Translational Control of Hemoglobin Synthesis by an Initiation Factor Required for Recycling of Ribosomes and for their Binding to Messenger RNA

PubMed Central

Kaempfer, Raymond; Kaufman, Jennifer

1972-01-01

The continued recycling of ribosomes during protein synthesis in rabbit reticulocyte lysates at 37° requires an initiation factor whose activity is rapidly lost in the absence of added heme. Partially purified factor (i) fully maintains the polysomes; (ii) inhibits the association of 40S and 60S ribosomal subunits into single ribosomes; (iii) promotes the quantitative entry of added 60S subunits into polysomes; (iv) allows the accumulation of ribosomal subunits, instead of single ribosomes, when initiation is blocked with aurin tricarboxylate; and (v) is absolutely required for the binding of globin messenger RNA to ribosomes. These properties suggest that this mammalian initiation factor functions analogously to bacterial IF-3. In addition, the translational control of globin synthesis by heme is exerted, directly or indirectly, through this factor. PMID:4508325

Infection of orthopedic implants with emphasis on bacterial adhesion process and techniques used in studying bacterial-material interactions

PubMed Central

Ribeiro, Marta; Monteiro, Fernando J.; Ferraz, Maria P.

2012-01-01

Staphylococcus comprises up to two-thirds of all pathogens in orthopedic implant infections and they are the principal causative agents of two major types of infection affecting bone: septic arthritis and osteomyelitis, which involve the inflammatory destruction of joint and bone. Bacterial adhesion is the first and most important step in implant infection. It is a complex process influenced by environmental factors, bacterial properties, material surface properties and by the presence of serum or tissue proteins. Properties of the substrate, such as chemical composition of the material, surface charge, hydrophobicity, surface roughness and the presence of specific proteins at the surface, are all thought to be important in the initial cell attachment process. The biofilm mode of growth of infecting bacteria on an implant surface protects the organisms from the host immune system and antibiotic therapy. The research for novel therapeutic strategies is incited by the emergence of antibiotic-resistant bacteria. This work will provide an overview of the mechanisms and factors involved in bacterial adhesion, the techniques that are currently being used studying bacterial-material interactions as well as provide insight into future directions in the field. PMID:23507884

Antagonistic interactions are sufficient to explain self-assemblage of bacterial communities in a homogeneous environment: a computational modeling approach

PubMed Central

Zapién-Campos, Román; Olmedo-Álvarez, Gabriela; Santillán, Moisés

2015-01-01

Most of the studies in Ecology have been devoted to analyzing the effects the environment has on individuals, populations, and communities, thus neglecting the effects of biotic interactions on the system dynamics. In the present work we study the structure of bacterial communities in the oligotrophic shallow water system of Churince, Cuatro Cienegas, Mexico. Since the physicochemical conditions of this water system are homogeneous and quite stable in time, it is an excellent candidate to study how biotic factors influence the structure of bacterial communities. In a previous study, the binary antagonistic interactions of 78 bacterial strains, isolated from Churince, were experimentally determined. We employ these data to develop a computer algorithm to simulate growth experiments in a cellular grid representing the pond. Remarkably, in our model, the dynamics of all the simulated bacterial populations is determined solely by antagonistic interactions. Our results indicate that all bacterial strains (even those that are antagonized by many other bacteria) survive in the long term, and that the underlying mechanism is the formation of bacterial community patches. Patches corresponding to less antagonistic and highly susceptible strains are consistently isolated from the highly-antagonistic bacterial colonies by patches of neutral strains. These results concur with the observed features of the bacterial community structure previously reported. Finally, we study how our findings depend on factors like initial population size, differential population growth rates, homogeneous population death rates, and enhanced bacterial diffusion. PMID:26052318

Eosinophilic pustular folliculitis: a sterile folliculitis of unknown cause?

PubMed

Brenner, S; Wolf, R; Ophir, J

1994-08-01

Eosinophilic pustular folliculitis (EPF) was initially defined as a sterile folliculitis of unknown cause. Because attempts to demonstrate bacterial organisms have been unsuccessful, and antibiotic therapy is usually ineffective, a bacterial infection is not considered a plausible causative factor for this disease. Our purpose was to describe five patients with the clinical and histologic characteristics of EPF and to report the results of bacterial cultures. Biopsy specimens were examined and pustules were cultured. In three of the five patients, Pseudomonas infection of the hair follicle was the cause of the disease as proven by repeated cultures and the response to specific therapy. Three patients had a systemic disorder known to cause immunologic alteration: AIDS in one and a myeloproliferative disorder in two. Although EPF was initially defined as a sterile folliculitis of unknown origin, three of our patients had an identifiable and treatable cause. We believe that these cases warrant the diagnosis of EPF.

Pathogenic flora composition and overview of the trends used for bacterial pathogenicity identifications.

PubMed

Orji, Frank Anayo; Ugbogu, Ositadinma Chinyere; Ugbogu, Eziuche Amadike; Barbabosa-Pliego, Alberto; Monroy, Jose Cedillo; Elghandour, Mona M M Y; Salem, Abdelfattah Z M

2018-05-05

Over 250 species of resident flora in the class of bacteria are known to be associated with humans. These conventional flora compositions is often determined by factors which may not be limited to genetics, age, sex, stress and nutrition of humans. Man is constantly in contact with bacteria through media such as air, water, soil and food. This paper reviews the concept of bacterial pathogenesis from the sequential point of colonization to tissue injury. The paper in addition to examination of the factors which enhance virulence in bacterial pathogens also x-rayed the concept of pathogenicity islands and the next generation approaches or rather current trends/methods used in the bacterial pathogenicity investigations. In terms of pathogenicity which of course is the capacity to cause disease in animals, requires that the attacking bacterial strain is virulent, and has ability to bypass the host immune defensive mechanisms. In order to achieve or exhibit pathogenicity, the virulence factors required by microorganisms include capsule, pigments, enzymes, iron acquisition through siderophores. Bacterial Pathogenicity Islands as a distinct concept in bacterial pathogenesis are just loci on the chromosome or extra chromosomal units which are acquired by horizontal gene transfer within pathogens in a microbial community or biofilm. In the area of laboratory investigations, bacterial pathogenesis was initially carried out using culture dependent approaches, which can only detect about 1% of human and veterinary-important pathogens. However, in the recent paradigms shift, the use of proteomics, metagenomics, phylogenetic tree analyses, spooligotyping, and finger printing etc. have made it possible that 100% of the bacterial pathogens in nature can be extensively studied. Copyright © 2018 Elsevier Ltd. All rights reserved.

Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations

PubMed Central

Perron, Gabriel G.; Lee, Alexander E. G.; Wang, Yun; Huang, Wei E.; Barraclough, Timothy G.

2012-01-01

Bacterial recombination is believed to be a major factor explaining the prevalence of multi-drug-resistance (MDR) among pathogenic bacteria. Despite extensive evidence for exchange of resistance genes from retrospective sequence analyses, experimental evidence for the evolutionary benefits of bacterial recombination is scarce. We compared the evolution of MDR between populations of Acinetobacter baylyi in which we manipulated both the recombination rate and the initial diversity of strains with resistance to single drugs. In populations lacking recombination, the initial presence of multiple strains resistant to different antibiotics inhibits the evolution of MDR. However, in populations with recombination, the inhibitory effect of standing diversity is alleviated and MDR evolves rapidly. Moreover, only the presence of DNA harbouring resistance genes promotes the evolution of resistance, ruling out other proposed benefits for recombination. Together, these results provide direct evidence for the fitness benefits of bacterial recombination and show that this occurs by mitigation of functional interference between genotypes resistant to single antibiotics. Although analogous to previously described mechanisms of clonal interference among alternative beneficial mutations, our results actually highlight a different mechanism by which interactions among co-occurring strains determine the benefits of recombination for bacterial evolution. PMID:22048956

Mitochondrial translational-initiation and elongation factors in Saccharomyces cerevisiae.

PubMed

Vambutas, A; Ackerman, S H; Tzagoloff, A

1991-11-01

C155 and E252 are respiratory-defective mutants of Saccharomyces cerevisiae, previously assigned to complementation groups G37 and G142, respectively. The following evidence suggested that both mutants were likely to have lesions in components of the mitochondrial translational machinery: C155 and E252 display a pleiotropic deficiency in cytochromes a, a3 and b; both strains are severly limited in their ability to incorporate radioactive methionine into the mitochondrial translation products and, in addition, display a tendency to loose wild-type mitochondrial DNA. This set of characteristics is commonly found in strains affected in mitochondrial protein synthesis. To identify the biochemical lesions, each mutant was transformed with a wild-type yeast genomic library and clones complemented for the respiratory defect were selected for growth on a non-fermentable substrate. Analysis of the cloned genes revealed that C155 has a mutation in a protein which has high sequence similarity to bacterial elongation factor G and that E252 has a mutation in a protein homologous to bacterial initiation factor 2. Disruption of the chromosomal copy of each gene in a wild-type haploid yeast induced a phenotype analogous to that of the original mutants, but does not affect cell viability. These results indicate that both gene products function exclusively in mitochondrial protein synthesis. Subcloning of the IFM1 gene, coding for the mitochondrial initiation factor, indicates that the amino-terminal 423 residues of the protein are sufficient to promote peptide-chain initiation in vivo.

Streptococcal pharyngitis and rheumatic heart disease: the superantigen hypothesis revisited.

PubMed

Hurst, Jacklyn R; Kasper, Katherine J; Sule, Akshay N; McCormick, John K

2018-07-01

Streptococcus pyogenes is a human-specific and globally prominent bacterial pathogen that despite causing numerous human infections, this bacterium is normally found in an asymptomatic carrier state. This review provides an overview of both bacterial and human factors that likely play an important role in nasopharyngeal colonization and pharyngitis, as well as the development of acute rheumatic fever and rheumatic heart disease. Here we highlight a recently described role for bacterial superantigens in promoting acute nasopharyngeal infection, and discuss how these immune system activating toxins could be crucial to initiate the autoimmune process in rheumatic heart disease. Copyright © 2018. Published by Elsevier B.V.

Role of the σ 54 Activator Interacting Domain in Bacterial Transcription Initiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Siegel, Alexander R.; Wemmer, David E.

Bacterial sigma factors are subunits of RNA polymerase that direct the holoenzyme to specific sets of promoters in the genome and are a central element of regulating transcription. Most polymerase holoenzymes open the promoter and initiate transcription rapidly after binding. However, polymerase containing the members of the σ 54 family must be acted on by a transcriptional activator before DNA opening and initiation occur. A key domain in these transcriptional activators forms a hexameric AAA + ATPase that acts through conformational changes brought on by ATP hydrolysis. Contacts between the transcriptional activator and σ 54 are primarily made through anmore » N-terminal σ 54 activator interacting domain (AID). To better understand this mechanism of bacterial transcription initiation, we characterized the σ 54 AID by NMR spectroscopy and other biophysical methods and show that it is an intrinsically disordered domain in σ 54 alone. In this paper, we identified a minimal construct of the Aquifex aeolicus σ 54 AID that consists of two predicted helices and retains native-like binding affinity for the transcriptional activator NtrC1. Using the NtrC1 ATPase domain, bound with the non-hydrolyzable ATP analog ADP-beryllium fluoride, we studied the NtrC1–σ 54 AID complex using NMR spectroscopy. We show that the σ 54 AID becomes structured after associating with the core loops of the transcriptional activators in their ATP state and that the primary site of the interaction is the first predicted helix. Finally, understanding this complex, formed as the first step toward initiation, will help unravel the mechanism of σ 54 bacterial transcription initiation.« less

Role of antibiotic therapy for bacterial vaginosis and intermediate flora in pregnancy.

PubMed

Ugwumadu, Austin

2007-06-01

Bacterial vaginosis and intermediate flora are associated with late miscarriage and preterm delivery. The mechanisms involved are not yet fully understood. Clinical trials of antibiotic therapy to reduce these complications have yielded conflicting results. These trials, however, were conducted in mixed populations of pregnant women with variable risk profiles for preterm delivery. Furthermore, investigators used different criteria for diagnosis, treated with different antibiotics at different doses and via different routes, and initiated treatment at different gestational ages. Over 80% of pregnant women with abnormal vaginal flora have a good outcome, and in some populations the presence of bacterial vaginosis is not associated with preterm delivery, suggesting that other host factors may modify the risk. Recent studies have examined the roles of genetic regulation of host immune response, bacterial pathogenic factors, and enzymes in the vagina, and how these factors interact to drive a given outcome. These markers have the potential to better define the women at maximal risk and therefore guide future interventions. This chapter aims to appraise the current state of treatment of abnormal vaginal flora in pregnancy and suggest appropriate management based on the available evidence.

Contribution of host, bacterial factors and antibiotic treatment to mortality in adult patients with bacteraemic pneumococcal pneumonia.

PubMed

Naucler, Pontus; Darenberg, Jessica; Morfeldt, Eva; Ortqvist, Ake; Henriques Normark, Birgitta

2013-06-01

Host and bacterial factors as well as different treatment regimens are likely to influence the outcome in patients with bacteraemic pneumococcal pneumonia. To estimate the relative contribution of host factors as well as bacterial factors and antibiotic treatment to mortality in bacteraemic pneumococcal pneumonia. A cohort study of 1580 adult patients with community-acquired bacteraemic pneumococcal pneumonia was conducted between 2007 and 2009 in Sweden. Data on host factors and initial antibiotic treatment were collected from patient records. Antibiotic resistance and serotype were determined for bacterial isolates. Logistic regression analyses were performed to assess risk factors for 30-day mortality. Smoking, alcohol abuse, solid tumour, liver disease and renal disease attributed to 14.9%, 13.1%, 13.1%, 8.0% and 7.4% of the mortality, respectively. Age was the strongest predictor, and mortality increased exponentially from 1.3% in patients <45 years of age to 26.1% in patients aged ≥85 years. There was considerable confounding by host factors on the association between serotype and mortality. Increasing age, liver disease and serotype were associated with mortality in patients admitted to the ICU. Combined treatment with β-lactam antibiotics and macrolide/quinolone was associated with reduced mortality in patients in the ICU, although confounding could not be ruled out. Host factors appear to be more important than the specific serotype as determinants of mortality in patients with bacteraemic pneumococcal pneumonia. Several host factors were identified that contribute to mortality, which is important for prognosis and to guide targeted prevention strategies.

Influence of type-I fimbriae and fluid shear stress on bacterial behavior and multicellular architecture of early Escherichia coli biofilms at single-cell resolution.

PubMed

Wang, Liyun; Keatch, Robert; Zhao, Qi; Wright, John A; Bryant, Clare E; Redmann, Anna L; Terentjev, Eugene M

2018-01-12

Biofilm formation on abiotic surfaces in food and medical industry can cause severe contamination and infection, yet how biological and physical factors determine cellular architecture of early biofilms and bacterial behavior of the constituent cells remains largely unknown. In this study we examine the specific role of type-I fimbriae in nascent stages of biofilm formation and the response of micro-colonies to environmental flow shear at single-cell resolution. The results show that type-I fimbriae are not required for reversible adhesion from plankton, but critical for irreversible adhesion of Escherichia coli ( E.coli ) MG1655 forming biofilms on polyethylene terephthalate (PET) surfaces. Besides establishing a firm cell-surface contact, the irreversible adhesion seems necessary to initiate the proliferation of E.coli on the surface. After application of shear stress, bacterial retention is dominated by the 3D architecture of colonies independent of the population and the multi-layered structure could protect the embedded cells from being insulted by fluid shear, while cell membrane permeability mainly depends on the biofilm population and the duration time of the shear stress. Importance Bacterial biofilms could lead to severe contamination problems in medical devices and food processing equipment. However, biofilms are usually studied at a rough macroscopic level, thus little is known about how individual bacterial behavior within biofilms and multicellular architecture are influenced by bacterial appendages (e.g. pili/fimbriae) and environmental factors during early biofilm formation. We apply Confocal Laser Scanning Microscopy (CLSM) to visualize E.coli micro-colonies at single-cell resolution. Our findings suggest that type-I fimbriae are vital to the initiation of bacterial proliferation on surfaces and that the responses of biofilm architecture and cell membrane permeability of constituent bacteria to fluid shear stress are different, which are respectively regulated by the 3D morphology and the population of micro-colonies. Copyright © 2018 American Society for Microbiology.

Initial insights into bacterial succession during human decomposition.

PubMed

Hyde, Embriette R; Haarmann, Daniel P; Petrosino, Joseph F; Lynne, Aaron M; Bucheli, Sibyl R

2015-05-01

Decomposition is a dynamic ecological process dependent upon many factors such as environment, climate, and bacterial, insect, and vertebrate activity in addition to intrinsic properties inherent to individual cadavers. Although largely attributed to microbial metabolism, very little is known about the bacterial basis of human decomposition. To assess the change in bacterial community structure through time, bacterial samples were collected from several sites across two cadavers placed outdoors to decompose and analyzed through 454 pyrosequencing and analysis of variable regions 3-5 of the bacterial 16S ribosomal RNA (16S rRNA) gene. Each cadaver was characterized by a change in bacterial community structure for all sites sampled as time, and decomposition, progressed. Bacteria community structure is variable at placement and before purge for all body sites. At bloat and purge and until tissues began to dehydrate or were removed, bacteria associated with flies, such as Ignatzschineria and Wohlfahrtimonas, were common. After dehydration and skeletonization, bacteria associated with soil, such as Acinetobacter, were common at most body sites sampled. However, more cadavers sampled through multiple seasons are necessary to assess major trends in bacterial succession.

Bacterial community initial development in proglacial soils of Larsemann hill, East Antarctica

NASA Astrophysics Data System (ADS)

Ma, H.; Yan, W.; Shi, G.; Sun, B.; Zhang, Y.; Xiao, X.

2016-12-01

Glacial forefields are considered ideal places to explore how microbial communities will response to climate-driven environmental changes. Our knowledge of how the bacterial community activities and structure was influenced by changing environment due to glacier retreat is still very limited, especially at the initial stage of glacier retreat. The short gradient soil samples including the ice free and ice covered sites were sampled in the forehead of East Antarctica ice sheet, in Larsemann Hills. By employing the Miseq sequencing methods, 1.8 x104 high-quality sequences were gotten for each sample and the bacterial diversity including abundant bacteria and rare bacteria were studied and compared between the gradient samples. Even though in such an extreme stress condition, the bacterial diversity was high. The coefficient of variance between the five sites of abundant group was 0.886 which was higher than that of the top 20 rare group (0.159) significantly (unpaired t test, p-value<0.0001) suggesting that the abundant bacterial communities were more sensitive to the ice sheet change in the initial stage than rare bacteria did. And the abundant bacteria contributed the community structure more than the rare bacteria did. The rare group acted more like seed bank to keep the community functionality in the forehead of sheet. And the ice thickness was the major factor to affect the abundant bacterial community. Given the fact that Antarctica environment was more sensitive to the global warming, the study about abundant and rare bacteria response to condition change will be helpful to precisely predict community response to climate change in polar region. This finding will improve the understanding about the relationship between community structure and environment condition in extreme stress condition.

Aseptic and Bacterial Meningitis: Evaluation, Treatment, and Prevention.

PubMed

Mount, Hillary R; Boyle, Sean D

2017-09-01

The etiologies of meningitis range in severity from benign and self-limited to life-threatening with potentially severe morbidity. Bacterial meningitis is a medical emergency that requires prompt recognition and treatment. Mortality remains high despite the introduction of vaccinations for common pathogens that have reduced the incidence of meningitis worldwide. Aseptic meningitis is the most common form of meningitis with an annual incidence of 7.6 per 100,000 adults. Most cases of aseptic meningitis are viral and require supportive care. Viral meningitis is generally self-limited with a good prognosis. Examination maneuvers such as Kernig sign or Brudzinski sign may not be useful to differentiate bacterial from aseptic meningitis because of variable sensitivity and specificity. Because clinical findings are also unreliable, the diagnosis relies on the examination of cerebrospinal fluid obtained from lumbar puncture. Delayed initiation of antibiotics can worsen mortality. Treatment should be started promptly in cases where transfer, imaging, or lumbar puncture may slow a definitive diagnosis. Empiric antibiotics should be directed toward the most likely pathogens and should be adjusted by patient age and risk factors. Dexamethasone should be administered to children and adults with suspected bacterial meningitis before or at the time of initiation of antibiotics. Vaccination against the most common pathogens that cause bacterial meningitis is recommended. Chemoprophylaxis of close contacts is helpful in preventing additional infections.

Bacterial Sepsis in Patients with Visceral Leishmaniasis in Northwest Ethiopia

PubMed Central

Takele, Yegnasew; Woldeyohannes, Desalegn; Tiruneh, Moges; Mohammed, Rezika; Lynen, Lutgarde; van Griensven, Johan

2014-01-01

Background and Objectives. Visceral leishmaniasis (VL) is one of the neglected diseases affecting the poorest segment of world populations. Sepsis is one of the predictors for death of patients with VL. This study aimed to assess the prevalence and factors associated with bacterial sepsis, causative agents, and their antimicrobial susceptibility patterns among patients with VL. Methods. A cross-sectional study was conducted among parasitologically confirmed VL patients suspected of sepsis admitted to the University of Gondar Hospital, Northwest Ethiopia, from February 2012 to May 2012. Blood cultures and other clinical samples were collected and cultured following the standard procedures. Results. Among 83 sepsis suspected VL patients 16 (19.3%) had culture confirmed bacterial sepsis. The most frequently isolated organism was Staphylococcus aureus (68.8%; 11/16), including two methicillin-resistant isolates (MRSA). Patients with focal bacterial infection were more likely to have bacterial sepsis (P < 0.001). Conclusions. The prevalence of culture confirmed bacterial sepsis was high, predominantly due to S. aureus. Concurrent focal bacterial infection was associated with bacterial sepsis, suggesting that focal infections could serve as sources for bacterial sepsis among VL patients. Careful clinical evaluation for focal infections and prompt initiation of empiric antibiotic treatment appears warranted in VL patients. PMID:24895569

Predictive factors of bacterial meningitis in the patients seen in emergency departments.

PubMed

Morales-Casado, María Isabel; Julián-Jiménez, Agustín; Lobato-Casado, Paula; Cámara-Marín, Belén; Pérez-Matos, Julio Alberto; Martínez-Maroto, Tamara

2017-04-01

To analyse and compare predictive factors of bacterial meningitis in the patients seen in the Emergency Departments (ED) due to an episode of acute meningitis (AM). A prospective, observational study was carried out in patients aged 15 years and older seen in ED due to AM between August 2009 and November 2015. Thirty-two variables for predicting bacterial meningitis were assessed. They covered epidemiological, comorbidity, clinical and analytical factors. Multivariate logistic regression analysis was performed. The study included 154 patients. The diagnosis was bacterial meningitis in 53 (34.4%) patients. Four variables were significantly associated with bacterial aetiology: cerebrospinal fluid (CSF) lactate concentration ≥33mg/dl (odds ratio [OR] 50.84; 95% confidence interval [CI]: 21.63-119.47, P<.001), serum procalcitonin (PCT) ≥0.8ng/ml (OR 46.34; 95%CI: 19.71-108.89; P<.001), CSF glucose <60% of blood value (OR 20.82; 95%CI: 8.86-48.96; P=.001), CSF polymorphonuclears greater than 50% (OR 20.19; 95%CI: 8.31-49.09; P=.002]. The area under the curve for the model serum PCT≥0.8ng/ml plus CSF lactate ≥33mg/dl was 0.992 (95%CI: 0.979-1; P<.001), and achieved 99% sensitivity and 98% specificity for predicting bacterial meningitis. Serum PCT with CSF lactate, CSF glucose and CSF polymorphonuclears evaluated in an initial assessment in the ED for patients with AM, achieved an excellent diagnostic usefulness for predicting bacterial meningitis. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

Bacterial Community Succession in Pine-Wood Decomposition.

PubMed

Kielak, Anna M; Scheublin, Tanja R; Mendes, Lucas W; van Veen, Johannes A; Kuramae, Eiko E

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities.

Bacterial Community Succession in Pine-Wood Decomposition

PubMed Central

Kielak, Anna M.; Scheublin, Tanja R.; Mendes, Lucas W.; van Veen, Johannes A.; Kuramae, Eiko E.

2016-01-01

Though bacteria and fungi are common inhabitants of decaying wood, little is known about the relationship between bacterial and fungal community dynamics during natural wood decay. Based on previous studies involving inoculated wood blocks, strong fungal selection on bacteria abundance and community composition was expected to occur during natural wood decay. Here, we focused on bacterial and fungal community compositions in pine wood samples collected from dead trees in different stages of decomposition. We showed that bacterial communities undergo less drastic changes than fungal communities during wood decay. Furthermore, we found that bacterial community assembly was a stochastic process at initial stage of wood decay and became more deterministic in later stages, likely due to environmental factors. Moreover, composition of bacterial communities did not respond to the changes in the major fungal species present in the wood but rather to the stage of decay reflected by the wood density. We concluded that the shifts in the bacterial communities were a result of the changes in wood properties during decomposition and largely independent of the composition of the wood-decaying fungal communities. PMID:26973611

Rhizobium meliloti lipooligosaccharide nodulation factors: different structural requirements for bacterial entry into target root hair cells and induction of plant symbiotic developmental responses.

PubMed

Ardourel, M; Demont, N; Debellé, F; Maillet, F; de Billy, F; Promé, J C; Dénarié, J; Truchet, G

1994-10-01

Rhizobium meliloti produces lipochitooligosaccharide nodulation NodRm factors that are required for nodulation of legume hosts. NodRm factors are O-acetylated and N-acylated by specific C16-unsaturated fatty acids. nodL mutants produce non-O-acetylated factors, and nodFE mutants produce factors with modified acyl substituents. Both mutants exhibited a significantly reduced capacity to elicit infection thread (IT) formation in alfalfa. However, once initiated, ITs developed and allowed the formation of nitrogen-fixing nodules. In contrast, double nodF/nodL mutants were unable to penetrate into legume hosts and to form ITs. Nevertheless, these mutants induced widespread cell wall tip growth in trichoblasts and other epidermal cells and were also able to elicit cortical cell activation at a distance. NodRm factor structural requirements are thus clearly more stringent for bacterial entry than for the elicitation of developmental plant responses.

Initial Bacterial Adhesion on Different Yttria-Stabilized Tetragonal Zirconia Implant Surfaces in Vitro

PubMed Central

Karygianni, Lamprini; Jähnig, Andrea; Schienle, Stefanie; Bernsmann, Falk; Adolfsson, Erik; Kohal, Ralf J.; Chevalier, Jérôme; Hellwig, Elmar; Al-Ahmad, Ali

2013-01-01

Bacterial adhesion to implant biomaterials constitutes a virulence factor leading to biofilm formation, infection and treatment failure. The aim of this study was to examine the initial bacterial adhesion on different implant materials in vitro. Four implant biomaterials were incubated with Enterococcus faecalis, Staphylococcus aureus and Candida albicans for 2 h: 3 mol % yttria-stabilized tetragonal zirconia polycrystal surface (B1a), B1a with zirconium oxide (ZrO2) coating (B2a), B1a with zirconia-based composite coating (B1b) and B1a with zirconia-based composite and ZrO2 coatings (B2b). Bovine enamel slabs (BES) served as control. The adherent microorganisms were quantified and visualized using scanning electron microscopy (SEM); DAPI and live/dead staining. The lowest bacterial count of E. faecalis was detected on BES and the highest on B1a. The fewest vital C. albicans strains (42.22%) were detected on B2a surfaces, while most E. faecalis and S. aureus strains (approximately 80%) were vital overall. Compared to BES; coated and uncoated zirconia substrata exhibited no anti-adhesive properties. Further improvement of the material surface characteristics is essential. PMID:28788415

Initial Bacterial Adhesion on Different Yttria-Stabilized Tetragonal Zirconia Implant Surfaces in Vitro.

PubMed

Karygianni, Lamprini; Jähnig, Andrea; Schienle, Stefanie; Bernsmann, Falk; Adolfsson, Erik; Kohal, Ralf J; Chevalier, Jérôme; Hellwig, Elmar; Al-Ahmad, Ali

2013-12-04

Bacterial adhesion to implant biomaterials constitutes a virulence factor leading to biofilm formation, infection and treatment failure. The aim of this study was to examine the initial bacterial adhesion on different implant materials in vitro . Four implant biomaterials were incubated with Enterococcus faecalis , Staphylococcus aureus and Candida albicans for 2 h: 3 mol % yttria-stabilized tetragonal zirconia polycrystal surface (B1a), B1a with zirconium oxide (ZrO₂) coating (B2a), B1a with zirconia-based composite coating (B1b) and B1a with zirconia-based composite and ZrO₂ coatings (B2b). Bovine enamel slabs (BES) served as control. The adherent microorganisms were quantified and visualized using scanning electron microscopy (SEM); DAPI and live/dead staining. The lowest bacterial count of E. faecalis was detected on BES and the highest on B1a. The fewest vital C. albicans strains (42.22%) were detected on B2a surfaces, while most E. faecalis and S. aureus strains (approximately 80%) were vital overall. Compared to BES; coated and uncoated zirconia substrata exhibited no anti-adhesive properties. Further improvement of the material surface characteristics is essential.

Dexamethasone enhances agonist induction of tissue factor in monocytes but not in endothelial cells.

PubMed

Bottles, K D; Morrissey, J H

1993-06-01

Stimulation of monocytic cells by inflammatory agents such as bacterial lipopolysaccharide or tumour necrosis factor-alpha leads to the rapid and transient expression of tissue factor, the major cellular initiator of the extrinsic coagulation cascade in both haemostasis and tissue inflammation. In this study we investigated whether the synthetic anti-inflammatory glucocorticoid, dexamethasone, would inhibit agonist induction of tissue factor expression in both monocytes and endothelial cells. Surprisingly, dexamethasone significantly enhanced the induction of tissue factor expression by peripheral blood mononuclear cells and an established monocytic cell line, THP-1, in response to lipopolysaccharide or tumour necrosis factor-alpha. However, unlike monocytic cells, dexamethasone did not enhance agonist induction of tissue factor in endothelial cells. Synergistic enhancement of tissue factor expression by dexamethasone was also reflected in tissue factor mRNA levels in THP-1 cells, but was not the result of improved TF mRNA stability. Synergism between bacterial lipopolysaccharide and glucocorticoid in the induction of monocyte effector function is extremely unusual and may help to explain the variable outcome of glucocorticoid treatment of septic shock.

Competition for space during bacterial colonization of a surface.

PubMed

Lloyd, Diarmuid P; Allen, Rosalind J

2015-09-06

Competition for space is ubiquitous in the ecology of both microorganisms and macro-organisms. We introduce a bacterial model system in which the factors influencing competition for space during colonization of an initially empty habitat can be tracked directly. Using fluorescence microscopy, we follow the fate of individual Escherichia coli bacterial cell lineages as they undergo expansion competition (the race to be the first to colonize a previously empty territory), and as they later compete at boundaries between clonal territories. Our experiments are complemented by computer simulations of a lattice-based model. We find that both expansion competition, manifested as differences in individual cell lag times, and boundary competition, manifested as effects of neighbour cell geometry, can play a role in colonization success, particularly when lineages expand exponentially. This work provides a baseline for investigating how ecological interactions affect colonization of space by bacterial populations, and highlights the potential of bacterial model systems for the testing and development of ecological theory. © 2015 The Authors.

Competition for space during bacterial colonization of a surface

PubMed Central

Lloyd, Diarmuid P.; Allen, Rosalind J.

2015-01-01

Competition for space is ubiquitous in the ecology of both microorganisms and macro-organisms. We introduce a bacterial model system in which the factors influencing competition for space during colonization of an initially empty habitat can be tracked directly. Using fluorescence microscopy, we follow the fate of individual Escherichia coli bacterial cell lineages as they undergo expansion competition (the race to be the first to colonize a previously empty territory), and as they later compete at boundaries between clonal territories. Our experiments are complemented by computer simulations of a lattice-based model. We find that both expansion competition, manifested as differences in individual cell lag times, and boundary competition, manifested as effects of neighbour cell geometry, can play a role in colonization success, particularly when lineages expand exponentially. This work provides a baseline for investigating how ecological interactions affect colonization of space by bacterial populations, and highlights the potential of bacterial model systems for the testing and development of ecological theory. PMID:26333814

A growth-dependent transcription initiation factor (TIF-IA) interacting with RNA polymerase I regulates mouse ribosomal RNA synthesis.

PubMed

Schnapp, A; Pfleiderer, C; Rosenbauer, H; Grummt, I

1990-09-01

Control of mouse ribosomal RNA synthesis in response to extracellular signals is mediated by TIF-IA, a regulatory factor whose amount or activity correlates with cell proliferation. Factor TIF-IA interacts with RNA polymerase I (pol I), thus converting it into a transcriptionally active holoenzyme, which is able to initiate specifically at the rDNA promoter in the presence of the other auxiliary transcription initiation factors, designated TIF-IB, TIF-IC and UBF. With regard to several criteria, the growth-dependent factor TIF-IA behaves like a bacterial sigma factor: (i) it associates physically with pol I, (ii) it is required for initiation of transcription, (iii) it is present in limiting amounts and (iv) under certain salt conditions, it is chromatographically separable from the polymerase. In addition, evidence is presented that dephosphorylation of pol I abolishes in vitro transcription initiation from the ribosomal gene promoter without significantly affecting the polymerizing activity of the enzyme at nonspecific templates. The involvement of both a regulatory factor and post-translational modification of the transcribing enzyme provides an efficient and versatile mechanism of rDNA transcription regulation which enables the cell to adapt ribosome synthesis rapidly to a variety of extracellular signals.

A 15-year retrospective analysis of prognostic factors in childhood bacterial meningitis.

PubMed

Wee, Liang Yi Justin; Tanugroho, Raymond Reinaldo; Thoon, Koh Cheng; Chong, Chia Yin; Choong, Chew Thye; Krishnamoorthy, Subramania; Maiwald, Matthias; Tee, Nancy Wen Sim; Tan, Natalie Woon Hui

2016-01-01

This retrospective chart review aimed to identify factors in childhood bacterial meningitis that predicted disease severity and long-term outcome. The study included 112 episodes of microbiologically confirmed bacterial meningitis in children aged three days to 15 years who were admitted to a Singapore hospital from 1998 to 2013. The mortality rate was 6%, and 44% required intensive care unit (ICU) admission. Predictive factors associated with ICU admission included pneumococcal meningitis, with an odds ratio (OR) of 5.2 and 95% confidence interval (CI) of 1.5-18.2, leukopenia (OR 5.6, 95% CI 1.7-17.9) and a cerebrospinal fluid (CSF):serum glucose ratio <0.25 (OR 4.5, 95% CI 1.4-14.4). An initial CSF white blood cell count >1000/mm(3) (OR 0.26, 95% CI 0.086-0.76) was negatively associated with ICU admission. Five years after meningitis, 32% had residual sequelae, and the associated prognostic factors were Haemophilus influenzae type b (Hib) meningitis (OR 29.5, 95% CI 2-429), seizures during their inpatient stay (OR 10.6, 95% CI 1.9-60.2) and septic shock (OR 8.4, 95% CI 1.1-62.1). As mortality was low in this bacterial meningitis study, ICU admission was used as a marker of disease severity. These findings underscore the importance of the pneumococcal and Hib meningitis vaccines. ©2015 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

Bacteria between protists and phages: from antipredation strategies to the evolution of pathogenicity.

PubMed

Brüssow, Harald

2007-08-01

Bacteriophages and protists are major causes of bacterial mortality. Genomics suggests that phages evolved well before eukaryotic protists. Bacteria were thus initially only confronted with phage predators. When protists evolved, bacteria were caught between two types of predators. One successful antigrazing strategy of bacteria was the elaboration of toxins that would kill the grazer. The released cell content would feed bystander bacteria. I suggest here that, to fight grazing protists, bacteria teamed up with those phage predators that concluded at least a temporary truce with them in the form of lysogeny. Lysogeny was perhaps initially a resource management strategy of phages that could not maintain infection chains. Subsequently, lysogeny might have evolved into a bacterium-prophage coalition attacking protists, which became a food source for them. When protists evolved into multicellular animals, the lysogenic bacteria tracked their evolving food source. This hypothesis could explain why a frequent scheme of bacterial pathogenicity is the survival in phagocytes, why a significant fraction of bacterial pathogens have prophage-encoded virulence genes, and why some virulence factors of animal pathogens are active against unicellular eukaryotes. Bacterial pathogenicity might thus be one playing option of the stone-scissor-paper game played between phages-bacteria-protists, with humans getting into the crossfire.

Novel model for multispecies biofilms that uses rigid gas-permeable lenses.

PubMed

Peyyala, Rebecca; Kirakodu, Sreenatha S; Ebersole, Jeffrey L; Novak, Karen F

2011-05-01

Oral biofilms comprise complex multispecies consortia aided by specific inter- and intraspecies interactions occurring among commensals and pathogenic bacterial species. Oral biofilms are primary initiating factors of periodontal disease, although complex multifactorial biological influences, including host cell responses, contribute to the individual outcome of the disease. To provide a system to study initial stages of interaction between oral biofilms and the host cells that contribute to the disease process, we developed a novel in vitro model system to grow biofilms on rigid gas-permeable contact lenses (RGPLs), which enable oxygen to permeate through the lens material. Bacterial species belonging to early- and late-colonizing groups were successfully established as single- or three-species biofilms, with each group comprising Streptococcus gordonii, Streptococcus oralis, and Streptococcus sanguinis; S. gordonii, Actinomyces naeslundii, and Fusobacterium nucleatum; or S. gordonii, F. nucleatum, and Porphyromonas gingivalis. Quantification of biofilm numbers by quantitative PCR (qPCR) revealed substantial differences in the magnitude of bacterial numbers in single-species and multispecies biofilms. We evaluated cell-permeable conventional nucleic acid stains acridine orange, hexidium iodide, and Hoechst 33258 and novel SYTO red, blue, and green fluorochromes for their effect on bacterial viability and fluorescence yield to allow visualization of the aggregates of individual bacterial species by confocal laser scanning microscopy (CLSM). Substantial differences in the quantity and distribution of the species in the multispecies biofilms were identified. The specific features of these biofilms may help us better understand the role of various bacteria in local challenge of oral tissues.

Distribution and diversity of ribosome binding sites in prokaryotic genomes.

PubMed

Omotajo, Damilola; Tate, Travis; Cho, Hyuk; Choudhary, Madhusudan

2015-08-14

Prokaryotic translation initiation involves the proper docking, anchoring, and accommodation of mRNA to the 30S ribosomal subunit. Three initiation factors (IF1, IF2, and IF3) and some ribosomal proteins mediate the assembly and activation of the translation initiation complex. Although the interaction between Shine-Dalgarno (SD) sequence and its complementary sequence in the 16S rRNA is important in initiation, some genes lacking an SD ribosome binding site (RBS) are still well expressed. The objective of this study is to examine the pattern of distribution and diversity of RBS in fully sequenced bacterial genomes. The following three hypotheses were tested: SD motifs are prevalent in bacterial genomes; all previously identified SD motifs are uniformly distributed across prokaryotes; and genes with specific cluster of orthologous gene (COG) functions differ in their use of SD motifs. Data for 2,458 bacterial genomes, previously generated by Prodigal (PROkaryotic DYnamic programming Gene-finding ALgorithm) and currently available at the National Center for Biotechnology Information (NCBI), were analyzed. Of the total genes examined, ~77.0% use an SD RBS, while ~23.0% have no RBS. Majority of the genes with the most common SD motifs are distributed in a manner that is representative of their abundance for each COG functional category, while motifs 13 (5'-GGA-3'/5'-GAG-3'/5'-AGG-3') and 27 (5'-AGGAGG-3') appear to be predominantly used by genes for information storage and processing, and translation and ribosome biogenesis, respectively. These findings suggest that an SD sequence is not obligatory for translation initiation; instead, other signals, such as the RBS spacer, may have an overarching influence on translation of mRNAs. Subsequent analyses of the 5' secondary structure of these mRNAs may provide further insight into the translation initiation mechanism.

Positive Bacteriological Analyses in Individuals With Diabetes Mellitus: Preliminary Results From a Forensic Study.

PubMed

Palmiere, Cristian; Tettamanti, Camilla

2018-06-01

Increased infection susceptibility in the diabetic population is a controversial issue in the clinical field. The greater frequency of infections in diabetic patients has been speculated as caused by the hyperglycemic environment that favors immune dysfunction. The aim of this study was to investigate the proportion of positive bacterial cultures in a series of diabetic individuals who underwent forensic investigations and assess the frequency of hyperglycemia at the time of death in these cases as well as the percentage of diabetics with cause of death due to bacterial infection. Forensic autopsy cases characterized by positive bacterial cultures and pre-existing diagnosis of diabetes mellitus were included in the study. Initial findings revealed that 12% (7/58 cases) of positive bacterial cultures concerned individuals with a pre-existing diagnosis of diabetes mellitus. Bacterial infection was considered to be the cause of death in 22% (7/31 cases) of diabetics with positive bacterial cultures. Hyperglycemia could be identified in 1 case only at the time of death. These preliminary results highlight the usefulness of systematically performing postmortem bacteriology in the forensic setting to more precisely characterize infectious risk factors in diabetics.

Symbiotic factors in Burkholderia essential for establishing an association with the bean bug, Riptortus pedestris.

PubMed

Kim, Jiyeun Kate; Lee, Bok Luel

2015-01-01

Symbiotic bacteria are common in insects and intimately affect the various aspects of insect host biology. In a number of insect symbiosis models, it has been possible to elucidate the effects of the symbiont on host biology, whereas there is a limited understanding of the impact of the association on the bacterial symbiont, mainly due to the difficulty of cultivating insect symbionts in vitro. Furthermore, the molecular features that determine the establishment and persistence of the symbionts in their host (i.e., symbiotic factors) have remained elusive. However, the recently established model, the bean bug Riptortus pedestris, provides a good opportunity to study bacterial symbiotic factors at a molecular level through their cultivable symbionts. Bean bugs acquire genus Burkholderia cells from the environment and harbor them as gut symbionts in the specialized posterior midgut. The genome of the Burkholderia symbiont was sequenced, and the genomic information was used to generate genetically manipulated Burkholderia symbiont strains. Using mutant symbionts, we identified several novel symbiotic factors necessary for establishing a successful association with the host gut. In this review, these symbiotic factors are classified into three categories based on the colonization dynamics of the mutant symbiont strains: initiation, accommodation, and persistence factors. In addition, the molecular characteristics of the symbiotic factors are described. These newly identified symbiotic factors and on-going studies of the Riptortus-Burkholderia symbiosis are expected to contribute to the understanding of the molecular cross-talk between insects and bacterial symbionts that are of ecological and evolutionary importance. © 2014 Wiley Periodicals, Inc.

A review of infectious bovine rhinotracheitis, shipping fever pneumonia and viral-bacterial synergism in respiratory disease of cattle.

PubMed Central

Yates, W D

1982-01-01

Unanswered questions on the etiology and prevention of shipping fever pneumonia have allowed this disease to remain one of the most costly to the North American cattle industry. Research in this area has indirected that while Pasteurella haemolytica and, to a lesser extent, P. multocida are involved in most cases, they seem to require additional factors to help initiate the disease process. Bovine herpes virus 1 has been shown experimentally to be one such factor. This review examines in some detail the topics of infectious bovine rhinotracheitis, shipping fever, and viral-bacterial interactions in the production of respiratory disease in various species. It deals with history, definitions, etiologies, clinical signs and lesions, and considers exposure levels, transmission and various pathogenetic mechanisms that are postulated or known to occur. PMID:6290011

Photodynamic antimicrobial chemotherapy using zinc phthalocyanine derivative for bacterial skin infection

NASA Astrophysics Data System (ADS)

Chen, Zhuo; Zhang, Yaxin; Li, Linsen; Zhou, Shanyong; Chen, Jincan; Hu, Ping; Huang, Mingdong

2014-09-01

Folliculitis, furunculosis and acne vulgaris are very common skin disorders of the hair follicles and are associated with large grease-producing (sebaceous) glands. Although the detailed mechanisms involved these skin disorders are not fully understood, it is believed that the bacteria Propionibacterium acnes and Staphylococcus aureus are the key pathogenic factors involved. Conventional treatments targeting the pathogenic factors include a variety of topical and oral medications such as antibiotics. The wide use of antibiotics leads to bacterial resistance, and hence there is a need for new alternatives in above bacterial skin treatment. Photodynamic antimicrobial chemotherapy (PACT) is based on an initial photosensitization of the infected area, followed by irradiation with visible light, producing singlet oxygen which is cytotoxic to bacteria. Herein we reported a zinc phthalocyanine derivative, pentalysine β-carbonylphthalocyanine zinc (ZnPc-(Lys)5) and its PACT effect for the bacteria involved in these skin infections. Our results demonstrated strong bactericidal effects of this photosensitizer on both strains of the bacteria, suggesting ZnPc-(Lys)5 as a promising antimicrobial photosensitizer for the treatment of infectious diseases caused by these bacteria.

Composition and extracellular enzymatic function of pelagic, particle-associated, and benthic bacterial communities in the central Arctic Ocean

NASA Astrophysics Data System (ADS)

Balmonte, J. P.; Teske, A.; Arnosti, C.

2016-02-01

The structure and function of Arctic bacterial communities have rarely been studied in concert, but are crucial to our understanding of biogeochemical cycles. As the Arctic transitions to become seasonally-ice free, a critical priority is to elucidate the present ecological role and environmental dependence of Arctic bacterial communities. We investigated the depth and regional variations in Central Arctic bacterial community composition (BCC) and extracellular enzymatic activities (EEA)—the initial step in organic matter breakdown—to explore links between community structure and function. Samples were collected across a gradient of sea-ice cover (open ocean, first year ice, multi-year ice) from 79°N to 88°N and from surface to bottom waters ( 3.5 to 4.5 km). Pelagic BCC most strongly varies with hydrography and with particle-association, which likely selects for a specialized community of heterotrophic opportunists; benthic BCC show little regional variation. In contrast, EEA reveal significant depth and regional differences in hydrolysis rates as well as in the spectrum of substrates hydrolyzed. Particle-associated EEA reveal an equal or greater range of enzymatic capabilities than in bulk-seawater measurements, supporting previous findings that particles are hotspots of microbial heterotrophic activity. These patterns suggest a complex relationship between BCC, EEA, and the environment: while water mass characteristics consistently differentiate bacterial communities, additional local factors shape their capabilities to hydrolyze organic matter. Multivariate analyses will be used to further explore the relationships between composition and function as well as their correlations with environmental data. Our findings provide a baseline for future comparisons and initial insight into the functionality and biogeography of Arctic bacterial communities.

Structural Basis of Mitochondrial Transcription Initiation.

PubMed

Hillen, Hauke S; Morozov, Yaroslav I; Sarfallah, Azadeh; Temiakov, Dmitry; Cramer, Patrick

2017-11-16

Transcription in human mitochondria is driven by a single-subunit, factor-dependent RNA polymerase (mtRNAP). Despite its critical role in both expression and replication of the mitochondrial genome, transcription initiation by mtRNAP remains poorly understood. Here, we report crystal structures of human mitochondrial transcription initiation complexes assembled on both light and heavy strand promoters. The structures reveal how transcription factors TFAM and TFB2M assist mtRNAP to achieve promoter-dependent initiation. TFAM tethers the N-terminal region of mtRNAP to recruit the polymerase to the promoter whereas TFB2M induces structural changes in mtRNAP to enable promoter opening and trapping of the DNA non-template strand. Structural comparisons demonstrate that the initiation mechanism in mitochondria is distinct from that in the well-studied nuclear, bacterial, or bacteriophage transcription systems but that similarities are found on the topological and conceptual level. These results provide a framework for studying the regulation of gene expression and DNA replication in mitochondria. Copyright © 2017 Elsevier Inc. All rights reserved.

Complement Regulator Factor H Mediates a Two-step Uptake of Streptococcus pneumoniae by Human Cells*

PubMed Central

Agarwal, Vaibhav; Asmat, Tauseef M.; Luo, Shanshan; Jensch, Inga; Zipfel, Peter F.; Hammerschmidt, Sven

2010-01-01

Streptococcus pneumoniae, a human pathogen, recruits complement regulator factor H to its bacterial cell surface. The bacterial PspC protein binds Factor H via short consensus repeats (SCR) 8–11 and SCR19–20. In this study, we define how bacterially bound Factor H promotes pneumococcal adherence to and uptake by epithelial cells or human polymorphonuclear leukocytes (PMNs) via a two-step process. First, pneumococcal adherence to epithelial cells was significantly reduced by heparin and dermatan sulfate. However, none of the glycosaminoglycans affected binding of Factor H to pneumococci. Adherence of pneumococci to human epithelial cells was inhibited by monoclonal antibodies recognizing SCR19–20 of Factor H suggesting that the C-terminal glycosaminoglycan-binding region of Factor H mediates the contact between pneumococci and human cells. Blocking of the integrin CR3 receptor, i.e. CD11b and CD18, of PMNs or CR3-expressing epithelial cells reduced significantly the interaction of pneumococci with both cell types. Similarly, an additional CR3 ligand, Pra1, derived from Candida albicans, blocked the interaction of pneumococci with PMNs. Strikingly, Pra1 inhibited also pneumococcal uptake by lung epithelial cells but not adherence. In addition, invasion of Factor H-coated pneumococci required the dynamics of host-cell actin microfilaments and was affected by inhibitors of protein-tyrosine kinases and phosphatidylinositol 3-kinase. In conclusion, pneumococcal entry into host cells via Factor H is based on a two-step mechanism. The first and initial contact of Factor H-coated pneumococci is mediated by glycosaminoglycans expressed on the surface of human cells, and the second step, pneumococcal uptake, is integrin-mediated and depends on host signaling molecules such as phosphatidylinositol 3-kinase. PMID:20504767

Effects of Cover Crop Species and Season on Population Dynamics of Escherichia coli and Listeria innocua in Soil

PubMed Central

Reed-Jones, Neiunna L.; Marine, Sasha Cahn; Everts, Kathryne L.

2016-01-01

Cover crops provide several ecosystem services, but their impact on enteric bacterial survival remains unexplored. The influence of cover cropping on foodborne pathogen indicator bacteria was assessed in five cover crop/green manure systems: cereal rye, hairy vetch, crimson clover, hairy vetch-rye and crimson clover-rye mixtures, and bare ground. Cover crop plots were inoculated with Escherichia coli and Listeria innocua in the fall of 2013 and 2014 and tilled into the soil in the spring to form green manure. Soil samples were collected and the bacteria enumerated. Time was a factor for all bacterial populations studied in all fields (P < 0.001). E. coli levels declined when soil temperatures dipped to <5°C and were detected only sporadically the following spring. L. innocua diminished somewhat but persisted, independently of season. In an organic field, the cover crop was a factor for E. coli in year 1 (P = 0.004) and for L. innocua in year 2 (P = 0.011). In year 1, E. coli levels were highest in the rye and hairy vetch-rye plots. In year 2, L. innocua levels were higher in hairy vetch-rye (P = 0.01) and hairy vetch (P = 0.03) plots than in the rye plot. Bacterial populations grew (P < 0.05) or remained the same 4 weeks after green manure incorporation, although initial reductions in L. innocua numbers were observed after tilling (P < 0.05). Green manure type was a factor only for L. innocua abundance in a transitional field (P < 0.05). Overall, the impacts of cover crops/green manures on bacterial population dynamics in soil varied, being influenced by bacterial species, time from inoculation, soil temperature, rainfall, and tillage; this reveals the need for long-term studies. PMID:26729724

Bacterial Cytolysin during Meningitis Disrupts the Regulation of Glutamate in the Brain, Leading to Synaptic Damage

PubMed Central

Wippel, Carolin; Maurer, Jana; Förtsch, Christina; Hupp, Sabrina; Bohl, Alexandra; Ma, Jiangtao; Mitchell, Timothy J.; Bunkowski, Stephanie; Brück, Wolfgang; Nau, Roland; Iliev, Asparouh I.

2013-01-01

Streptococcus pneumoniae (pneumococcal) meningitis is a common bacterial infection of the brain. The cholesterol-dependent cytolysin pneumolysin represents a key factor, determining the neuropathogenic potential of the pneumococci. Here, we demonstrate selective synaptic loss within the superficial layers of the frontal neocortex of post-mortem brain samples from individuals with pneumococcal meningitis. A similar effect was observed in mice with pneumococcal meningitis only when the bacteria expressed the pore-forming cholesterol-dependent cytolysin pneumolysin. Exposure of acute mouse brain slices to only pore-competent pneumolysin at disease-relevant, non-lytic concentrations caused permanent dendritic swelling, dendritic spine elimination and synaptic loss. The NMDA glutamate receptor antagonists MK801 and D-AP5 reduced this pathology. Pneumolysin increased glutamate levels within the mouse brain slices. In mouse astrocytes, pneumolysin initiated the release of glutamate in a calcium-dependent manner. We propose that pneumolysin plays a significant synapto- and dendritotoxic role in pneumococcal meningitis by initiating glutamate release from astrocytes, leading to subsequent glutamate-dependent synaptic damage. We outline for the first time the occurrence of synaptic pathology in pneumococcal meningitis and demonstrate that a bacterial cytolysin can dysregulate the control of glutamate in the brain, inducing excitotoxic damage. PMID:23785278

Novel Model for Multispecies Biofilms That Uses Rigid Gas-Permeable Lenses ▿

PubMed Central

Peyyala, Rebecca; Kirakodu, Sreenatha S.; Ebersole, Jeffrey L.; Novak, Karen F.

2011-01-01

Oral biofilms comprise complex multispecies consortia aided by specific inter- and intraspecies interactions occurring among commensals and pathogenic bacterial species. Oral biofilms are primary initiating factors of periodontal disease, although complex multifactorial biological influences, including host cell responses, contribute to the individual outcome of the disease. To provide a system to study initial stages of interaction between oral biofilms and the host cells that contribute to the disease process, we developed a novel in vitro model system to grow biofilms on rigid gas-permeable contact lenses (RGPLs), which enable oxygen to permeate through the lens material. Bacterial species belonging to early- and late-colonizing groups were successfully established as single- or three-species biofilms, with each group comprising Streptococcus gordonii, Streptococcus oralis, and Streptococcus sanguinis; S. gordonii, Actinomyces naeslundii, and Fusobacterium nucleatum; or S. gordonii, F. nucleatum, and Porphyromonas gingivalis. Quantification of biofilm numbers by quantitative PCR (qPCR) revealed substantial differences in the magnitude of bacterial numbers in single-species and multispecies biofilms. We evaluated cell-permeable conventional nucleic acid stains acridine orange, hexidium iodide, and Hoechst 33258 and novel SYTO red, blue, and green fluorochromes for their effect on bacterial viability and fluorescence yield to allow visualization of the aggregates of individual bacterial species by confocal laser scanning microscopy (CLSM). Substantial differences in the quantity and distribution of the species in the multispecies biofilms were identified. The specific features of these biofilms may help us better understand the role of various bacteria in local challenge of oral tissues. PMID:21421785

Development of a molecular method for testing the effectiveness of UV systems on-site.

PubMed

Nizri, Limor; Vaizel-Ohayon, Dalit; Ben-Amram, Hila; Sharaby, Yehonatan; Halpern, Malka; Mamane, Hadas

2017-12-15

We established a molecular method for quantifying ultraviolet (UV) disinfection efficacy using total bacterial DNA in a water sample. To evaluate UV damage to the DNA, we developed the "DNA damage" factor, which is a novel cultivation-independent approach that reveals UV-exposure efficiency by applying a simple PCR amplification method. The study's goal was to prove the feasibility of this method for demonstrating the efficiency of UV systems in the field using flow-through UV reactors. In laboratory-based experiments using seeded bacteria, the DNA damage tests demonstrated a good correlation between PCR products and UV dose. In the field, natural groundwater sampled before and after being subjected to the full-scale UV reactors was filtered, and the DNA extracted from the filtrate was subjected to PCR amplification for a 900-bp fragment of the 16S rRNA gene with initial DNA concentrations of 0.1 and 1 ng/μL. In both cases, the UV dose predicted and explained a significant proportion of the variance in the log inactivation ratio and DNA damage factor. Log inactivation ratio was very low, as expected in groundwater due to low initial bacterial counts, whereas the DNA damage factor was within the range of values obtained in the laboratory-based experiments. Consequently, the DNA damage factor reflected the true performance of the full-scale UV system during operational water flow by using the indigenous bacterial array present in a water sample. By applying this method, we were able to predict with high confidence, the UV reactor inactivation potential. For method validation, laboratory and field iterations are required to create a practical field calibration curve that can be used to determine the expected efficiency of the full-scale UV system in the field under actual operation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Responses of Baltic Sea Ice and Open-Water Natural Bacterial Communities to Salinity Change

PubMed Central

Kaartokallio, Hermanni; Laamanen, Maria; Sivonen, Kaarina

2005-01-01

To investigate the responses of Baltic Sea wintertime bacterial communities to changing salinity (5 to 26 practical salinity units), an experimental study was conducted. Bacterial communities of Baltic seawater and sea ice from a coastal site in southwest Finland were used in two batch culture experiments run for 17 or 18 days at 0°C. Bacterial abundance, cell volume, and leucine and thymidine incorporation were measured during the experiments. The bacterial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) of PCR-amplified partial 16S rRNA genes with sequencing of DGGE bands from initial communities and communities of day 10 or 13 of the experiment. The sea ice-derived bacterial community was metabolically more active than the open-water community at the start of the experiment. Ice-derived bacterial communities were able to adapt to salinity change with smaller effects on physiology and community structure, whereas in the open-water bacterial communities, the bacterial cell volume evolution, bacterial abundance, and community structure responses indicated the presence of salinity stress. The closest relatives for all eight partial 16S rRNA gene sequences obtained were either organisms found in polar sea ice and other cold habitats or those found in summertime Baltic seawater. All sequences except one were associated with the α- and γ-proteobacteria or the Cytophaga-Flavobacterium-Bacteroides group. The overall physiological and community structure responses were parallel in ice-derived and open-water bacterial assemblages, which points to a linkage between community structure and physiology. These results support previous assumptions of the role of salinity fluctuation as a major selective factor shaping the sea ice bacterial community structure. PMID:16085826

Increasing RpoS expression causes cell death in Borrelia burgdorferi.

PubMed

Chen, Linxu; Xu, Qilong; Tu, Jiagang; Ge, Yihe; Liu, Jun; Liang, Fang Ting

2013-01-01

RpoS, one of the two alternative σ factors in Borrelia burgdorferi, is tightly controlled by multiple regulators and, in turn, determines expression of many critical virulence factors. Here we show that increasing RpoS expression causes cell death. The immediate effect of increasing RpoS expression was to promote bacterial division and as a consequence result in a rapid increase in cell number before causing bacterial death. No DNA fragmentation or degradation was observed during this induced cell death. Cryo-electron microscopy showed induced cells first formed blebs, which were eventually released from dying cells. Apparently blebbing initiated cell disintegration leading to cell death. These findings led us to hypothesize that increasing RpoS expression triggers intracellular programs and/or pathways that cause spirochete death. The potential biological significance of induced cell death may help B. burgdorferi regulate its population to maintain its life cycle in nature.

Study on the biodegradation of crude oil by free and immobilized bacterial consortium in marine environment.

PubMed

Chen, Qingguo; Li, Jingjing; Liu, Mei; Sun, Huiling; Bao, Mutai

2017-01-01

Five strains of bacteria, namely, Exiguobacterium sp. ASW-1, Pseudomonas aeruginosa strain ASW-2, Alcaligenes sp. ASW-3, Alcaligenes sp. ASS-1, and Bacillus sp. ASS-2, were isolated from the Zhejiang coast in China. The mixed flora of the five strains performed well with degrading 75.1% crude oil (1%, w/v) in 7 days. The calcium alginate-activated carbon embedding carrier was used to immobilize bacterial consortium. Immobilized cells performed better than free ones in variations of environmental factors containing incubated temperature, initial pH, salinity of the medium and crude oil concentration. The degradation process of crude oil by immobilized bacteria was accelerated compared with that of the free ones. Bacterial consortium showed better performance on biodegradation of normal alkanes than that of PAHs. Improvement of immobilization on the biodegradation efficiency of normal alkanes (31.9%) was apparently high than that of PAHs (1.9%).

Mortality from bacterial meningitis in children in Kosovo.

PubMed

Namani, Sadie; Milenkovic, Zvonko; Kuchar, Ernest; Koci, Remzie; Mehmeti, Murat

2012-01-01

Bacterial meningitis is a severe infection responsible for high mortality. This prospective study of 277 pediatric bacterial meningitis cases was done to identify factors predicting death in children <16 years of age living and treated in a limited-resources country (Kosovo). Of the 277 children enrolled, 60 patients (22%) developed neurologic complications, and 15 children died (5%). The following variables were strongly correlated with mortality: altered mental status on admission (relative risk [RR] = 29.9), presentation of the initial cerebrospinal fluid as thick pus (RR = 29.9), prehospital seizures (RR = 23.5) and their recurrence >24 hours after admission (RR = 11.5), age <1 month (RR = 19.3), the use of inotropic agents (RR = 11.5), and admission after 5 days' duration of illness (P < .001). The mortality rate in children in Kosovo is similar to those reported from developing countries, and this is most likely due to the unfavorable living conditions.

Study on the biodegradation of crude oil by free and immobilized bacterial consortium in marine environment

PubMed Central

Li, Jingjing; Liu, Mei; Sun, Huiling; Bao, Mutai

2017-01-01

Five strains of bacteria, namely, Exiguobacterium sp. ASW-1, Pseudomonas aeruginosa strain ASW-2, Alcaligenes sp. ASW-3, Alcaligenes sp. ASS-1, and Bacillus sp. ASS-2, were isolated from the Zhejiang coast in China. The mixed flora of the five strains performed well with degrading 75.1% crude oil (1%, w/v) in 7 days. The calcium alginate—activated carbon embedding carrier was used to immobilize bacterial consortium. Immobilized cells performed better than free ones in variations of environmental factors containing incubated temperature, initial pH, salinity of the medium and crude oil concentration. The degradation process of crude oil by immobilized bacteria was accelerated compared with that of the free ones. Bacterial consortium showed better performance on biodegradation of normal alkanes than that of PAHs. Improvement of immobilization on the biodegradation efficiency of normal alkanes (31.9%) was apparently high than that of PAHs (1.9%). PMID:28346510

Brood size modifications affect plumage bacterial assemblages of European starlings.

PubMed

Lucas, Françoise S; Moureau, Benoit; Jourdie, Violaine; Heeb, Philipp

2005-02-01

During reproduction, birds face trade-offs between time and energy devoted to parental effort and traits associated with self-maintenance. We manipulated brood sizes to investigate the effects of such trade-offs on feather bacterial densities and the structure of bacterial assemblages on feathers in adult European starlings, Sturnus vulgaris, and in vitro feather degradation. As predicted by a trade-off between parental effort and self-maintenance, we found that birds with enlarged broods had more free-living bacteria on their feathers than birds with reduced broods. Furthermore, we found a significant interaction between brood manipulation and original brood size on free-living bacterial densities suggesting that the trade-off is mediated by the adults' initial reproductive investment. In contrast, brood size manipulations had no significant effect on densities of attached bacteria. Using ribosomal intergenic spacer analysis (RISA), we demonstrated that brood manipulations significantly modified the structure (band pattern) of feather-degrading bacterial assemblages, but had no significant effect on their richness (number of bands) or the in vitro feather degradation. In vitro feather degradation varied in relation to the premanipulation brood size and positively with the richness of the feather degrading bacterial community. Besides brood manipulation effect, we found that ecological factors and individual traits, such as the age, the nest location or the capture date, shaped bacterial assemblages and feather degradation capacities.

[Acute care of patients with bacterial meningitis].

PubMed

Stetefeld, H R; Dohmen, C

2016-04-01

Bacterial meningitis is a life-threatening emergency that is still associated with high mortality and poor outcome. The purpose of this article is to provide a review of clinical presentation, diagnostic procedure, therapy, and prognosis in bacterial meningitis. Prognostic factors which could be influenced positively are identified and a focused procedure in the emergency setting and for the treatment of complications are provided. This work is based on a literature search (PubMed, guidelines) and personal experience (standard operating procedures, SOP). Despite improved health care, bacterial meningitis is still associated with high mortality and poor neurological outcome, which has remained largely unaltered during recent decades. Diagnosis and, more importantly, effective therapy of bacterial meningitis are often delayed, having an immediate negative influence on clinical outcome. Neurological and nonneurological complications often necessitate intensive care and may occur rapidly or in the further course of the disease. Immediate initiation of effective therapy is crucial to positively influence mortality and neurological outcome. Antibiotics should be administered within 30 min after admission. To achieve this, a focused and well-organized procedure in the emergency setting is necessary. Because of intra- and extracranial complications, patients need to be treated on intensive care units including neurological expertise and interdisciplinary support.

The absence of the N-acyl-homoserine-lactone autoinducer synthase genes tral and ngrl increases the copy number of the symbiotic plasmid in Sinorhizobium fredii NGR234

USDA-ARS?s Scientific Manuscript database

Plant-released flavonoids induce the transcription of symbiotic genes in rhizobia and one of the first bacterial responses is the synthesis of so called Nod factors. They are responsible for the initial root hair curling during onset of root nodule development. This signal exchange is believed to be...

Uncovering stability mechanisms in microbial ecosystems - combining microcosm experiments, computational modelling and ecological theory in a multidisciplinary approach

NASA Astrophysics Data System (ADS)

Worrich, Anja; König, Sara; Banitz, Thomas; Centler, Florian; Frank, Karin; Kästner, Matthias; Miltner, Anja; Thullner, Martin; Wick, Lukas

2015-04-01

Although bacterial degraders in soil are commonly exposed to fluctuating environmental conditions, the functional performance of the biodegradation processes can often be maintained by resistance and resilience mechanisms. However, there is still a gap in the mechanistic understanding of key factors contributing to the stability of such an ecosystem service. Therefore we developed an integrated approach combining microcosm experiments, simulation models and ecological theory to directly make use of the strengths of these disciplines. In a continuous interplay process, data, hypotheses, and central questions are exchanged between disciplines to initiate new experiments and models to ultimately identify buffer mechanisms and factors providing functional stability. We focus on drying and rewetting-cycles in soil ecosystems, which are a major abiotic driver for bacterial activity. Functional recovery of the system was found to depend on different spatial processes in the computational model. In particular, bacterial motility is a prerequisite for biodegradation if either bacteria or substrate are heterogeneously distributed. Hence, laboratory experiments focussing on bacterial dispersal processes were conducted and confirmed this finding also for functional resistance. Obtained results will be incorporated into the model in the next step. Overall, the combination of computational modelling and laboratory experiments identified spatial processes as the main driving force for functional stability in the considered system, and has proved a powerful methodological approach.

Composition and development of oral bacterial communities.

PubMed

Palmer, Robert J

2014-02-01

The oral bacterial microbiome encompasses approximately 700 commonly occurring phylotypes, approximately half of which can be present at any time in any individual. These bacteria are largely indigenous to the oral cavity; this limited habitat range suggests that interactions between the various phylotypes, and between the phylotypes and their environment, are crucial for their existence. Molecular cataloging has confirmed many basic observations on the composition of the oral microbiome that were formulated well before ribosomal RNA-based systematics, but the power and the scope of molecular taxonomy have resulted in the discovery of new phylotypes and, more importantly, have made possible a level of bacterial community analysis that was unachievable with classical methods. Bacterial community structure varies with location within the mouth, and changes in community structure are related to disease initiation and disease progression. Factors that influence the formation and the evolution of communities include selective adherence to epithelial or tooth surfaces, specific cell-to-cell binding as a driver of early community composition, and interorganismal interaction leading to alteration of the local environment, which represents the first step on the road to oral disease. A comprehensive understanding of how these factors interact to drive changes in the composition of the oral microbial community can lead to new strategies for the inhibition of periodontal diseases and dental caries. Published 2013. This article is a US Government work and is in the public domain in the USA.

[Clinical outcome and prognosis of neonatal bacterial meningitis].

PubMed

Ben Hamouda, H; Ben Haj Khalifa, A; Hamza, M A; Ayadi, A; Soua, H; Khedher, M; Sfar, M T

2013-09-01

To study the epidemiological, clinical, and bacteriological aspects as well as the outcome of neonatal bacterial meningitis and analyze the factors of poor prognosis of this condition. We report a retrospective analysis of 44 cases of neonatal bacterial meningitis hospitalized in the pediatric unit of Tahar Sfar Hospital in Mahdia, Tunisia, between January 1996 and December 2010. Inclusion criteria were infants less than 29 days of age who were hospitalized for bacterial meningitis diagnosed on either the presence of bacteria in cerebrospinal fluid or with more than 50 cells/mm(3), predominance of neutrophils, and the protein level greater than 1.2g/l. Clinical data were obtained through the analysis of patient files. Statistical analysis was based on the Chi(2) test, and P-values less than 0.05 were considered statistically significant. The incidence of neonatal bacterial meningitis was 0.49 per 1000 live births. The patients were premature in 20.4 % and low birth weight in 13.6 % of cases. The clinical presentation was not specific for most cases. The main signs at admission were hyperthermia (43.2 %), refusal to nurse (20.4 %), seizures (18.2 %), and respiratory distress (13.6 %). The cerebrospinal fluid culture was positive in 36.4 % of cases. The group B streptococcus was the most frequently isolated (62.5 %) followed by Escherichia coli (12.5 %). The association of cefotaxime-ampicillin-gentamicin was used as the first treatment in all cases. Ofloxacin was associated with initial antibiotic therapy during the first 5 days in 20.4 % of cases. The mortality rate was 15.9 % and the rate of neurological sequelae in survivors was 21.6 %. Prematurity, low birth weight, shock, respiratory distress, and pleocytosis of less than 500 cells/mm(3) were the main factors of a poor prognosis. The addition of ofloxacin to the initial antibiotic therapy was associated with a decreased rate of neurological sequelae in survivors (11 % vs. 25 %, P=0.042). This study emphasizes the severity of neonatal bacterial meningitis with high rates of mortality and neurological sequelae, especially in premature and low birth weight infants. An early diagnosis and effective antibiotic therapy is needed to improve the prognosis. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Characterization of initial events in bacterial surface colonization by two Pseudomonas species using image analysis.

PubMed

Mueller, R F; Characklis, W G; Jones, W L; Sears, J T

1992-05-01

The processes leading to bacterial colonization on solid-water interfaces are adsorption, desorption, growth, and erosion. These processes have been measured individually in situ in a flowing system in real time using image analysis. Four different substrata (copper, silicon, 316 stainless-steel and glass) and 2 different bacterial species (Pseudomonas aeruginosa and Pseudomonas fluorescens) were used in the experiments. The flow was laminar (Re = 1.4) and the shear stress was kept constant during all experiments at 0.75 N m(-2). The surface roughness varied among the substrata from 0.002 microm (for silicon) to 0.015 microm (for copper). Surface free energies varied from 25.1 dynes cm(-1) for silicon to 31.2 dynes cm(-1) for copper. Cell curface hydrophobicity, reported as hydrocarbon partitioning values, ranged from 0.67 for Ps. fluorescens to 0.97 for Ps. aeruginosa.The adsorption rate coefficient varied by as much as a factor of 10 among the combinations of bacterial strain and substratum material, and was positively correlated with surface free energy, the surface roughness of the substratum, and the hydrophobicity of the cells. The probability of desorption decreased with increasing surface free energy and surface roughness of the substratum. Cell growth was inhibited on copper, but replication of cells overlying an initial cell layer was observed with increased exposure time to the cell-containing bulk water. A mathematical model describing cell accumulation on a substratum is presented.

Temperature adaptation of bacterial communities in experimentally warmed forest soils.

PubMed

Rousk, Johannes; Frey, Serita D; Bååth, Erland

2012-10-01

A detailed understanding of the influence of temperature on soil microbial activity is critical to predict future atmospheric CO 2 concentrations and feedbacks to anthropogenic warming. We investigated soils exposed to 3-4 years of continuous 5 °C-warming in a field experiment in a temperate forest. We found that an index for the temperature adaptation of the microbial community, T min for bacterial growth, increased by 0.19 °C per 1 °C rise in temperature, showing a community shift towards one adapted to higher temperature with a higher temperature sensitivity (Q 10(5-15 °C) increased by 0.08 units per 1 °C). Using continuously measured temperature data from the field experiment we modelled in situ bacterial growth. Assuming that warming did not affect resource availability, bacterial growth was modelled to become 60% higher in warmed compared to the control plots, with the effect of temperature adaptation of the community only having a small effect on overall bacterial growth (<5%). However, 3 years of warming decreased bacterial growth, most likely due to substrate depletion because of the initially higher growth in warmed plots. When this was factored in, the result was similar rates of modelled in situ bacterial growth in warmed and control plots after 3 years, despite the temperature difference. We conclude that although temperature adaptation for bacterial growth to higher temperatures was detectable, its influence on annual bacterial growth was minor, and overshadowed by the direct temperature effect on growth rates. © 2012 Blackwell Publishing Ltd.

Exploring the cause of initially reactive bovine brains on rapid tests for BSE

PubMed Central

Dudas, Sandor; James, Jace; Anderson, Renee; Czub, Stefanie

2015-01-01

ABSTRACT Bovine spongiform encephalopathy (BSE) is an invariably fatal prion disease of cattle. The identification of the zoonotic potential of BSE prompted safety officials to initiate surveillance testing for this disease. In Canada, BSE surveillance is primarily focused on high risk cattle including animals which are dead, down and unable to rise, diseased or distressed. This targeted surveillance results in the submission of brain samples with a wide range of tissue autolysis and associated contaminants. These contaminants have the potential to interfere with important steps of surveillance tests resulting in initially positive test results requiring additional testing to confirm the disease status of the animal. The current tests used for BSE screening in Canada utilize the relative protease resistance of the prion protein gained when it misfolds from PrPC to PrPSc as part of the disease process. Proteinase K completely digests PrPC in normal brains, but leaves most of the PrPSc in BSE positive brains intact which is detected using anti-prion antibodies. These tests are highly reliable but occasionally give rise to initially reactive/false positive results. Test results for these reactive samples were close to the positive/negative cut-off on a sub set of test platforms. This is in contrast to all of the previous Canadian positive samples whose numeric values on these same test platforms were 10 to 100 fold greater than the test positive/negative cut-off. Here we explore the potential reason why a sample is repeatedly positive on a sub-set of rapid surveillance tests, but negative on other test platforms. In order to better understand and identify what might cause these initial reactions, we have conducted a variety of rapid and confirmatory assays as well as bacterial isolation and identification on BSE positive, negative and initially reactive samples. We observed high levels of viable bacterial contamination in initially reactive samples suggesting that the reactivity may be related to bacterial factors. Several bacteria isolated from the initially reactive samples have characteristics of biofilm forming bacteria and this extracellular matrix might play a role in preventing complete digestion of PrPC in these samples. PMID:26689488

THE RELATIONSHIP OF THE CHEMOTACTIC BEHAVIOR OF THE COMPLEMENT-DERIVED FACTORS, C3a, C5a, AND C567, AND A BACTERIAL CHEMOTACTIC FACTOR TO THEIR ABILITY TO ACTIVATE THE PROESTERASE 1 OF RABBIT POLYMORPHONUCLEAR LEUKOCYTES

PubMed Central

Becker, Elmer L.

1972-01-01

The inhibition profiles obtained when a series of p-nitrophenyl ethyl alkylphosphonates and of p-nitrophenyl ethyl chloroalkylphosphonates were used to interfere with the chemotactic activity of polymorphonuclear leukocytes stimulated by C3a, C5a, and bacterial factor were the same as found previously when C567 was the chemotactic agent. This indicates that as in the chemotactic activity induced by C567, an obligatory step in the chemotaxis caused by C3a, C5a, and bacterial factor is the activation of proesterase 1 of the rabbit polymorphonuclear leukocyte. C5a and C3a activate proesterase 1 of peripheral blood polymophonuclear leukocytes as measured by the increase of acetyl DL-phenylalanine β-naphthyl esterase activity. Attempts to detect in a like manner the proesterase 1 of the same leukocytes using bacterial factor under varying circumstances have consistently failed. It is concluded that bacterial factor, for unknown reasons, is unable to activate proesterase 1 to the same extent as the complement-derived chemotactic factors. The hypothesis of there being a quantitative difference in the ability of bacterial factor to activate proesterase 1 compared with the complement-derived factors explains the previous observations that bacterial factor can not deactivate to itself or to the complement-derived factors, although these latter factors can deactivate to themselves, to each other, and to the bacterial factor. The quantitative difference in the ability of bacterial factor to activate proesterase 1 compared to the complement-derived factors is also associated with and explains the finding that the maximal chemotactic activity attainable when bacterial factor is the chemotactic agent is distinctly less than that obtained using either C3a, C5a, or C567. These results indicate that the activation of proesterase 1 is a general requirement for the chemotactic activity of rabbit polymorphonuclear leukocytes with known macromolecular chemotactic agents and suggest that under several different circumstances the level of chemotactic activity attained is related to the degree of such activation. PMID:4551218

Streptococcus pyogenes CAMP factor promotes bacterial adhesion and invasion in pharyngeal epithelial cells without serum via PI3K/Akt signaling pathway.

PubMed

Kurosawa, Mie; Oda, Masataka; Domon, Hisanori; Isono, Toshihito; Nakamura, Yuki; Saitoh, Issei; Hayasaki, Haruaki; Yamaguchi, Masaya; Kawabata, Shigetada; Terao, Yutaka

2018-01-01

Streptococcus pyogenes is a bacterium that causes systemic diseases, such as pharyngitis and toxic shock syndrome, via oral- or nasal-cavity infection. S. pyogenes produces various molecules known to function with serum components that lead to bacterial adhesion and invasion in human tissues. In this study, we identified a novel S. pyogenes adhesin/invasin. Our results revealed that CAMP factor promoted streptococcal adhesion and invasion in pharyngeal epithelial Detroit562 cells without serum. Recombinant CAMP factor initially localized on the membranes of cells and then became internalized in the cytosol following S. pyogenes infection. Additionally, CAMP factor phosphorylated phosphoinositide 3-kinase and serine-threonine kinase in the cells. ELISA results demonstrate that CAMP factor affected the amount of phosphorylated phosphoinositide 3-kinase and serine-threonine kinase in Detroit562 cells. Furthermore, CAMP factor did not reverse the effect of phosphoinositide 3-kinase knockdown by small interfering RNA in reducing the level of adhesion and invasion of S. pyogenes isogenic cfa-deficient mutant. These results suggested that S. pyogenes CAMP factor activated the phosphoinositide 3-kinase/serine-threonine kinase signaling pathway, promoting S. pyogenes invasion of Detroit562 cells without serum. Our findings suggested that CAMP factor played an important role on adhesion and invasion in pharyngeal epithelial cells. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Disease notes - Bacterial root rot

USDA-ARS?s Scientific Manuscript database

Bacterial root rot initiated by lactic acid bacteria, particularly Leuconostoc, occurs every year in Idaho sugarbeet fields. Hot fall weather seems to make the problem worse. Although Leuconostoc initiates the rot, other bacteria and yeast frequently invade the tissue as well. The acetic acid bac...

Structure, Function, and Assembly of Adhesive Organelles by Uropathogenic Bacteria

PubMed Central

Chahales, Peter; Thanassi, David G.

2015-01-01

Bacteria assemble a wide range of adhesive proteins, termed adhesins, to mediate binding to receptors and colonization of surfaces. For pathogenic bacteria, adhesins are critical for early stages of infection, allowing the bacteria to initiate contact with host cells, colonize different tissues, and establish a foothold within the host. The adhesins expressed by a pathogen are also critical for bacterial-bacterial interactions and the formation of bacterial communities such as biofilms. The ability to adhere to host tissues is particularly important for bacteria that colonize sites such as the urinary tract, where the flow of urine functions to maintain sterility by washing away non-adherent pathogens. Adhesins vary from monomeric proteins that are directly anchored to the bacterial surface to polymeric, hairlike fibers that extend out from the cell surface. These latter fibers are termed pili or fimbriae, and were among the first identified virulence factors of uropathogenic Escherichia coli. Studies since then have identified a range of both pilus and non-pilus adhesins that contribute to bacterial colonization of the urinary tract, and have revealed molecular details of the structures, assembly pathways, and functions of these adhesive organelles. In this review, we describe the different types of adhesins expressed by both Gram-negative and Gram-positive uropathogens, what is known about their structures, how they are assembled on the bacterial surface, and the functions of specific adhesins in the pathogenesis of urinary tract infections. PMID:26542038

Effects of Cover Crop Species and Season on Population Dynamics of Escherichia coli and Listeria innocua in Soil.

PubMed

Reed-Jones, Neiunna L; Marine, Sasha Cahn; Everts, Kathryne L; Micallef, Shirley A

2016-01-04

Cover crops provide several ecosystem services, but their impact on enteric bacterial survival remains unexplored. The influence of cover cropping on foodborne pathogen indicator bacteria was assessed in five cover crop/green manure systems: cereal rye, hairy vetch, crimson clover, hairy vetch-rye and crimson clover-rye mixtures, and bare ground. Cover crop plots were inoculated with Escherichia coli and Listeria innocua in the fall of 2013 and 2014 and tilled into the soil in the spring to form green manure. Soil samples were collected and the bacteria enumerated. Time was a factor for all bacterial populations studied in all fields (P < 0.001). E. coli levels declined when soil temperatures dipped to <5°C and were detected only sporadically the following spring. L. innocua diminished somewhat but persisted, independently of season. In an organic field, the cover crop was a factor for E. coli in year 1 (P = 0.004) and for L. innocua in year 2 (P = 0.011). In year 1, E. coli levels were highest in the rye and hairy vetch-rye plots. In year 2, L. innocua levels were higher in hairy vetch-rye (P = 0.01) and hairy vetch (P = 0.03) plots than in the rye plot. Bacterial populations grew (P < 0.05) or remained the same 4 weeks after green manure incorporation, although initial reductions in L. innocua numbers were observed after tilling (P < 0.05). Green manure type was a factor only for L. innocua abundance in a transitional field (P < 0.05). Overall, the impacts of cover crops/green manures on bacterial population dynamics in soil varied, being influenced by bacterial species, time from inoculation, soil temperature, rainfall, and tillage; this reveals the need for long-term studies. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Microbial plant litter decomposition in aquatic and terrestrial boreal systems along a natural fertility gradient

NASA Astrophysics Data System (ADS)

Soares, A. Margarida P. M.; Kritzberg, Emma S.; Rousk, Johannes

2017-04-01

Plant litter decomposition is a global ecosystem process, with a crucial role in carbon and nutrient cycling. The majority of litter processing occurs in terrestrial systems, but an important fraction also takes place in inland waters. Among environmental factors, pH impacts the litter decomposition through its selective influence on microbial decomposers. Fungal communities are less affected by pH than bacteria, possibly owing to a wider pH tolerance by this group. On the other hand, bacterial pH optima are constrained to a narrower range of pH values. The microbial decomposition of litter is universally nutrient limited; but few comparisons exist between terrestrial and aquatic systems. We investigated the microbial colonisation and decomposition of plant litter along a fertility gradient, which varied in both pH and N availability in both soil and adjacent water. To do this we installed litterbags with birch (Betula pendula) in streams and corresponding soils in adjacent riparian areas in a boreal system, in Krycklan, Sweden. During the four months covering the ice-free growth season we monitored the successional dynamics of fungal (acetate incorporation into ergosterol) and bacterial growth (thymidine incorporation), microbial respiration in leaf litter, and quantitative and qualitative changes in litter over time. We observed that bacterial growth rates were initially higher in litter decomposing in streams than those in soils, but differences between terrestrial and aquatic bacterial production converged towards the end of the experiment. In litter bags installed in soils, bacterial growth was lower at sites with more acidic pH and lower N availability, while aquatic bacteria were relatively unaffected by the fertility level. Fungal growth rates were two-fold higher for litter decomposing in streams than in soils. In aquatic systems, fungal growth was initially lower in low fertility sites, but differences gradually disappeared over the time course. Fungal growth rates measured on litter-bags in soils were relatively stable over time, with unclear links to fertility. Microbial respiration rates were highest in litterbags buried in soils, and only initially negatively affected by pH. There was a large decrease in litter mass loss initially in aquatic systems. Subsequently the rates of loss stabilized to similar values to those in terrestrial systems, to finally be exceeded by the rates of loss in terrestrial systems. In conclusion, initial decomposition of litter appeared to be N-limited in aquatic systems, which was associated with a fungal dominance. In contrast, litter decomposition in terrestrial systems appeared to be lower in acidic sites, which coincided with lower growth rates of bacteria. Litter degradation was initially faster in aquatic systems, but overall mass-loss over the full time course was higher in terrestrial systems.

Exploring lot-to-lot variation in spoilage bacterial communities on commercial modified atmosphere packaged beef.

PubMed

Säde, Elina; Penttinen, Katri; Björkroth, Johanna; Hultman, Jenni

2017-04-01

Understanding the factors influencing meat bacterial communities is important as these communities are largely responsible for meat spoilage. The composition and structure of a bacterial community on a high-O 2 modified-atmosphere packaged beef product were examined after packaging, on the use-by date and two days after, to determine whether the communities at each stage were similar to those in samples taken from different production lots. Furthermore, we examined whether the taxa associated with product spoilage were distributed across production lots. Results from 16S rRNA amplicon sequencing showed that while the early samples harbored distinct bacterial communities, after 8-12 days storage at 6 °C the communities were similar to those in samples from different lots, comprising mainly of common meat spoilage bacteria Carnobacterium spp., Brochothrix spp., Leuconostoc spp. and Lactococcus spp. Interestingly, abundant operational taxonomic units associated with product spoilage were shared between the production lots, suggesting that the bacteria enable to spoil the product were constant contaminants in the production chain. A characteristic succession pattern and the distribution of common spoilage bacteria between lots suggest that both the packaging type and the initial community structure influenced the development of the spoilage bacterial community. Copyright © 2016 Elsevier Ltd. All rights reserved.

Microbiological changes associated with dental prophylaxis.

PubMed

Goodson, J Max; Palys, Michael D; Carpino, Elizabeth; Regan, Elizabeth O; Sweeney, Michael; Socransky, Sigmund S

2004-11-01

Despite the common application of dental prophylaxis as part of patient therapy, there is little reported that describes the microbiological impact of this treatment. The authors gave 20 healthy college-aged subjects three dental prophylaxes with a fluoride-containing prophylaxis paste during a two-week period and instructed them in oral hygiene. They evaluated the microbiological composition of dental plaque samples collected before and after treatment using DNA probe analysis. They analyzed 40 representative bacterial species in seven bacterial complexes by checkerboard DNA-DNA hybridization assay techniques. After three dental prophylaxes, the patients' mean Gingival Index score decreased from 0.82 to 0.77, the mean Plaque Index score decreased from 0.72 to zero, and the total number of bacteria per tooth decreased to approximately one-third of the original number. The authors computed two different measures of bacterial presence. The reduction in bacterial numbers was statistically significant and occurred in many species. Bacterial proportion (DNA percentage or percentage of the bacteria per tooth) did not change significantly. Greater reductions in bacterial count occurred in species that showed high numbers before treatment. The total bacterial count decreased by approximately 72 percent of its original level before prophylaxis was initiated. Professional dental prophylaxis did not target any particular bacteria or bacterial groups but removed bacteria nonspecifically and in proportion to their initial numbers. Repeated dental prophylaxes effect a reduction in bacterial amount that is commensurate with the initial amount, but they do does not alter composition. This suggests that mild gingivitis may be a bacterially nonspecific effect of plaque accumulation and emphasizes the need for regular plaque removal to maintain optimal gingival health.

Are Uncultivated Bacteria Really Uncultivable?

PubMed Central

Puspita, Indun Dewi; Kamagata, Yoichi; Tanaka, Michiko; Asano, Kozo; Nakatsu, Cindy H.

2012-01-01

Many strategies have been used to increase the number of bacterial cells that can be grown from environmental samples but cultivation efficiency remains a challenge for microbial ecologists. The difficulty of cultivating a fraction of bacteria in environmental samples can be classified into two non-exclusive categories. Bacterial taxa with no cultivated representatives for which appropriate laboratory conditions necessary for growth are yet to be identified. The other class is cells in a non-dividing state (also known as dormant or viable but not culturable cells) that require the removal or addition of certain factors to re-initiate growth. A number of strategies, from simple to high throughput techniques, are reviewed that have been used to increase the cultivation efficiency of environmental samples. Some of the underlying mechanisms that contribute to the success of these cultivation strategies are described. Overall this review emphasizes the need of researchers to first understand the factors that are hindering cultivation to identify the best strategies to improve cultivation efficiency. PMID:23059723

Gut microbiota and allergy: the importance of the pregnancy period.

PubMed

Abrahamsson, Thomas R; Wu, Richard You; Jenmalm, Maria C

2015-01-01

Limited microbial exposure is suggested to underlie the increase of allergic diseases in affluent countries, and bacterial diversity seems to be more important than specific bacteria taxa. Prospective studies indicate that the gut microbiota composition during the first months of life influences allergy development, and support the theory that factors influencing the early maturation of the immune system might be important for subsequent allergic disease. However, recent research indicates that microbial exposure during pregnancy may be even more important for the preventative effects against allergic disease. This review gives a background of the epidemiology, immunology, and microbiology literature in this field. It focuses on possible underlying mechanisms such as immune-regulated epigenetic imprinting and bacterial translocation during pregnancy, potentially providing the offspring with a pioneer microbiome. We suggest that a possible reason for the initial exposure of bacterial molecular patterns to the fetus in utero is to prime the immune system and/or the epithelium to respond appropriately to pathogens and commensals after birth.

Dynamic metabolic exchange governs a marine algal-bacterial interaction.

PubMed

Segev, Einat; Wyche, Thomas P; Kim, Ki Hyun; Petersen, Jörn; Ellebrandt, Claire; Vlamakis, Hera; Barteneva, Natasha; Paulson, Joseph N; Chai, Liraz; Clardy, Jon; Kolter, Roberto

2016-11-18

Emiliania huxleyi is a model coccolithophore micro-alga that generates vast blooms in the ocean. Bacteria are not considered among the major factors influencing coccolithophore physiology. Here we show through a laboratory model system that the bacterium Phaeobacter inhibens , a well-studied member of the Roseobacter group, intimately interacts with E. huxleyi. While attached to the algal cell, bacteria initially promote algal growth but ultimately kill their algal host. Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone indole-3-acetic acid. Bacterial production of indole-3-acetic acid and attachment to algae are significantly increased by tryptophan, which is exuded from the algal cell. Algal death triggered by bacteria involves activation of pathways unique to oxidative stress response and programmed cell death. Our observations suggest that bacteria greatly influence the physiology and metabolism of E. huxleyi. Coccolithophore-bacteria interactions should be further studied in the environment to determine whether they impact micro-algal population dynamics on a global scale.

Ligand-induced expansion of the S1' site in the anthrax toxin lethal factor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maize, Kimberly M.; Kurbanov, Elbek K.; Johnson, Rodney L.

2016-07-05

The Bacillus anthracis lethal factor (LF) is one component of a tripartite exotoxin partly responsible for persistent anthrax cytotoxicity after initial bacterial infection. Inhibitors of the zinc metalloproteinase have been investigated as potential therapeutic agents, but LF is a challenging target because inhibitors lack sufficient selectivity or possess poor pharmaceutical properties. These structural studies reveal an alternate conformation of the enzyme, induced upon binding of specific inhibitors, that opens a previously unobserved deep pocket termed S1'* which might afford new opportunities to design selective inhibitors that target this subsite.

[The quantitative recovery of microbes during testing of disinfectants for instruments].

PubMed

Höller, C; Gundermann, K O

1990-02-01

The efficacy of a disinfectant can only be determined exactly, when quantitative as well as qualitative tests are being performed. Aim of this study was to ascertain whether the earlier published method of a germ carrier test could be applied also to the testing of disinfectants for instruments. Rubber tubes of 1 cm length were used as germ carriers, Staph. aureus, Pseud. aerug., Proteus mir., E. coli and Cand. alb. as test organisms. The culture media were CASO-agar and -broth, latter containing 20% defibrinated sheep blood in some experiments. Two disinfectants on aldehyde-basis and one disinfectant on phenol-basis and on biguanide-basis, respectively, were used for the disinfectant tests. The rubber tubes were contaminated with bacterial suspension, dried upright on sterile filters and then put into 10 ml CASO-broth. After high speed vortexing of the germ carriers the bacterial count was determined. Following factors that were believed to probably having an influence on the recovery rate of bacteria were investigated: 1. the amount of fluid staying on the rubber tubes; 2. the drying time; 3. the vortexing time; 4. repeated vortexing; 5. variations of the initial concentration of bacteria on the rubber tubes; 6. addition of inactivating substances. ad 1. The mean amount of fluid staying on the tubes was 0.0056 g. ad 2. Drying times longer than 30 to 60 min resulted partly in considerably lower bacterial counts. ad. 3. and 4. Neither extension of vortexing time nor repeated vortexing of the same germ carrier could raise the recovery rate of bacteria. ad 5. Higher initial concentration of bacteria on the rubber tubes could not be achieved. The recovery rate of bacteria was reliable even when the initial bacterial concentration was low. ad 6. Addition of inactivating substances to the CASO-broth had no influence on the recovery rate of bacteria. The test method was checked by testing four disinfectants for instruments and proved itself a good and reliable quantitative method.

Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms

NASA Astrophysics Data System (ADS)

Ghanbari, Azadeh; Dehghany, Jaber; Schwebs, Timo; Müsken, Mathias; Häussler, Susanne; Meyer-Hermann, Michael

2016-09-01

Pseudomonas aeruginosa often colonises immunocompromised patients and the lungs of cystic fibrosis patients. It exhibits resistance to many antibiotics by forming biofilms, which makes it hard to eliminate. P. aeruginosa biofilms form mushroom-shaped structures under certain circumstances. Bacterial motility and the environment affect the eventual mushroom morphology. This study provides an agent-based model for the bacterial dynamics and interactions influencing bacterial biofilm shape. Cell motility in the model relies on recently published experimental data. Our simulations show colony formation by immotile cells. Motile cells escape from a single colony by nutrient chemotaxis and hence no mushroom shape develops. A high number density of non-motile colonies leads to migration of motile cells onto the top of the colonies and formation of mushroom-shaped structures. This model proposes that the formation of mushroom-shaped structures can be predicted by parameters at the time of bacteria inoculation. Depending on nutrient levels and the initial number density of stalks, mushroom-shaped structures only form in a restricted regime. This opens the possibility of early manipulation of spatial pattern formation in bacterial colonies, using environmental factors.

Inoculation density and nutrient level determine the formation of mushroom-shaped structures in Pseudomonas aeruginosa biofilms.

PubMed

Ghanbari, Azadeh; Dehghany, Jaber; Schwebs, Timo; Müsken, Mathias; Häussler, Susanne; Meyer-Hermann, Michael

2016-09-09

Pseudomonas aeruginosa often colonises immunocompromised patients and the lungs of cystic fibrosis patients. It exhibits resistance to many antibiotics by forming biofilms, which makes it hard to eliminate. P. aeruginosa biofilms form mushroom-shaped structures under certain circumstances. Bacterial motility and the environment affect the eventual mushroom morphology. This study provides an agent-based model for the bacterial dynamics and interactions influencing bacterial biofilm shape. Cell motility in the model relies on recently published experimental data. Our simulations show colony formation by immotile cells. Motile cells escape from a single colony by nutrient chemotaxis and hence no mushroom shape develops. A high number density of non-motile colonies leads to migration of motile cells onto the top of the colonies and formation of mushroom-shaped structures. This model proposes that the formation of mushroom-shaped structures can be predicted by parameters at the time of bacteria inoculation. Depending on nutrient levels and the initial number density of stalks, mushroom-shaped structures only form in a restricted regime. This opens the possibility of early manipulation of spatial pattern formation in bacterial colonies, using environmental factors.

Comparative evaluation of aggressiveness traits in staphylococcal strains from severe infections versus nasopharyngeal carriage.

PubMed

Săndulescu, Oana; Bleotu, Coralia; Matei, Lilia; Streinu-Cercel, Anca; Oprea, Mihaela; Drăgulescu, Elena Carmina; Chifiriuc, Mariana Carmen; Rafila, Alexandru; Pirici, Daniel; Tălăpan, Daniela; Dorobăţ, Olga Mihaela; Neguţ, Alina Cristina; Oţelea, Dan; Berciu, Ioana; Ion, Daniela Adriana; Codiţă, Irina; Calistru, Petre Iacob; Streinu-Cercel, Adrian

2017-01-01

Despite their commensal status, staphylococci can become problematic pathogens expressing multiple and redundant virulence factors. This study aimed to evaluate aggressiveness markers comparatively in staphylococcal strains isolated from severe infections versus asymptomatic carriage in order to identify clinically relevant bacterial traits that could easily be detected in clinical practice and could be suggestive for particular host-pathogen interactions such as cyto-adhesion or biofilm formation, ultimately orienting the clinical decision-making process. We have used in vitro phenotypic methods to assess adhesion to and invasion of eukaryotic cells, biofilm development, and expression of soluble virulence factors in 92 Staphylococcus spp. strains. The adhesion index, invasion capacity, biofilm formation and expression of soluble factors did not differ significantly between clinical and commensal strains. The major bacterial traits we found to be significantly more prevalent in clinical staphylococci were the aggregative adhesion pattern (P = 0.012), cluster adhesion (P = 0.001) and tetrad morphology (P = 0.018). The aggregative adhesion pattern was correlated with higher cyto-adhesion (P < 0.001), higher invasion capacity (P = 0.003) and lower Carmeli scores (P = 0.002). Three major bacterial traits, namely tetrad morphology, aggregative adhesion pattern, and resistance to methicillin (acronym: TAM), can be used to compute an aggressiveness score (SAS) predictive of the staphylococcal strain's virulence and capacity to initiate and develop a biofilm-driven chronic infectious process versus a fulminant acute infection, in a susceptible host. Copyright © 2016 Elsevier Ltd. All rights reserved.

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

DOE PAGES

Christensen, Geoffrey A.; Moon, Ji Won; Veach, Allison M.; ...

2018-03-20

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion ofmore » the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.« less

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

PubMed Central

Moon, JiWon; Veach, Allison M.; Mosher, Jennifer J.; Wymore, Ann M.; van Nostrand, Joy D.; Zhou, Jizhong; Hazen, Terry C.; Arkin, Adam P.; Elias, Dwayne A.

2018-01-01

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion of the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems. PMID:29558522

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christensen, Geoffrey A.; Moon, Ji Won; Veach, Allison M.

Using in-field bioreactors, we investigated the influence of exogenous microorganisms in groundwater planktonic and biofilm microbial communities as part of the Integrated Field Research Challenge (IFRC). After an acclimation period with source groundwater, bioreactors received either filtered (0.22 μM filter) or unfiltered well groundwater in triplicate and communities were tracked routinely for 23 days after filtration was initiated. To address geochemical influences, the planktonic phase was assayed periodically for protein, organic acids, physico-/geochemical measurements and bacterial community (via 16S rRNA gene sequencing), while biofilms (i.e. microbial growth on sediment coupons) were targeted for bacterial community composition at the completion ofmore » the experiment (23 d). Based on Bray-Curtis distance, planktonic bacterial community composition varied temporally and between treatments (filtered, unfiltered bioreactors). Notably, filtration led to an increase in the dominant genus, Zoogloea relative abundance over time within the planktonic community, while remaining relatively constant when unfiltered. At day 23, biofilm communities were more taxonomically and phylogenetically diverse and substantially different from planktonic bacterial communities; however, the biofilm bacterial communities were similar regardless of filtration. These results suggest that although planktonic communities were sensitive to groundwater filtration, bacterial biofilm communities were stable and resistant to filtration. Bioreactors are useful tools in addressing questions pertaining to microbial community assembly and succession. These data provide a first step in understanding how an extrinsic factor, such as a groundwater inoculation and flux of microbial colonizers, impact how microbial communities assemble in environmental systems.« less

Applying Central Composite Design and Response Surface Methodology to Optimize Growth and Biomass Production of Haemophilus influenzae Type b.

PubMed

Momen, Seyed Bahman; Siadat, Seyed Davar; Akbari, Neda; Ranjbar, Bijan; Khajeh, Khosro

2016-06-01

Haemophilus influenzae type b (Hib) is the leading cause of bacterial meningitis, otitis media, pneumonia, cellulitis, bacteremia, and septic arthritis in infants and young children. The Hib capsule contains the major virulence factor, and is composed of polyribosyl ribitol phosphate (PRP) that can induce immune system response. Vaccines consisting of Hib capsular polysaccharide (PRP) conjugated to a carrier protein are effective in the prevention of the infections. However, due to costly processes in PRP production, these vaccines are too expensive. To enhance biomass, in this research we focused on optimizing Hib growth with respect to physical factors such as pH, temperature, and agitation by using a response surface methodology (RSM). We employed a central composite design (CCD) and a response surface methodology to determine the optimum cultivation conditions for growth and biomass production of H. influenzae type b. The treatment factors investigated were initial pH, agitation, and temperature, using shaking flasks. After Hib cultivation and determination of dry biomass, analysis of experimental data was performed by the RSM-CCD. The model showed that temperature and pH had an interactive effect on Hib biomass production. The dry biomass produced in shaking flasks was about 5470 mg/L, which was under an initial pH of 8.5, at 250 rpm and 35° C. We found CCD and RSM very effective in optimizing Hib culture conditions, and Hib biomass production was greatly influenced by pH and incubation temperature. Therefore, optimization of the growth factors to maximize Hib production can lead to 1) an increase in bacterial biomass and PRP productions, 2) lower vaccine prices, 3) vaccination of more susceptible populations, and 4) lower risk of Hib infections.

Taking Root: Enduring Effect of Rhizosphere Bacterial Colonization in Mangroves

PubMed Central

Pinto, Fernando N.; Egas, Conceição; Almeida, Adelaide; Cunha, Angela; Mendonça-Hagler, Leda C. S.; Smalla, Kornelia

2010-01-01

Background Mangrove forests are of global ecological and economic importance, but are also one of the world's most threatened ecosystems. Here we present a case study examining the influence of the rhizosphere on the structural composition and diversity of mangrove bacterial communities and the implications for mangrove reforestation approaches using nursery-raised plants. Methodology/Principal Findings A barcoded pyrosequencing approach was used to assess bacterial diversity in the rhizosphere of plants in a nursery setting, nursery-raised transplants and native (non-transplanted) plants in the same mangrove habitat. In addition to this, we also assessed bacterial composition in the bulk sediment in order to ascertain if the roots of mangrove plants affect sediment bacterial composition. We found that mangrove roots appear to influence bacterial abundance and composition in the rhizosphere. Due to the sheer abundance of roots in mangrove habitat, such an effect can have an important impact on the maintenance of bacterial guilds involved in nutrient cycling and other key ecosystem functions. Surprisingly, we also noted a marked impact of initial nursery conditions on the rhizosphere bacterial composition of replanted mangrove trees. This result is intriguing because mangroves are periodically inundated with seawater and represent a highly dynamic environment compared to the more controlled nursery environment. Conclusions/Significance In as far as microbial diversity and composition influences plant growth and health, this study indicates that nursery conditions and early microbial colonization patterns of the replants are key factors that should be considered during reforestation projects. In addition to this, our results provide information on the role of the mangrove rhizosphere as a habitat for bacteria from estuarine sediments. PMID:21124923

Bacterial colonization patterns in mechanically ventilated patients with traumatic and medical head injury. Incidence, risk factors, and association with ventilator-associated pneumonia.

PubMed

Ewig, S; Torres, A; El-Ebiary, M; Fábregas, N; Hernández, C; González, J; Nicolás, J M; Soto, L

1999-01-01

We prospectively evaluated the relation of upper airway, lower airway, and gastric colonization patterns with the development of pneumonia and its etiology in 48 patients with surgical (n = 25) and medical (n = 23) head injury. Initial colonization was assessed by cultures of nasal and pharyngeal swabs, tracheobronchial aspirates, gastric juice, and bronchoscopically retrieved protected specimen brush. Follow-up colonization was determined until the end points extubation, suspected ventilator-associated pneumonia (VAP), or death. The initial colonization rate at any site at ICU admission was 39/47 (83%). It mainly accounted for Group I pathogens (Streptococcus pneumoniae, Staphylococcus aureus, Hemophilus influenzae) of the upper and lower airways. At follow-up, colonization rates with Group II pathogens (Gram-negative enteric bacilli and Pseudomonas spp.) increased significantly. The high initial bacterial load with Group I pathogens of the upper airways and trachea decreased during Days 2 to 4, whereas that of Group II pathogens increased. Upper airway colonization was an independent predictor of follow-up tracheobronchial colonization (odds ratio [OR], 9.9; 95% confidence interval [CI], 1.8 to 56.3 for initial colonization with Group I pathogens; OR, 23.9; 95% CI, 3.8 to 153.3 for follow-up colonization with Group II pathogens). Previous (short-term) antibiotics had a protective effect against colonization with Group I pathogens of the lower respiratory tract (OR, 0.2; 95% CI, 0.05 to 0.86), but they were a risk factor for colonization with Group II pathogens (OR, 6.1; 95% CI, 1.3 to 29). Initial tracheobronchial colonization with Group I pathogens was associated with a higher probability of early onset pneumonia (OR, 4. 1; 95% CI, 0.7 to 23.3), whereas prolonged antibiotic treatment (> 24 h) independently predicted late-onset pneumonia (OR, 9.2; 95% CI, 1.7 to 51.3). We conclude that patients with head injury are colonized in the airways mainly by Group I pathogens early in the evolution of illness. The upper airways represent the main reservoir for subsequent lower airway colonization with Group I pathogens. Previous (short-term) antibiotic treatment is protective against initial tracheobronchial colonization with Group I pathogens, but it represents a risk factor for subsequent lower airway colonization by Group II pathogens.

Barrier dysfunction and bacterial uptake in the follicle-associated epithelium of ileal Crohn's disease.

PubMed

Keita, Asa V; Söderholm, Johan D

2012-07-01

The ability to control uptake across the mucosa and protect from harmful substances in the gut lumen is defined as intestinal barrier function. The etiology of Crohn's disease is unknown, but genetic, environmental, and immunological factors all contribute. The frontline between these factors lies in the intestinal barrier. The most important inflammation-driving environmental factor in Crohn's disease is the microbiota, where Esherichia coli strains have been assigned a key role. The first observable signs of Crohn's disease are small aphtoid ulcers over Peyer's patches and lymphoid follicles. The overlaying follicle-associated epithelium (FAE) is specialized for luminal sampling and is an entry site for antigens and bacteria. We have demonstrated increased E. coli uptake across the FAE in Crohn's disease, which may initiate inflammation. This short review will discuss barrier dysfunction and bacteria in the context of ileal Crohn's disease, and how the FAE might be the site of initial inflammation. © 2012 New York Academy of Sciences.

Quantitative PCR Method for Diagnosis of Citrus Bacterial Canker†

PubMed Central

Cubero, J.; Graham, J. H.; Gottwald, T. R.

2001-01-01

For diagnosis of citrus bacterial canker by PCR, an internal standard is employed to ensure the quality of the DNA extraction and that proper requisites exist for the amplification reaction. The ratio of PCR products from the internal standard and bacterial target is used to estimate the initial bacterial concentration in citrus tissues with lesions. PMID:11375206

Bacterial Community Profiling of Plastic Litter in the Belgian Part of the North Sea.

PubMed

De Tender, Caroline A; Devriese, Lisa I; Haegeman, Annelies; Maes, Sara; Ruttink, Tom; Dawyndt, Peter

2015-08-18

Bacterial colonization of marine plastic litter (MPL) is known for over four decades. Still, only a few studies on the plastic colonization process and its influencing factors are reported. In this study, seafloor MPL was sampled at different locations across the Belgian part of the North Sea to study bacterial community structure using 16S metabarcoding. These marine plastic bacterial communities were compared with those of sediment and seawater, and resin pellets sampled on the beach, to investigate the origin and uniqueness of plastic bacterial communities. Plastics display great variation of bacterial community composition, while each showed significant differences from those of sediment and seawater, indicating that plastics represent a distinct environmental niche. Various environmental factors correlate with the diversity of MPL bacterial composition across plastics. In addition, intrinsic plastic-related factors such as pigment content may contribute to the differences in bacterial colonization. Furthermore, the differential abundance of known primary and secondary colonizers across the various plastics may indicate different stages of bacterial colonization, and may confound comparisons of free-floating plastics. Our studies provide insights in the factors that shape plastic bacterial colonization and shed light on the possible role of plastic as transport vehicle for bacteria through the aquatic environment.

Prevalence of bacterial vaginosis among pregnant women attending antenatal care in Tikur Anbessa University Hospital, Addis Ababa, Ethiopia.

PubMed

Mengistie, Zemenu; Woldeamanuel, Yimtubezinash; Asrat, Daniel; Adera, Addis

2014-11-20

Bacterial vaginosis is one of the most common genital tract infections among reproductive age group. The prevalence of bacterial vaginosis varies from country to country even in the same country it varies among populations of interest. Different social and sexual factors can contribute to the development of bacterial vaginosis. The aim of this study was to determine the prevalence of bacterial vaginosis and to identify the possible risk factors associated among pregnant women attending antenatal care in Tikur Anbessa University Hospital, Addis Ababa, Ethiopia. Randomly selected 57 symptomatic and 195 asymptomatic pregnant women aged between 18 and 40 years visiting obstetric and gynecological clinic from November 2011 to April 2012 screenedusing Gram stain Nugent scoring system. Statistical analysis like univariate analysis to calculate frequencies and proportions, bivariate analysis to see association of selected exposure variables with the outcome variable, and multivariate analysis to check the association of possible factors with bacterial vaginosis by adjusting potential confounding factors was calculated using SPSS (Version 16.0). The prevalence of bacterial vaginosis is 19.4% using Gram stain Nugent scoring system. In addition, prevalence of bacterial vaginosis is 31.6% and 15.9% among symptomatic and asymptomatic pregnant women respectively. A high percentage of bacterial vaginosis positive pregnant women were asymptomatic (63.3%). 36.7% bacterial vaginosis positive pregnant women reported abnormal vaginal discharge with or without unpleasant smell. Multiple lifetime sexual partner (OR: 8.6; 95% CI: 2.5, 29) and previous history of spontaneous abortion (OR: 5.9; 95% CI: 1.5, 23) had remained significantly associated with prevalence of bacterial vaginosis. The prevalence of bacterial vaginosis is higher among asymptomatic pregnant women and associated with the factors previous history of multiple lifetime sexual partner and spontaneous abortion.

Uncoupling of Bacterial and Terrigenous Dissolved Organic Matter Dynamics in Decomposition Experiments

PubMed Central

Herlemann, Daniel P. R.; Manecki, Marcus; Meeske, Christian; Pollehne, Falk; Labrenz, Matthias; Schulz-Bull, Detlef; Dittmar, Thorsten; Jürgens, Klaus

2014-01-01

The biodegradability of terrigenous dissolved organic matter (tDOM) exported to the sea has a major impact on the global carbon cycle, but our understanding of tDOM bioavailability is fragmentary. In this study, the effects of preparative tDOM isolation on microbial decomposition were investigated in incubation experiments consisting of mesocosms containing mesohaline water from the Baltic Sea. Dissolved organic carbon (DOC) consumption, molecular DOM composition, bacterial activities, and shifts in bacterial community structure were compared between mesocosms supplemented with riverine tDOM, either as filtered, particle-free river water or as a concentrate obtained by lyophilization/tangential ultrafiltration, and those containing only Baltic Sea water or river water. As shown using ultra-high-resolution mass spectrometry (15 Tesla Fourier-transform ion cyclotron resonance mass spectrometry, FT-ICR-MS) covering approximately 4600 different DOM compounds, the three DOM preparation protocols resulted in distinct patterns of molecular DOM composition. However, despite DOC losses of 4–16% and considerable bacterial production, there was no significant change in DOM composition during the 28-day experiment. Moreover, tDOM addition affected neither DOC degradation nor bacterial dynamics significantly, regardless of the tDOM preparation. This result suggested that the introduced tDOM was largely not bioavailable, at least on the temporal scale of our experiment, and that the observed bacterial activity and DOC decomposition mainly reflected the degradation of unknown, labile, colloidal and low-molecular weight DOM, both of which escape the analytical window of FT-ICR-MS. In contrast to the different tDOM preparations, the initial bacterial inoculum and batch culture conditions determined bacterial community succession and superseded the effects of tDOM addition. The uncoupling of tDOM and bacterial dynamics suggests that mesohaline bacterial communities cannot efficiently utilize tDOM and that in subarctic estuaries other factors are responsible for the removal of imported tDOM. PMID:24718626

Domestication of Lambda Phage Genes into a Putative Third Type of Replicative Helicase Matchmaker

PubMed Central

Brézellec, Pierre; Petit, Marie-Agnès; Pasek, Sophie; Vallet-Gely, Isabelle; Possoz, Christophe

2017-01-01

Abstract At the onset of the initiation of chromosome replication, bacterial replicative helicases are recruited and loaded on the DnaA-oriC nucleoprotein platform, assisted by proteins like DnaC/DnaI or DciA. Two orders of bacteria appear, however, to lack either of these factors, raising the question of the essentiality of these factors in bacteria. Through a phylogenomic approach, we identified a pair of genes that could have substituted for dciA. The two domesticated genes are specific of the dnaC/dnaI- and dciA-lacking organisms and apparently domesticated from lambdoid phage genes. They derive from λO and λP and were renamed dopC and dopE, respectively. DopE is expected to bring the replicative helicase to the bacterial origin of replication, while DopC might assist DopE in this function. The confirmation of the implication of DopCE in the handling of the replicative helicase at the onset of replication in these organisms would generalize to all bacteria and therefore to all living organisms the need for specific factors dedicated to this function. PMID:28854626

Repeated disturbances affect functional but not compositional resistance and resilience in an aquatic bacterioplankton community.

PubMed

Sjöstedt, Johanna; Langenheder, Silke; Kritzberg, Emma; Karlsson, Christofer M G; Lindström, Eva S

2018-05-07

Disturbances are believed to be one of the main factors influencing variations in community diversity and functioning. Here we investigated if exposure to a pH press disturbance affected the composition and functional performance of a bacterial community and its resistance, recovery and resilience to a second press disturbance (salt addition). Lake bacterial assemblages were initially exposed to reduced pH in six mesocosms whereas another six mesocosms were kept as reference. Seven days after the pH disturbance, three tanks from each treatment were exposed to a salt disturbance. Both bacterial production and enzyme activity were negatively affected by the salt treatment, regardless if the communities had been subject to a previous disturbance or not. However, cell-specific enzyme activity had a higher resistance in communities pre-exposed to the pH disturbance compared to the reference treatment. In contrast, for cell-specific bacterial production resistance was not affected, but recovery was faster in the communities that had previously been exposed to the pH disturbance. Over time, bacterial community composition diverged among treatments, in response to both pH and salinity. The difference in functional recovery, resilience and resistance may depend on differences in community composition caused by the pH disturbance, niche breadth or acquired stress resistance. This article is protected by copyright. All rights reserved. © 2018 Society for Applied Microbiology and John Wiley & Sons Ltd.

In vitro combined effect of co-amoxiclav concentrations achievable in serum after a 2000/125 mg oral dose, and polymorphonuclear neutrophils against strains of Streptococcus pneumoniae exhibiting decreased susceptibility to amoxicillin.

PubMed

Amores, Raquel; Alou, Luis; Giménez, María José; Sevillano, David; Gómez-Lus, María Luisa; Aguilar, Lorenzo; Prieto, José

2004-07-01

The in vitro effect that the presence of components of non-specific immunity (serum plus polymorphonuclear neutrophils) has on the bactericidal activity of co-amoxiclav was explored against Streptococcus pneumoniae strains exhibiting an amoxicillin MIC > or =4 mg/L. Eight penicillin-resistant clinical isolates non-susceptible to co-amoxiclav with MICs of 4 (two strains), 8 (four strains) and 16 mg/L (two strains) were used. Values of MBC were identical to MIC values in all cases. Time-kill curves were performed with co-amoxiclav concentrations achievable in serum after a single oral dose administration of the new 2000/125 mg sustained-release formulation. Results were expressed as percentage of reduction of initial inocula after 3 h incubation. Control curves showed growth with no reduction of initial inocula. Against strains with MIC of 4 and 8 mg/L, the results obtained with the antibiotic alone or with the presence of factors of non-specific immunity were similar, with a weak combined effect due to the intrinsic activity of co-amoxiclav (reductions of initial inocula ranging from 70 to 99.16%). Against strains with MIC of 16 mg/L, the addition of PMN in the presence of serum increased the reduction of bacterial load provided by the aminopenicillin, even at sub-inhibitory concentrations (25.8% versus 51.1% at 0.5 x MIC concentration--8/0.5 mg/L). This combined activity against strains with an amoxicillin MIC of 16 mg/L which decreased the bacterial load may be important in preventing bacterial proliferation within the host and the transmission of resistant clones to others.

Periodic growth of bacterial colonies

NASA Astrophysics Data System (ADS)

Yamazaki, Yoshihiro; Ikeda, Takemasa; Shimada, Hirotoshi; Hiramatsu, Fumiko; Kobayashi, Naoki; Wakita, Jun-ichi; Itoh, Hiroto; Kurosu, Sayuri; Nakatsuchi, Michio; Matsuyama, Tohey; Matsushita, Mitsugu

2005-06-01

The formation of concentric ring colonies by bacterial species Bacillus subtilis and Proteus mirabilis has been investigated experimentally, focusing our attention on the dependence of local cell density upon the bacterial motility. It has been confirmed that these concentric ring colonies reflect the periodic change of the bacterial motility between motile cell state and immotile cell state. We conclude that this periodic change is macroscopically determined neither by biological factors (i.e., biological clock) nor by chemical factors (chemotaxis as inhibitor). And our experimental results strongly suggest that the essential factor for the change of the bacterial motility during concentric ring formation is the local cell density.

Biliary bacterial factors determine the path of gallstone formation.

PubMed

Stewart, Lygia; Grifiss, J McLeod; Jarvis, Gary A; Way, Lawrence W

2006-11-01

Bacteria cause pigment gallstones and can act as a nidus for cholesterol gallstone formation. Bacterial factors that facilitate gallstone formation include beta-glucuronidase (bG), phospholipase (PhL), and slime. The current study sought to determine whether bacterial factors influence the path of gallstone formation. A total of 382 gallstones were cultured and/or examined using scanning electron microscopy (SEM). Bacteria were tested for bG and slime production. Gallstone composition was determined using infrared spectrography. Ca-palmitate presence documented bacterial PhL production. Groups were identified based upon bacterial factors present: slime and bGPhL (slime/bGPhL), bGPhL only, and slime only. Influence of bacterial stone-forming factors on gallstone composition and morphology was analyzed. Bacteria were present in 75% of pigment, 76% of mixed, and 20% of cholesterol stones. Gallstones with bGPhL producing bacteria contained more pigment (71% vs. 26%, P < .0001). The slime/bGPhL group was associated (79%) with pigment stones, bGPhL was associated (56%) with mixed stones, while slime (or none) only was associated (67%) with cholesterol stones (P < .031, all comparisons). Bacterial properties determined the path of gallstone formation. Bacteria that produced all stone-forming factors promoted pigment stone formation, while those that produced only bGPhL promoted mixed stone formation. Bacteria that only produced slime lacked the ability to generate pigment solids, and consequently were more common in the centers of cholesterol stones. This shows how bacterial characteristics may govern the process of gallstone formation.

D-amino acids inhibit initial bacterial adhesion: thermodynamic evidence.

PubMed

Xing, Su-Fang; Sun, Xue-Fei; Taylor, Alicia A; Walker, Sharon L; Wang, Yi-Fu; Wang, Shu-Guang

2015-04-01

Bacterial biofilms are structured communities of cells enclosed in a self-produced hydrated polymeric matrix that can adhere to inert or living surfaces. D-Amino acids were previously identified as self-produced compounds that mediate biofilm disassembly by causing the release of the protein component of the polymeric matrix. However, whether exogenous D-amino acids could inhibit initial bacterial adhesion is still unknown. Here, the effect of the exogenous amino acid D-tyrosine on initial bacterial adhesion was determined by combined use of chemical analysis, force spectroscopic measurement, and theoretical predictions. The surface thermodynamic theory demonstrated that the total interaction energy increased with more D-tyrosine, and the contribution of Lewis acid-base interactions relative to the change in the total interaction energy was much greater than the overall nonspecific interactions. Finally, atomic force microscopy analysis implied that the hydrogen bond numbers and adhesion forces decreased with the increase in D-tyrosine concentrations. D-Tyrosine contributed to the repulsive nature of the cell and ultimately led to the inhibition of bacterial adhesion. This study provides a new way to regulate biofilm formation by manipulating the contents of D-amino acids in natural or engineered systems. © 2014 Wiley Periodicals, Inc.

Bacterial superantigens bypass Lck-dependent T cell receptor signaling by activating a Galpha11-dependent, PLC-beta-mediated pathway.

PubMed

Bueno, Clara; Lemke, Caitlin D; Criado, Gabriel; Baroja, Miren L; Ferguson, Stephen S G; Rahman, A K M Nur-Ur; Tsoukas, Constantine D; McCormick, John K; Madrenas, Joaquin

2006-07-01

The paradigm to explain antigen-dependent T cell receptor (TCR) signaling is based on the activation of the CD4 or CD8 coreceptor-associated kinase Lck. It is widely assumed that this paradigm is also applicable to signaling by bacterial superantigens. However, these bacterial toxins can activate human T cells lacking Lck, suggesting the existence of an additional pathway of TCR signaling. Here we showed that this alternative pathway operates in the absence of Lck-dependent tyrosine-phosphorylation events and was initiated by the TCR-dependent activation of raft-enriched heterotrimeric Galpha11 proteins. This event, in turn, activated a phospholipase C-beta and protein kinase C-mediated cascade that turned on the mitogen-activated protein kinases ERK-1 and ERK-2, triggered Ca(2+) influx, and translocated the transcription factors NF-AT and NF-kappaB to the nucleus, ultimately inducing the production of interleukin-2 in Lck-deficient T cells. The triggering of this alternative pathway by superantigens suggests that these toxins use a G protein-coupled receptor as a coreceptor on T cells.

Dynamic metabolic exchange governs a marine algal-bacterial interaction

PubMed Central

Segev, Einat; Wyche, Thomas P; Kim, Ki Hyun; Petersen, Jörn; Ellebrandt, Claire; Vlamakis, Hera; Barteneva, Natasha; Paulson, Joseph N; Chai, Liraz; Clardy, Jon; Kolter, Roberto

2016-01-01

Emiliania huxleyi is a model coccolithophore micro-alga that generates vast blooms in the ocean. Bacteria are not considered among the major factors influencing coccolithophore physiology. Here we show through a laboratory model system that the bacterium Phaeobacter inhibens, a well-studied member of the Roseobacter group, intimately interacts with E. huxleyi. While attached to the algal cell, bacteria initially promote algal growth but ultimately kill their algal host. Both algal growth enhancement and algal death are driven by the bacterially-produced phytohormone indole-3-acetic acid. Bacterial production of indole-3-acetic acid and attachment to algae are significantly increased by tryptophan, which is exuded from the algal cell. Algal death triggered by bacteria involves activation of pathways unique to oxidative stress response and programmed cell death. Our observations suggest that bacteria greatly influence the physiology and metabolism of E. huxleyi. Coccolithophore-bacteria interactions should be further studied in the environment to determine whether they impact micro-algal population dynamics on a global scale. DOI: http://dx.doi.org/10.7554/eLife.17473.001 PMID:27855786

A dual switch controls bacterial enhancer-dependent transcription

PubMed Central

Wiesler, Simone C.; Burrows, Patricia C.; Buck, Martin

2012-01-01

Bacterial RNA polymerases (RNAPs) are targets for antibiotics. Myxopyronin binds to the RNAP switch regions to block structural rearrangements needed for formation of open promoter complexes. Bacterial RNAPs containing the major variant σ54 factor are activated by enhancer-binding proteins (bEBPs) and transcribe genes whose products are needed in pathogenicity and stress responses. We show that (i) enhancer-dependent RNAPs help Escherichia coli to survive in the presence of myxopyronin, (ii) enhancer-dependent RNAPs partially resist inhibition by myxopyronin and (iii) ATP hydrolysis catalysed by bEBPs is obligatory for functional interaction of the RNAP switch regions with the transcription start site. We demonstrate that enhancer-dependent promoters contain two barriers to full DNA opening, allowing tight regulation of transcription initiation. bEBPs engage in a dual switch to (i) allow propagation of nucleated DNA melting from an upstream DNA fork junction and (ii) complete the formation of the transcription bubble and downstream DNA fork junction at the RNA synthesis start site, resulting in switch region-dependent RNAP clamp closure and open promoter complex formation. PMID:22965125

Bacterial body plans

PubMed Central

Rieger, Tomáš; Neubauer, Zdeněk; Blahůšková, Anna; Cvrčková, Fatima

2008-01-01

The bacterium Serratia marcescens produces a plethora of multicellular shapes of different colorations on solid substrates, allowing immediate visual detection of varieties. Such a plasticity allows studies on multicellular community scale spanning two extremes, from well-elaborated individual colonies to undifferentiated cell mass. For a single strain and medium, we obtained a range of different multicellular bodies, depending on the layout of initial plating. Four principal factors affecting the morphogenetic pathways of such bodies can be distinguished: (1) amount, density and distribution pattern of founder cells; (2) the configuration of surrounding free medium; (3) the presence and character of other bacterial bodies sharing the same niche; and (4) self-perception, resulting in delimitation towards other bodies. The last feature results in an ability of well-formed multicellular individuals to maintain their identity upon a close mutual contact, as well as in spontaneous separation of cell masses in experimental chimeras. We propose an “embryo-like” colony model where multicellular bacterial bodies develop along genuine ontogenetic pathways inherent to the given species (clone), while external shaping forces (like nutrient gradients, pH, etc.,) exert not formative, but only regulative roles in the process. PMID:19513204

Mechanisms for Differential Protein Production in Toxin–Antitoxin Systems

PubMed Central

Deter, Heather S.; Jensen, Roderick V.; Mather, William H.; Butzin, Nicholas C.

2017-01-01

Toxin–antitoxin (TA) systems are key regulators of bacterial persistence, a multidrug-tolerant state found in bacterial species that is a major contributing factor to the growing human health crisis of antibiotic resistance. Type II TA systems consist of two proteins, a toxin and an antitoxin; the toxin is neutralized when they form a complex. The ratio of antitoxin to toxin is significantly greater than 1.0 in the susceptible population (non-persister state), but this ratio is expected to become smaller during persistence. Analysis of multiple datasets (RNA-seq, ribosome profiling) and results from translation initiation rate calculators reveal multiple mechanisms that ensure a high antitoxin-to-toxin ratio in the non-persister state. The regulation mechanisms include both translational and transcriptional regulation. We classified E. coli type II TA systems into four distinct classes based on the mechanism of differential protein production between toxin and antitoxin. We find that the most common regulation mechanism is translational regulation. This classification scheme further refines our understanding of one of the fundamental mechanisms underlying bacterial persistence, especially regarding maintenance of the antitoxin-to-toxin ratio. PMID:28677629

Bacterial body plans: Colony ontogeny in Serratia marcescens.

PubMed

Rieger, Tomás; Neubauer, Zdenek; Blahůsková, Anna; Cvrcková, Fatima; Markos, Anton

2008-01-01

The bacterium Serratia marcescens produces a plethora of multicellular shapes of different colorations on solid substrates, allowing immediate visual detection of varieties. Such a plasticity allows studies on multicellular community scale spanning two extremes, from well-elaborated individual colonies to undifferentiated cell mass.For a single strain and medium, we obtained a range of different multicellular bodies, depending on the layout of initial plating. Four principal factors affecting the morphogenetic pathways of such bodies can be distinguished: (1) amount, density and distribution pattern of founder cells; (2) the configuration of surrounding free medium; (3) the presence and character of other bacterial bodies sharing the same niche; and (4) self-perception, resulting in delimitation towards other bodies. The last feature results in an ability of well-formed multicellular individuals to maintain their identity upon a close mutual contact, as well as in spontaneous separation of cell masses in experimental chimeras. We propose an "embryo-like" colony model where multicellular bacterial bodies develop along genuine ontogenetic pathways inherent to the given species (clone), while external shaping forces (like nutrient gradients, pH, etc.,) exert not formative, but only regulative roles in the process.

Two cases of bacterial meningitis accompanied by thalidomide therapy in patients with multiple myeloma: is thalidomide associated with bacterial meningitis?

PubMed

Pasa, Semir; Altintas, Abdullah; Cil, Timucin; Ustun, Cemal; Bayan, Kadim; Danis, Ramazan; Urakci, Zuhat; Tuzun, Yekta; Ayyildiz, Orhan

2009-01-01

Morbidity and mortality in multiple myeloma is often attributed to life-threatening infections. A defect in humoral immunity has been proposed for the predisposition to bacterial infections. Most of the infections are of bacterial origin, and the most serious are septicemia, meningitis, and pneumonia. Thalidomide is a drug with pleiotropic effects. The immunomodulatory effects of thalidomide are at least partially mediated through its ability to down-regulate the pathogenic over-production of tumor necrosis factor-alpha (TNF-alpha). TNF-alpha is a cytokine that plays a central role in the regulation of the host immune and inflammatory response to infection. In the central nervous system, TNF-alpha is involved in induction of a fever response and triggers the release of other cytokines, and may also influence transport of compounds into the brain, leading to cerebrospinal fluid leukocytosis, increased protein influx, and lactate accumulation. Thalidomide has been shown to down-regulate the production of TNF-alpha. On the other hand, knowledge of the effects of thalidomide on granulocyte functions is limited. Thalidomide has been shown to attenuate neutrophil adhesion and chemotaxis. We present herein two cases of Streptococcus pneumoniae bacterial meningitis that developed soon after the initiation of thalidomide treatment, and discuss the effect of thalidomide on the immune system. Although, it is not clear whether thalidomide caused the development of the bacterial infections and meningitis, or what its pathogenetic mechanisms are, physicians should be alert for signs and symptoms of meningitis in patients with multiple myeloma who are treated with thalidomide, especially those in neutropenic states.

Aim-less translation: loss of Saccharomyces cerevisiae mitochondrial translation initiation factor mIF3/Aim23 leads to unbalanced protein synthesis.

PubMed

Kuzmenko, Anton; Derbikova, Ksenia; Salvatori, Roger; Tankov, Stoyan; Atkinson, Gemma C; Tenson, Tanel; Ott, Martin; Kamenski, Piotr; Hauryliuk, Vasili

2016-01-05

The mitochondrial genome almost exclusively encodes a handful of transmembrane constituents of the oxidative phosphorylation (OXPHOS) system. Coordinated expression of these genes ensures the correct stoichiometry of the system's components. Translation initiation in mitochondria is assisted by two general initiation factors mIF2 and mIF3, orthologues of which in bacteria are indispensible for protein synthesis and viability. mIF3 was thought to be absent in Saccharomyces cerevisiae until we recently identified mitochondrial protein Aim23 as the missing orthologue. Here we show that, surprisingly, loss of mIF3/Aim23 in S. cerevisiae does not indiscriminately abrogate mitochondrial translation but rather causes an imbalance in protein production: the rate of synthesis of the Atp9 subunit of F1F0 ATP synthase (complex V) is increased, while expression of Cox1, Cox2 and Cox3 subunits of cytochrome c oxidase (complex IV) is repressed. Our results provide one more example of deviation of mitochondrial translation from its bacterial origins.

The Composition and Spatial Patterns of Bacterial Virulence Factors and Antibiotic Resistance Genes in 19 Wastewater Treatment Plants

PubMed Central

Zhang, Bing; Xia, Yu; Wen, Xianghua; Wang, Xiaohui; Yang, Yunfeng; Zhou, Jizhong; Zhang, Yu

2016-01-01

Bacterial pathogenicity and antibiotic resistance are of concern for environmental safety and public health. Accumulating evidence suggests that wastewater treatment plants (WWTPs) are as an important sink and source of pathogens and antibiotic resistance genes (ARGs). Virulence genes (encoding virulence factors) are good indicators for bacterial pathogenic potentials. To achieve a comprehensive understanding of bacterial pathogenic potentials and antibiotic resistance in WWTPs, bacterial virulence genes and ARGs in 19 WWTPs covering a majority of latitudinal zones of China were surveyed by using GeoChip 4.2. A total of 1610 genes covering 13 virulence factors and 1903 genes belonging to 11 ARG families were detected respectively. The bacterial virulence genes exhibited significant spatial distribution patterns of a latitudinal biodiversity gradient and a distance-decay relationship across China. Moreover, virulence genes tended to coexist with ARGs as shown by their strongly positive associations. In addition, key environmental factors shaping the overall virulence gene structure were identified. This study profiles the occurrence, composition and distribution of virulence genes and ARGs in current WWTPs in China, and uncovers spatial patterns and important environmental variables shaping their structure, which may provide the basis for further studies of bacterial virulence factors and antibiotic resistance in WWTPs. PMID:27907117

Comparison of the structural basis for thermal stability between archaeal and bacterial proteins.

PubMed

Ding, Yanrui; Cai, Yujie; Han, Yonggang; Zhao, Bingqiang

2012-01-01

In this study, the structural basis for thermal stability in archaeal and bacterial proteins was investigated. There were many common factors that confer resistance to high temperature in both archaeal and bacterial proteins. These factors include increases in the Lys content, the bends and blanks of secondary structure, the Glu content of salt bridge; decreases in the number of main-side chain hydrogen bond and exposed surface area, and changes in the bends and blanks of amino acids. Certainly, the utilization of charged amino acids to form salt bridges is a primary factor. In both heat-resistant archaeal and bacterial proteins, most Glu and Asp participate in the formation of salt bridges. Other factors may influence either archaeal or bacterial protein thermostability, which includes the more frequent occurrence of shorter 3(10)-helices and increased hydrophobicity in heat-resistant archaeal proteins. However, there were increases in average helix length, the Glu content in salt bridges, temperature factors and decreases in the number of main-side chain hydrogen bonds, uncharged-uncharged hydrogen bonds, hydrophobicity, and buried and exposed polar surface area in heat-resistant bacterial proteins. Evidently, there are few similarities and many disparities between the heat-resistant mechanisms of archaeal and bacterial proteins.

Soil bacterial diversity patterns and drivers along an elevational gradient on Shennongjia Mountain, China

PubMed Central

Zhang, Yuguang; Cong, Jing; Lu, Hui; Li, Guangliang; Xue, Yadong; Deng, Ye; Li, Hui; Zhou, Jizhong; Li, Diqiang

2015-01-01

Understanding biological diversity elevational pattern and the driver factors are indispensable to develop the ecological theories. Elevational gradient may minimize the impact of environmental factors and is the ideal places to study soil microbial elevational patterns. In this study, we selected four typical vegetation types from 1000 to 2800 m above the sea level on the northern slope of Shennongjia Mountain in central China, and analysed the soil bacterial community composition, elevational patterns and the relationship between soil bacterial diversity and environmental factors by using the 16S rRNA Illumina sequencing and multivariate statistical analysis. The results revealed that the dominant bacterial phyla were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Verrucomicrobia, which accounted for over 75% of the bacterial sequences obtained from tested samples, and the soil bacterial operational taxonomic unit (OTU) richness was a significant monotonous decreasing (P < 0.01) trend with the elevational increasing. The similarity of soil bacterial population composition decreased significantly (P < 0.01) with elevational distance increased as measured by the Jaccard and Bray–Curtis index. Canonical correspondence analysis and Mantel test analysis indicated that plant diversity and soil pH were significantly correlated (P < 0.01) with the soil bacterial community. Therefore, the soil bacterial diversity on Shennongjia Mountain had a significant and different elevational pattern, and plant diversity and soil pH may be the key factors in shaping the soil bacterial spatial pattern. PMID:26032124

Structure of the protein core of translation initiation factor 2 in apo, GTP-bound and GDP-bound forms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simonetti, Angelita; Marzi, Stefano; Fabbretti, Attilio

2013-06-01

The crystal structures of the eubacterial translation initiation factor 2 in apo form and with bound GDP and GTP reveal conformational changes upon nucleotide binding and hydrolysis, notably of the catalytically important histidine in the switch II region. Translation initiation factor 2 (IF2) is involved in the early steps of bacterial protein synthesis. It promotes the stabilization of the initiator tRNA on the 30S initiation complex (IC) and triggers GTP hydrolysis upon ribosomal subunit joining. While the structure of an archaeal homologue (a/eIF5B) is known, there are significant sequence and functional differences in eubacterial IF2, while the trimeric eukaryotic IF2more » is completely unrelated. Here, the crystal structure of the apo IF2 protein core from Thermus thermophilus has been determined by MAD phasing and the structures of GTP and GDP complexes were also obtained. The IF2–GTP complex was trapped by soaking with GTP in the cryoprotectant. The structures revealed conformational changes of the protein upon nucleotide binding, in particular in the P-loop region, which extend to the functionally relevant switch II region. The latter carries a catalytically important and conserved histidine residue which is observed in different conformations in the GTP and GDP complexes. Overall, this work provides the first crystal structure of a eubacterial IF2 and suggests that activation of GTP hydrolysis may occur by a conformational repositioning of the histidine residue.« less

Topical Corticosteroids in the Management of Bacterial Keratitis.

PubMed

Tuli, Sonal S

2013-12-01

Bacterial keratitis can cause significant morbidity from ulceration of the cornea and the resultant scarring. The use of steroids to decrease these complications is controversial with arguments for and against their use. The SCUT (Steroids for Corneal Ulcers Trial) was initiated in 2006 to definitively determine whether steroids in bacterial keratitis were beneficial or harmful. While the SCUT showed no benefit or harm overall, subgroup analyses showed that larger, more central ulcers with very poor initial visual acuity may benefit. On the other hand, Nocardia ulcers that were treated with steroids had worse outcomes. The study did have some limitations as the patient population was not typical for bacterial keratitis in the United States, and there were some criticisms of the therapeutic approach so the question is still not definitively answered.

Impact of egg disinfection of hatching eggs on the eggshell microbiome and bacterial load.

PubMed

Olsen, R; Kudirkiene, E; Thøfner, I; Pors, S; Karlskov-Mortensen, P; Li, L; Papasolomontos, S; Angastiniotou, C; Christensen, J

2017-09-01

Disinfection of hatching eggs is essential to ensure high quality production of broilers. Different protocols are followed in different hatcheries; however, only limited scientific evidence on how the disinfection procedures impact the microbiome is available. The aim of the present study was to characterize the microbiome and aerobic bacterial load of hatching eggs before disinfection and during the subsequent disinfection steps. The study included a group of visibly clean and a group of visibly dirty eggs. For dirty eggs, an initial wash in chlorine was performed, hereafter all eggs were submitted to two times fumigation and finally spray disinfection. The eggshell microbiome was characterized by sequencing of the total amount of 16S rRNA extracted from each sample, consisting of shell surface swabs of five eggs from the same group. In addition, the number of colony forming units (cfu) under aerobic conditions was established for each disinfection step. The disinfection procedure reduced the bacterial load from more than 104 cfu (initially visibly clean eggs) and 105 cfu (initially visibly dirty eggs) to less than 10 cfu per sample after disinfection for both groups of eggs. The microbiome of both initially visibly clean and initially visibly dirty eggs had the highest abundances of the phyla Firmicutes, Proteobacteria and Bacteroidetes. Within the phyla Firmicutes the relative abundances of Clostridiales decreased while Lactobacillus increased from before to after final disinfection. In conclusion, the investigated disinfection procedure is effective in reducing the bacterial load, and by adding a chlorine wash for initially visibly dirty eggs, the microbiome of initially visibly clean and initially visibly dirty eggs had a highly similar microflora after the final disinfection step. © 2017 Poultry Science Association Inc.

The Third Intron of the Interferon Regulatory Factor-8 Is an Initiator of Repressed Chromatin Restricting Its Expression in Non-Immune Cells

PubMed Central

Barnea-Yizhar, Ofer; Ram, Sigal; Kovalev, Ekaterina; Azriel, Aviva; Rand, Ulfert; Nakayama, Manabu; Hauser, Hansjörg; Gepstein, Lior; Levi, Ben-Zion

2016-01-01

Interferon Regulatory Factor-8 (IRF-8) serves as a key factor in the hierarchical differentiation towards monocyte/dendritic cell lineages. While much insight has been accumulated into the mechanisms essential for its hematopoietic specific expression, the mode of restricting IRF-8 expression in non-hematopoietic cells is still unknown. Here we show that the repression of IRF-8 expression in restrictive cells is mediated by its 3rd intron. Removal of this intron alleviates the repression of Bacterial Artificial Chromosome (BAC) IRF-8 reporter gene in these cells. Fine deletion analysis points to conserved regions within this intron mediating its restricted expression. Further, the intron alone selectively initiates gene silencing only in expression-restrictive cells. Characterization of this intron’s properties points to its role as an initiator of sustainable gene silencing inducing chromatin condensation with suppressive histone modifications. This intronic element cannot silence episomal transgene expression underlining a strict chromatin-dependent silencing mechanism. We validated this chromatin-state specificity of IRF-8 intron upon in-vitro differentiation of induced pluripotent stem cells (iPSCs) into cardiomyocytes. Taken together, the IRF-8 3rd intron is sufficient and necessary to initiate gene silencing in non-hematopoietic cells, highlighting its role as a nucleation core for repressed chromatin during differentiation. PMID:27257682

Regional Similarities and Consistent Patterns of Local Variation in Beach Sand Bacterial Communities throughout the Northern Hemisphere

PubMed Central

Staley, Christopher

2016-01-01

ABSTRACT Recent characterization of the bacterial community structure in beach sands has revealed patterns of biogeography similar to those observed in aquatic environments. Studies to date, however, have mainly focused on subtidal sediments from marine beaches. Here, we investigate the bacterial diversity, using Illumina-based sequencing of the V5-V6 region of the 16S rRNA gene, at 11 beaches representing those next to the Great Lakes, Florida, and the Pacific Ocean. The alpha diversity differed significantly among regions (P < 0.0001), while the within-region diversity was more similar. The beta diversity also differed by region (P < 0.001), where freshwater sands had significantly higher abundances of taxa within the Actinobacteria, Betaproteobacteria, and Verrucomicrobia than marine environments. In contrast, marine sands harbored greater abundances of Gammaproteobacteria and Planctomycetes, and those from Florida had more Deltaproteobacteria and Firmicutes. Marine beaches had significantly different phylogenetic community structures (P ≤ 0.018), but freshwater and Florida beaches showed fewer within-region phylogenetic differences. Furthermore, regionally distinct patterns in taxonomic variation were observed in backshore sands, which had communities distinct from those in nearshore sands (P < 0.001). Sample depth minimally influenced the community composition. The results of this study reveal distinct bacterial community structures in sand on a broad geographic scale but moderate regional similarity and suggest that local variation is primarily related to the distance from the shoreline. This study offers a novel comparison of the bacterial communities in freshwater and marine beach sands and provides an important basis for future comparisons and analyses to elucidate factors affecting microbial ecology in this underexplored environment. IMPORTANCE This study presents a large-scale geographic characterization of the bacterial communities present in beach sands. While previous studies have evaluated how environmental factors influence bacterial community composition, few have evaluated bacterial communities in freshwater sands. Furthermore, the use of a consistent methodology to characterize bacterial communities here allowed a novel comparison of communities across geographic regions. We reveal that while the community composition in sands at individual beaches is distinct, beach sands within the same region harbor similar assemblages of bacteria and these assemblages differ greatly between regions. In addition, moisture, associated with distance from the shoreline, strongly influences the bacteria present in sands and more strongly influences the bacteria present than sample depth does. Thus, the data presented here offer an important basis for a broader characterization of the ecology of bacteria in sands, which may also be relevant to public health and resource management initiatives. PMID:26921429

Update on the combination effect of macrolide antibiotics in community-acquired pneumonia.

PubMed

Emmet O'Brien, M; Restrepo, Marcos I; Martin-Loeches, Ignacio

2015-09-01

Community-acquired pneumonia (CAP) is a leading cause of death from an infectious cause worldwide. Guideline-concordant antibiotic therapy initiated in a timely manner is associated with improved treatment responses and patient outcomes. In the post-antibiotic era, much of the morbidity and mortality of CAP is as a result of the interaction between bacterial virulence factors and host immune responses. In patients with severe CAP, or who are critically ill, there is a lot of emerging observational evidence demonstrating improved survival rates when treatment using combination therapy with a β-lactam and a macrolide is initiated, as compared to other antibiotic regimes without a macrolide. Macrolides in combination with a β-lactam antibiotic provide broader coverage for the atypical organisms implicated in CAP, and may contribute to antibacterial synergism. However, it has been postulated that the documented immunomodulatory effects of macrolides are the primary mechanism for improved patient outcomes through attenuation of bacterial virulence factors and host systemic inflammatory responses. Despite concerns regarding the limitations of observational evidence and the lack of confirmatory randomized controlled trials, the potential magnitude of mortality benefits estimated at 20-50% cannot be overlooked. In light of recent data from a number of trials showing that combination treatment with a macrolide and a suitable second agent is justified in all patients with severe CAP, such treatment should be obligatory for those admitted to an intensive care setting. Copyright © 2015 The Japanese Respiratory Society. Published by Elsevier B.V. All rights reserved.

Ecological fitness and strategies of adaptation of Bartonella species to their hosts and vectors☆

PubMed Central

Chomel, Bruno B.; Boulouis, Henri-Jean; Breitschwerdt, Edward B.; Kasten, Rickie W.; Vayssier-Taussat, Muriel; Birtles, Richard J.; Koehler, Jane E.; Dehio, Christoph

2009-01-01

Bartonella spp. are facultative intracellular bacteria that cause characteristic host-restricted hemotropic infections in mammals and are typically transmitted by blood-sucking arthropods. In the mammalian reservoir, these bacteria initially infect a yet unrecognized primary niche, which seeds organisms into the blood stream leading to the establishment of a long-lasting intra-erythrocytic bacteremia as the hall-mark of infection. Bacterial type IV secretion systems, which are supra-molecular transporters ancestrally related to bacterial conjugation systems, represent crucial pathogenicity factors that have contributed to a radial expansion of the Bartonella lineage in nature by facilitating adaptation to unique mammalian hosts. On the molecular level, the type IV secretion system VirB/VirD4 is known to translocate a cocktail of different effector proteins into host cells, which subvert multiple cellular functions to the benefit of the infecting pathogen. Furthermore, bacterial adhesins mediate a critical, early step in the pathogenesis of the bartonellae by binding to extracellular matrix components of host cells, which leads to firm bacterial adhesion to the cell surface as a prerequisite for the efficient translocation of type IV secretion effector proteins. The best-studied adhesins in bartonellae are the orthologous trimeric autotransporter adhesins, BadA in Bartonella henselae and the Vomp family in Bartonella quintana. Genetic diversity and strain variability also appear to enhance the ability of bartonellae to invade not only specific reservoir hosts, but also accidental hosts, as shown for B. henselae. Bartonellae have been identified in many different blood-sucking arthropods, in which they are typically found to cause extracellular infections of the mid-gut epithelium. Adaptation to specific vectors and reservoirs seems to be a common strategy of bartonellae for transmission and host diversity. However, knowledge regarding arthropod specificity/restriction, the mode of transmission, and the bacterial factors involved in arthropod infection and transmission is still limited. PMID:19284965

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning.

PubMed

Dini-Andreote, Francisco; de Cássia Pereira e Silva, Michele; Triadó-Margarit, Xavier; Casamayor, Emilio O; van Elsas, Jan Dirk; Salles, Joana Falcão

2014-10-01

The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time.

Dynamics of bacterial community succession in a salt marsh chronosequence: evidences for temporal niche partitioning

PubMed Central

Dini-Andreote, Francisco; de Cássia Pereira e Silva, Michele; Triadó-Margarit, Xavier; Casamayor, Emilio O; van Elsas, Jan Dirk; Salles, Joana Falcão

2014-01-01

The mechanisms underlying community assembly and promoting temporal succession are often overlooked in microbial ecology. Here, we studied an undisturbed salt marsh chronosequence, spanning over a century of ecosystem development, to understand bacterial succession in soil. We used 16S rRNA gene-based quantitative PCR to determine bacterial abundance and multitag 454 pyrosequencing for community composition and diversity analyses. Despite 10-fold lower 16S rRNA gene abundances, the initial stages of soil development held higher phylogenetic diversities than the soil at late succession. Temporal variations in phylogenetic β-diversity were greater at initial stages of soil development, possibly as a result of the great dynamism imposed by the daily influence of the tide, promoting high immigration rates. Allogenic succession of bacterial communities was mostly driven by shifts in the soil physical structure, as well as variations in pH and salinity, which collectively explained 84.5% of the variation concerning community assemblage. The community assembly data for each successional stage were integrated into a network co-occurrence analysis, revealing higher complexity at initial stages, coinciding with great dynamism in turnover and environmental variability. Contrary to a spatial niche-based perspective of bacterial community assembly, we suggest temporal niche partitioning as the dominant mechanism of assembly (promoting more phylotype co-occurrence) in the initial stages of succession, where continuous environmental change results in the existence of multiple niches over short periods of time. PMID:24739625

Bacterial community changes in response to oil contamination and perennial crop cultivation.

PubMed

Yan, Lijuan; Penttinen, Petri; Mikkonen, Anu; Lindström, Kristina

2018-05-01

We investigated bacterial community dynamics in response to used motor oil contamination and perennial crop cultivation by 16S rRNA gene amplicon sequencing in a 4-year field study. Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes were the major bacterial phyla, and Rhodococcus was the most abundant genus. Initially, oil contamination decreased the overall bacterial diversity. Actinobacteria, Betaproteobacteria, and Gammaproteobacteria were sensitive to oil contamination, exhibiting clear succession with time. However, bacterial communities changed over time, regardless of oil contamination and crop cultivation. The abundance difference of most OTUs between oil-contaminated and non-contaminated plots remained the same in later sampling years after the initial abundance difference induced by oil spike. The abundances of three oil-favored actinobacteria (Lysinimonas, Microbacteriaceae, and Marmoricola) and one betaproteobacterium (Aquabacterium) changed in different manner over time in oil-contaminated and non-contaminated soil. We propose that these taxa are potential bio-indicators for monitoring recovery from motor oil contamination in boreal soil. The effect of crop cultivation on bacterial communities became significant only after the crops achieved stable growth, likely associated with plant material decomposition by Bacteroidetes, Armatimonadetes and Fibrobacteres.

Factors contributing to bacterial bulb rots of onion

USDA-ARS?s Scientific Manuscript database

The incidence of bacterial rots of onion bulbs is increasing and has become a serious problem for growers. This increase is likely due to a combination of factors, such as high bacterial populations in soils and irrigation water, heavy rains flooding production fields, higher temperatures, etc. It m...

Analysis of Salmonella sp bacterial contamination on Vannamei Shrimp using binary logit model approach

NASA Astrophysics Data System (ADS)

Oktaviana, P. P.; Fithriasari, K.

2018-04-01

Mostly Indonesian citizen consume vannamei shrimp as their food. Vannamei shrimp also is one of Indonesian exports comodities mainstay. Vannamei shrimp in the ponds and markets could be contaminated by Salmonella sp bacteria. This bacteria will endanger human health. Salmonella sp bacterial contamination on vannamei shrimp could be affected by many factors. This study is intended to identify what factors that supposedly influence the Salmonella sp bacterial contamination on vannamei shrimp. The researchers used the testing result of Salmonella sp bacterial contamination on vannamei shrimp as response variable. This response variable has two categories: 0 = if testing result indicate that there is no Salmonella sp on vannamei shrimp; 1 = if testing result indicate that there is Salmonella sp on vannamei shrimp. There are four factors that supposedly influence the Salmonella sp bacterial contamination on vannamei shrimp, which are the testing result of Salmonella sp bacterial contamination on farmer hand swab; the subdistrict of vannamei shrimp ponds; the fish processing unit supplied by; and the pond are in hectare. This four factors used as predictor variables. The analysis used is Binary Logit Model Approach according to the response variable that has two categories. The analysis result indicates that the factors or predictor variables which is significantly affect the Salmonella sp bacterial contamination on vannamei shrimp are the testing result of Salmonella sp bacterial contamination on farmer hand swab and the subdistrict of vannamei shrimp ponds.

Biogeographical distribution and diversity of bacterial communities in surface sediments of the South China Sea.

PubMed

Li, Tao; Wang, Peng

2013-05-01

This paper aims at an investigation of the features of bacterial communities in surface sediments of the South China Sea (SCS). In particular, biogeographical distribution patterns and the phylogenetic diversity of bacteria found in sediments collected from a coral reef platform, a continental slope, and a deep-sea basin were determined. Bacterial diversity was measured by an observation of 16S rRNA genes, and 18 phylogenetic groups were identified in the bacterial clone library. Planctomycetes, Deltaproteobacteria, candidate division OP11, and Alphaproteobacteria made up the majority of the bacteria in the samples, with their mean bacterial clones being 16%, 15%, 12%, and 9%, respectively. By comparison, the bacterial communities found in the SCS surface sediments were significantly different from other previously observed deep-sea bacterial communities. This research also emphasizes the fact that geographical factors have an impact on the biogeographical distribution patterns of bacterial communities. For instance, canonical correspondence analyses illustrated that the percentage of sand weight and water depth are important factors affecting the bacterial community composition. Therefore, this study highlights the importance of adequately determining the relationship between geographical factors and the distribution of bacteria in the world's seas and oceans.

Role and mechanism of the Hsp70 molecular chaperone machines in bacterial pathogens.

PubMed

Ghazaei, Ciamak

2017-03-01

Heat shock proteins are highly conserved, stress-inducible, ubiquitous proteins that maintain homeostasis in both eukaryotes and prokaryotes. Hsp70 proteins belong to the heat shock protein family and enhance bacterial survival in hostile environments. Hsp70, known as DnaK in prokaryotes, supports numerous processes such as the assembly and disassembly of protein complexes, the refolding of misfolded and clustered proteins, membrane translocation and the regulation of regulatory proteins. The chaperone-based activity of Hsp70 depends on dynamic interactions between its two domains, known as the ATPase domain and the substrate-binding domain. It also depends on interactions between these domains and other co-chaperone molecules such as the Hsp40 protein family member DnaJ and nucleotide exchange factors. DnaJ is the primary chaperone that interacts with nascent polypeptide chains and functions to prevent their premature release from the ribosome and misfolding before it is targeted by DnaK. Adhesion of bacteria to host cells is mediated by both host and bacterial Hsp70. Following infection of the host, bacterial Hsp70 (DnaK) is in a position to initiate bacterial survival processes and trigger an immune response by the host. Any mutations in the dnaK gene have been shown to decrease the viability of bacteria inside the host. This review will give insights into the structure and mechanism of Hsp70 and its role in regulating the protein activity that contributes to pathogenesis.

Studying the effect of administration route and treatment dose on the selection of enrofloxacin resistance in commensal Escherichia coli in broilers.

PubMed

Chantziaras, Ilias; Smet, Annemieke; Haesebrouck, Freddy; Boyen, Filip; Dewulf, Jeroen

2017-07-01

Factors potentially contributing to fluoroquinolone resistance selection in commensal Escherichia coli strains in poultry were studied through a series of in vivo experiments. The effect of the initial prevalence of enrofloxacin resistance in the E. coli gut microbiota, effect of the bacterial fitness of the enrofloxacin-resistant strain and effect of treatment with enrofloxacin (effect of dose and effect of route of administration) were assessed. Four in vivo studies with broiler chickens were performed. Right after hatching, the chicks were inoculated with either a bacteriologically fit or a bacteriologically non-fit fluoroquinolone-resistant strain as either a minority or the majority of the total E. coli population. Six days later, the chicks were treated for three consecutive days either orally or parenterally and using three different doses (under-, correct- and over-dose) of enrofloxacin. The faecal shedding of E. coli strains was quantified by plating on agar plates either supplemented or not supplemented with enrofloxacin. Linear mixed models were used to assess the effect of the aforementioned variables on the selection of enrofloxacin resistance. The factors that significantly contributed were treatment ( P  <   0.001), bacterial fitness of the resistant donor strain ( P  <   0.001), administration route ( P  =   0.052) and interactions between bacterial fitness and administration route ( P  <   0.001). In the currently used models, fluoroquinolone resistance selection was influenced by treatment, bacterial fitness of the inoculation strain and administration route. The use of oral treatment seems to select more for fluoroquinolone resistance, particularly in the model where a non-fit strain was used for inoculation. © The Author 2017. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Risk factors for community-acquired bacterial meningitis.

PubMed

Lundbo, Lene Fogt; Benfield, Thomas

2017-06-01

Bacterial meningitis is a significant burden of disease and mortality in all age groups worldwide despite the development of effective conjugated vaccines. The pathogenesis of bacterial meningitis is based on complex and incompletely understood host-pathogen interactions. Some of these are pathogen-specific, while some are shared between different bacteria. We searched the database PubMed to identify host risk factors for bacterial meningitis caused by the pathogens Streptococcus pneumoniae, Neisseria meningitidis and Haemophilus influenzae type b, because they are three most common causative bacteria beyond the neonatal period. We describe a number of risk factors; including socioeconomic factors, age, genetic variation of the host and underlying medical conditions associated with increased susceptibility to invasive bacterial infections in both children and adults. As conjugated vaccines are available for these infections, it is of utmost importance to identify high risk patients to be able to prevent invasive disease.

Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis

PubMed Central

Chauhan, Rinki; Ravi, Janani; Datta, Pratik; Chen, Tianlong; Schnappinger, Dirk; Bassler, Kevin E.; Balázsi, Gábor; Gennaro, Maria Laura

2016-01-01

Accessory sigma factors, which reprogram RNA polymerase to transcribe specific gene sets, activate bacterial adaptive responses to noxious environments. Here we reconstruct the complete sigma factor regulatory network of the human pathogen Mycobacterium tuberculosis by an integrated approach. The approach combines identification of direct regulatory interactions between M. tuberculosis sigma factors in an E. coli model system, validation of selected links in M. tuberculosis, and extensive literature review. The resulting network comprises 41 direct interactions among all 13 sigma factors. Analysis of network topology reveals (i) a three-tiered hierarchy initiating at master regulators, (ii) high connectivity and (iii) distinct communities containing multiple sigma factors. These topological features are likely associated with multi-layer signal processing and specialized stress responses involving multiple sigma factors. Moreover, the identification of overrepresented network motifs, such as autoregulation and coregulation of sigma and anti-sigma factor pairs, provides structural information that is relevant for studies of network dynamics. PMID:27029515

Initial nitrogen enrichment conditions determines variations in nitrogen substrate utilization by heterotrophic bacterial isolates.

PubMed

Ghosh, Suchismita; Ayayee, Paul A; Valverde-Barrantes, Oscar J; Blackwood, Christopher B; Royer, Todd V; Leff, Laura G

2017-04-04

The nitrogen (N) cycle consists of complex microbe-mediated transformations driven by a variety of factors, including diversity and concentrations of N compounds. In this study, we examined taxonomic diversity and N substrate utilization by heterotrophic bacteria isolated from streams under complex and simple N-enrichment conditions. Diversity estimates differed among isolates from the enrichments, but no significant composition were detected. Substrate utilization and substrate range of bacterial assemblages differed within and among enrichments types, and not simply between simple and complex N-enrichments. N substrate use patterns differed between isolates from some complex and simple N-enrichments while others were unexpectedly similar. Taxonomic composition of isolates did not differ among enrichments and was unrelated to N use suggesting strong functional redundancy. Ultimately, our results imply that the available N pool influences physiology and selects for bacteria with various abilities that are unrelated to their taxonomic affiliation.

Using the rate of bacterial clearance determined by real-time polymerase chain reaction as a timely surrogate marker to evaluate the appropriateness of antibiotic usage in critical patients with Acinetobacter baumannii bacteremia.

PubMed

Chuang, Yu-Chung; Chang, Shan-Chwen; Wang, Wei-Kung

2012-08-01

Bacteremia caused by Acinetobacter baumannii is becoming more frequent among critically ill patients, and has been associated with high mortality and prolonged hospital stay. Multidrug resistance and delay in blood culture have been shown to be significant barriers to appropriate antibiotic treatment. Quantitative polymerase chain reaction assays were recently used to monitor bacterial loads; we hypothesized that the rate of bacterial clearance determined by quantitative polymerase chain reaction can be used as a timely surrogate marker to evaluate the appropriateness of antibiotic usage. Prospective observational study. University hospital and research laboratory. Patients with culture-proven A. baumannii bacteremia in the intensive care units were prospectively enrolled from April 2008 to February 2009. Plasmid Oxa-51/pCRII-TOPO, which contained a 431-bp fragment of the A. baumannii-specific Oxa-51 gene in a pCRII-TOPO vector, was used as the standard. Sequential bacterial DNA loads in the blood were measured by a quantitative polymerase chain reaction assay. We enrolled 51 patients with A. baumannii bacteremia, and examined 318 sequential whole blood samples. The initial mean bacterial load was 2.15 log copies/mL, and the rate of bacterial clearance was 0.088 log copies/mL/day. Multivariate linear regression using the generalized estimation equation approach revealed that the use of immunosuppressants was an independent predictor for slower bacterial clearance (coefficient, 1.116; p<.001), and appropriate antibiotic usage was an independent predictor for more rapid bacterial clearance (coefficient, -0.995; p<.001). Patients with a slower rate of bacterial clearance experienced higher in-hospital mortality (odds ratio, 2.323; p=.04) Immunosuppression and appropriate antibiotic usage were independent factors affecting the rate of clearance of A. baumannii bacteremia in critical patients. These findings highlight the importance of appropriate antibiotic usage and development of effective antibiotics against A. baumannii in an era of emerging antibiotic resistance. The rate of bacterial clearance could serve as a timely surrogate marker for evaluating the appropriateness of antibiotics.

[Analysis of false-positive reaction for bacterial detection of blood samples with the automated microbial detection system BacT/ALERT 3D].

PubMed

Zhu, Li-Wei; Yang, Xue-Mei; Xu, Xiao-Qin; Xu, Jian; Lu, Huang-Jun; Yan, Li-Xing

2008-10-01

This study was aimed to analyze the results of false positive reaction in bacterial detection of blood samples with BacT/ALERT 3D system, to evaluate the specificity of this system, and to decrease the false positive reaction. Each reaction flasks in past five years were processed for bacteria isolation and identification. When the initial cultures were positive, the remaining samples and the corresponding units were recultured if still available. 11395 blood samples were detected. It is worthy of note that the incubator temperature should be stabilized, avoiding fluctuation; when the cultures were alarmed, the reaction flasks showed be kept some hours for further incubation so as to trace a sharply increasing signal to support the judgement of true bacterial growth. The results indicated that 122 samples (1.07%) wee positive at initial culture, out of them 107 samples (88.7%) were found bacterial, and 15 samples (12.3%) were found nothing. The detection curves of positive samples resulted from bacterial growth showed ascent. In conclusion, maintenance of temperature stability and avoidance of temperature fluctuation in incubator could decrease the occurrence of false-positive reaction in detection process. The reaction flasks with positive results at initial culture should be recultured, and whether existence of a sharply ascending logarilhimic growth phase in bacterial growth curve should be further detected, which are helpful to distinguish false-positive reactions from true positive, and thus increase the specificity of the BacT/ALERT system.

Risk Factor Analysis of Ciprofloxacin-Resistant and Extended Spectrum Beta-Lactamases Pathogen-Induced Acute Bacterial Prostatitis in Korea.

PubMed

Lee, Young; Lee, Dong Gi; Lee, Sang Hyub; Yoo, Koo Han

2016-11-01

The objectives of this study were to investigate risk factors and the incidence of ciprofloxacin resistance and extended-spectrum beta-lactamases (ESBL) in patients with acute bacterial prostatitis (ABP). We reviewed the medical records of 307 patients who were diagnosed with ABP between January 2006 and December 2015. The etiologic pathogens and risk factors for ciprofloxacin-resistant E. coli and ESBL-producing microbes, susceptibility to ciprofloxacin, and the incidence of ESBL in patients with ABP were described. History of prior urologic manipulation was an independent risk factor for ciprofloxacin-resistant (P = 0.005) and ESBL-producing microbes (P = 0.005). Advanced age (over 60 years) was an independent risk factor for ciprofloxacin-resistant microbes (P = 0.022). The ciprofloxacin susceptibility for Escherichia coli in groups without prior manipulation was documented 85.7%. For groups with prior manipulation, the susceptibility was 10.0%. Incidence of ESBL-producing microbes by pathogen was 3.8% for E. coli and 1.0% for Klebsiella pneumonia in the absence of manipulation group, and 20% and 33.3% in the presence of manipulation group, respectively. Initial treatment of ABP must consider patient's age and the possibility of prior manipulation to optimize patient treatment. With the high rate of resistance to fluoroquinolone, cephalosporins with amikacin, or carbapenems, or extended-spectrum penicillin with beta lactamase inhibitor should be considered as the preferred empirical ABP treatment in the patients with history of prior urologic manipulation.

Effect of lag time distribution on the lag phase of bacterial growth - a Monte Carlo analysis

USDA-ARS?s Scientific Manuscript database

The objective of this study is to use Monte Carlo simulation to evaluate the effect of lag time distribution of individual bacterial cells incubated under isothermal conditions on the development of lag phase. The growth of bacterial cells of the same initial concentration and mean lag phase durati...

AtlA Mediates Extracellular DNA Release, Which Contributes to Streptococcus mutans Biofilm Formation in an Experimental Rat Model of Infective Endocarditis

PubMed Central

Hsu, Ron-Bin; Shun, Chia-Tung; Hsu, Chih-Chieh

2017-01-01

ABSTRACT Host factors, such as platelets, have been shown to enhance biofilm formation by oral commensal streptococci, inducing infective endocarditis (IE), but how bacterial components contribute to biofilm formation in vivo is still not clear. We demonstrated previously that an isogenic mutant strain of Streptococcus mutans deficient in autolysin AtlA (ΔatlA) showed a reduced ability to cause vegetation in a rat model of bacterial endocarditis. However, the role of AtlA in bacterial biofilm formation is unclear. In this study, confocal laser scanning microscopy analysis showed that extracellular DNA (eDNA) was embedded in S. mutans GS5 floes during biofilm formation on damaged heart valves, but an ΔatlA strain could not form bacterial aggregates. Semiquantification of eDNA by PCR with bacterial 16S rRNA primers demonstrated that the ΔatlA mutant strain produced dramatically less eDNA than the wild type. Similar results were observed with in vitro biofilm models. The addition of polyanethol sulfonate, a chemical lysis inhibitor, revealed that eDNA release mediated by bacterial cell lysis is required for biofilm initiation and maturation in the wild-type strain. Supplementation of cultures with calcium ions reduced wild-type growth but increased eDNA release and biofilm mass. The effect of calcium ions on biofilm formation was abolished in ΔatlA cultures and by the addition of polyanethol sulfonate. The VicK sensor, but not CiaH, was found to be required for the induction of eDNA release or the stimulation of biofilm formation by calcium ions. These data suggest that calcium ion-regulated AtlA maturation mediates the release of eDNA by S. mutans, which contributes to biofilm formation in infective endocarditis. PMID:28674029

Promoter Recognition by Extracytoplasmic Function σ Factors: Analyzing DNA and Protein Interaction Motifs

PubMed Central

Guzina, Jelena

2016-01-01

ABSTRACT Extracytoplasmic function (ECF) σ factors are the largest and the most diverse group of alternative σ factors, but their mechanisms of transcription are poorly studied. This subfamily is considered to exhibit a rigid promoter structure and an absence of mixing and matching; both −35 and −10 elements are considered necessary for initiating transcription. This paradigm, however, is based on very limited data, which bias the analysis of diverse ECF σ subgroups. Here we investigate DNA and protein recognition motifs involved in ECF σ factor transcription by a computational analysis of canonical ECF subfamily members, much less studied ECF σ subgroups, and the group outliers, obtained from recently sequenced bacteriophages. The analysis identifies an extended −10 element in promoters for phage ECF σ factors; a comparison with bacterial σ factors points to a putative 6-amino-acid motif just C-terminal of domain σ2, which is responsible for the interaction with the identified extension of the −10 element. Interestingly, a similar protein motif is found C-terminal of domain σ2 in canonical ECF σ factors, at a position where it is expected to interact with a conserved motif further upstream of the −10 element. Moreover, the phiEco32 ECF σ factor lacks a recognizable −35 element and σ4 domain, which we identify in a homologous phage, 7-11, indicating that the extended −10 element can compensate for the lack of −35 element interactions. Overall, the results reveal greater flexibility in promoter recognition by ECF σ factors than previously recognized and raise the possibility that mixing and matching also apply to this group, a notion that remains to be biochemically tested. IMPORTANCE ECF σ factors are the most numerous group of alternative σ factors but have been little studied. Their promoter recognition mechanisms are obscured by the large diversity within the ECF σ factor group and the limited similarity with the well-studied housekeeping σ factors. Here we extensively compare bacterial and bacteriophage ECF σ factors and their promoters in order to infer DNA and protein recognition motifs involved in transcription initiation. We predict a more flexible promoter structure than is recognized by the current paradigm, which assumes rigidness, and propose that ECF σ promoter elements may complement (mix and match with) each other's strengths. These results warrant the refocusing of research efforts from the well-studied housekeeping σ factors toward the physiologically highly important, but insufficiently understood, alternative σ factors. PMID:27137497

Bacterial keratitis: predisposing factors, clinical and microbiological review of 300 cases

PubMed Central

Bourcier, T; Thomas, F; Borderie, V; Chaumeil, C; Laroche, L

2003-01-01

Aim: To identify predisposing factors and to define clinical and microbiological characteristics of bacterial keratitis in current practice. Methods: A retrospective analysis of the hospital records of patients presenting with bacterial keratitis and treated at the Quinze-Vingts National Center of Ophthalmology, Paris, France, was performed during a 20 month period. A bacterial keratitis was defined as a suppurative corneal infiltrate and overlying epithelial defect associated with presence of bacteria on corneal scraping and/or that was cured with antibiotic therapy. Risk factors, clinical and microbiological data were collected. Results: 300 cases (291 patients) of presumed bacterial keratitis were included. Potential predisposing factors, usually multiple, were identified in 90.6% of cases. Contact lens wear was the main risk factor (50.3%). Trauma or a history of keratopathy was found in 15% and 21% of cases, respectively. An organism was identified in 201 eyes (68%). 83% of the infections involved Gram positive bacteria, 17% involved Gram negative bacteria, and 2% were polymicrobial. Gram negative bacteria were associated with severe anterior chamber inflammation (p=0.004), as well as greater surface of infiltrates (p=0.01). 99% of ulcers resolved with treatment, but only 60% of patients had visual acuity better than the level at admission, and 5% had very poor visual outcome. Conclusions: Contact lens wear is the most important risk factor. Most community acquired bacterial ulcers resolve with appropriate treatment. PMID:12812878

The Influence of Prior Modes of Growth, Temperature, Medium, and Substrate Surface on Biofilm Formation by Antibiotic-Resistant Campylobacter jejuni.

PubMed

Teh, Amy Huei Teen; Lee, Sui Mae; Dykes, Gary A

2016-12-01

Campylobacter jejuni is one of the most common causes of bacterial gastrointestinal food-borne infection worldwide. It has been suggested that biofilm formation may play a role in survival of these bacteria in the environment. In this study, the influence of prior modes of growth (planktonic or sessile), temperatures (37 and 42 °C), and nutrient conditions (nutrient broth and Mueller-Hinton broth) on biofilm formation by eight C. jejuni strains with different antibiotic resistance profiles was examined. The ability of these strains to form biofilm on different abiotic surfaces (stainless steel, glass, and polystyrene) as well as factors potentially associated with biofilm formation (bacterial surface hydrophobicity, auto-aggregation, and initial attachment) was also determined. The results showed that cells grown as sessile culture generally have a greater ability to form biofilm (P < 0.05) compared to their planktonic counterparts. Biofilm was also greater (P < 0.05) in lower nutrient media, while growth at different temperatures affects biofilm formation in a strain-dependent manner. The strains were able to attach and form biofilms on different abiotic surfaces, but none of them demonstrated strong, complex, or structured biofilm formation. There were no clear trends between the bacterial surface hydrophobicity, auto-aggregation, attachment, and biofilm formation by the strains. This finding suggests that environmental factors did affect biofilm formation by C. jejuni, and they are more likely to persist in the environment in the form of mixed-species rather than monospecies biofilms.

STATIC AND KINETIC SITE-SPECIFIC PROTEIN-DNA PHOTOCROSSLINKING: ANALYSIS OF BACTERIAL TRANSCRIPTION INITIATION COMPLEXES

PubMed Central

Naryshkin, Nikolai; Druzhinin, Sergei; Revyakin, Andrei; Kim, Younggyu; Mekler, Vladimir; Ebright, Richard H.

2009-01-01

Static site-specific protein-DNA photocrosslinking permits identification of protein-DNA interactions within multiprotein-DNA complexes. Kinetic site-specific protein-DNA photocrosslinking--involving rapid-quench-flow mixing and pulsed-laser irradiation--permits elucidation of pathways and kinetics of formation of protein-DNA interactions within multiprotein-DNA complexes. We present detailed protocols for application of static and kinetic site-specific protein-DNA photocrosslinking to bacterial transcription initiation complexes. PMID:19378179

Hydrodynamics of bacterial colonies: Phase diagrams

NASA Astrophysics Data System (ADS)

Lega, J.; Passot, T.

2004-09-01

We present numerical simulations of a recent hydrodynamic model describing the growth of bacterial colonies on agar plates. We show that this model is able to qualitatively reproduce experimentally observed phase diagrams, which relate a colony shape to the initial quantity of nutrients on the plate and the initial wetness of the agar. We also discuss the principal features resulting from the interplay between hydrodynamic motions and colony growth, as described by our model.

Influence of carbon steel grade on the initial attachment of bacteria and microbiologically influenced corrosion.

PubMed

Javed, M A; Neil, W C; Stoddart, P R; Wade, S A

2016-01-01

The influence of the composition and microstructure of different carbon steel grades on the initial attachment (≤ 60 min) of Escherichia coli and subsequent longer term (28 days) corrosion was investigated. The initial bacterial attachment increased with time on all grades of carbon steel. However, the rate and magnitude of bacterial attachment varied on the different steel grades and was significantly less on the steels with a higher pearlite phase content. The observed variations in the number of bacterial cells attached across different steel grades were significantly reduced by applying a fixed potential to the steel samples. Longer term immersion studies showed similar levels of biofilm formation on the surface of the different grades of carbon steel. The measured corrosion rates were significantly higher in biotic conditions compared to abiotic conditions and were found to be positively correlated with the pearlite phase content of the different grades of carbon steel coupons.

Impact of contraceptive initiation on vaginal microbiota.

PubMed

Achilles, Sharon L; Austin, Michele N; Meyn, Leslie A; Mhlanga, Felix; Chirenje, Zvavahera M; Hillier, Sharon L

2018-06-01

Data evaluating the impact of contraceptives on the vaginal microbiome are limited and inconsistent. We hypothesized that women initiating copper intrauterine device use would have increased bacterial vaginosis and bacterial vaginosis-associated microbes with use compared to women initiating and using hormonal contraceptive methods. Vaginal swabs (N = 1047 from 266 participants seeking contraception) for Nugent score determination of bacterial vaginosis and quantitative polymerase chain reaction analyses for assessment of specific microbiota were collected from asymptomatic, healthy women aged 18-35 years in Harare, Zimbabwe, who were confirmed to be free of nonstudy hormones by mass spectrometry at each visit. Contraception was initiated with an injectable (depot medroxyprogesterone acetate [n = 41], norethisterone enanthate [n = 44], or medroxyprogesterone acetate and ethinyl estradiol [n = 40]), implant (levonorgestrel [n = 45] or etonogestrel [n = 48]), or copper intrauterine device (n = 48) and repeat vaginal swabs were collected after 30, 90, and 180 days of continuous use. Self-reported condom use was similar across all arms at baseline. Quantitative polymerase chain reaction was used to detect Lactobacillus crispatus, L jensenii, L gasseri/johnsonii group, L vaginalis, L iners, Gardnerella vaginalis, Atopobium vaginae, and Megasphaera-like bacterium phylotype I from swabs. Modified Poisson regression and mixed effects linear models were used to compare marginal prevalence and mean difference in quantity (expressed as gene copies/swab) prior to and during contraceptive use. Bacterial vaginosis prevalence increased in women initiating copper intrauterine devices from 27% at baseline, 35% at 30 days, 40% at 90 days, and 49% at 180 days (P = .005 compared to marginal prevalence at enrollment). Women initiating hormonal methods had no change in bacterial vaginosis prevalence over 180 days. The mean increase in Nugent score was 1.2 (95% confidence interval, 0.5-2.0; P = .001) in women using copper intrauterine devices. Although the frequency and density of beneficial lactobacilli did not change among intrauterine device users over 6 months, there was an increase in the log concentration of G vaginalis (4.7, 5.2, 5.8, 5.9; P = .046) and A vaginae (3.0, 3.8, 4.6, 5.1; P = .002) between baseline and 30, 90, and 180 days after initiation. Among other contraceptive groups, women using depot medroxyprogesterone acetate had decreased L iners (mean decrease log concentration = 0.8; 95% confidence interval, 0.3-1.5; P = .004) and there were no significant changes in beneficial Lactobacillus species over 180 days regardless of contraceptive method used. Copper intrauterine device use may increase colonization by bacterial vaginosis-associated microbiota, resulting in increased prevalence of bacterial vaginosis. Use of most hormonal contraception does not alter vaginal microbiota. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

The Role of Viral, Host, and Secondary Bacterial Factors in Influenza Pathogenesis

PubMed Central

Kash, John C.; Taubenberger, Jeffery K.

2016-01-01

Influenza A virus infections in humans generally cause self-limited infections, but can result in severe disease, secondary bacterial pneumonias, and death. Influenza viruses can replicate in epithelial cells throughout the respiratory tree and can cause tracheitis, bronchitis, bronchiolitis, diffuse alveolar damage with pulmonary edema and hemorrhage, and interstitial and airspace inflammation. The mechanisms by which influenza infections result in enhanced disease, including development of pneumonia and acute respiratory distress, are multifactorial, involving host, viral, and bacterial factors. Host factors that enhance risk of severe influenza disease include underlying comorbidities, such as cardiac and respiratory disease, immunosuppression, and pregnancy. Viral parameters enhancing disease risk include polymerase mutations associated with host switch and adaptation, viral proteins that modulate immune and antiviral responses, and virulence factors that increase disease severity, which can be especially prominent in pandemic viruses and some zoonotic influenza viruses causing human infections. Influenza viral infections result in damage to the respiratory epithelium that facilitates secondary infection with common bacterial pneumopathogens and can lead to secondary bacterial pneumonias that greatly contribute to respiratory distress, enhanced morbidity, and death. Understanding the molecular mechanisms by which influenza and secondary bacterial infections, coupled with the role of host risk factors, contribute to enhanced morbidity and mortality is essential to develop better therapeutic strategies to treat severe influenza. PMID:25747532

Possible mechanism for preterm labor associated with bacterial infection. I. Stimulation of phosphoinositide metabolism by endotoxin in endometrial fibroblasts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khan, A.A.; Imai, A.; Tamaya, T.

Growing evidence suggests an association between intra-amniotic infection and premature initiation of parturition. We recently demonstrated that some factor(s) including endotoxin produced by the organism stimulates endogenous phospholipase A2 resulting in liberation of arachidonic acid and prostaglandin formation. The studies presented in this report were designated to evaluate the mechanism for endotoxin to stimulate phospholipase A2 using human endometrial fibroblasts. Exposure of the fibroblasts to endotoxin from Escherichia coli in the presence of ({sup 32}P) phosphate increased {sup 32}P-labeling of phosphatidic acid (PA) and phosphatidyl-inositol (PI) in a dose-dependent and a time-dependent manners. The PA labeling occurred without a measurablemore » lag time. These findings demonstrate that the endotoxin stimulates phosphoinositide metabolism in human endometrial fibroblasts by a receptor-mediated mechanism. Membrane phosphoinositide turnover stimulated by endotoxin results in cytosolic Ca{sup 2+} increment, liberation of arachidonic acid, which may be involved in the initiation of parturition.« less

Box-Behnken experimental design for chromium(VI) ions removal by bacterial cellulose-magnetite composites.

PubMed

Stoica-Guzun, Anicuta; Stroescu, Marta; Jinga, Sorin Ion; Mihalache, Nicoleta; Botez, Adriana; Matei, Cristian; Berger, Daniela; Damian, Celina Maria; Ionita, Valentin

2016-10-01

In this study bacterial cellulose-magnetite composites were synthesised for the removal of chromium(VI) from aqueous solutions. Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), X-ray diffraction (XRD), thermogravimetric analysis and X-ray Photoelectron Spectroscopy (XPS) were used to characterize the bacterial cellulose-magnetite composites and to reveal the uniform dispersion of nanomagnetite in the BC matrix. Magnetic properties were also measured to confirm the magnetite immobilization on bacterial cellulose membrane. The effects of initial Cr(VI) concentration, solution pH and solid/liquid ratio upon chromium removal were examined using the statistical Box-Behnken Design. Because of the possibility of magnetite dissolution during chromium(VI) adsorption, the degree of iron leaching was also analysed in the same conditions as Cr(VI) adsorption. From the factors affecting chromium(VI) adsorption the most important was solution pH. The highest Cr(VI) removal efficiency was observed at pH 4, accompanied by the lowest iron leaching in the solution. The adsorption experiments also indicated that the adsorption process of chromium(VI) is well described by Freundlich adsorption model. Our results proved that the BC-magnetite composites could be used for an efficient removal of chromium(VI) from diluted solutions with a minimum magnetite dissolution during operation. Copyright © 2016 Elsevier B.V. All rights reserved.

Transcription termination factor Rho and microbial phenotypic heterogeneity.

PubMed

Bidnenko, Elena; Bidnenko, Vladimir

2018-06-01

Populations of genetically identical microorganisms exhibit high degree of cell-to-cell phenotypic diversity even when grown in uniform environmental conditions. Heterogeneity is a genetically determined trait, which ensures bacterial adaptation and survival in the ever changing environmental conditions. Fluctuations in gene expression (noise) at the level of transcription initiation largely contribute to cell-to-cell variability within population. Not surprisingly, the analyses of the mechanisms driving phenotypic heterogeneity are mainly focused on the activity of promoters and transcriptional factors. Less attention is currently given to a role of intrinsic and factor-dependent transcription terminators. Here, we discuss recent advances in understanding the regulatory role of the multi-functional transcription termination factor Rho, the major inhibitor of pervasive transcription in bacteria and the emerging global regulator of gene expression. We propose that termination activity of Rho might be among the mechanisms by which cells manage the intensity of transcriptional noise, thus affecting population heterogeneity.

Anti-Biofilm Performance of Three Natural Products against Initial Bacterial Attachment

PubMed Central

Salta, Maria; Wharton, Julian A.; Dennington, Simon P.; Stoodley, Paul; Stokes, Keith R.

2013-01-01

Marine bacteria contribute significantly towards the fouling consortium, both directly (modern foul release coatings fail to prevent “slime” attachment) and indirectly (biofilms often excrete chemical cues that attract macrofouling settlement). This study assessed the natural product anti-biofilm performance of an extract of the seaweed, Chondrus crispus, and two isolated compounds from terrestrial sources, (+)-usnic acid and juglone, against two marine biofilm forming bacteria, Cobetia marina and Marinobacter hydrocarbonoclasticus. Bioassays were developed using quantitative imaging and fluorescent labelling to test the natural products over a range of concentrations against initial bacterial attachment. All natural products affected bacterial attachment; however, juglone demonstrated the best anti-biofilm performance against both bacterial species at a concentration range between 5–20 ppm. In addition, for the first time, a dose-dependent inhibition (hormetic) response was observed for natural products against marine biofilm forming bacteria. PMID:24192819

Diversity of protists and bacteria determines predation performance and stability.

PubMed

Saleem, Muhammad; Fetzer, Ingo; Harms, Hauke; Chatzinotas, Antonis

2013-10-01

Predation influences prey diversity and productivity while it effectuates the flux and reallocation of organic nutrients into biomass at higher trophic levels. However, it is unknown how bacterivorous protists are influenced by the diversity of their bacterial prey. Using 456 microcosms, in which different bacterial mixtures with equal initial cell numbers were exposed to single or multiple predators (Tetrahymena sp., Poterioochromonas sp. and Acanthamoeba sp.), we showed that increasing prey richness enhanced production of single predators. The extent of the response depended, however, on predator identity. Bacterial prey richness had a stabilizing effect on predator performance in that it reduced variability in predator production. Further, prey richness tended to enhance predator evenness in the predation experiment including all three protists predators (multiple predation experiment). However, we also observed a negative relationship between prey richness and predator production in multiple predation experiments. Mathematical analysis of potential ecological mechanisms of positive predator diversity-functioning relationships revealed predator complementarity as a factor responsible for both enhanced predator production and prey reduction. We suggest that the diversity at both trophic levels interactively determines protistan performance and might have implications in microbial ecosystem processes and services.

Gut Microbiota Linked to Sexual Preference and HIV Infection.

PubMed

Noguera-Julian, Marc; Rocafort, Muntsa; Guillén, Yolanda; Rivera, Javier; Casadellà, Maria; Nowak, Piotr; Hildebrand, Falk; Zeller, Georg; Parera, Mariona; Bellido, Rocío; Rodríguez, Cristina; Carrillo, Jorge; Mothe, Beatriz; Coll, Josep; Bravo, Isabel; Estany, Carla; Herrero, Cristina; Saz, Jorge; Sirera, Guillem; Torrela, Ariadna; Navarro, Jordi; Crespo, Manel; Brander, Christian; Negredo, Eugènia; Blanco, Julià; Guarner, Francisco; Calle, Maria Luz; Bork, Peer; Sönnerborg, Anders; Clotet, Bonaventura; Paredes, Roger

2016-03-01

The precise effects of HIV-1 on the gut microbiome are unclear. Initial cross-sectional studies provided contradictory associations between microbial richness and HIV serostatus and suggested shifts from Bacteroides to Prevotella predominance following HIV-1 infection, which have not been found in animal models or in studies matched for HIV-1 transmission groups. In two independent cohorts of HIV-1-infected subjects and HIV-1-negative controls in Barcelona (n = 156) and Stockholm (n = 84), men who have sex with men (MSM) predominantly belonged to the Prevotella-rich enterotype whereas most non-MSM subjects were enriched in Bacteroides, independently of HIV-1 status, and with only a limited contribution of diet effects. Moreover, MSM had a significantly richer and more diverse fecal microbiota than non-MSM individuals. After stratifying for sexual orientation, there was no solid evidence of an HIV-specific dysbiosis. However, HIV-1 infection remained consistently associated with reduced bacterial richness, the lowest bacterial richness being observed in subjects with a virological-immune discordant response to antiretroviral therapy. Our findings indicate that HIV gut microbiome studies must control for HIV risk factors and suggest interventions on gut bacterial richness as possible novel avenues to improve HIV-1-associated immune dysfunction.

Selection of peptides targeting helix 31 of bacterial 16S ribosomal RNA by screening M13 phage-display libraries.

PubMed

Lamichhane, Tek N; Abeydeera, N Dinuka; Duc, Anne-Cécile E; Cunningham, Philip R; Chow, Christine S

2011-01-28

Ribosomal RNA is the catalytic portion of ribosomes, and undergoes a variety of conformational changes during translation. Structural changes in ribosomal RNA can be facilitated by the presence of modified nucleotides. Helix 31 of bacterial 16S ribosomal RNA harbors two modified nucleotides, m²G966 and m⁵C967, that are highly conserved among bacteria, though the degree and nature of the modifications in this region are different in eukaryotes. Contacts between helix 31 and the P-site tRNA, initiation factors, and ribosomal proteins highlight the importance of this region in translation. In this work, a heptapeptide M13 phage-display library was screened for ligands that target the wild-type, naturally modified bacterial helix 31. Several peptides, including TYLPWPA, CVRPFAL, TLWDLIP, FVRPFPL, ATPLWLK, and DIRTQRE, were found to be prevalent after several rounds of screening. Several of the peptides exhibited moderate affinity (in the high nM to low µM range) to modified helix 31 in biophysical assays, including surface plasmon resonance (SPR), and were also shown to bind 30S ribosomal subunits. These peptides also inhibited protein synthesis in cell-free translation assays.

Bacterial Communities in the Groundwater of Xikuangshan Antimony Mine, China

NASA Astrophysics Data System (ADS)

Wu, M.; Wang, H.; Wang, N.; Wang, M.

2017-12-01

Xikuangshan (XKS) is the biggest antimony (Sb) mine around the word, which causes serious environmental contamination due to the mining actives. To fully understand the bacterial compositions in the groundwater around the mining area in XKS and their correlation with environmental factors, groundwater samples were collected and subject to 16S rDNA high throughput sequencing. Results indicated that Proteobacteria (especially Gamma-Proteobacteria) dominated bacterial communities in high-Sb groundwater samples, whereas Bacteroidetes predominated in low-Sb groundwater. Furthermore, antimony concentration was found to be the most significant factor shaping bacterial communities (P=0.002) with an explanation of 9.16% of the variation. Other factors such as pH, contents of Mg, Ca and orthophosphate were also observed to significantly correlate with bacterial communities. This was the first report to show the important impact of Sb concentration on bacterial community structure in the groundwater in the mining area. Our results will enhance the understanding of subsurface biogeochemical processes mediated by microbes.

Plasma Deactivation of Oral Bacteria Seeded on Hydroxyapatite Disks as Tooth Enamel Analogue

PubMed Central

Blumhagen, Adam; Singh, Prashant; Mustapha, Azlin; Chen, Meng; Wang, Yong; Yu, Qingsong

2014-01-01

Purpose To study the plasma treatment effects on deactivation of oral bacteria seeded on a tooth enamel analogue. Methods A non-thermal atmospheric pressure argon plasma brush was used to treat two different Gram-positive oral bacteria including Lactobacillus acidophilus (L. acidophilus) and Streptococcus mutans (S. mutans). The bacteria were seeded on hydroxyapatite (HA) disks used as tooth enamel analogue with three initial bacterial seeding concentrations: a low inoculum concentration between 2.1×108 and 2.4×108 cfu/mL, a medium inoculum concentration between 9.8×108 and 2.4×109 cfu/mL, and a high inoculum concentration between 1.7×1010 and 3.5×1010 cfu/mL. The bacterial survivability upon plasma exposure was examined in terms of plasma exposure time and oxygen addition into the plasmas. SEM was performed to examine bacterial morphological changes after plasma exposure. Results The experimental data indicated that 13 second plasma exposure time completely killed all the bacteria when initial bacterial seeding density on HA surfaces were less than 6.9×106 cfu/cm2 for L. acidophilus and 1.7×107 cfu/cm2 for S. mutans, which were resulted from low initial seeding inoculum concentration between 2.1×108 and 2.4×108 cfu/mL. Plasma exposure of the bacteria at higher initial bacterial seeding density obtained with high initial seeding inoculum concentration, however, only resulted in ~ 1.5 to 2 log reduction and ~ 2 to 2.5 log reduction for L. acidophilus and S. mutans, respectively. It was also noted that oxygen addition into the argon plasma brush did not affect the plasma deactivation effectiveness. SEM images showed that plasma deactivation mainly occurred with the top layer bacteria, while shadowing effects from the resulting bacterial debris reduced the plasma deactivation of the underlying bacteria. Clinical Significance The experimental results indicate that, with direct contact, nonthermal atmospheric pressure argon plasmas could rapidly and effectively deactivate oral bacteria seeded on HA surfaces and thus could be a promising technique in various dental clinical applications. PMID:25000666

In vitro bacterial isolate susceptibility to empirically selected antimicrobials in 111 dogs with bacterial pneumonia.

PubMed

Proulx, Alexandre; Hume, Daniel Z; Drobatz, Kenneth J; Reineke, Erica L

2014-01-01

To determine the proportion of airway bacterial isolates resistant to both empirically selected and recently administered antimicrobials, and to assess the impact of inappropriate initial empiric antimicrobials selection on length of hospital stay and survival to discharge in dogs with bacterial pneumonia. Retrospective study. University veterinary teaching hospital. One hundred and eleven dogs with a clinical diagnosis of bacterial pneumonia that had aerobic bacterial culture and susceptibility testing performed from a tracheal wash sample. None. Overall, 26% (29/111) of the dogs had at least 1 bacterial isolate that was resistant to empirically selected antimicrobials. In dogs with a history of antimicrobial administration within the preceding 4 weeks, a high incidence (57.4%, 31/54) of in vitro bacterial resistance to those antimicrobials was found: 64.7% (11/17) in the community-acquired pneumonia group, 55.2% (16/29) in the aspiration pneumonia group, and 50.0% (4/8) in the other causes of bacterial pneumonia group. No statistically significant association was found between bacterial isolate resistance to empirically selected antimicrobials and length of hospital stay or mortality. The high proportion of in vitro airway bacterial resistance to empiric antimicrobials would suggest that airway sampling for bacterial culture and susceptibility testing may be helpful in guiding antimicrobial therapy and recently administered antimicrobials should be avoided when empirically selecting antimicrobials. Although no relationship was found between inappropriate initial empiric antimicrobial selection and length of hospital stay or mortality, future prospective studies using standardized airway-sampling techniques, treatment modalities, and stratification of disease severity based on objective values, such as arterial blood gas analysis in all dogs with pneumonia, would be needed to determine if a clinical effect of in vitro bacterial resistance to empirically administered antimicrobials truly exists or not. © Veterinary Emergency and Critical Care Society 2013.

Development of a Model to Predict the Primary Infection Date of Bacterial Spot (Xanthomonas campestris pv. vesicatoria) on Hot Pepper.

PubMed

Kim, Ji-Hoon; Kang, Wee-Soo; Yun, Sung-Chul

2014-06-01

A population model of bacterial spot caused by Xanthomonas campestris pv. vesicatoria on hot pepper was developed to predict the primary disease infection date. The model estimated the pathogen population on the surface and within the leaf of the host based on the wetness period and temperature. For successful infection, at least 5,000 cells/ml of the bacterial population were required. Also, wind and rain were necessary according to regression analyses of the monitored data. Bacterial spot on the model is initiated when the pathogen population exceeds 10(15) cells/g within the leaf. The developed model was validated using 94 assessed samples from 2000 to 2007 obtained from monitored fields. Based on the validation study, the predicted initial infection dates varied based on the year rather than the location. Differences in initial infection dates between the model predictions and the monitored data in the field were minimal. For example, predicted infection dates for 7 locations were within the same month as the actual infection dates, 11 locations were within 1 month of the actual infection, and only 3 locations were more than 2 months apart from the actual infection. The predicted infection dates were mapped from 2009 to 2012; 2011 was the most severe year. Although the model was not sensitive enough to predict disease severity of less than 0.1% in the field, our model predicted bacterial spot severity of 1% or more. Therefore, this model can be applied in the field to determine when bacterial spot control is required.

Development of a Model to Predict the Primary Infection Date of Bacterial Spot (Xanthomonas campestris pv. vesicatoria) on Hot Pepper

PubMed Central

Kim, Ji-Hoon; Kang, Wee-Soo; Yun, Sung-Chul

2014-01-01

A population model of bacterial spot caused by Xanthomonas campestris pv. vesicatoria on hot pepper was developed to predict the primary disease infection date. The model estimated the pathogen population on the surface and within the leaf of the host based on the wetness period and temperature. For successful infection, at least 5,000 cells/ml of the bacterial population were required. Also, wind and rain were necessary according to regression analyses of the monitored data. Bacterial spot on the model is initiated when the pathogen population exceeds 1015 cells/g within the leaf. The developed model was validated using 94 assessed samples from 2000 to 2007 obtained from monitored fields. Based on the validation study, the predicted initial infection dates varied based on the year rather than the location. Differences in initial infection dates between the model predictions and the monitored data in the field were minimal. For example, predicted infection dates for 7 locations were within the same month as the actual infection dates, 11 locations were within 1 month of the actual infection, and only 3 locations were more than 2 months apart from the actual infection. The predicted infection dates were mapped from 2009 to 2012; 2011 was the most severe year. Although the model was not sensitive enough to predict disease severity of less than 0.1% in the field, our model predicted bacterial spot severity of 1% or more. Therefore, this model can be applied in the field to determine when bacterial spot control is required. PMID:25288995

Meteorological factors had more impact on airborne bacterial communities than air pollutants.

PubMed

Zhen, Quan; Deng, Ye; Wang, Yaqing; Wang, Xiaoke; Zhang, Hongxing; Sun, Xu; Ouyang, Zhiyun

2017-12-01

Airborne bacteria have gained increasing attention because they affect ecological balance and pose potential risks on human health. Recently, some studies have focused on the abundance and composition of airborne bacteria under heavy, hazy polluted weather in China, but they reached different conclusions about the comparisons with non-polluted days. In this study, we tested the hypothesis that meteorological factors could have a higher impact on shaping airborne bacterial communities than air pollutants by systematically monitoring the communities for 1year. Total suspended particles in Beijing were sampled for 20 consecutive days in each season of 2015. Bacterial abundance varied from 8.71×10 3 to 2.14×10 7 ribosomal operons per cubic meter according to the quantitative PCR analysis. There were relatively higher bacterial counts in spring and in autumn than in winter and summer. Airborne bacterial communities displayed a strong seasonality, according to the hierarchical cluster analysis. Only two exceptions overtook the seasonal trend, and both occurred in or after violent meteorological changes (sandstorm or rain). Aggregated boosted tree analysis performed on bacterial abundance showed that the dominant factors shaping bacterial communities were meteorological. They were air pressure in winter, air temperature and relative humidity in spring, RH in summer, and vapor pressure in autumn. Variation partition analysis on community structure showed that meteorological factors explained more variations than air pollutants. Therefore, both of the two models verified our hypothesis that the differences in airborne bacterial communities in polluted days or non-polluted days were mainly driven by the discrepancies of meteorological factors rather than by the presence of air pollutants. Copyright © 2017 Elsevier B.V. All rights reserved.

AtaT blocks translation initiation by N-acetylation of the initiator tRNAfMet.

PubMed

Jurėnas, Dukas; Chatterjee, Sneha; Konijnenberg, Albert; Sobott, Frank; Droogmans, Louis; Garcia-Pino, Abel; Van Melderen, Laurence

2017-06-01

Toxin-antitoxin (TA) loci are prevalent in bacterial genomes. They are suggested to play a central role in dormancy and persister states. Under normal growth conditions, TA toxins are neutralized by their cognate antitoxins, and under stress conditions, toxins are freed and inhibit essential cellular processes using a variety of mechanisms. Here we characterize ataR-ataT, a novel TA system, from enterohemorrhagic Escherichia coli. We show that the toxin AtaT is a GNAT family enzyme that transfers an acetyl group from acetyl coenzyme A to the amine group of the methionyl aminoacyl moiety of initiator tRNA. AtaT specifically modifies Met-tRNA fMet , but no other aminoacyl-tRNAs, including the elongator Met-tRNA Met . We demonstrate that once acetylated, AcMet-tRNA fMet fails to interact with initiation factor-2 (IF2), resulting in disruption of the translation initiation complex. This work reveals a new mechanism of translation inhibition and confirms Met-tRNA fMet as a prime target to efficiently block cell growth.

Bacterial meningitis - principles of antimicrobial treatment.

PubMed

Jawień, Miroslaw; Garlicki, Aleksander M

2013-01-01

Bacterial meningitis is associated with significant morbidity and mortality despite the availability of effective antimicrobial therapy. The management approach to patients with suspected or proven bacterial meningitis includes emergent cerebrospinal fluid analysis and initiation of appropriate antimicrobial and adjunctive therapies. The choice of empirical antimicrobial therapy is based on the patient's age and underlying disease status; once the infecting pathogen is isolated, antimicrobial therapy can be modified for optimal treatment. Successful treatment of bacterial meningitis requires the knowledge on epidemiology including prevalence of antimicrobial resistant pathogens, pathogenesis of meningitis, pharmacokinetics and pharmacodynamics of antimicrobial agents. The emergence of antibiotic-resistant bacterial strains in recent years has necessitated the development of new strategies for empiric antimicrobial therapy for bacterial meningitis.

Chemical Genetics Reveals Bacterial and Host Cell Functions Critical for Type IV Effector Translocation by Legionella pneumophila

PubMed Central

Charpentier, Xavier; Gabay, Joëlle E.; Reyes, Moraima; Zhu, Jing W.; Weiss, Arthur; Shuman, Howard A.

2009-01-01

Delivery of effector proteins is a process widely used by bacterial pathogens to subvert host cell functions and cause disease. Effector delivery is achieved by elaborate injection devices and can often be triggered by environmental stimuli. However, effector export by the L. pneumophila Icm/Dot Type IVB secretion system cannot be detected until the bacterium encounters a target host cell. We used chemical genetics, a perturbation strategy that utilizes small molecule inhibitors, to determine the mechanisms critical for L. pneumophila Icm/Dot activity. From a collection of more than 2,500 annotated molecules we identified specific inhibitors of effector translocation. We found that L. pneumophila effector translocation in macrophages requires host cell factors known to be involved in phagocytosis such as phosphoinositide 3-kinases, actin and tubulin. Moreover, we found that L. pneumophila phagocytosis and effector translocation also specifically require the receptor protein tyrosine phosphate phosphatases CD45 and CD148. We further show that phagocytosis is required to trigger effector delivery unless intimate contact between the bacteria and the host is artificially generated. In addition, real-time analysis of effector translocation suggests that effector export is rate-limited by phagocytosis. We propose a model in which L. pneumophila utilizes phagocytosis to initiate an intimate contact event required for the translocation of pre-synthesized effector molecules. We discuss the need for host cell participation in the initial step of the infection and its implications in the L. pneumophila lifestyle. Chemical genetic screening provides a novel approach to probe the host cell functions and factors involved in host–pathogen interactions. PMID:19578436

Enamel pearl on an unusual location associated with localized periodontal disease: A clinical report

PubMed Central

Sharma, Shivani; Malhotra, Sumit; Baliga, Vidya; Hans, Manoj

2013-01-01

Bacterial plaque has been implicated as the primary etiologic factor in the initiation and progression of periodontal disease. Anatomic factors (such as enamel pearls) are often associated with advanced localized periodontal destruction. The phenomenon of ectopic development of enamel on the root surface, variedly referred to as enameloma, enamel pearl, enamel drop or enamel nodule, is not well-understood. Such an anomaly may facilitate the progression of periodontal breakdown. A rare case of enamel pearl on the lingual aspect of mandibular central incisor associated with localized periodontal disease is presented. Removal and treatment of enamel pearl along with possible mechanisms to account for the pathogenesis of ectopic enamel formation are also discussed. PMID:24554894

Common themes in microbial pathogenicity revisited.

PubMed Central

Finlay, B B; Falkow, S

1997-01-01

Bacterial pathogens employ a number of genetic strategies to cause infection and, occasionally, disease in their hosts. Many of these virulence factors and their regulatory elements can be divided into a smaller number of groups based on the conservation of similar mechanisms. These common themes are found throughout bacterial virulence factors. For example, there are only a few general types of toxins, despite a large number of host targets. Similarly, there are only a few conserved ways to build the bacterial pilus and nonpilus adhesins used by pathogens to adhere to host substrates. Bacterial entry into host cells (invasion) is a complex mechanism. However, several common invasion themes exist in diverse microorganisms. Similarly, once inside a host cell, pathogens have a limited number of ways to ensure their survival, whether remaining within a host vacuole or by escaping into the cytoplasm. Avoidance of the host immune defenses is key to the success of a pathogen. Several common themes again are employed, including antigenic variation, camouflage by binding host molecules, and enzymatic degradation of host immune components. Most virulence factors are found on the bacterial surface or secreted into their immediate environment, yet virulence factors operate through a relatively small number of microbial secretion systems. The expression of bacterial pathogenicity is dependent upon complex regulatory circuits. However, pathogens use only a small number of biochemical families to express distinct functional factors at the appropriate time that causes infection. Finally, virulence factors maintained on mobile genetic elements and pathogenicity islands ensure that new strains of pathogens evolve constantly. Comprehension of these common themes in microbial pathogenicity is critical to the understanding and study of bacterial virulence mechanisms and to the development of new "anti-virulence" agents, which are so desperately needed to replace antibiotics. PMID:9184008

Bacterial secondary production on vascular plant detritus: relationships to detritus composition and degradation rate.

PubMed Central

Moran, M A; Hodson, R E

1989-01-01

Bacterial production at the expense of vascular plant detritus was measured for three emergent plant species (Juncus effusus, Panicum hemitomon, and Typha latifolia) degrading in the littoral zone of a thermally impacted lake. Bacterial secondary production, measured as tritiated thymidine incorporation into DNA, ranged from 0.01 to 0.81 microgram of bacterial C mg of detritus-1 day-1. The three plant species differed with respect to the amount of bacterial productivity they supported per milligram of detritus, in accordance with the predicted biodegradability of the plant material based on initial nitrogen content, lignin content, and C/N ratio. Bacterial production also varied throughout the 22 weeks of in situ decomposition and was positively related to the nitrogen content and lignin content of the remaining detritus, as well as to the temperature of the lake water. Over time, production was negatively related to the C/N ratio and cellulose content of the degrading plant material. Bacterial production on degrading plant material was also calculated on the basis of plant surface area and ranged from 0.17 to 1.98 micrograms of bacterial C cm-2 day-1. Surface area-based calculations did not correlate well with either initial plant composition or changing composition of the remaining detritus during decomposition. The rate of bacterial detritus degradation, calculated from measured production of surface-attached bacteria, was much lower than the actual rate of weight loss of plant material. This discrepancy may be attributable to the importance of nonbacterial organisms in the degradation and loss of plant material from litterbags or to the microbially mediated solubilization of particulate material prior to bacterial utilization, or both. PMID:2802603

Bacterial Profile, Antibacterial Resistance Pattern, and Associated Factors from Women Attending Postnatal Health Service at University of Gondar Teaching Hospital, Northwest Ethiopia.

PubMed

Bitew Kifilie, Abebaw; Dagnew, Mulat; Tegenie, Birhanemeskel; Yeshitela, Biruk; Howe, Rawleigh; Abate, Ebba

2018-01-01

Surgical site infection is a vital cause of maternal mortality and morbidity, especially in resource-limited countries. The rise of antibiotic resistance bacterial infection poses a big threat to this vulnerable population. However, there is lack of studies around the study area. The purpose of this study was to identify bacterial profile, antibacterial resistance pattern, and associated factors among mothers attending postnatal care health service. Institutional based cross-sectional study was conducted on 107 study participants at University of Gondar Teaching Hospital from 1 January 2016 to 30 May 2016. Wound swab, aspirate, and biopsy were collected and performed for culture and drug resistance testing. Data were entered and analyzed by using SPSS version 20. Bivariate and multivariate logistic regression models were fitted to determine the associated factors for bacterial infection. Odds ratio (95% CI) was calculated to determine the strength of statistically significant associated factors. Bacterial growth was confirmed in 90 (84.1%) of 107 study participants suspected to have surgical site infection. The predominant bacterial isolates were S. aureus (41.6%), E. coli (19.8%), K. pneumoniae (13.9%), coagulase negative Staphylococcus (12.9%), and Enterobacter spp. (4%). The majority of isolates were resistant to ampicillin, amoxicillin, and tetracycline but susceptible to ceftriaxone and amikacin. Multidrug-resistant bacteria species were isolated. Using a procedure such as cesarean section and episiotomy for delivery and premature rapture of membrane had strong association with bacterial infection. The high prevalence of bacterial profile and isolation of multidrug-resistant bacteria pose a big threat to postnatal mothers and their children. Factors such as cesarean section, episiotomy for delivery, and premature rapture of membrane were predictors for bacterial infection. Therefore, there should be done a continuous surveillance as well as rational use of antibiotics and a longitudinal study using phenotypic and genotypic methods will be done.

Intrinsic factors of Peltigera lichens influence the structure of the associated soil bacterial microbiota.

PubMed

Leiva, Diego; Clavero-León, Claudia; Carú, Margarita; Orlando, Julieta

2016-11-01

Definition of lichens has evolved from bi(tri)partite associations to multi-species symbioses, where bacteria would play essential roles. Besides, although soil bacterial communities are known to be affected by edaphic factors, when lichens grow upon them these could become less preponderant. We hypothesized that the structure of both the lichen microbiota and the microbiota in the soil underneath lichens is shaped by lichen intrinsic and extrinsic factors. In this work, intrinsic factors corresponded to mycobiont and cyanobiont identities of Peltigera lichens, metabolite diversity and phenoloxidase activity and extrinsic factors involved the site of the forest where lichens grow. Likewise, the genetic and metabolic structure of the lichen and soil bacterial communities were analyzed by fingerprinting. Among the results, metabolite diversity was inversely related to the genetic structure of bacterial communities of lichens and soils, highlighting the far-reaching effect of these substances; while phenoloxidase activity was inversely related to the metabolic structure only of the lichen bacterial microbiota, presuming a more limited effect of the products of these enzymes. Soil bacterial microbiota was different depending on the site and, strikingly, according to the cyanobiont present in the lichen over them, which could indicate an influence of the photobiont metabolism on the availability of soil nutrients. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Differential growth responses of soil bacterial taxa to carbon substrates of varying chemical recalcitrance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goldfarb, K.C.; Karaoz, U.; Hanson, C.A.

2011-04-18

Soils are immensely diverse microbial habitats with thousands of co-existing bacterial, archaeal, and fungal species. Across broad spatial scales, factors such as pH and soil moisture appear to determine the diversity and structure of soil bacterial communities. Within any one site however, bacterial taxon diversity is high and factors maintaining this diversity are poorly resolved. Candidate factors include organic substrate availability and chemical recalcitrance, and given that they appear to structure bacterial communities at the phylum level, we examine whether these factors might structure bacterial communities at finer levels of taxonomic resolution. Analyzing 16S rRNA gene composition of nucleotide analog-labeledmore » DNA by PhyloChip microarrays, we compare relative growth rates on organic substrates of increasing chemical recalcitrance of >2,200 bacterial taxa across 43 divisions/phyla. Taxa that increase in relative abundance with labile organic substrates (i.e., glycine, sucrose) are numerous (>500), phylogenetically clustered, and occur predominantly in two phyla (Proteobacteria and Actinobacteria) including orders Actinomycetales, Enterobacteriales, Burkholderiales, Rhodocyclales, Alteromonadales, and Pseudomonadales. Taxa increasing in relative abundance with more chemically recalcitrant substrates (i.e., cellulose, lignin, or tannin-protein) are fewer (168) but more phylogenetically dispersed, occurring across eight phyla and including Clostridiales, Sphingomonadalaes, Desulfovibrionales. Just over 6% of detected taxa, including many Burkholderiales increase in relative abundance with both labile and chemically recalcitrant substrates. Estimates of median rRNA copy number per genome of responding taxa demonstrate that these patterns are broadly consistent with bacterial growth strategies. Taken together, these data suggest that changes in availability of intrinsically labile substrates may result in predictable shifts in soil bacterial composition.« less

Motility and Adhesiveness in Human Neutrophils

PubMed Central

Smith, C. Wayne; Hollers, James C.; Patrick, Richard A.; Hassett, Clare

1979-01-01

Human peripheral blood neutrophils (PMN) obtained from healthy adults were examined in vitro with techniques adapted to assess the effects of chemotactic factors (CF) on cellular configuration and adhesiveness. The results were compared with those that use certain conventional techniques for assessing chemotaxis and chemokinesis. Exposure of PMN to N-formyl-l-methionyl-l-phenylalanine (f-Met-Phe), zymosan-activated serum, bacterial chemotactic factor, or a low molecular weight chemotactic factor from activated serum (C5a) in the absence of a gradient resulted in a change in cellular shape from a spherical to a polarized configuration in a high percentage of cells. This occurred rapidly in suspension, under conditions designed to exclude a role for cell adhesiveness, and was reversible upon removal of the CF. Restimulation of cells with the CF resulted in reappearance of the polarized configuration to the same extent as on initial stimulation with one exception: f-Met-Phe pretreated cells failed to respond to f-Met-Phe, though they responded fully to the other CF. Each CF caused a significant increase in PMN attachment to protein-coated glass. This enhanced adhesiveness was not reversible upon removal of the CF when the cells were treated under conditions shown to produce chemotactic deactivation. Cells treated under these conditions also exhibited significantly reduced motility on glass and in micropore filters in the absence of a gradient of CF. Bacterial chemotactic factor, even at high concentrations, failed to produce deactivation and did not cause a sustained enhancement of adhesiveness. Images PMID:372238

Efficacy of a mouthrinse based on hydroxyapatite to reduce initial bacterial colonisation in situ.

PubMed

Kensche, A; Holder, C; Basche, S; Tahan, N; Hannig, C; Hannig, M

2017-08-01

The present in situ - investigation aimed to specify the impact of pure hydroxyapatite microclusters on initial bioadhesion and bacterial colonization at the tooth surface. Pellicle formation was carried out in situ on bovine enamel slabs (9 subjects). After 1min of pellicle formation rinses with 8ml of hydroxyapatite (HA) microclusters (5%) in bidestilled water or chlorhexidine 0.2% were performed. As negative control no rinse was adopted. In situ biofilm formation was promoted by the intraoral slab exposure for 8h overnight. Afterwards initial bacterial adhesion was quantified by DAPI staining and bacterial viability was determined in vivo/in vitro by live/dead-staining (BacLight). SEM analysis evaluated the efficacy of the mouthrinse to accumulate hydroxyapatite microclusters at the specimens' surface and spit-out samples of the testsolution were investigated by TEM. Compared to the control (2.36×10 6 ±2.01×10 6 bacteria/cm 2 ), significantly reduced amounts of adherent bacteria were detected on specimens rinsed with chlorhexidine 0.2% (8.73×10 4 ±1.37×10 5 bacteria/cm 2 ) and likewise after rinses with the hydroxyapatite testsolution (2.08×10 5 ±2.85×10 5 bacteria/cm 2 , p<0.001). No demonstrable effect of HA-particles on Streptococcus mutans viability could be shown. SEM analysis confirmed the temporary adsorption of hydroxyapatite microclusters at the tooth surface. Adhesive interactions of HA-particles with oral bacteria were shown by TEM. Hydroxyapatite microclusters reduced initial bacterial adhesion to enamel in situ considerably and could therefore sensibly supplement current approaches in dental prophylaxis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Ralstonia insidiosa induces cell aggregation by Listeria monocytogenes

USDA-ARS?s Scientific Manuscript database

Biofilm formation is an important strategy for foodborne bacterial pathogens to survive in stressful environments such as fresh produce processing facilities. Bacterial cell aggregation strongly promotes the initiation of microcolonies and the formation of biofilms on abiological surfaces. We previ...

Growth phase-dependent induction of stationary-phase promoters of Escherichia coli in different gram-negative bacteria.

PubMed Central

Miksch, G; Dobrowolski, P

1995-01-01

RSF1010-derived plasmids carrying a fusion of a promoterless lacZ gene with the sigma s-dependent growth phase-regulated promoters of Escherichia coli, bolAp1 and fic, were constructed. The plasmids were mobilized into the gram-negative bacterial species Acetobacter methanolicus, Xanthomonas campestris, Pseudomonas putida, and Rhizobium meliloti. The beta-galactosidase activities of bacterial cultures were determined during exponential and stationary growth phases. Transcriptional activation of the fic promoter in the different bacteria was growth phase dependent as in E. coli and was initiated generally during the transition to stationary phase. The induction of the bolA promoter was also growth phase dependent in the bacteria tested. While the expression in E. coli and R. meliloti was initiated during the transition from exponential to stationary phase, the induction in A. methanolicus, P. putida, and X. campestris started some hours after stationary growth phase was reached. In all the species tested, DNA fragments hybridizing with the rpoS gene of E. coli were detected. The results show that in different gram-negative bacteria, stationary-phase-specific sigma factors which are structurally and functionally homologous to sigma s and are able to recognize the promoter sequences of both bolA and fic exist. PMID:7665531

[Bacterial translocation: gap in the shield].

PubMed

Rosero, Olivér; Kovács, Tibor; Onody, Péter; Harsányi, László; Szijártó, Attila

2014-02-23

The gastrointestinal tract is not only regarded as a system where nutrient absorption takes place, but also as a vital barrier against intraluminal pathogens entering the circulation and the maintenance of immune homeostasis. Bacterial translocation is defined as the penetration of viable bacteria or bacterial compounds from the gastrointestinal tract to extraintestinal sites. This disorder has been described in several clinical conditions. The main promoting factors for bacterial translocation have been proposed to be changes in the intestinal microflora, mucosal barrier failure and defects in host immunity. The presence of bacterial translocation has been associated with higher complications and mortality rates; therefore it should be taken into account in the therapeutic strategies of patients with predisposing factors.

[Preoperatiove Airway Bacterial Colonization: the Missing Link between Non-small Cell Lung Cancer Following Lobectomy and Postoperative Pneumonia?

PubMed

Gao, Ke; Lai, Yutian; Huang, Jian; Wang, Yifan; Wang, Xiaowei; Che, Guowei

2017-04-20

Surgical procedure is the main method of treating lung cancer. Meanwhile, postoperative pneumonia (POP) is the major cause of perioperative mortality in lung cancer surgery. The preoperative pathogenic airway bacterial colonization is an independent risk factor causing postoperative pulmonary complications (PPC). This cross-sectional study aimed to explore the relationship between preoperative pathogenic airway bacterial colonization and POP in lung cancer and to identify the high-risk factors of preoperative pathogenic airway bacterial colonization. A total of 125 patients with non-small cell lung cancer (NSCLC) underwent thoracic surgery in six hospitals of Chengdu between May 2015 and January 2016. Preoperative pathogenic airway bacterial colonization was detected in all patients via fiber bronchoscopy. Patients' PPC, high-risk factors, clinical characteristics, and the serum surfactant protein D (SP-D) level were also analyzed. The incidence of preoperative pathogenic airway bacterial colonization among NSCLC patients was 15.2% (19/125). Up to 22 strains were identified in the colonization positive group, with Gram-negative bacteria being dominant (86.36%, 19/22). High-risk factors of pathogenic airway bacterial colonization were age (≥75 yr) and smoking index (≥400 cigarettes/year). PPC incidence was significantly higher in the colonization-positive group (42.11%, 8/19) than that in the colonization-negative group (16.04%, 17/106)(P=0.021). POP incidence was significantly higher in the colonization-positive group (26.32%, 5/19) than that in the colonization-negative group (6.60%, 7/106)(P=0.019). The serum SP-D level of patients in the colonization-positive group was remarkably higher than that in the colonization-negative group [(31.25±6.09) vs (28.17±5.23)](P=0.023). The incidence of preoperative pathogenic airway bacterial colonization among NSCLC patients with POP was 41.67% (5/12). This value was 3.4 times higher than that among the patients without POP (OR=3.363, 95%CI: 1.467-7.711). An intimate correlation was observed between POP and pathogenic airway bacterial colonization in lung cancer. The high-risk factors of pathogenic airway bacterial colonization were age and smoking index.

Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin.

PubMed

Brown, Richard G; Marchesi, Julian R; Lee, Yun S; Smith, Ann; Lehne, Benjamin; Kindinger, Lindsay M; Terzidou, Vasso; Holmes, Elaine; Nicholson, Jeremy K; Bennett, Phillip R; MacIntyre, David A

2018-01-24

Preterm prelabour rupture of the fetal membranes (PPROM) precedes 30% of preterm births and is a risk factor for early onset neonatal sepsis. As PPROM is strongly associated with ascending vaginal infection, prophylactic antibiotics are widely used. The evolution of vaginal microbiota compositions associated with PPROM and the impact of antibiotics on bacterial compositions are unknown. We prospectively assessed vaginal microbiota prior to and following PPROM using MiSeq-based sequencing of 16S rRNA gene amplicons and examined the impact of erythromycin prophylaxis on bacterial load and community structures. In contrast to pregnancies delivering at term, vaginal dysbiosis characterised by Lactobacillus spp. depletion was present prior to the rupture of fetal membranes in approximately a third of cases (0% vs. 27%, P = 0.026) and persisted following membrane rupture (31%, P = 0.005). Vaginal dysbiosis was exacerbated by erythromycin treatment (47%, P = 0.00009) particularly in women initially colonised by Lactobacillus spp. Lactobacillus depletion and increased relative abundance of Sneathia spp. were associated with subsequent funisitis and early onset neonatal sepsis. Our data show that vaginal microbiota composition is a risk factor for subsequent PPROM and is associated with adverse short-term maternal and neonatal outcomes. This highlights vaginal microbiota as a potentially modifiable antenatal risk factor for PPROM and suggests that routine use of erythromycin for PPROM be re-examined.

Synthesis and characterization of anti-bacterial and anti-fungal citrate-based mussel-inspired bioadhesives

PubMed Central

Guo, Jinshan; Wang, Wei; Hu, Jianqing; Xie, Denghui; Gerhard, Ethan; Nisic, Merisa; Shan, Dingying; Qian, Guoying; Zheng, Siyang; Yang, Jian

2016-01-01

Bacterial and fungal infections in the use of surgical devices and medical implants remain a major concern. Traditional bioadhesives fail to incorporate anti-microbial properties, necessitating additional anti-microbial drug injection. Herein, by the introduction of the clinically used and inexpensive anti-fungal agent, 10-undecylenic acid (UA), into our recently developed injectable citrate-based mussel-inspired bioadhesives (iCMBAs), a new family of anti-bacterial and anti-fungal iCMBAs (AbAf iCs) was developed. AbAf iCs not only showed strong wet tissue adhesion strength, but also exhibited excellent in vitro cyto-compatibility, fast degradation, and strong initial and considerable long-term anti-bacterial and anti-fungal ability. For the first time, the biocompatibility and anti-microbial ability of sodium metaperiodate (PI), an oxidant used as a cross-linking initiator in the AbAf iCs system, was also thoroughly investigated. Our results suggest that the PI-based bioadhesives showed better anti-microbial properties compared to the unstable silver-based bioadhesive materials. In conclusion, AbAf iCs family can serve as excellent anti-bacterial and anti-fungal bioadhesive candidates for tissue/wound closure, wound dressing, and bone regeneration, especially when bacterial or fungal infections are a major concern. PMID:26874283

Synthesis and characterization of anti-bacterial and anti-fungal citrate-based mussel-inspired bioadhesives.

PubMed

Guo, Jinshan; Wang, Wei; Hu, Jianqing; Xie, Denghui; Gerhard, Ethan; Nisic, Merisa; Shan, Dingying; Qian, Guoying; Zheng, Siyang; Yang, Jian

2016-04-01

Bacterial and fungal infections in the use of surgical devices and medical implants remain a major concern. Traditional bioadhesives fail to incorporate anti-microbial properties, necessitating additional anti-microbial drug injection. Herein, by the introduction of the clinically used and inexpensive anti-fungal agent, 10-undecylenic acid (UA), into our recently developed injectable citrate-based mussel-inspired bioadhesives (iCMBAs), a new family of anti-bacterial and anti-fungal iCMBAs (AbAf iCs) was developed. AbAf iCs not only showed strong wet tissue adhesion strength, but also exhibited excellent in vitro cyto-compatibility, fast degradation, and strong initial and considerable long-term anti-bacterial and anti-fungal ability. For the first time, the biocompatibility and anti-microbial ability of sodium metaperiodate (PI), an oxidant used as a cross-linking initiator in the AbAf iCs system, was also thoroughly investigated. Our results suggest that the PI-based bioadhesives showed better anti-microbial properties compared to the unstable silver-based bioadhesive materials. In conclusion, AbAf iCs family can serve as excellent anti-bacterial and anti-fungal bioadhesive candidates for tissue/wound closure, wound dressing, and bone regeneration, especially when bacterial or fungal infections are a major concern. Copyright © 2016 Elsevier Ltd. All rights reserved.

Silver nanoparticle-doped zirconia capillaries for enhanced bacterial filtration.

PubMed

Wehling, Julia; Köser, Jan; Lindner, Patrick; Lüder, Christian; Beutel, Sascha; Kroll, Stephen; Rezwan, Kurosch

2015-03-01

Membrane clogging and biofilm formation are the most serious problems during water filtration. Silver nanoparticle (Agnano) coatings on filtration membranes can prevent bacterial adhesion and the initiation of biofilm formation. In this study, Agnano are immobilized via direct reduction on porous zirconia capillary membranes to generate a nanocomposite material combining the advantages of ceramics being chemically, thermally and mechanically stable with nanosilver, an efficient broadband bactericide for water decontamination. The filtration of bacterial suspensions of the fecal contaminant Escherichia coli reveals highly efficient bacterial retention capacities of the capillaries of 8 log reduction values, fulfilling the requirements on safe drinking water according to the U.S. Environmental Protection Agency. Maximum bacterial loading capacities of the capillary membranes are determined to be 3×10(9)bacterialcells/750mm(2) capillary surface until back flushing is recommendable. The immobilized Agnano remain accessible and exhibit strong bactericidal properties by killing retained bacteria up to maximum bacterial loads of 6×10(8)bacterialcells/750mm(2) capillary surface and the regenerated membranes regain filtration efficiencies of 95-100%. Silver release is moderate as only 0.8% of the initial silver loading is leached during a three-day filtration experiment leading to average silver contaminant levels of 100μg/L. Copyright © 2014 Elsevier B.V. All rights reserved.

Consequences of packaging on bacterial growth. Meat is an ecological niche.

PubMed

Labadie, J

1999-07-01

Meat is a good support for bacterial growth and particularly for bacteria which are specific of meat and meat products. Little is known about the physiological and biochemical factors which could explain why some bacterial species are only isolated from meat. This review tentatively points out, from an ecological point of view, some of these factors in Gram negative and Gram positive micro-organisms influencing storage life.

Klebsiella pneumoniae Siderophores Induce Inflammation, Bacterial Dissemination, and HIF-1α Stabilization during Pneumonia.

PubMed

Holden, Victoria I; Breen, Paul; Houle, Sébastien; Dozois, Charles M; Bachman, Michael A

2016-09-13

Klebsiella pneumoniae is a Gram-negative pathogen responsible for a wide range of infections, including pneumonia and bacteremia, and is rapidly acquiring antibiotic resistance. K. pneumoniae requires secretion of siderophores, low-molecular-weight, high-affinity iron chelators, for bacterial replication and full virulence. The specific combination of siderophores secreted by K. pneumoniae during infection can impact tissue localization, systemic dissemination, and host survival. However, the effect of these potent iron chelators on the host during infection is unknown. In vitro, siderophores deplete epithelial cell iron, induce cytokine secretion, and activate the master transcription factor hypoxia inducible factor-1α (HIF-1α) protein that controls vascular permeability and inflammatory gene expression. Therefore, we hypothesized that siderophore secretion by K. pneumoniae directly contributes to inflammation and bacterial dissemination during pneumonia. To examine the effects of siderophore secretion independently of bacterial growth, we performed infections with tonB mutants that persist in vivo but are deficient in siderophore import. Using a murine model of pneumonia, we found that siderophore secretion by K. pneumoniae induces the secretion of interleukin-6 (IL-6), CXCL1, and CXCL2, as well as bacterial dissemination to the spleen, compared to siderophore-negative mutants at an equivalent bacterial number. Furthermore, we determined that siderophore-secreting K. pneumoniae stabilized HIF-1α in vivo and that bacterial dissemination to the spleen required alveolar epithelial HIF-1α. Our results indicate that siderophores act directly on the host to induce inflammatory cytokines and bacterial dissemination and that HIF-1α is a susceptibility factor for bacterial invasion during pneumonia. Klebsiella pneumoniae causes a wide range of bacterial diseases, including pneumonia, urinary tract infections, and sepsis. To cause infection, K. pneumoniae steals iron from its host by secreting siderophores, small iron-chelating molecules. Classically, siderophores are thought to worsen infections by promoting bacterial growth. In this study, we determined that siderophore-secreting K. pneumoniae causes lung inflammation and bacterial dissemination to the bloodstream independently of bacterial growth. Furthermore, we determined that siderophore-secreting K. pneumoniae activates a host protein, hypoxia inducible factor (HIF)-1α, and requires it for siderophore-dependent bacterial dissemination. Although HIF-1α can protect against some infections, it appears to worsen infection with K. pneumoniae Together, these results indicate that bacterial siderophores directly alter the host response to pneumonia in addition to providing iron for bacterial growth. Therapies that disrupt production of siderophores could provide a two-pronged attack against K. pneumoniae infection by preventing bacterial growth and preventing bacterial dissemination to the blood. Copyright © 2016 Holden et al.

Phylogenetic congruence of armored scale insects (Hemiptera: Diaspididae) and their primary endosymbionts from the phylum Bacteroidetes.

PubMed

Gruwell, Matthew E; Morse, Geoffrey E; Normark, Benjamin B

2007-07-01

Insects in the sap-sucking hemipteran suborder Sternorrhyncha typically harbor maternally transmitted bacteria housed in a specialized organ, the bacteriome. In three of the four superfamilies of Sternorrhyncha (Aphidoidea, Aleyrodoidea, Psylloidea), the bacteriome-associated (primary) bacterial lineage is from the class Gammaproteobacteria (phylum Proteobacteria). The fourth superfamily, Coccoidea (scale insects), has a diverse array of bacterial endosymbionts whose affinities are largely unexplored. We have amplified fragments of two bacterial ribosomal genes from each of 68 species of armored scale insects (Diaspididae). In spite of initially using primers designed for Gammaproteobacteria, we consistently amplified sequences from a different bacterial phylum: Bacteroidetes. We use these sequences (16S and 23S, 2105 total base pairs), along with previously published sequences from the armored scale hosts (elongation factor 1alpha and 28S rDNA) to investigate phylogenetic congruence between the two clades. The Bayesian tree for the bacteria is roughly congruent with that of the hosts, with 67% of nodes identical. Partition homogeneity tests found no significant difference between the host and bacterial data sets. Of thirteen Shimodaira-Hasegawa tests, comparing the original Bayesian bacterial tree to bacterial trees with incongruent clades forced to match the host tree, 12 found no significant difference. A significant difference in topology was found only when the entire host tree was compared with the entire bacterial tree. For the bacterial data set, the treelengths of the most parsimonious host trees are only 1.8-2.4% longer than that of the most parsimonious bacterial trees. The high level of congruence between the topologies indicates that these Bacteroidetes are the primary endosymbionts of armored scale insects. To investigate the phylogenetic affinities of these endosymbionts, we aligned some of their 16S rDNA sequences with other known Bacteroidetes endosymbionts and with other similar sequences identified by BLAST searches. Although the endosymbionts of armored scales are only distantly related to the endosymbionts of the other sternorrhynchan insects, they are closely related to bacteria associated with eriococcid and margarodid scale insects, to cockroach and auchenorrynchan endosymbionts (Blattabacterium and Sulcia), and to male-killing endosymbionts of ladybird beetles. We propose the name "Candidatus Uzinura diaspidicola" for the primary endosymbionts of armored scale insects.

Neuroprotective action of bacterial melanin in rats after corticospinal tract lesions.

PubMed

Petrosyan, Tigran R; Gevorkyan, Olga V; Meliksetyan, Irina B; Hovsepyan, Anna S; Manvelyan, Levon R

2012-04-01

Experiments were performed on 48 albino rats. Part of the experimental animals were initially trained to a balancing instrumental conditioned reflex (ICR). Unilateral bulbar pyramidotomy performed in all rats caused contralateral hemiparesis. On the next day following the operation 24 rats were injected intramuscularly with bacterial melanin solution. 12 of these rats were initially trained to ICR. Recovery periods of ICR and paralyzed hindlimb movements were registered for melanin injected rats (n=24) and for operated rats, not treated with melanin (n=24). In rats injected with bacterial melanin the posttraumatic recovery is shorter than in animals not treated with melanin. The fastest and complete recovery was registered in rats initially trained to ICR and injected after the operation with bacterial melanin. Electrophysiological experiments were performed in transected animals treated with melanin, transected animals without melanin treatment and intact animals. Spiking activity of motoneurons was registered in lumbar motoneurons of rats in response to high frequency stimulation above the corticospinal tract transection. Spiking activity was very similar in motoneurons of melanin injected and intact or non operated animals. In animals, not dosed with bacterial melanin after the operation, areactivity or no change in firing rate was registered in response to stimulus. Stimulation of the corticospinal tract of melanin injected rats produced potentiation of the motoneuronal firing rate and is an evidence of regeneration in corticospinal tract. Similarity in spiking activity of intact and melanin injected rats shows the recovery of conductance in pyramidal tract. Morphohistochemical examination was carried out to confirm the results of behavioral and electrophysiological experiments. Medulla slices were prepared to trace the regeneration of nerve fibers. Examination of transection area revealed that bacterial melanin increases vascularization, dilates the capillaries in nervous tissue and stimulates the process of sprouting. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates

PubMed Central

Olm, Matthew R.; Brown, Christopher T.; Brooks, Brandon; Firek, Brian; Baker, Robyn; Burstein, David; Soenjoyo, Karina; Thomas, Brian C.; Morowitz, Michael; Banfield, Jillian F.

2017-01-01

The initial microbiome impacts the health and future development of premature infants. Methodological limitations have led to gaps in our understanding of the habitat range and subpopulation complexity of founding strains, as well as how different body sites support microbial growth. Here, we used metagenomics to reconstruct genomes of strains that colonized the skin, mouth, and gut of two hospitalized premature infants during the first month of life. Seven bacterial populations, considered to be identical given whole-genome average nucleotide identity of >99.9%, colonized multiple body sites, yet none were shared between infants. Gut-associated Citrobacter koseri genomes harbored 47 polymorphic sites that we used to define 10 subpopulations, one of which appeared in the gut after 1 wk but did not spread to other body sites. Differential genome coverage was used to measure bacterial population replication rates in situ. In all cases where the same bacterial population was detected in multiple body sites, replication rates were faster in mouth and skin compared to the gut. The ability of identical strains to colonize multiple body sites underscores the habit flexibility of initial colonists, whereas differences in microbial replication rates between body sites suggest differences in host control and/or resource availability. Population genomic analyses revealed microdiversity within bacterial populations, implying initial inoculation by multiple individual cells with distinct genotypes. Overall, however, the overlap of strains across body sites implies that the premature infant microbiome can exhibit very low microbial diversity. PMID:28073918

Analysis of Bacterial and Archaeal Communities along a High-Molecular-Weight Polyacrylamide Transportation Pipeline System in an Oil Field

PubMed Central

Li, Cai-Yun; Li, Jing-Yan; Mbadinga, Serge Maurice; Liu, Jin-Feng; Gu, Ji-Dong; Mu, Bo-Zhong

2015-01-01

Viscosity loss of high-molecular-weight partially hydrolyzed polyacrylamide (HPAM) solution was observed in a water injection pipeline before being injected into subterranean oil wells. In order to investigate the possible involvement of microorganisms in HPAM viscosity loss, both bacterial and archaeal community compositions of four samples collected from different points of the transportation pipeline were analyzed using PCR-amplification of the 16S rRNA gene and clone library construction method together with the analysis of physicochemical properties of HPAM solution and environmental factors. Further, the relationship between environmental factors and HPAM properties with microorganisms were delineated by canonical correspondence analysis (CCA). Diverse bacterial and archaeal groups were detected in the four samples. The microbial community of initial solution S1 gathered from the make-up tank is similar to solution S2 gathered from the first filter, and that of solution S3 obtained between the first and the second filter is similar to that of solution S4 obtained between the second filter and the injection well. Members of the genus Acinetobacter sp. were detected with high abundance in S3 and S4 in which HPAM viscosity was considerably reduced, suggesting that they likely played a considerable role in HPAM viscosity loss. This study presents information on microbial community diversity in the HPAM transportation pipeline and the possible involvement of microorganisms in HPAM viscosity loss and biodegradation. The results will help to understand the microbial community contribution made to viscosity change and are beneficial for providing information for microbial control in oil fields. PMID:25849654

Analysis of bacterial and archaeal communities along a high-molecular-weight polyacrylamide transportation pipeline system in an oil field.

PubMed

Li, Cai-Yun; Li, Jing-Yan; Mbadinga, Serge Maurice; Liu, Jin-Feng; Gu, Ji-Dong; Mu, Bo-Zhong

2015-04-02

Viscosity loss of high-molecular-weight partially hydrolyzed polyacrylamide (HPAM) solution was observed in a water injection pipeline before being injected into subterranean oil wells. In order to investigate the possible involvement of microorganisms in HPAM viscosity loss, both bacterial and archaeal community compositions of four samples collected from different points of the transportation pipeline were analyzed using PCR-amplification of the 16S rRNA gene and clone library construction method together with the analysis of physicochemical properties of HPAM solution and environmental factors. Further, the relationship between environmental factors and HPAM properties with microorganisms were delineated by canonical correspondence analysis (CCA). Diverse bacterial and archaeal groups were detected in the four samples. The microbial community of initial solution S1 gathered from the make-up tank is similar to solution S2 gathered from the first filter, and that of solution S3 obtained between the first and the second filter is similar to that of solution S4 obtained between the second filter and the injection well. Members of the genus Acinetobacter sp. were detected with high abundance in S3 and S4 in which HPAM viscosity was considerably reduced, suggesting that they likely played a considerable role in HPAM viscosity loss. This study presents information on microbial community diversity in the HPAM transportation pipeline and the possible involvement of microorganisms in HPAM viscosity loss and biodegradation. The results will help to understand the microbial community contribution made to viscosity change and are beneficial for providing information for microbial control in oil fields.

Consistent effects of nitrogen fertilization on soil bacterial communities in black soils for two crop seasons in China.

PubMed

Zhou, Jing; Jiang, Xin; Wei, Dan; Zhao, Baisuo; Ma, Mingchao; Chen, Sanfeng; Cao, Fengming; Shen, Delong; Guan, Dawei; Li, Jun

2017-06-12

Long-term use of inorganic nitrogen (N) fertilization has greatly influenced the bacterial community in black soil of northeast China. It is unclear how N affects the bacterial community in two successive crop seasons in the same field for this soil type. We sampled soils from a long-term fertilizer experimental field in Harbin city with three N gradients. We applied sequencing and quantitative PCR targeting at the 16S rRNA gene to examine shifts in bacterial communities and test consistent shifts and driving-factors bacterial responses to elevated N additions. N addition decreased soil pH and bacterial 16S rDNA copy numbers, and increased soil N and crop yield. N addition consistently decreased bacterial diversity and altered bacterial community composition, by increasing the relative abundance of Proteobacteria, and decreasing that of Acidobacteria and Nitrospirae in both seasons. Consistent changes in the abundant classes and genera, and the structure of the bacterial communities across both seasons were observed. Our results suggest that increases in N inputs had consistent effects on the richness, diversity and composition of soil bacterial communities across the crop seasons in two continuous years, and the N addition and the subsequent edaphic changes were important factors in shaping bacterial community structures.

Morphodynamics of growing bacterial colony

NASA Astrophysics Data System (ADS)

Ghosh, Pushpita; Perlekar, Prasad; Rana, Navdeep

Self-organization into multicellular communities is a natural trend of most of the bacteria. Mutual interactions and competition among the bacterial cells in such multicellular organization play essential role in governing the spatiotemporal dynamics. We here present the spatiotemporal dynamics of growing bacterial colony using theory and a particle-based or individual-based simulation model of nonmotile cells growing utilizing a diffusing nutrient/food on a semi-solid surface by their growth and division forces and by pushing each-other through sliding motility. We show how the resource competition over a fixed amount of food, the diffusion coefficient of the nutrient and the random genetic noise govern the morphodynamics of a single species and a well-mixed two-species bacterial colonies. Our results show that for a very low initial food concentrations, colony develops fingering pattern at the front, while for intermediate values of initial food sources, the colony undergoes transitions to branched structures at the periphery and for very high values of food colony develops smoother fronts.

Isolation and characterization of a novel 2-methyl-4-chlorophenoxyacetic acid-degrading Enterobacter sp. strain SE08.

PubMed

Tan, Lin; Hu, Qiulong; Xiong, Xingyao; Su, Xiaojun; Huang, Yanning; Jiang, Ziwei; Zhou, Qingming; Zhao, Songyi; Zeng, Wei-ai

2013-10-01

A bacterial strain (SE08) capable of utilizing 2-methyl-4-chlorophenoxy acetic acid (MCPA) as the sole carbon and energy source for growth was isolated by continuous enrichment culturing in minimal salt medium (MSM) from a long term MCPA exposed soil. This bacterial strain was identified as Enterobacter sp. based on morphological, physiological and biochemical tests, as well as 16S rRNA sequence analysis. Its ability to degrade MCPA was determined using high performance liquid chromatography. The strain SE08 can tolerate unusually high MCPA concentrations (125-2000mg/L). The influences of culturing factors (initial concentration, pH, and temperature) on the bacterial growth and substrate degradation were studied. The results showed that the optimal MCPA degradation occurred at an MCPA concentration of 500mg/L, 30°C and pH 6.0. Under these conditions, 68.5 percent of MCPA in MSM was degraded by SE08, and the OD600nm reached 0.64 after culturing for 72h. The degradation of MCPA could be enhanced by addition of both carbon and nitrogen sources. At an initial MCPA concentration of 500mg/L, when 5g/L glucose and 2.5g/L yeast extract were added into the MSM media, the MCPA degradation was significantly increased to 83.8 percent, and OD600nm was increased to 1.09 after incubation at 30°C and pH 6.0 for 72h. This is the first study showing that an Enterobacter sp. strain is capable of degrading MCPA, which might provide a new approach for the remediation of MCPA contaminated soil and contribute to the limited knowledge about the function of Enterobacter species. Crown Copyright © 2013. Published by Elsevier Inc. All rights reserved.

Biosorption of heavy metals by Bacillus thuringiensis strain OSM29 originating from industrial effluent contaminated north Indian soil

PubMed Central

Oves, Mohammad; Khan, Mohammad Saghir; Zaidi, Almas

2012-01-01

The study was navigated to examine the metal biosorbing ability of bacterial strain OSM29 recovered from rhizosphere of cauliflower grown in soil irrigated consistently with industrial effluents. The metal tolerant bacterial strain OSM29 was identified as Bacillus thuringiensis following 16S rRNA gene sequence analysis. In the presence of the varying concentrations (25–150 mgl−1) of heavy metals, such as cadmium, chromium, copper, lead and nickel, the B. thuringiensis strain OSM29 showed an obvious metal removing potential. The effect of certain physico-chemical factors such as pH, initial metal concentration, and contact time on biosorption was also assessed. The optimum pH for nickel and chromium removal was 7, while for cadmium, copper and lead, it was 6. The optimal contact time was 30 min. for each metal at 32 ± 2 °C by strain OSM29. The biosorption capacity of the strain OSM29 for the metallic ions was highest for Ni (94%) which was followed by Cu (91.8%), while the lowest sorption by bacterial biomass was recorded for Cd (87%) at 25 mgl−1 initial metal ion concentration. The regression coefficients obtained for heavy metals from the Freundlich and Langmuir models were significant. The surface chemical functional groups of B. thuringiensis biomass identified by Fourier transform infrared (FTIR) were amino, carboxyl, hydroxyl, and carbonyl groups, which may be involved in the biosorption of heavy metals. The biosorption ability of B. thuringiensis OSM29 varied with metals and was pH and metal concentration dependent. The biosorption of each metal was fairly rapid which could be an advantage for large scale treatment of contaminated sites. PMID:24115905

Two-Partner Secretion: Combining Efficiency and Simplicity in the Secretion of Large Proteins for Bacteria-Host and Bacteria-Bacteria Interactions

PubMed Central

Guérin, Jeremy; Bigot, Sarah; Schneider, Robert; Buchanan, Susan K.; Jacob-Dubuisson, Françoise

2017-01-01

Initially identified in pathogenic Gram-negative bacteria, the two-partner secretion (TPS) pathway, also known as Type Vb secretion, mediates the translocation across the outer membrane of large effector proteins involved in interactions between these pathogens and their hosts. More recently, distinct TPS systems have been shown to secrete toxic effector domains that participate in inter-bacterial competition or cooperation. The effects of these systems are based on kin vs. non-kin molecular recognition mediated by specific immunity proteins. With these new toxin-antitoxin systems, the range of TPS effector functions has thus been extended from cytolysis, adhesion, and iron acquisition, to genome maintenance, inter-bacterial killing and inter-bacterial signaling. Basically, a TPS system is made up of two proteins, the secreted TpsA effector protein and its TpsB partner transporter, with possible additional factors such as immunity proteins for protection against cognate toxic effectors. Structural studies have indicated that TpsA proteins mainly form elongated β helices that may be followed by specific functional domains. TpsB proteins belong to the Omp85 superfamily. Open questions remain on the mechanism of protein secretion in the absence of ATP or an electrochemical gradient across the outer membrane. The remarkable dynamics of the TpsB transporters and the progressive folding of their TpsA partners at the bacterial surface in the course of translocation are thought to be key elements driving the secretion process. PMID:28536673

Plasmid-Mediated Bioaugmentation for the Bioremediation of Contaminated Soils

PubMed Central

Garbisu, Carlos; Garaiyurrebaso, Olatz; Epelde, Lur; Grohmann, Elisabeth; Alkorta, Itziar

2017-01-01

Bioaugmentation, or the inoculation of microorganisms (e.g., bacteria harboring the required catabolic genes) into soil to enhance the rate of contaminant degradation, has great potential for the bioremediation of soils contaminated with organic compounds. Regrettably, cell bioaugmentation frequently turns into an unsuccessful initiative, owing to the rapid decrease of bacterial viability and abundance after inoculation, as well as the limited dispersal of the inoculated bacteria in the soil matrix. Genes that encode the degradation of organic compounds are often located on plasmids and, consequently, they can be spread by horizontal gene transfer into well-established, ecologically competitive, indigenous bacterial populations. Plasmid-mediated bioaugmentation aims to stimulate the spread of contaminant degradation genes among indigenous soil bacteria by the introduction of plasmids, located in donor cells, harboring such genes. But the acquisition of plasmids by recipient cells can affect the host’s fitness, a crucial aspect for the success of plasmid-mediated bioaugmentation. Besides, environmental factors (e.g., soil moisture, temperature, organic matter content) can play important roles for the transfer efficiency of catabolic plasmids, the expression of horizontally acquired genes and, finally, the contaminant degradation activity. For plasmid-mediated bioaugmentation to be reproducible, much more research is needed for a better selection of donor bacterial strains and accompanying plasmids, together with an in-depth understanding of indigenous soil bacterial populations and the environmental conditions that affect plasmid acquisition and the expression and functioning of the catabolic genes of interest. PMID:29062312

Initial Characterization of the Pig Skin Bacteriome and Its Effect on In Vitro Models of Wound Healing

PubMed Central

McIntyre, Matthew K.; Peacock, Trent J.; Akers, Kevin S.

2016-01-01

Elucidating the roles and composition of the human skin microbiome has revealed a delicate interplay between resident microbes and wound healing. Evolutionarily speaking, normal cutaneous flora likely has been selected for because it potentiates or, at minimum, does not impede wound healing. While pigs are the gold standard model for wound healing studies, the porcine skin microbiome has not been studied in detail. Herein, we performed 16S rDNA sequencing to characterize the pig skin bacteriome at several anatomical locations. Additionally, we used bacterial conditioned-media with in vitro techniques to examine the paracrine effects of bacterial-derived proteins on human keratinocytes (NHEK) and fibroblasts (NHDF). We found that at the phyla level, the pig skin bacteriome is similar to that of humans and largely consists of Firmicutes (55.6%), Bacteroidetes (20.8%), Actinobacteria (13.3%), and Proteobacteria (5.1%) however species-level differences between anatomical locations exist. Studies of bacterial supernatant revealed location-dependent effects on NHDF migration and NHEK apoptosis and growth factor release. These results expand the limited knowledge of the cutaneous bacteriome of healthy swine, and suggest that naturally occurring bacterial flora affects wound healing differentially depending on anatomical location. Ultimately, the pig might be considered the best surrogate for not only wound healing studies but also the cutaneous microbiome. This would not only facilitate investigations into the microbiome’s role in recovery from injury, but also provide microbial targets for enhancing or accelerating wound healing. PMID:27824921

Role of Streptococcus sanguinis sortase A in bacterial colonization.

PubMed

Yamaguchi, Masaya; Terao, Yutaka; Ogawa, Taiji; Takahashi, Toshihito; Hamada, Shigeyuki; Kawabata, Shigetada

2006-10-01

Streptococcus sanguinis, a normal inhabitant of the human oral cavity, has low cariogenicity, though colonization on tooth surfaces by this bacterium initiates aggregation by other oral bacteria and maturation of dental plaque. Additionally, S. sanguinis is frequently isolated from infective endocarditis patients. We investigated the functions of sortase A (SrtA), which cleaves LPXTG-containing proteins and anchors them to the bacterial cell wall, as a possible virulence factor of S. sanguinis. We identified the srtA gene of S. sanguinis by searching a homologous gene of Streptococcus mutans in genome databases. Next, we constructed an srtA-deficient mutant strain of S. sanguinis by insertional inactivation and compared it to the wild type strain. In the case of the mutant strain, some surface proteins could not anchor to the cell wall and were partially released into the culture supernatant. Furthermore, adherence to saliva-coated hydroxyapatite beads and polystyrene plates, as well as adherence to and invasion of human epithelial cells were reduced significantly in the srtA-deficient strain when compared to the wild type. In addition, antiopsonization levels and bacterial survival of the srtA-deficient mutant were decreased in human whole blood. This is the first known study to report that SrtA contributes to antiopsonization in streptococci. Our results suggest that SrtA anchors surface adhesins as well as some proteins that function as antiopsonic molecules as a means of evading the human immune system. Furthermore, they demonstrate that SrtA of S. sanguinis plays important roles in bacterial colonization.

Genome-wide analysis of alternative splicing during dendritic cell response to a bacterial challenge.

PubMed

Rodrigues, Raquel; Grosso, Ana Rita; Moita, Luís

2013-01-01

The immune system relies on the plasticity of its components to produce appropriate responses to frequent environmental challenges. Dendritic cells (DCs) are critical initiators of innate immunity and orchestrate the later and more specific adaptive immunity. The generation of diversity in transcriptional programs is central for effective immune responses. Alternative splicing is widely considered a key generator of transcriptional and proteomic complexity, but its role has been rarely addressed systematically in immune cells. Here we used splicing-sensitive arrays to assess genome-wide gene- and exon-level expression profiles in human DCs in response to a bacterial challenge. We find widespread alternative splicing events and splicing factor transcriptional signatures induced by an E. coli challenge to human DCs. Alternative splicing acts in concert with transcriptional modulation, but these two mechanisms of gene regulation affect primarily distinct functional gene groups. Alternative splicing is likely to have an important role in DC immunobiology because it affects genes known to be involved in DC development, endocytosis, antigen presentation and cell cycle arrest.

Step-wise loss of bacterial flagellar torsion confers progressive phagocytic evasion.

PubMed

Lovewell, Rustin R; Collins, Ryan M; Acker, Julie L; O'Toole, George A; Wargo, Matthew J; Berwin, Brent

2011-09-01

Phagocytosis of bacteria by innate immune cells is a primary method of bacterial clearance during infection. However, the mechanisms by which the host cell recognizes bacteria and consequentially initiates phagocytosis are largely unclear. Previous studies of the bacterium Pseudomonas aeruginosa have indicated that bacterial flagella and flagellar motility play an important role in colonization of the host and, importantly, that loss of flagellar motility enables phagocytic evasion. Here we use molecular, cellular, and genetic methods to provide the first formal evidence that phagocytic cells recognize bacterial motility rather than flagella and initiate phagocytosis in response to this motility. We demonstrate that deletion of genes coding for the flagellar stator complex, which results in non-swimming bacteria that retain an initial flagellar structure, confers resistance to phagocytic binding and ingestion in several species of the gamma proteobacterial group of Gram-negative bacteria, indicative of a shared strategy for phagocytic evasion. Furthermore, we show for the first time that susceptibility to phagocytosis in swimming bacteria is proportional to mot gene function and, consequently, flagellar rotation since complementary genetically- and biochemically-modulated incremental decreases in flagellar motility result in corresponding and proportional phagocytic evasion. These findings identify that phagocytic cells respond to flagellar movement, which represents a novel mechanism for non-opsonized phagocytic recognition of pathogenic bacteria.

Step-Wise Loss of Bacterial Flagellar Torsion Confers Progressive Phagocytic Evasion

PubMed Central

Lovewell, Rustin R.; Collins, Ryan M.; Acker, Julie L.; O'Toole, George A.; Wargo, Matthew J.; Berwin, Brent

2011-01-01

Phagocytosis of bacteria by innate immune cells is a primary method of bacterial clearance during infection. However, the mechanisms by which the host cell recognizes bacteria and consequentially initiates phagocytosis are largely unclear. Previous studies of the bacterium Pseudomonas aeruginosa have indicated that bacterial flagella and flagellar motility play an important role in colonization of the host and, importantly, that loss of flagellar motility enables phagocytic evasion. Here we use molecular, cellular, and genetic methods to provide the first formal evidence that phagocytic cells recognize bacterial motility rather than flagella and initiate phagocytosis in response to this motility. We demonstrate that deletion of genes coding for the flagellar stator complex, which results in non-swimming bacteria that retain an initial flagellar structure, confers resistance to phagocytic binding and ingestion in several species of the gamma proteobacterial group of Gram-negative bacteria, indicative of a shared strategy for phagocytic evasion. Furthermore, we show for the first time that susceptibility to phagocytosis in swimming bacteria is proportional to mot gene function and, consequently, flagellar rotation since complementary genetically- and biochemically-modulated incremental decreases in flagellar motility result in corresponding and proportional phagocytic evasion. These findings identify that phagocytic cells respond to flagellar movement, which represents a novel mechanism for non-opsonized phagocytic recognition of pathogenic bacteria. PMID:21949654

Insights into the gut microbiota of freshwater shrimp and its associations with the surrounding microbiota and environmental factors.

PubMed

Zhao, Yanting; Duan, Cuilan; Zhang, Xuxiang; Chen, Huangen; Ren, Hongqiang; Yin, Ying; Ye, Lin

2018-04-23

The gut microbiota of aquatic animals plays a crucial role in host health through nutrient acquisition and outcompetition of pathogens. In this study, based on the high-throughput sequencing of 16S rRNA gene amplicons, we examined the bacterial communities in the gut of freshwater shrimp ( Macrobrachium nipponense ) and in their living environments (sediment and pond water) and analyzed the effects of abiotic and biotic factors on the shrimp gut bacterial communities. High bacterial heterogeneity was observed in the freshwater shrimp gut samples, and the result indicated that both the surrounding bacterial community and water quality factors (particularly dissolved oxygen and temperature) could affect the shrimp gut bacterial community. Despite the observed heterogeneity, 57 genera, constituting 38~99% of the total genera in each of the 40 shrimp gut samples, were identified as the main bacterial population in the gut of M. nipponense . In addition, a high diversity and abundance of lactic acid bacteria (26 genera), which could play significant roles in the digestion process in shrimp, were observed in the shrimp gut samples. Overall, this study provides insights into the gut bacterial communities of freshwater shrimp and basic information for shrimp farming regarding the application of probiotics and disease prevention.

Bacterial and fungal communities and contribution of physicochemical factors during cattle farm waste composting.

PubMed

Huhe; Jiang, Chao; Wu, Yanpei; Cheng, Yunxiang

2017-12-01

During composting, the composition of microbial communities is subject to constant change owing to interactions with fluctuating physicochemical parameters. This study explored the changes in bacterial and fungal communities during cattle farm waste composting and aimed to identify and prioritize the contributing physicochemical factors. Microbial community compositions were determined by high-throughput sequencing. While the predominant phyla in the bacterial and fungal communities were largely consistent during the composting, differences in relative abundances were observed. Bacterial and fungal community diversity and relative abundance varied significantly, and inversely, over time. Relationships between physicochemical factors and microbial community compositions were evaluated by redundancy analysis. The variation in bacterial community composition was significantly related to water-soluble organic carbon (WSOC), and pile temperature and moisture (p < .05), while the largest portions of variation in fungal community composition were explained by pile temperature, WSOC, and C/N (p < .05). These findings indicated that those parameters are the most likely ones to influence, or be influenced by the bacterial and fungal communities. Variation partitioning analyses indicated that WSOC and pile temperature had predominant effects on bacterial and fungal community composition, respectively. Our findings will be useful for improving the quality of cattle farm waste composts. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Bioextraction of Copper from Printed Circuit Boards: Influence of Initial Concentration of Ferrous Iron

NASA Astrophysics Data System (ADS)

Yamane, Luciana Harue; Espinosa, Denise Crocce Romano; Tenório, Jorge Alberto Soares

Printed circuit boards are found in all electric and electronic equipment and are particularly problematic to recycle because of the heterogeneous mix of organic material, metals, and fiberglass. Additionally, printed circuit boards can be considered a secondary source of copper and bacterial leaching can be applied to copper recovery. This study investigated the influence of initial concentration of ferrous iron on bacterial leaching to recover copper from printed circuit boards using Acidithiobacillus ferrooxidans-LR. Printed circuit boards from computers were comminuted using a hammer mill. The powder obtained was magnetically separated and the non magnetic material used in this study. A shake flask study was carried out on the non magnetic material using a rotary shaker at 30°C, 170 rpm and different initial concentrations of ferrous iron (gL-1): 6.75; 13.57 and 16.97. Abiotic controls were also run in parallel. The monitored parameters were pH, Eh, ferrous iron concentration and copper extraction (spectroscopy of atomic absorption). The results showed that using initial concentration of ferrous iron of 6.75gL-1 were extracted 99% of copper by bacterial leaching.

Endotoxins and other sepsis triggers.

PubMed

Opal, Steven M

2010-01-01

Endotoxin, or more accurately termed bacterial lipopolysaccharide (LPS), is recognized as the most potent microbial mediator implicated in the pathogenesis of sepsis and septic shock. Yet despite its discovery well over a century ago, the fundamental role of circulating endotoxin in the blood of most patients with septic shock remains enigmatic and a subject of considerable controversy. LPS is the most prominent 'alarm molecule' sensed by the host's early warning system of innate immunity presaging the threat of invasion of the internal milieu by Gram-negative bacterial pathogens. In small doses within a localized tissue space, LPS signaling is advantageous to the host in orchestrating an appropriate antimicrobial defense and bacterial clearance mechanisms. Conversely, the sudden release of large quantities of LPS into the bloodstream is clearly deleterious to the host, initiating the release of a dysregulated and potentially lethal array of inflammatory mediators and procoagulant factors in the systemic circulation. The massive host response to this single bacterial pattern recognition molecule is sufficient to generate diffuse endothelial injury, tissue hypoperfusion, disseminated intravascular coagulation and refractory shock. Numerous attempts to block endotoxin activity in clinical trials with septic patients have met with inconsistent and largely negative results. Yet the groundbreaking discoveries within the past decade into the precise molecular basis for LPS-mediated cellular activation and tissue injury has rekindled optimism that a new generation of therapies that specifically disrupt LPS signaling might succeed. Other microbial mediators found in Gram-positive bacterial and viral and fungal pathogens are now appreciated to activate many of the same host defense networks induced by LPS. This information is providing novel interventions in the continuing effots to improve the care of septic patients. Copyright 2010 S. Karger AG, Basel.

Wine fermentation microbiome: a landscape from different Portuguese wine appellations

PubMed Central

Pinto, Cátia; Pinho, Diogo; Cardoso, Remy; Custódio, Valéria; Fernandes, Joana; Sousa, Susana; Pinheiro, Miguel; Egas, Conceição; Gomes, Ana C.

2015-01-01

Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation – Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of regional wines. PMID:26388852

Climate-related changes of soil characteristics affect bacterial community composition and function of high altitude and latitude lakes.

PubMed

Rofner, Carina; Peter, Hannes; Catalán, Núria; Drewes, Fabian; Sommaruga, Ruben; Pérez, María Teresa

2017-06-01

Lakes at high altitude and latitude are typically unproductive ecosystems where external factors outweigh the relative importance of in-lake processes, making them ideal sentinels of climate change. Climate change is inducing upward vegetation shifts at high altitude and latitude regions that translate into changes in the pools of soil organic matter. Upon mobilization, this allochthonous organic matter may rapidly alter the composition and function of lake bacterial communities. Here, we experimentally simulate this potential climate-change effect by exposing bacterioplankton of two lakes located above the treeline, one in the Alps and one in the subarctic region, to soil organic matter from below and above the treeline. Changes in bacterial community composition, diversity and function were followed for 72 h. In the subarctic lake, soil organic matter from below the treeline reduced bulk and taxon-specific phosphorus uptake, indicating that bacterial phosphorus limitation was alleviated compared to organic matter from above the treeline. These effects were less pronounced in the alpine lake, suggesting that soil properties (phosphorus and dissolved organic carbon availability) and water temperature further shaped the magnitude of response. The rapid bacterial succession observed in both lakes indicates that certain taxa directly benefited from soil sources. Accordingly, the substrate uptake profiles of initially rare bacteria (copiotrophs) indicated that they are one of the main actors cycling soil-derived carbon and phosphorus. Our work suggests that climate-induced changes in soil characteristics affect bacterioplankton community structure and function, and in turn, the cycling of carbon and phosphorus in high altitude and latitude aquatic ecosystems. © 2016 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing

PubMed Central

Eastman, Alexander W.; Yuan, Ze-Chun

2015-01-01

Advances in sequencing technology have drastically increased the depth and feasibility of bacterial genome sequencing. However, little information is available that details the specific techniques and procedures employed during genome sequencing despite the large numbers of published genomes. Shotgun approaches employed by second-generation sequencing platforms has necessitated the development of robust bioinformatics tools for in silico assembly, and complete assembly is limited by the presence of repetitive DNA sequences and multi-copy operons. Typically, re-sequencing with multiple platforms and laborious, targeted Sanger sequencing are employed to finish a draft bacterial genome. Here we describe a novel strategy based on the identification and targeted sequencing of repetitive rDNA operons to expedite bacterial genome assembly and finishing. Our strategy was validated by finishing the genome of Paenibacillus polymyxa strain CR1, a bacterium with potential in sustainable agriculture and bio-based processes. An analysis of the 38 contigs contained in the P. polymyxa strain CR1 draft genome revealed 12 repetitive rDNA operons with varied intragenic and flanking regions of variable length, unanimously located at contig boundaries and within contig gaps. These highly similar but not identical rDNA operons were experimentally verified and sequenced simultaneously with multiple, specially designed primer sets. This approach also identified and corrected significant sequence rearrangement generated during the initial in silico assembly of sequencing reads. Our approach reduces the required effort associated with blind primer walking for contig assembly, increasing both the speed and feasibility of genome finishing. Our study further reinforces the notion that repetitive DNA elements are major limiting factors for genome finishing. Moreover, we provided a step-by-step workflow for genome finishing, which may guide future bacterial genome finishing projects. PMID:25653642

Changes in Bacterial and Fungal Communities across Compost Recipes, Preparation Methods, and Composting Times

PubMed Central

Neher, Deborah A.; Weicht, Thomas R.; Bates, Scott T.; Leff, Jonathan W.; Fierer, Noah

2013-01-01

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties. PMID:24278144

Changes in bacterial and fungal communities across compost recipes, preparation methods, and composting times.

PubMed

Neher, Deborah A; Weicht, Thomas R; Bates, Scott T; Leff, Jonathan W; Fierer, Noah

2013-01-01

Compost production is a critical component of organic waste handling, and compost applications to soil are increasingly important to crop production. However, we know surprisingly little about the microbial communities involved in the composting process and the factors shaping compost microbial dynamics. Here, we used high-throughput sequencing approaches to assess the diversity and composition of both bacterial and fungal communities in compost produced at a commercial-scale. Bacterial and fungal communities responded to both compost recipe and composting method. Specifically, bacterial communities in manure and hay recipes contained greater relative abundances of Firmicutes than hardwood recipes with hay recipes containing relatively more Actinobacteria and Gemmatimonadetes. In contrast, hardwood recipes contained a large relative abundance of Acidobacteria and Chloroflexi. Fungal communities of compost from a mixture of dairy manure and silage-based bedding were distinguished by a greater relative abundance of Pezizomycetes and Microascales. Hay recipes uniquely contained abundant Epicoccum, Thermomyces, Eurotium, Arthrobotrys, and Myriococcum. Hardwood recipes contained relatively abundant Sordariomycetes. Holding recipe constant, there were significantly different bacterial and fungal communities when the composting process was managed by windrow, aerated static pile, or vermicompost. Temporal dynamics of the composting process followed known patterns of degradative succession in herbivore manure. The initial community was dominated by Phycomycetes, followed by Ascomycota and finally Basidiomycota. Zygomycota were associated more with manure-silage and hay than hardwood composts. Most commercial composters focus on the thermophilic phase as an economic means to insure sanitation of compost from pathogens. However, the community succeeding the thermophilic phase begs further investigation to determine how the microbial dynamics observed here can be best managed to generate compost with the desired properties.

Wine fermentation microbiome: a landscape from different Portuguese wine appellations.

PubMed

Pinto, Cátia; Pinho, Diogo; Cardoso, Remy; Custódio, Valéria; Fernandes, Joana; Sousa, Susana; Pinheiro, Miguel; Egas, Conceição; Gomes, Ana C

2015-01-01

Grapes and wine musts harbor a complex microbiome, which plays a crucial role in wine fermentation as it impacts on wine flavour and, consequently, on its final quality and value. Unveiling the microbiome and its dynamics, and understanding the ecological factors that explain such biodiversity, has been a challenge to oenology. In this work, we tackle this using a metagenomics approach to describe the natural microbial communities, both fungal and bacterial microorganisms, associated with spontaneous wine fermentations. For this, the wine microbiome, from six Portuguese wine appellations, was fully characterized as regards to three stages of fermentation - Initial Musts (IM), and Start and End of alcoholic fermentations (SF and EF, respectively). The wine fermentation process revealed a higher impact on fungal populations when compared with bacterial communities, and the fermentation evolution clearly caused a loss of the environmental microorganisms. Furthermore, significant differences (p < 0.05) were found in the fungal populations between IM, SF, and EF, and in the bacterial population between IM and SF. Fungal communities were characterized by either the presence of environmental microorganisms and phytopathogens in the IM, or yeasts associated with alcoholic fermentations in wine must samples as Saccharomyces and non-Saccharomyces yeasts (as Lachancea, Metschnikowia, Hanseniaspora, Hyphopichia, Sporothrix, Candida, and Schizosaccharomyces). Among bacterial communities, the most abundant family was Enterobacteriaceae; though families of species associated with the production of lactic acid (Lactobacillaceae, Leuconostocaceae) and acetic acid (Acetobacteriaceae) were also detected. Interestingly, a biogeographical correlation for both fungal and bacterial communities was identified between wine appellations at IM suggesting that each wine region contains specific and embedded microbial communities which may contribute to the uniqueness of regional wines.

Bacterial reproductive pathogens of cats and dogs.

PubMed

Graham, Elizabeth M; Taylor, David J

2012-05-01

With the notable exception of Brucella canis, exogenous bacterial pathogens are uncommon causes of reproductive disease in cats and dogs. Most bacterial reproductive infections are endogenous, and predisposing factors for infection are important. This article reviews the etiology, pathogenesis, clinical presentation, diagnosis, treatment, and public health significance of bacterial reproductive pathogens in cats and dogs.

Simultaneous recovery of Ni and Cu from computer-printed circuit boards using bioleaching: statistical evaluation and optimization.

PubMed

Arshadi, M; Mousavi, S M

2014-12-01

Computer printed circuit boards (CPCBs) have a rich metal content and are produced in high volume, making them an important component of electronic waste. The present study used a pure culture of Acidithiobacillus ferrooxidans to leach Cu and Ni from CPCBs waste. The adaptation phase began at 1g/l CPCBs powder with 10% inoculation and final pulp density was reached at 20g/l after about 80d. Four effective factors including initial pH, particle size, pulp density, and initial Fe(3+) concentration were optimized to achieve maximum simultaneous recovery of Cu and Ni. Their interactions were also identified using central composite design in response surface methodology. The suggested optimal conditions were initial pH 3, initial Fe(3+) 8.4g/l, pulp density 20g/l and particle size 95μm. Nearly 100% of Cu and Ni were simultaneously recovered under optimum conditions. Finally, bacterial growth characteristics versus time at optimum conditions were plotted. Copyright © 2014 Elsevier Ltd. All rights reserved.

Bacterial plaque retention on oral hard materials: effect of surface roughness, surface composition, and physisorbed polycarboxylate.

PubMed

McConnell, Marla D; Liu, Yu; Nowak, Andrew P; Pilch, Shira; Masters, James G; Composto, Russell J

2010-03-15

Bacterial adhesion to oral hard materials is dependent on various factors, for example, surface roughness and surface composition. In this study, bacteria retention on three oral hard substrates, hydroxyapatite (HAP), enamel, and polished enamel (p-enamel) were investigated. The surface morphology and roughness of the three substrates were measured by scanning probe microscopy. HAP had the roughest surface, followed by enamel and polished enamel. For each individual substrate type, the roughness was shown to increase with scan size up to 50 microm x 50 microm. For HAP and enamel, roughness decreased considerably after formation of a pellicle, while addition of polymer coating to the pellicle layer reduced roughness much less in comparison. Bacterial surface coverage was measured at 30 min, 3 h, and 24 h on both native and surface-modified substrates, which were coated with two different polycarboxylate-based polymers, Gantrez S97 and Carbopol 940. As a result, the polymer coated surfaces had reduced bacteria coverage compared with the native surfaces over all time points and substrates measured. The reduction is the combined effect of electrostatic repulsion and sequestering of Ca(2+) ions at the surface, which plays a key role in the initial adhesion of bacteria to enamel surfaces in models of plaque formation. (c) 2009 Wiley Periodicals, Inc.

Gut Microbiota Linked to Sexual Preference and HIV Infection

PubMed Central

Noguera-Julian, Marc; Rocafort, Muntsa; Guillén, Yolanda; Rivera, Javier; Casadellà, Maria; Nowak, Piotr; Hildebrand, Falk; Zeller, Georg; Parera, Mariona; Bellido, Rocío; Rodríguez, Cristina; Carrillo, Jorge; Mothe, Beatriz; Coll, Josep; Bravo, Isabel; Estany, Carla; Herrero, Cristina; Saz, Jorge; Sirera, Guillem; Torrela, Ariadna; Navarro, Jordi; Crespo, Manel; Brander, Christian; Negredo, Eugènia; Blanco, Julià; Guarner, Francisco; Calle, Maria Luz; Bork, Peer; Sönnerborg, Anders; Clotet, Bonaventura; Paredes, Roger

2016-01-01

The precise effects of HIV-1 on the gut microbiome are unclear. Initial cross-sectional studies provided contradictory associations between microbial richness and HIV serostatus and suggested shifts from Bacteroides to Prevotella predominance following HIV-1 infection, which have not been found in animal models or in studies matched for HIV-1 transmission groups. In two independent cohorts of HIV-1-infected subjects and HIV-1-negative controls in Barcelona (n = 156) and Stockholm (n = 84), men who have sex with men (MSM) predominantly belonged to the Prevotella-rich enterotype whereas most non-MSM subjects were enriched in Bacteroides, independently of HIV-1 status, and with only a limited contribution of diet effects. Moreover, MSM had a significantly richer and more diverse fecal microbiota than non-MSM individuals. After stratifying for sexual orientation, there was no solid evidence of an HIV-specific dysbiosis. However, HIV-1 infection remained consistently associated with reduced bacterial richness, the lowest bacterial richness being observed in subjects with a virological-immune discordant response to antiretroviral therapy. Our findings indicate that HIV gut microbiome studies must control for HIV risk factors and suggest interventions on gut bacterial richness as possible novel avenues to improve HIV-1-associated immune dysfunction. PMID:27077120

Microscopic Analysis of Bacterial Motility at High Pressure

PubMed Central

Nishiyama, Masayoshi; Sowa, Yoshiyuki

2012-01-01

The bacterial flagellar motor is a molecular machine that converts an ion flux to the rotation of a helical flagellar filament. Counterclockwise rotation of the filaments allows them to join in a bundle and propel the cell forward. Loss of motility can be caused by environmental factors such as temperature, pH, and solvation. Hydrostatic pressure is also a physical inhibitor of bacterial motility, but the detailed mechanism of this inhibition is still unknown. Here, we developed a high-pressure microscope that enables us to acquire high-resolution microscopic images, regardless of applied pressures. We also characterized the pressure dependence of the motility of swimming Escherichia coli cells and the rotation of single flagellar motors. The fraction and speed of swimming cells decreased with increased pressure. At 80 MPa, all cells stopped swimming and simply diffused in solution. After the release of pressure, most cells immediately recovered their initial motility. Direct observation of the motility of single flagellar motors revealed that at 80 MPa, the motors generate torque that should be sufficient to join rotating filaments in a bundle. The discrepancy in the behavior of free swimming cells and individual motors could be due to the applied pressure inhibiting the formation of rotating filament bundles that can propel the cell body in an aqueous environment. PMID:22768943

Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors.

PubMed

Chehoud, Christel; Stieh, Daniel J; Bailey, Aubrey G; Laughlin, Alice L; Allen, Shannon A; McCotter, Kerrie L; Sherrill-Mix, Scott A; Hope, Thomas J; Bushman, Frederic D

2017-04-24

We sought to investigate the effects of HIV infection on the vaginal microbiota and associations with treatment and demographic factors. We thus compared vaginal microbiome samples from HIV-infected (HIV+) and HIV-uninfected (HIV-) women collected at two Chicago area hospitals. We studied vaginal microbiome samples from 178 women analyzed longitudinally (n = 324 samples) and collected extensive data on clinical status and demographic factors. We used 16S rRNA gene sequencing to characterize the bacterial lineages present, then UniFrac, Shannon diversity, and other measures to compare community structure with sample metadata. Differences in microbiota measures were modest in the comparison of HIV+ and HIV- samples, in contrast to several previous studies, consistent with effective antiretroviral therapy. Proportions of healthy Lactobacillus species were not higher in HIV- patients overall, but were significantly higher when analyzed within each hospital in isolation. Rates of bacterial vaginosis were higher among African-American women and HIV+ women. Bacterial vaginosis was associated with higher frequency of HIV+. Unexpectedly, African-American women were more likely to switch bacterial vaginosis status between sampling times; switching was not associated with HIV+ status. The influence of HIV infection on the vaginal microbiome was modest for this cohort of well suppressed urban American women, consistent with effective antiretroviral therapy. HIV+ was found to be associated with bacterial vaginosis. Although bacterial vaginosis has previously been associated with HIV transmission, most of the women studied here became HIV+ many years before our test for bacterial vaginosis, thus implicating additional mechanisms linking HIV infection and bacterial vaginosis.

Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria

PubMed Central

Takada, Toshihiko; Nagata, Yuriko; Kado, Shoichi; Kushiro, Akira

2017-01-01

Each species of intestinal bacteria requires a nutritional source to maintain its population in the intestine. Dietary factors are considered to be major nutrients; however, evidence directly explaining the in situ utilization of dietary factors is limited. Microscale bacterial distribution would provide clues to understand bacterial lifestyle and nutrient utilization. However, the detailed bacterial localization around dietary factors in the intestine remains uninvestigated. Therefore, we explored microscale habitats in the murine intestine by using histology and fluorescent in situ hybridization, focusing on dietary factors. This approach successfully revealed several types of bacterial colonization. In particular, bifidobacterial colonization and adhesion on granular starch was frequently and commonly observed in the jejunum and distal colon. To identify the bacterial composition of areas around starch granules and areas without starch, laser microdissection and next-generation sequencing-based 16S rRNA microbial profiling was performed. It was found that Bifidobacteriaceae were significantly enriched by 4.7 fold in peri-starch areas compared to ex-starch areas. This family solely consisted of Bifidobacterium pseudolongum. In contrast, there was no significant enrichment among the other major families. This murine intestinal B. pseudolongum had starch-degrading activity, confirmed by isolation from the mouse feces and in vitro analysis. Collectively, our results demonstrate the significance of starch granules as a major habitat and potential nutritional niche for murine intestinal B. pseudolongum. Moreover, our results suggest that colonizing bifidobacteria effectively utilize starch from the closest location and maintain the location. This may be a bacterial strategy to monopolize solid dietary nutrients. We believe that our analytical approach could possibly be applied to other nutritional factors, and can be a powerful tool to investigate in vivo relationships between bacteria and environmental factors in the intestine. PMID:28394924

Microscale spatial analysis provides evidence for adhesive monopolization of dietary nutrients by specific intestinal bacteria.

PubMed

Nagara, Yusuke; Takada, Toshihiko; Nagata, Yuriko; Kado, Shoichi; Kushiro, Akira

2017-01-01

Each species of intestinal bacteria requires a nutritional source to maintain its population in the intestine. Dietary factors are considered to be major nutrients; however, evidence directly explaining the in situ utilization of dietary factors is limited. Microscale bacterial distribution would provide clues to understand bacterial lifestyle and nutrient utilization. However, the detailed bacterial localization around dietary factors in the intestine remains uninvestigated. Therefore, we explored microscale habitats in the murine intestine by using histology and fluorescent in situ hybridization, focusing on dietary factors. This approach successfully revealed several types of bacterial colonization. In particular, bifidobacterial colonization and adhesion on granular starch was frequently and commonly observed in the jejunum and distal colon. To identify the bacterial composition of areas around starch granules and areas without starch, laser microdissection and next-generation sequencing-based 16S rRNA microbial profiling was performed. It was found that Bifidobacteriaceae were significantly enriched by 4.7 fold in peri-starch areas compared to ex-starch areas. This family solely consisted of Bifidobacterium pseudolongum. In contrast, there was no significant enrichment among the other major families. This murine intestinal B. pseudolongum had starch-degrading activity, confirmed by isolation from the mouse feces and in vitro analysis. Collectively, our results demonstrate the significance of starch granules as a major habitat and potential nutritional niche for murine intestinal B. pseudolongum. Moreover, our results suggest that colonizing bifidobacteria effectively utilize starch from the closest location and maintain the location. This may be a bacterial strategy to monopolize solid dietary nutrients. We believe that our analytical approach could possibly be applied to other nutritional factors, and can be a powerful tool to investigate in vivo relationships between bacteria and environmental factors in the intestine.

Spatial variations of bacterial community and its relationship with water chemistry in Sanya Bay, South China Sea as determined by DGGE fingerprinting and multivariate analysis.

PubMed

Ling, Juan; Zhang, Yan-Ying; Dong, Jun-De; Wang, You-Shao; Feng, Jing-Bing; Zhou, Wei-Hua

2015-10-01

Bacteria play important roles in the structure and function of marine food webs by utilizing nutrients and degrading the pollutants, and their distribution are determined by surrounding water chemistry to a certain extent. It is vital to investigate the bacterial community's structure and identifying the significant factors by controlling the bacterial distribution in the paper. Flow cytometry showed that the total bacterial abundance ranged from 5.27 × 10(5) to 3.77 × 10(6) cells/mL. Molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequencing has been employed to investigate the bacterial community composition. The results were then interpreted through multivariate statistical analysis and tended to explain its relationship to the environmental factors. A total of 270 bands at 83 different positions were detected in DGGE profiles and 29 distinct DGGE bands were sequenced. The predominant bacteria were related to Phyla Protebacteria species (31 %, nine sequences), Cyanobacteria (37.9 %, eleven sequences) and Actinobacteria (17.2 %, five sequences). Other phylogenetic groups identified including Firmicutes (6.9 %, two sequences), Bacteroidetes (3.5 %, one sequences) and Verrucomicrobia (3.5 %, one sequences). Conical correspondence analysis was used to elucidate the relationships between the bacterial community compositions and environmental factors. The results showed that the spatial variations in the bacterial community composition was significantly related to phosphate (P = 0.002, P < 0.01), dissolved organic carbon (P = 0.004, P < 0.01), chemical oxygen demand (P = 0.010, P < 0.05) and nitrite (P = 0.016, P < 0.05). This study revealed the spatial variations of bacterial community and significant environmental factors driving the bacterial composition shift. These results may be valuable for further investigation on the functional microbial structure and expression quantitatively under the polluted environments in the world.

Urinary tract infections and bacterial prostatitis in men.

PubMed

Wagenlehner, Florian M E; Weidner, Wolfgang; Pilatz, Adrian; Naber, Kurt G

2014-02-01

The purpose of this review is to highlight advances in research on urinary tract infections (UTIs) and bacterial prostatitis in men in the preceding year. The antiseptic properties of the prostate secretions might be an important factor for prevention of recurrency. Risk factors for UTI in men include prostate enlargement and urological interventions, such as transrectal prostate biopsy. Preventive treatment of prostate enlargement has been demonstrated to reduce frequency of UTI. Ensuing infections after prostate biopsy, such as UTI and bacterial prostatitis, are increasing due to increasing rates of fluoroquinolone resistance. The increasing global antibiotic resistance also significantly affects management of UTI in men, and therefore calls for alternative strategies.Apart from prevention of complicating factors leading to UTI, a more thorough understanding of the pathophysiology may play a more important role in the future, to define new targets for treatment. Interesting results that might interfere with the intracellular mucosal bacterial load in the bladder wall have been found in the last years. UTI in men and bacterial prostatitis are currently underrepresented in the medical literature. Increasing antibacterial resistance calls for novel strategies in the prevention and management of UTI and bacterial prostatitis in men.

The Patterns and Drivers of Bacterial and Fungal β-Diversity in a Typical Dryland Ecosystem of Northwest China.

PubMed

Wang, Jianming; Zhang, Tianhan; Li, Liping; Li, Jingwen; Feng, Yiming; Lu, Qi

2017-01-01

Dryland ecosystems cover more than 30% of the terrestrial area of China, while processes that shape the biogeographic patterns of bacterial and fungal β-diversity have rarely been evaluated synchronously. To compare the biogeographic patterns and its drivers of bacterial and fungal β-diversity, we collected 62 soil samples from a typical dryland region of northwest China. We assessed bacterial and fungal communities by sequencing bacterial 16S rRNA gene and fungal ITS data. Meanwhile, the β-diversity was decomposed into two components: species replacement (species turnover) and nestedness to further explore the bacterial and fungal β-diversity patterns and its causes. The results show that both bacterial and fungal β-diversity were derived almost entirely from species turnover rather than from species nestedness. Distance-decay relationships confirmed that the geographic patterns of bacterial and fungal β-diversity were significantly different. Environmental factors had the dominant influence on both the bacterial and fungal β-diversity and species turnover, however, the role of geographic distance varied across bacterial and fungal communities. Furthermore, both bacterial and fungal nestedness did not significantly respond to the environmental and geographic distance. Our findings suggest that the different response of bacterial and fungal species turnover to dispersal limitation and other, unknown processes may result in different biogeographic patterns of bacterial and fungal β-diversity in the drylands of northwest China. Together, we highlight that the drivers of β-diversity patterns vary between bacterial and fungal communities, and microbial β-diversity are driven by multiple factors in the drylands of northwest China.

Ionic solution and nanoparticle assisted MALDI-MS as bacterial biosensors for rapid analysis of yogurt.

PubMed

Lee, Chia-Hsun; Gopal, Judy; Wu, Hui-Fen

2012-01-15

Bacterial analysis from food samples is a highly challenging task because food samples contain intensive interferences from proteins and carbohydrates. Three different conditions of yogurt were analyzed: (1) the fresh yogurt immediately after purchasing, (2) the yogurt after expiry date stored in the refrigerator and (3) the yogurt left outside, without refrigeration. The shelf lives of both these yogurt was compared in terms of the decrease in bacterial signals. AB which initially contained 10(9) cells/mL drastically reduced to 10(7) cells/mL. However, Lin (Feng-Yin) yogurt which initially (fresh) had 10(8) cells/mL, even after two weeks beyond the expiry period showed no marked drop in bacterial count. Conventional MALDI-MS analysis showed limited sensitivity for analysis of yogurt bacteria amidst the complex milk proteins present in yogurt. A cost effective ionic solution, CrO(4)(2-) solution was used to enable the successful detection of bacterial signals (40-fold increased in sensitivity) selectively without the interference of the milk proteins. 0.035 mg of Ag nanoparticles (NPs) were also found to improve the detection of bacteria 2-6 times in yogurt samples. The current approach can be further applied as a rapid, sensitive and effective platform for bacterial analysis from food. Copyright © 2011 Elsevier B.V. All rights reserved.

Impact of phenolic compounds in the acyl homoserine lactone-mediated quorum sensing regulatory pathways.

PubMed

Hossain, Md Akil; Lee, Seung-Jin; Park, Na-Hye; Mechesso, Abraham Fikru; Birhanu, Biruk Tesfaye; Kang, JeongWoo; Reza, Md Ahsanur; Suh, Joo-Won; Park, Seung-Chun

2017-09-06

Quorum sensing (QS) is a cell density-dependent regulation of virulent bacterial gene expression by autoinducers that potentially pertains in the epidemic of bacterial virulence. This study was initially designed to evaluate the effect of 5 phenolic compounds in the modulation of QS and virulence factors of Chromobacterium violaceum and Pseudomonas aeruginosa, and to determine the mechanisms of their effects. Biosensor strains were used to assess antibacterial and anti-QS effect of these compounds. Only methyl gallate (MG) among these compounds demonstrated profound anti-QS effect in the preliminary study, and thus only MG was utilized further to evaluate the effects on the synthesis and activity of acyl homoserine lactone (AHL) in C. violaceum and on the modulation of biofilm, motility, proteolytic, elastase, pyocyanin, and rhamnolipid activity in P. aeruginosa. Finally, the effect of MG on the expression of QS-regulated genes of P. aeruginosa was verified. MG suppressed both the synthesis and activity of AHL in C. violaceum. It also restricted the biofilm formation and other QS-associated virulence factor of P. aeruginosa. MG concentration-dependently suppressed the expression of lasI/R, rhlI/R, and pqsA of P. aeruginosa and was non-toxic in in vitro study. This is the first report of the anti-QS mechanism of MG.

3,4-dichloropropionaniline suppresses normal macrophage function.

PubMed

Ustyugova, Irina V; Frost, Laura L; Van Dyke, Knox; Brundage, Kathleen M; Schafer, Rosana; Barnett, John B

2007-06-01

Macrophages are a critical part of the innate immune response and natural surveillance mechanisms. As such, proper macrophage function is crucial for engulfing bacterial pathogens through phagocytosis and destroying them by generation of reactive oxygen species (ROS) and reactive nitrogen species (RNS). The production of a number of cytokines by macrophages, such as tumor necrosis factor-alpha (TNF-alpha), interleukin (IL)-1beta, and IL-6, plays an important role in the initiation of the acquired immune response creating an inflammatory environment favorable for fighting a bacterial infection. 3,4-Dichloropropionaniline (DCPA) suppresses several inflammatory parameters, including TNF-alpha production through a mechanism where nuclear factor-kappaB (NF-kappaB)-DNA binding is inhibited but not entirely abrogated. The goal of the present study was to evaluate the effects of DCPA on the inflammatory mediators of macrophages, including ROS and RNS in both murine peritoneal exudate cells and the human monocytic cell line, THP-1. The ability to perform phagocytosis and directly kill Listeria monocytogenes was also assessed. The results indicate that DCPA decreases the ability of both types of macrophages to phagocytize beads and generate both types of reactive species, which was correlated with a decrement in listericidal activity. These results demonstrate that DCPA has profound effects on macrophage function and provide insight into the potential mechanisms of immunosuppression by DCPA.

Inflammation and fertility in the mare.

PubMed

Christoffersen, M; Troedsson, Mht

2017-08-01

A transient uterine inflammation post-breeding is a normal physiological reaction in the mare, and it is believed that the inflammatory response is necessary to eliminate bacteria and excess spermatozoa introduced into the uterine lumen. A tight balance between multiple pro- and anti-inflammatory factors is required for resolving the breeding-induced inflammation within 24-36 hr in the reproductively healthy mare, whereas a subpopulation of mares is susceptible to development of a persistent infection that can interfere with fertility. The aetiology of persistent endometritis can be either bacterial or semen-induced and both scenarios can threaten the establishment of pregnancy. Several factors associated with susceptibility to persistent endometritis have been identified including altered innate immune response in the early inflammatory process, reduced myometrial contractions and impaired opsonization; however, the pathogenesis to susceptibility has not been fully elucidated. Current research focuses on the initial hours of uterine inflammatory responses to semen and bacteria, and potential treatments to modify this altered innate immune response. An increased understanding of the mechanisms involved in the disease progression is necessary to improve the treatment and management of these mares. This review attempts to summarize the current knowledge of the uterine inflammatory and immunological responses to breeding-induced endometritis, persistent breeding-induced endometritis (PBIE) and bacterial endometritis in the mare. © 2017 Blackwell Verlag GmbH.

An innate immune system-mimicking, real-time biosensing of infectious bacteria.

PubMed

Seo, Sung-Min; Jeon, Jin-Woo; Kim, Tae-Yong; Paek, Se-Hwan

2015-09-07

An animal cell-based biosensor was investigated to monitor bacterial contamination in an unattended manner by mimicking the innate immune response. The cells (RAW 264.7 cell line) were first attached onto the solid surfaces of a 96-well microtiter plate and co-incubated in the culture medium with a sample that might contain bacterial contaminants. As Toll-like receptors were present on the cell membrane surfaces, they acted as a sentinel by binding to pathogen-associated molecular patterns (PAMPs) of any contaminant. Such biological recognition initiates signal transmission along various pathways to produce different proinflammatory mediators, one of which, tumor necrosis factor-α (TNF-α) was measured using an immunosensor. To demonstrate automated bacterium monitoring, a capture antibody specific for TNF-α was immobilized on an optical fiber sensor tip and then used to measure complex formation in a label-free sensor system (e.g., Octet Red). The sensor response time depended significantly on the degree of agitation of the culture medium, controlling the biological recognition and further autocrine/paracrine signaling by cytokines. The response, particularly under non-agitated conditions, was also influenced by the medium volume, revealing a local gradient change of the cytokine concentration and also acidity, caused by bacterial growth near the bottom surfaces. A biosensor system retaining 50 μL medium and not employing agitation could be used for the early detection of bacterial contamination. This novel biosensing model was applied to the real-time monitoring of different bacteria, Shigella sonnei, Staphylococcus aureus, and Listeria monocytogenes. They (<100 CFU mL(-1)) could be detected automatically within the working time. Such analysis was carried out without any manual handling regardless of the bacterial species, suggesting the concept of non-targeted bacterial real-time monitoring. This technique was further applied to real sample testing (e.g., with milk) to exemplify, for example, the food quality control process without using any additional sample pretreatment such as magnetic concentration.

AtlA Mediates Extracellular DNA Release, Which Contributes to Streptococcus mutans Biofilm Formation in an Experimental Rat Model of Infective Endocarditis.

PubMed

Jung, Chiau-Jing; Hsu, Ron-Bin; Shun, Chia-Tung; Hsu, Chih-Chieh; Chia, Jean-San

2017-09-01

Host factors, such as platelets, have been shown to enhance biofilm formation by oral commensal streptococci, inducing infective endocarditis (IE), but how bacterial components contribute to biofilm formation in vivo is still not clear. We demonstrated previously that an isogenic mutant strain of Streptococcus mutans deficient in autolysin AtlA (Δ atlA ) showed a reduced ability to cause vegetation in a rat model of bacterial endocarditis. However, the role of AtlA in bacterial biofilm formation is unclear. In this study, confocal laser scanning microscopy analysis showed that extracellular DNA (eDNA) was embedded in S. mutans GS5 floes during biofilm formation on damaged heart valves, but an Δ atlA strain could not form bacterial aggregates. Semiquantification of eDNA by PCR with bacterial 16S rRNA primers demonstrated that the Δ atlA mutant strain produced dramatically less eDNA than the wild type. Similar results were observed with in vitro biofilm models. The addition of polyanethol sulfonate, a chemical lysis inhibitor, revealed that eDNA release mediated by bacterial cell lysis is required for biofilm initiation and maturation in the wild-type strain. Supplementation of cultures with calcium ions reduced wild-type growth but increased eDNA release and biofilm mass. The effect of calcium ions on biofilm formation was abolished in Δ atlA cultures and by the addition of polyanethol sulfonate. The VicK sensor, but not CiaH, was found to be required for the induction of eDNA release or the stimulation of biofilm formation by calcium ions. These data suggest that calcium ion-regulated AtlA maturation mediates the release of eDNA by S. mutans , which contributes to biofilm formation in infective endocarditis. Copyright © 2017 American Society for Microbiology.

pH value promotes growth of Staphylococcus epidermidis in platelet concentrates.

PubMed

Störmer, Melanie; Kleesiek, Knut; Dreier, Jens

2008-05-01

The platelet (PLT) storage lesion is characterized metabolically by a pH value associated with lactic acid generation. PLT storage conditions support the growth of Staphylococcus epidermidis, the most common organism implicated in bacterial contamination of PLT concentrates (PCs). Here, different factors that influence bacterial growth in PCs are discussed and the relation between pH values of PCs and citrate plasma (CP) is studied, with emphasis on bacterial proliferation. The PLT lesion with regard to pH decrease and lactic acid production was monitored during storage and correlated to bacterial proliferation properties. A total of 115 coagulase-negative staphylococci, especially S. epidermidis isolates, were characterized for their proliferation in different blood components (CP, buffy coat-derived, and apheresis PCs). Furthermore, the influence of donor-specific, product-specific, species-specific, and strain-specific factors on bacterial proliferation was investigated. PCs showed a lower pH value in comparison to plasma during storage. Bacterial proliferation in PCs and the failure to grow in CP were determined with all organisms tested. No correlation to donor-specific, species-specific, or strain-specific factors was observed. Lowering the pH of CP resulted in bacterial proliferation, whereas a pH increase in the PC unit inhibited the proliferation of S. epidermidis. With emphasis on bacterial proliferation, the significant difference between PC and CP is the presence of metabolizing PLTs. The pH values of stored PLTs, but not those of stored plasma, support the growth of S. epidermidis.

Modifiable risk factors in periodontitis: at the intersection of aging and disease.

PubMed

Reynolds, Mark A

2014-02-01

Chronic inflammation is a prominent feature of aging and of common age-related diseases, including atherosclerosis, cancer and periodontitis. This volume examines modifiable risk factors for periodontitis and other chronic inflammatory diseases. Oral bacterial communities and viral infections, particularly with cytomegalovirus and other herpesviruses, elicit distinct immune responses and are central in the initiation of periodontal diseases. Risk of disease is dynamic and changes in response to complex interactions of genetic, environmental and stochastic factors over the lifespan. Many modifiable risk factors, such as smoking and excess caloric intake, contribute to increases in systemic markers of inflammation and can modify gene regulation through a variety of biologic mechanisms (e.g. epigenetic modifications). Periodontitis and other common chronic inflammatory diseases share multiple modifiable risk factors, such as tobacco smoking, psychological stress and depression, alcohol consumption, obesity, diabetes, metabolic syndrome and osteoporosis. Interventions that target modifiable risk factors have the potential to improve risk profiles for periodontitis as well as for other common chronic diseases. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Extremely productive microbial communities in shallow saline pools respond immediately to changing meteorological conditions.

PubMed

Kirschner, A K T; Eiler, A; Zechmeister, T C; Velimirov, B; Herzig, A; Mach, R; Farnleitner, A H

2002-09-01

Diel changes in bacterial and cyanobacterial numbers, as well as heterotrophic bacterial production, were examined in two shallow alkaline pools, harbouring dense populations of cyanobacteria (up to 1100 x 109 cells l-1) and bacteria (up to 500 x 109 cells l-1). Together with the recorded bacterial production rates (925 micro gC l-1x h-1), these values are the highest reported for natural aquatic ecosystems. The investigations were performed during a fair-weather situation, and during a rapid change after a long-term fair-weather situation to thunderstorms and heavy rainfall. During fair weather, bacterial growth was significantly correlated to the diurnal light and temperature cycle. Prokaryotic abundances were fairly constant, and loss by grazing and viral lysis must have been of significant importance. During the invasion of rainy weather, the prokaryotic community showed a strong and immediate response. A significant enhancement of bacterial growth followed after rainfall, suggesting that the high salt concentrations had inhibited bacterial activity. Changes in bacterial and cyanobacterial numbers were consistent with this pattern. From comparison with the available literature, we conclude that diel changes of bacterioplankton are regulated by a complex combination of environmental factors specific for each investigated ecosystem. In the soda pools investigated, external abiotic factors were dominant on a diel scale. In larger ecosystems, such factors are much more buffered and internal biotic interactions may prevail.

Bacterial lipoproteins and other factors released by Francisella tularensis modulate human neutrophil lifespan: Effects of a TLR1 SNP on apoptosis inhibition

PubMed Central

Kinkead, Lauren C.; Whitmore, Laura C.; McCracken, Jenna M.; Fletcher, Joshua R.; Ketelsen, Brandi B.; Kaufman, Justin W.; Jones, Bradley D.; Weiss, David S.; Barker, Jason H.

2017-01-01

Abstract Francisella tularensis infects several cell types including neutrophils, and aberrant neutrophil accumulation contributes to tissue destruction during tularaemia. We demonstrated previously that F. tularensis strains Schu S4 and live vaccine strain markedly delay human neutrophil apoptosis and thereby prolong cell lifespan, but the bacterial factors that mediate this aspect of virulence are undefined. Herein, we demonstrate that bacterial conditioned medium (CM) can delay apoptosis in the absence of direct infection. Biochemical analyses show that CM contained F. tularensis surface factors as well as outer membrane components. Our previous studies excluded roles for lipopolysaccharide and capsule in apoptosis inhibition, and current studies of [14C] acetate‐labelled bacteria argue against a role for other bacterial lipids in this process. At the same time, studies of isogenic mutants indicate that TolC and virulence factors whose expression requires FevR or MglA were also dispensable, demonstrating that apoptosis inhibition does not require Type I or Type VI secretion. Instead, we identified bacterial lipoproteins (BLPs) as active factors in CM. Additional studies of isolated BLPs demonstrated dose‐dependent neutrophil apoptosis inhibition via a TLR2‐dependent mechanism that is significantly influenced by a common polymorphism, rs5743618, in human TLR1. These data provide fundamental new insight into pathogen manipulation of neutrophil lifespan and BLP function. PMID:29063667

Development of protective immunity to Salmonella, a mucosal pathogen with a systemic agenda

PubMed Central

Griffin, Amanda J.; McSorley, Stephen J.

2014-01-01

Salmonella infections can cause a range of intestinal and systemic disease in human and animal hosts. While some Salmonella serovars initiate a localized intestinal inflammatory response, others use the intestine as a portal of entry to initiate a systemic infection. Considerable progress has been made in understanding bacterial invasion and dissemination strategies and the nature of the Salmonella-specific immune response to oral infection. Innate and adaptive immunity are rapidly initiated after oral infection but these effector responses can also be hindered by bacterial evasion strategies. Furthermore, although Salmonella resides within intramacrophage phagosomes, recent studies highlight a surprising collaboration of CD4 Th1, Th17, and B cell responses in mediating resistance to Salmonella infection. PMID:21307847

Heterotrophic bacterium Pseudomonas saponiphila and sunlight as impact factors on organo-mineral colloids transformations in boreal humic waters

NASA Astrophysics Data System (ADS)

Oleinikova, Olga; Drozdova, Olga; Shirokova, Liudmila; Lapitskiy, Sergey; Bychkov, Andrew; Pokrovsky, Oleg

2017-04-01

Two of the main factors of carbon balance in high latitudes, known to govern the CO2 flux from the lakes and rivers to the atmosphere, are bacterial mineralization (respiration) of allochthonous dissolved organic matter (DOM) and photochemical degradation of DOM. Yet, in contrast to large numbers of experimental and field studies on these factors impact on the utilization of DOM of different origin, the fate of metals bound to colloids during bacterial processing of DOM and behavior of trace element (TE) during photodegradation of DOM remains poorly constrained. This is especially important in view of essentially organic and organo-mineral colloidal status of TE in most boreal waters. To answer this questions, a monoculture of Pseudomonas saponiphila from a boreal creek in NW Karelia (Russia) was separated and allowed to interact with boreal peat leachate in nutrient-free media. We quantified colloidal transformation of the peat leachate during 5-days activity of live bacteria using 3 kDa, 50 kDa Amicon® centrifugal filtration and 0.45 µm syringe filtration. The total net decrease of the concentration of Dissolved Organic Carbon (DOC) over 93 h of exposure was within 5% of the initial value for all fractions except low molecular weight one (< 3 kDa), which yielded a 16%-decrease due to long-term bio-uptake or coagulation. Elements most affected by bacterial presence were Al, Mn, (Ni), Cu, Ga, REEs, Y, U which exhibited essentially the adsorption at the cell surface over first hrs of reaction, and Fe, Ti, (Zr), and Nb showing short-term adsorption and long-term assimilation. Towards a better understanding of concentration, size fractionation and speciation change of TE in boreal waters subjected to solar radiation, we conducted on-site photo-degradation experiments in stream and bog water from pristine zone of Northern Karelia (Russian subarctic). After 5 days of exposure, the DOM in stream photodegraded in a much smaller degree than that in the bog water with 25 and 60% removal of initial DOC, respectively. Specific UV absorption (SUVA254) decreased by a factor of 1.75 and 5 over 200 h of exposure in stream and bog water, respectively. The removal of Fe and Al occurred only in the bog water (90 % and 50% respectively, over 5 days of reaction), whereas no detectable decrease of Al and Fe concentration (< 0.22 µm) was observed in the boreal stream. The majority of colloidal constituents including DOC, Fe, Al, metal micronutrients are weakly affected by heterotrophic bacterial activity and as such the stability of peat soil colloids in boreal waters is expected to be high. In contrast to this, in bog waters, alkali, alkaline-earth metals and divalent metal micornutrients, present in the form of organic complexes (50-80%), may be completely degraded over a week of sunlight exposure. We acknowledge support from a RFBR research projects №№ 16-55-150002 HЦHИ_a, 15-05-05000_a, 14-05-00430_a, 16-05-00542_a. Experimental study was supported by RSF № 14-50-00029.

Bacterial interactions in dental biofilm development.

PubMed

Hojo, K; Nagaoka, S; Ohshima, T; Maeda, N

2009-11-01

Recent analyses with ribosomal RNA-based technologies have revealed the diversity of bacterial populations within dental biofilms, and have highlighted their important contributions to oral health and disease. Dental biofilms are exceedingly complex and multispecies ecosystems, where oral bacteria interact cooperatively or competitively with other members. Bacterial interactions that influence dental biofilm communities include various different mechanisms. During the early stage of biofilm formation, it is known that planktonic bacterial cells directly attach to surfaces of the oral cavity or indirectly bind to other bacterial cells that have already colonized. Adherence through co-aggregation may be critical for the temporary retention of bacteria on dental surfaces, and may facilitate eventual bacterial colonization. It is likely that metabolic communication, genetic exchange, production of inhibitory factors (e.g., bacteriocins, hydrogen peroxide, etc.), and quorum-sensing are pivotal regulatory factors that determine the bacterial composition and/or metabolism. Since each bacterium can easily access a neighboring bacterial cell and its metabolites, genetic exchanges and metabolic communication may occur frequently in dental biofilms. Quorum-sensing is defined as gene regulation in response to cell density, which influences various functions, e.g., virulence and bacteriocin production. In this review, we discuss these important interactions among oral bacteria within the dental biofilm communities.

Detecting macroecological patterns in bacterial communities across independent studies of global soils.

PubMed

Ramirez, Kelly S; Knight, Christopher G; de Hollander, Mattias; Brearley, Francis Q; Constantinides, Bede; Cotton, Anne; Creer, Si; Crowther, Thomas W; Davison, John; Delgado-Baquerizo, Manuel; Dorrepaal, Ellen; Elliott, David R; Fox, Graeme; Griffiths, Robert I; Hale, Chris; Hartman, Kyle; Houlden, Ashley; Jones, David L; Krab, Eveline J; Maestre, Fernando T; McGuire, Krista L; Monteux, Sylvain; Orr, Caroline H; van der Putten, Wim H; Roberts, Ian S; Robinson, David A; Rocca, Jennifer D; Rowntree, Jennifer; Schlaeppi, Klaus; Shepherd, Matthew; Singh, Brajesh K; Straathof, Angela L; Bhatnagar, Jennifer M; Thion, Cécile; van der Heijden, Marcel G A; de Vries, Franciska T

2018-02-01

The emergence of high-throughput DNA sequencing methods provides unprecedented opportunities to further unravel bacterial biodiversity and its worldwide role from human health to ecosystem functioning. However, despite the abundance of sequencing studies, combining data from multiple individual studies to address macroecological questions of bacterial diversity remains methodically challenging and plagued with biases. Here, using a machine-learning approach that accounts for differences among studies and complex interactions among taxa, we merge 30 independent bacterial data sets comprising 1,998 soil samples from 21 countries. Whereas previous meta-analysis efforts have focused on bacterial diversity measures or abundances of major taxa, we show that disparate amplicon sequence data can be combined at the taxonomy-based level to assess bacterial community structure. We find that rarer taxa are more important for structuring soil communities than abundant taxa, and that these rarer taxa are better predictors of community structure than environmental factors, which are often confounded across studies. We conclude that combining data from independent studies can be used to explore bacterial community dynamics, identify potential 'indicator' taxa with an important role in structuring communities, and propose hypotheses on the factors that shape bacterial biogeography that have been overlooked in the past.

Bacterial stimulation of adventitious rooting on in vitro cultured slash pine (Pinus elliottii Engelm.) seedling explants.

PubMed

Burns, J A; Schwarz, O J

1996-02-01

A bacterium has been isolated that initiates adventitious rooting when co-cultured under in vitro conditions with seedling-produced hypocotylary explants of slash pine (Pinus elliottii). Rooting efficiencies produced through bacterial-explant co-culture range from approximately 15% to greater than 90% over non-treated controls. Explant exposure to the root inducing bacterium has produced no obvious pathology in the regenerated plantlets. Seedling explants rooted by bacterial-explant co-culture have been successfully transitioned to ambient greenhouse conditions.

Core Principles of Bacterial Autoinducer Systems

PubMed Central

2015-01-01

SUMMARY Autoinduction (AI), the response to self-produced chemical signals, is widespread in the bacterial world. This process controls vastly different target functions, such as luminescence, nutrient acquisition, and biofilm formation, in different ways and integrates additional environmental and physiological cues. This diversity raises questions about unifying principles that underlie all AI systems. Here, we suggest that such core principles exist. We argue that the general purpose of AI systems is the homeostatic control of costly cooperative behaviors, including, but not limited to, secreted public goods. First, costly behaviors require preassessment of their efficiency by cheaper AI signals, which we encapsulate in a hybrid “push-pull” model. The “push” factors cell density, diffusion, and spatial clustering determine when a behavior becomes effective. The relative importance of each factor depends on each species' individual ecological context and life history. In turn, “pull” factors, often stress cues that reduce the activation threshold, determine the cellular demand for the target behavior. Second, control is homeostatic because AI systems, either themselves or through accessory mechanisms, not only initiate but also maintain the efficiency of target behaviors. Third, AI-controlled behaviors, even seemingly noncooperative ones, are generally cooperative in nature, when interpreted in the appropriate ecological context. The escape of individual cells from biofilms, for example, may be viewed as an altruistic behavior that increases the fitness of the resident population by reducing starvation stress. The framework proposed here helps appropriately categorize AI-controlled behaviors and allows for a deeper understanding of their ecological and evolutionary functions. PMID:25694124

Plumage bacterial assemblages in a breeding wild passerine: relationships with ecological factors and body condition.

PubMed

Saag, Pauli; Tilgar, Vallo; Mänd, Raivo; Kilgas, Priit; Mägi, Marko

2011-05-01

Microorganisms have been shown to play an important role in shaping the life histories of animals, and it has recently been suggested that feather-degrading bacteria influence the trade-off between parental effort and self-preening behavior in birds. We studied a wild breeding population of great tits (Parus major) to explore habitat-, seasonal-, and sex-related variation in feather-degrading and free-living bacteria inhabiting the birds' yellow ventral feathers and to investigate associations with body condition. The density and species richness of bacterial assemblages was studied using flow cytometry and ribosomal intergenic spacer analysis. The density of studied bacteria declined between the nest-building period and the first brood. The number of bacterial phylotypes per bird was higher in coniferous habitat, while bacterial densities were higher in deciduous habitat. Free-living bacterial density was positively correlated with female mass; conversely, there was a negative correlation between attached bacterial density and female mass during the period of peak reproductive effort. Bacterial species richness was sex dependent, with more diverse bacterial assemblages present on males than females. Thus, this study revealed that bacterial assemblages on the feathers of breeding birds are affected both by life history and ecological factors and are related to body condition.

A Greenhouse Assay on the Effect of Applied Urea Amount on the Rhizospheric Soil Bacterial Communities.

PubMed

Shang, Shuanghua; Yi, Yanli

2015-12-01

The rhizospheric bacteria play key role in plant nutrition and growth promotion. The effects of increased nitrogen inputs on plant rhizospheric soils also have impacted on whole soil microbial communities. In this study, we analyzed the effects of applied nitrogen (urea) on rhizospheric bacterial composition and diversity in a greenhouse assay using the high-throughput sequencing technique. To explore the environmental factors driving the abundance, diversity and composition of soil bacterial communities, the relationship between soil variables and the bacterial communities were also analyzed using the mantel test as well as the redundancy analysis. The results revealed significant bacterial diversity changes at different amounts of applied urea, especially between the control treatment and the N fertilized treatments. Mantel tests showed that the bacterial communities were significantly correlated with the soil nitrate nitrogen, available nitrogen, soil pH, ammonium nitrogen and total organic carbon. The present study deepened the understanding about the rhizospheric soil microbial communities under different amounts of applied urea in greenhouse conditions, and our work revealed the environmental factors affecting the abundance, diversity and composition of rhizospheric bacterial communities.

Succession of bacterial community composition over two consecutive years in two aquatic systems: a natural lake and a lake-reservoir.

PubMed

Boucher, Delphine; Jardillier, Ludwig; Debroas, Didier

2006-01-01

The succession in bacterial community composition was studied over two years in the epilimnion and hypolimnion of two freshwater systems: a natural lake (Pavin Lake) and a lake-reservoir (Sep Reservoir). The bacterial community composition was determined by cloning-sequencing of 16S rRNA and by terminal restriction fragment length polymorphism. Despite large hydrogeological differences, in the Sep Reservoir and Pavin Lake the dominant bacteria were from the same taxonomic divisions, particularly Actinobacteria and Betaproteobacteria. In both ecosystems, these major bacterial divisions showed temporal fluctuations that were much less marked than those occurring at a finer phylogenetic scale. Nutrient availability and mortality factors, the nature of which differed from one lake to another, covaried with the temporal variations in the bacterial community composition at all sampling depths, whereas factors related to seasonal forces (temperature and outflow for Sep Reservoir) seemed to account only for the variation of the hypolimnion bacterial community composition. No seasonal reproducibility in temporal evolution of bacterial community from one year to the next was observed.

Rifaximin has minor effects on bacterial composition, inflammation, and bacterial translocation in cirrhosis: A randomized trial.

PubMed

Kimer, Nina; Pedersen, Julie S; Tavenier, Juliette; Christensen, Jeffrey E; Busk, Troels M; Hobolth, Lise; Krag, Aleksander; Al-Soud, Waleed Abu; Mortensen, Martin S; Sørensen, Søren J; Møller, Søren; Bendtsen, Flemming

2018-01-01

Decompensated cirrhosis is characterized by disturbed hemodynamics, immune dysfunction, and high risk of infections. Translocation of viable bacteria and bacterial products from the gut to the blood is considered a key driver in this process. Intestinal decontamination with rifaximin may reduce bacterial translocation (BT) and decrease inflammation. A randomized, placebo-controlled trial investigated the effects of rifaximin on inflammation and BT in decompensated cirrhosis. Fifty-four out-patients with cirrhosis and ascites were randomized, mean age 56 years (± 8.4), and model for end-stage liver disease score 12 (± 3.9). Patients received rifaximin 550-mg BD (n = 36) or placebo BD (n = 18). Blood and fecal (n = 15) sampling were conducted at baseline and after 4 weeks. Bacterial DNA in blood was determined by real-time qPCR 16S rRNA gene quantification. Bacterial composition in feces was analyzed by 16S rRNA gene sequencing. Circulating markers of inflammation, including tumor necrosis factor alpha, interleukins 6, 10, and 18, stromal cell-derived factor 1-α, transforming growth factor β-1, and high sensitivity C-reactive protein, were unaltered by rifaximin treatment. Rifaximin altered abundance of bacterial taxa in blood marginally, only a decrease in Pseudomonadales was observed. In feces, rifaximin decreased bacterial richness, but effect on particular species was not observed. Subgroup analyses on patients with severely disturbed hemodynamics (n = 34) or activated lipopolysaccharide binding protein (n = 37) revealed no effect of rifaximin. Four weeks of treatment with rifaximin had no impact on the inflammatory state and only minor effects on BT and intestinal bacterial composition in stable, decompensated cirrhosis (NCT01769040). © 2017 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Impact of environmental factors on couplings between bacterial community composition and ectoenzymatic activities in a lacustrine ecosystem.

PubMed

Boucher, Delphine; Debroas, Didier

2009-10-01

This study examined the effects of temporal changes in bacterial community composition (BCC) and environmental factors on potential ectoenzymatic activities (alpha-glucosidase, beta-glucosidase, alkaline phosphatase and leucine aminopeptidase) in a lacustrine ecosystem (Sep reservoir, France). BCC was assessed by terminal restriction fragment length polymorphism. Physical parameters, and inorganic and organic nutrient concentrations (dissolved carbohydrates and proteins) were measured in lakes and tributaries. According to the multivariate statistics (redundancy analysis), physical and chemical factors explained the largest part of leucine aminopeptidase activity, whereas the temporal changes of other ectoenzymatic activities were partly dependent on the variations in the BCC. In particular, the occurrence of occasional bacterial populations seemed to explain a lot of the variation in rates and patterns of polymer hydrolysis. The relation observed in this study between the bacterial structure and activity is discussed within the framework of biodiversity-ecosystem functioning.

Development of practical diagnostic methods for monitoring rice bacterial panicle blight disease and evaluation of rice germplasm for resistance

USDA-ARS?s Scientific Manuscript database

A study was initiated to understand Burkholderia glumae, the major causal agent for bacterial panicle blight disease of rice; to develop practical diagnostic methods for monitoring the disease; and to evaluate rice germplasm for resistance. Burkholderia glumae was frequently isolated from infected p...

Development of practical diagnostic methods for monitoring rice bacterial panicle blight disease and evaluation of rice germplasm for resistance

USDA-ARS?s Scientific Manuscript database

A study was initiated to understand Burkholderia glumae (major causal agent for bacterial panicle blight disease of rice) to develop practical diagnostic methods for monitoring the disease; and to evaluate rice germplasm for resistance. B. glumae was frequently isolated from symptomatic panicles on...

Influence of long-term land application of class B biosolids on soil bacterial diversity

USDA-ARS?s Scientific Manuscript database

This project evaluated the influence of annual land applications of Class B biosolids on soil bacterial diversity monitored over a 20 year period. Each annual land application was followed by a cotton crop. The study was initiated in 1986 at the University of Arizona Marana Agricultural Center, 21 m...

Initiation of a pan-genomic research project for Xylella fastidiosa

USDA-ARS?s Scientific Manuscript database

Differences in genomic structure and nucleotide polymorphism among strains form the genetic basis for adaptability of a bacterial species. This can be described by a bacterial pan-genome, which is defined as the full complement of genes in all strains of a species. The pan-genome is composed of a "c...

Effect of oral bacterial lysates on serum immunoglobulins.

PubMed

Palma-Carlos, A G; Palma-Carlos, M L

1989-11-01

The level of serum immunoglobulins IgG, IgA, IgM and IgE has been studied before and after oral immunotherapy with a bacterial lysate in 88 patients with bronchial asthma, repeated respiratory infection and 12 cases of IgA deficiency. A significant increase in IgA has been observed in 9 patients presenting initially a decreased IgA serum level. In 3 patients without response to the standard treatment an increase in IgA was achieved increasing the dosage of oral bacterial lysate. Oral bacterial lysates could be an useful immunomodulating agent in repeated respiratory infections associated or not with IgA deficiency.

Determinative factors of competitive advantage between aerobic bacteria for niches at the air-liquid interface.

PubMed

Yamamoto, Kyosuke; Haruta, Shin; Kato, Souichiro; Ishii, Masaharu; Igarashi, Yasuo

2010-01-01

We focused on bacterial interspecies relationships at the air-liquid interface where the formation of pellicles by aerobes was observed. Although an obligate aerobe (Brevibacillus sp. M1-5) was initially dominant in the pellicle population, a facultative aerobe (Pseudoxanthomonas sp. M1-3) emerged and the viability of M1-5 rapidly decreased due to severe competition for oxygen. Supplementation of the medium with carbohydrates allowed the two species to coexist at the air-liquid interface. These results indicate that the population dynamics within pellicles are primarily governed by oxygen utilization which was affected by a combination of carbon sources.

Identification of regulatory targets for the bacterial Nus factor complex.

PubMed

Baniulyte, Gabriele; Singh, Navjot; Benoit, Courtney; Johnson, Richard; Ferguson, Robert; Paramo, Mauricio; Stringer, Anne M; Scott, Ashley; Lapierre, Pascal; Wade, Joseph T

2017-12-11

Nus factors are broadly conserved across bacterial species, and are often essential for viability. A complex of five Nus factors (NusB, NusE, NusA, NusG and SuhB) is considered to be a dedicated regulator of ribosomal RNA folding, and has been shown to prevent Rho-dependent transcription termination. Here, we identify an additional cellular function for the Nus factor complex in Escherichia coli: repression of the Nus factor-encoding gene, suhB. This repression occurs primarily by translation inhibition, followed by Rho-dependent transcription termination. Thus, the Nus factor complex can prevent or promote Rho activity depending on the gene context. Conservation of putative NusB/E binding sites upstream of Nus factor genes suggests that Nus factor autoregulation occurs in many bacterial species. Additionally, many putative NusB/E binding sites are also found upstream of other genes in diverse species, and we demonstrate Nus factor regulation of one such gene in Citrobacter koseri. We conclude that Nus factors have an evolutionarily widespread regulatory function beyond ribosomal RNA, and that they are often autoregulatory.

Microparticle-associated tissue factor activity correlates with plasma levels of bacterial lipopolysaccharides in meningococcal septic shock.

PubMed

Hellum, Marit; Øvstebø, Reidun; Brusletto, Berit S; Berg, Jens P; Brandtzaeg, Petter; Henriksson, Carola E

2014-03-01

The plasma level of bacterial lipopolysaccharides (LPS) is associated with activation of the coagulation system, inhibition of fibrinolysis and the nature of the clinical presentation and outcome in patients with meningococcal disease. Tissue factor (TF)-bearing microparticles (MPs) appear to contribute to the pathogenesis of disseminated intravascular coagulation (DIC). The aim of this study was to investigate the relationship between MP-associated TF activity and the level of bacterial LPS in plasma from patients with meningococcal septic shock and meningitis. MPs isolated from citrated plasmas were assessed for TF-dependent activity with both a plasma-based thrombin generation assay (CAT) and whole blood-based thromboelastometry (ROTEM). The LPS level was measured using a chromogenic Limulus amebocyte lysate assay. MPs obtained from patients with meningococcal septic shock initiated significantly more efficient and TF-dependent thrombin generation in the CAT assay compared to MPs from patients with meningococcal meningitis. Differences in MP-associated TF activity between the septic shock patients and the meningitis patients were also evident when MPs were added to whole blood using ROTEM. The level of plasma LPS in patients with septic shock (range 2-2,100 EU/mL) was correlated with thrombogram parameters in the CAT assay; lagtime (r(s)=-0.84), time to peak (rs=-0.83), peak (r(s)=0.85) and ETP (r(s)=0.83). MPs obtained from patients with meningococcal septic shock displayed more efficient TF-dependent thrombin generation and clot formation compared to MPs from meningitis patients. MP-associated TF activity was closely associated with plasma LPS levels in the septic shock group. Copyright © 2013 Elsevier Ltd. All rights reserved.

Novel inhibitors of the Pseudomonas aeruginosa virulence factor LasB: a potential therapeutic approach for the attenuation of virulence mechanisms in pseudomonal infection.

PubMed

Cathcart, George R A; Quinn, Derek; Greer, Brett; Harriott, Pat; Lynas, John F; Gilmore, Brendan F; Walker, Brian

2011-06-01

Pseudomonas elastase (LasB), a metalloprotease virulence factor, is known to play a pivotal role in pseudomonal infection. LasB is secreted at the site of infection, where it exerts a proteolytic action that spans from broad tissue destruction to subtle action on components of the host immune system. The former enhances invasiveness by liberating nutrients for continued growth, while the latter exerts an immunomodulatory effect, manipulating the normal immune response. In addition to the extracellular effects of secreted LasB, it also acts within the bacterial cell to trigger the intracellular pathway that initiates growth as a bacterial biofilm. The key role of LasB in pseudomonal virulence makes it a potential target for the development of an inhibitor as an antimicrobial agent. The concept of inhibition of virulence is a recently established antimicrobial strategy, and such agents have been termed "second-generation" antibiotics. This approach holds promise in that it seeks to attenuate virulence processes without bactericidal action and, hence, without selection pressure for the emergence of resistant strains. A potent inhibitor of LasB, N-mercaptoacetyl-Phe-Tyr-amide (K(i) = 41 nM) has been developed, and its ability to block these virulence processes has been assessed. It has been demonstrated that thes compound can completely block the action of LasB on protein targets that are instrumental in biofilm formation and immunomodulation. The novel LasB inhibitor has also been employed in bacterial-cell-based assays, to reduce the growth of pseudomonal biofilms, and to eradicate biofilm completely when used in combination with conventional antibiotics.

Amphypterygium adstringens anacardic acid mixture inhibits quorum sensing-controlled virulence factors of Chromobacterium violaceum and Pseudomonas aeruginosa.

PubMed

Castillo-Juárez, Israel; García-Contreras, Rodolfo; Velázquez-Guadarrama, Norma; Soto-Hernández, Marcos; Martínez-Vázquez, Mariano

2013-10-01

Quorum sensing (QS) is a process of bacterial cell-cell communication that controls a large number of systems affecting pathogenicity. Interrupting this communication system can provide nonvirulent pathogenic bacteria. The aim of this study was to evaluate the anti-quorum sensing (anti-QS) potential of an anacardic acids mixture isolated from Amphipterygium adstringens, a medicinal plant known as "cuachalalate", to prevent the onset of bacterial infections as an alternate to antibiotics. Initially we investigated the anti-QS activity of A. adstringens hexane extract (HE) by the inhibition of violacein production in Chromobacterium violaceum. From the active HE, an anacardic acid mixture (AAM) was obtained. The anti-quorum sensing activity of AAM was investigated by the rhamnolipid and pyocyanin production constraint as well as decrease of elastase activity, all being quorum sensing-controlled virulence factors expressed in the pathogenic bacteria Pseudomonas aeruginosa. HE induced a 91.6% of inhibition of the violecin production at 55 μg/mL concentration, whereas AAM showed 94% of inhibition at 166 μg/mL. In both cases, inhibition of violacein production did not affect the viability of the bacterium. AAM inhibited pyocyanin (86% at 200 μg/mL) and rhamnolipid (91% at 500 μg/mL) production in a dose/response form and decrease the elastase (75% at 500 μg/mL) activity in P. aeruginosa without affecting its development. Because an anacardic acids mixture isolated from A. adstringens demonstrated anti-QS, it could be further exploited for novel molecules to treat the emerging infections of antibiotic-resistant bacterial pathogens. Copyright © 2013 IMSS. Published by Elsevier Inc. All rights reserved.

Recent advances in recurrent urinary tract infection from pathogenesis and biomarkers to prevention.

PubMed

Jhang, Jia-Fong; Kuo, Hann-Chorng

2017-01-01

Recurrent urinary tract infection (UTI) might be one of the most common problems in urological clinics. Recent research has revealed novel evidence about recurrent UTI and it should be considered a different disease from the first infection. The pathogenesis of recurrent UTI might include two mechanisms, bacterial factors and deficiencies in host defense. Bacterial survival in the urinary bladder after antibiotic treatment and progression to form intracellular bacterial communities might be the most important bacterial factors. In host defense deficiency, a defect in pathogen recognition and urothelial barrier function impairment play the most important roles. Immunodeficiency and urogenital tract anatomical abnormalities have been considered the essential risk factors for recurrent UTI. In healthy women, voiding dysfunction and behavioral factors also increase the risk of recurrent UTI. Sexual intercourse and estrogen deficiency in postmenopausal women might have the strongest association with recurrent UTI. Traditional lifestyle factors such as fluid intake and diet are not considered independent risk factors now. Serum and urine biomarkers to predict recurrent UTI from the first infection have also attracted a wide attention recently. Current clinical evidence suggests that serum macrophage colony-stimulating factor and urinary nerve growth factor have potential predictive value for recurrent UTI. Clinical trials have proven the efficacy of the oral immunoactive agent OM-89 for the prevention of UTI. Vaccines for recurrent UTI are recommended by the latest guidelines and are available on the market.

Bacterial community structure in response to environmental impacts in the intertidal sediments along the Yangtze Estuary, China.

PubMed

Guo, Xing-Pan; Lu, Da-Pei; Niu, Zuo-Shun; Feng, Jing-Nan; Chen, Yu-Ru; Tou, Fei-Yun; Liu, Min; Yang, Yi

2018-01-01

This study was designed to investigate the characteristics of bacterial communities in intertidal sediments along the Yangtze Estuary and their responses to environmental factors. The results showed that bacterial abundance was significantly correlated with salinity, SO 4 2- and total organic carbon, while bacterial diversity was significantly correlated with SO 4 2- and total nitrogen. At different taxonomic levels, both the dominant taxa and their abundances varied among the eight samples, with Proteobacteria being the most dominant phylum in general. Cluster analysis revealed that the bacterial community structure was influenced by river runoff and sewerage discharge. Moreover, SO 4 2- , salinity and total phosphorus were the vital environmental factors that influenced the bacterial community structure. Quantitative PCR and sequencing of sulphate-reducing bacteria indicated that the sulphate reduction process occurs frequently in intertidal sediments. These findings are important to understand the microbial ecology and biogeochemical cycles in estuarine environments. Copyright © 2017 Elsevier Ltd. All rights reserved.

Raised Proinflammatory Cytokine Production Within Cerebrospinal Fluid Precedes Fever Onset in Patients With Neurosurgery-Associated Bacterial Meningitis.

PubMed

Liu, Zhuo-Hao; Tu, Po-Hsun; Chen, Nan-Yu; Yip, Ping K; Bowes, Amy L; Lee, Cheng-Chi; Chan, She-Hung; Kung, Chua-Chi; Wang, Alvin Yi-Chou; Wu, Chieh-Tsai; Lee, Shih-Tseng

2015-11-01

The objective of the present study was to determine whether selective inflammatory cytokine concentrations within cerebrospinal fluid are useful markers for the differential diagnosis of aseptic and bacterial meningitis within neurosurgical patients. Prospective, open-label, observational, cohort study. Neurosurgical ICU, Chang Gung Memorial Hospital. Thirty-two consecutive neurosurgical patients who had postoperative fever following external ventricular drain insertion for the treatment of brain injury underwent serial cerebrospinal fluid cytokine analysis pre and post fever to determine the value of such markers in ascertaining the differential diagnosis of meningitis. Cerebrospinal fluid samples were collected on the day of fever onset, as well as on day 2 and 4 pre and post fever development. Tumor necrosis factor-α, interleukin-1β, interleukin-6, interleukin-8, transforming growth factor-β, and procalcitonin were subsequently analyzed using enzyme-linked immunosorbent assay analysis techniques. Inflammatory marker levels were compared among febrile aseptic, bacterial, and nonmeningitis patients to determine cerebrospinal fluid inflammatory changes over time. Significant increases in cerebrospinal fluid tumor necrosis factor -α, interleukin-1β, interleukin-6, and interleukin-8 levels were observed within patients with bacterial meningitis at fever onset, which was not evident in aseptic or nonmeningitis patients. Furthermore, significant increases in cerebrospinal fluid tumor necrosis factor-α, interleukin-1β, interleukin-6, and interleukin-8 levels were detected as early as 4 days prior to fever onset within patients with bacterial meningitis when compared with both aseptic and nonmeningitis groups. Interestingly, procalcitonin was only significantly increased in patients with bacterial meningitis on the fourth day post fever. The present study suggests that raised cerebrospinal fluid tumor necrosis factor -α, interleukin-1β, and interleukin-8 in a temporal manner may indicate early bacterial meningitis development in neurosurgical patients, enabling earlier diagnostic certainty and improved patient outcomes.

Factors associated with negative T-SPOT.TB results among smear-negative tuberculosis patients in China.

PubMed

Kang, Wanli; Wu, Meiying; Yang, Kunyun; Ertai, A; Wu, Shucai; Geng, Shujun; Li, Zhihui; Li, Mingwu; Pang, Yu; Tang, Shenjie

2018-03-09

We compared the positive rates of T-SPOT.TB and bacterial culture in the smear-negative PTB, and analyzed the factors affecting the results of negative T-SPOT.TB and bacterial culture. Retrospective evaluation of data from smear-negative PTB patients who underwent T-SPOT.TB and bacterial culture were done. The agreement and concordance were analyzed between T-SPOT.TB and bacterial culture. Multivariable logistic regression analysis was used to explore the factors associated with positive results of T-SPOT.TB and bacterial culture in smear-negative PTB. 858 eligible smear-negative PTB patients were included in the study. The agreement rate was 25.6% (22.7~28.5%) between T-SPOT.TB and bacterial culture in smear- negative PTB patients. The positive rate of T-SPOT.TB was higher than that of bacterial culture in smear-negative PTB patients (p < 0.001). There were nearly no concordance between T-SPOT.TB and bacterial culture (p > 0.05). Using multivariable logistic regression analysis we found that older age ≥ 60 years (OR = 0.469, 95% CI: 0.287-0.768) and decreased albumin (OR = 0.614, 95% CI: 0.380-0.992) were associated with negative diagnostic results of T-SPOT.TB in smear-negative PTB patients. Female (OR = 0.654, 95% CI: 0.431-0.992) were associated with negative diagnostic results of bacteria culture in smear-negative PTB patients. Our results indicated that the older age and decreased albumin were independently associated with negative T-SPOT.TB responses.

Proteus mirabilis fimbriae- and urease-dependent clusters assemble in an extracellular niche to initiate bladder stone formation.

PubMed

Schaffer, Jessica N; Norsworthy, Allison N; Sun, Tung-Tien; Pearson, Melanie M

2016-04-19

The catheter-associated uropathogenProteus mirabilisfrequently causes urinary stones, but little has been known about the initial stages of bladder colonization and stone formation. We found thatP. mirabilisrapidly invades the bladder urothelium, but generally fails to establish an intracellular niche. Instead, it forms extracellular clusters in the bladder lumen, which form foci of mineral deposition consistent with development of urinary stones. These clusters elicit a robust neutrophil response, and we present evidence of neutrophil extracellular trap generation during experimental urinary tract infection. We identified two virulence factors required for cluster development: urease, which is required for urolithiasis, and mannose-resistantProteus-like fimbriae. The extracellular cluster formation byP. mirabilisstands in direct contrast to uropathogenicEscherichia coli, which readily formed intracellular bacterial communities but not luminal clusters or urinary stones. We propose that extracellular clusters are a key mechanism ofP. mirabilissurvival and virulence in the bladder.

The development and evaluation of ultrasound for the treatment of bacterial suspensions. A study of frequency, power and sonication time on cultured Bacillus species.

PubMed

Joyce, E; Phull, S S; Lorimer, J P; Mason, T J

2003-10-01

Some species of bacteria produce colonies and spores which agglomerate in spherical clusters (Bacillus subtilis) and this serves as a protection for the organisms inside against biocidal attack. Flocs of fine particles e.g. clay can entrap bacteria which can also protect them against the biocides. It is because of problems such as these that alternative methods of disinfecting water are under active investigation. One such method is the use of power ultrasound, either alone or in combination with other methods. Ultrasound is able to inactivate bacteria and deagglomerate bacterial clusters or flocs through a number of physical, mechanical and chemical effects arising from acoustic cavitation. The aim of this study was to investigate the effect of power ultrasound at different powers and frequencies on Bacillus subtilis. Viable plate count techniques were used as a measure of microbial activity. Results showed a significant increase in percent kill for Bacillus species with increasing duration of exposure and intensity of ultrasound in the low-kilohertz range (20 and 38 kHz). Results obtained at two higher frequencies (512 and 850 kHz) indicated a significant increase in bacteria count suggesting declumping. In assessing the bacterial kill with time under different sonication regimes three types of behaviour were characterized: High power ultrasound (lower frequencies) in low volumes of bacterial suspension results in a continuous reduction in bacterial cell numbers i.e. the kill rate predominates. High power ultrasound (lower frequencies) in larger volumes results in an initial rise in cell numbers suggesting declumping of the bacteria but this initial rise then falls as the declumping finishes and the kill rate becomes more important. Low intensity ultrasound (higher frequencies) gives an initial rise in cell numbers as a result of declumping. The kill rate is low and so there is no significant subsequent decrease in bacterial cell numbers.

Bacterial pneumonia in patients with liver cirrhosis, with or without HIV co-infection: a possible definition of antibiotic prophylaxis associated pneumonia (APAP).

PubMed

Cuomo, Gianluca; Brancaccio, Giuseppina; Stornaiuolo, Gianfranca; Manno, Daniela; Gaeta, Giuseppe L; Mussini, Cristina; Puoti, Massimo; Gaeta, Giovanni B

2018-02-01

Introducion: Bacterial infections frequently complicate liver cirrhosis. The aim of this study was to identify risk factors and clinical impact of bacterial pneumonia in patients with cirrhosis. Bacterial infection prevalence study: consecutive patients with cirrhosis were enroled over a six-month period in 13 Italian centres. Pneumonia and other infections were diagnosed by standard methods. Pneumonia study: cirrhotic patients with pneumonia were enroled for an additional six-month period and HIV-positive patients were included. Pneumonia was the fourth most frequent infection. In the two parts of the study, 79 cases of pneumonia were recorded and 441 patients with cirrhosis without infections served as controls. Seventy-eight patients had extra-pulmonary infections. There were no clinical differences between HIV-negative and -positive cases with pneumonia. Previous gastro-intestinal bleeding (p = .02) and long-term prophylactic antibiotic use (p < .0001) were associated with pneumonia. Hospital stay was longer and renal failure more frequent than in patients without infections. Pneumonia was hospital acquired (HAP) in 6 cases, healthcare associated (HCAP) in 24 and community acquired (CAP) in 28. A new category of antibiotic prophylaxis associated pneumonia (APAP) was proposed for 21 cases. Cultures were positive in 21/79 patients (26.6%) with Gram-positive isolates in 57%. Unfavourable outcomes were recorded in 11.4% of the cases (3.6% of CAP, 33% of HAP, 12.5% of HCAP and 14.3% of APAP). Receiving antibiotic prophylaxis was associated with pneumonia and the study identified a new sub-group of patients, who require broad spectrum initial antibiotic therapy.

Bacterial community composition and structure in an Urban River impacted by different pollutant sources.

PubMed

Ibekwe, A Mark; Ma, Jincai; Murinda, Shelton E

2016-10-01

Microbial communities in terrestrial fresh water are diverse and dynamic in composition due to different environmental factors. The goal of this study was to undertake a comprehensive analysis of bacterial composition along different rivers and creeks and correlate these to land-use practices and pollutant sources. Here we used 454 pyrosequencing to determine the total bacterial community composition, and bacterial communities that are potentially of fecal origin, and of relevance to water quality assessment. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, and community composition. Detrended correspondence analysis (DCA) and canonical correspondence analysis (CCA) were used to correlate bacterial composition in streams and creeks to different environmental parameters impacting bacterial communities in the sediment and surface water within the watershed. Bacteria were dominated by the phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Actinobacteria, with Bacteroidetes significantly (P<0.001) higher in all water samples than sediment, where as Acidobacteria and Actinobacteria where significantly higher (P<0.05) in all the sediment samples than surface water. Overall results, using the β diversity measures, coupled with PCoA and DCA showed that bacterial composition in sediment and surface water was significantly different (P<0.001). Also, there were differences in bacterial community composition between agricultural runoff and urban runoff based on parsimony tests using 454 pyrosequencing data. Fecal indicator bacteria in surface water along different creeks and channels were significantly correlated with pH (P<0.01), NO2 (P<0.03), and NH4N (P<0.005); and in the sediment with NO3 (P<0.015). Our results suggest that microbial community compositions were influenced by several environmental factors, and pH, NO2, and NH4 were the major environmental factors driving FIB in surface water based on CCA analysis, while NO3 was the only factor in sediment. Published by Elsevier B.V.

Pilot- and bench-scale testing of faecal indicator bacteria survival in marine beach sand near point sources.

PubMed

Mika, K B; Imamura, G; Chang, C; Conway, V; Fernandez, G; Griffith, J F; Kampalath, R A; Lee, C M; Lin, C-C; Moreno, R; Thompson, S; Whitman, R L; Jay, J A

2009-07-01

Factors affecting faecal indicator bacteria (FIB) and pathogen survival/persistence in sand remain largely unstudied. This work elucidates how biological and physical factors affect die-off in beach sand following sewage spills. Solar disinfection with mechanical mixing was pilot-tested as a disinfection procedure after a large sewage spill in Los Angeles. Effects of solar exposure, mechanical mixing, predation and/or competition, season, and moisture were tested at bench scale. First-order decay constants for Escherichia coli ranged between -0.23 and -1.02 per day, and for enterococci between -0.5 and -1.0 per day. Desiccation was a dominant factor for E. coli but not enterococci inactivation. Effects of season were investigated through a comparison of experimental results from winter, spring, and fall. Moisture was the dominant factor controlling E. coli inactivation kinetics. Initial microbial community and sand temperature were also important factors. Mechanical mixing, common in beach grooming, did not consistently reduce bacterial levels. Inactivation rates are mainly dependent on moisture and high sand temperature. Chlorination was an effective disinfection treatment in sand microcosms inoculated with raw influent.

Helicobacter pylori virulence genes and host genetic polymorphisms as risk factors for peptic ulcer disease.

PubMed

Miftahussurur, Muhammad; Yamaoka, Yoshio

2015-01-01

Helicobacter pylori infection plays an important role in the pathogenesis of peptic ulcer disease (PUD). Several factors have been proposed as possible H. pylori virulence determinants; for example, bacterial adhesins and gastric inflammation factors are associated with an increased risk of PUD. However, differences in bacterial virulence factors alone cannot explain the opposite ends of the PUD disease spectrum, that is duodenal and gastric ulcers; presumably, both bacterial and host factors contribute to the differential response. Carriers of the high-producer alleles of the pro-inflammatory cytokines IL-1B, IL-6, IL-8, IL-10, and TNF-α who also carry low-producer allele of anti-inflammatory cytokines have severe gastric mucosal inflammation, whereas carriers of the alternative alleles have mild inflammation. Recent reports have suggested that the PSCA and CYP2C19 ultra-rapid metabolizer genotypes are also associated with PUD.

Combined influence of multiple climatic factors on the incidence of bacterial foodborne diseases.

PubMed

Park, Myoung Su; Park, Ki Hwan; Bahk, Gyung Jin

2018-01-01

Information regarding the relationship between the incidence of foodborne diseases (FBD) and climatic factors is useful in designing preventive strategies for FBD based on anticipated future climate change. To better predict the effect of climate change on foodborne pathogens, the present study investigated the combined influence of multiple climatic factors on bacterial FBD incidence in South Korea. During 2011-2015, the relationships between 8 climatic factors and the incidences of 13 bacterial FBD, were determined based on inpatient stays, on a monthly basis using the Pearson correlation analyses, multicollinearity tests, principal component analysis (PCA), and the seasonal autoregressive integrated moving average (SARIMA) modeling. Of the 8 climatic variables, the combination of temperature, relative humidity, precipitation, insolation, and cloudiness was significantly associated with salmonellosis (P<0.01), vibriosis (P<0.05), and enterohemorrhagic Escherichia coli O157:H7 infection (P<0.01). The combined effects of snowfall, wind speed, duration of sunshine, and cloudiness were not significant for these 3 FBD. Other FBD, including campylobacteriosis, were not significantly associated with any combination of climatic factors. These findings indicate that the relationships between multiple climatic factors and bacterial FBD incidence can be valuable for the development of prediction models for future patterns of diseases in response to changes in climate. Copyright © 2017 Elsevier B.V. All rights reserved.

Development of small molecule biosensors by coupling the recognition of the bacterial allosteric transcription factor with isothermal strand displacement amplification.

PubMed

Yao, Yongpeng; Li, Shanshan; Cao, Jiaqian; Liu, Weiwei; Fan, Keqiang; Xiang, Wensheng; Yang, Keqian; Kong, Deming; Wang, Weishan

2018-05-08

Here, we demonstrate an easy-to-implement and general biosensing strategy by coupling the small-molecule recognition of the bacterial allosteric transcription factor (aTF) with isothermal strand displacement amplification (SDA) in vitro. Based on this strategy, we developed two biosensors for the detection of an antiseptic, p-hydroxybenzoic acid, and a disease marker, uric acid, using bacterial aTF HosA and HucR, respectively, highlighting the great potential of this strategy for the development of small-molecule biosensors.

Macrophage migration inhibitory factor deficiency is associated with impaired killing of gram-negative bacteria by macrophages and increased susceptibility to Klebsiella pneumoniae sepsis.

PubMed

Roger, Thierry; Delaloye, Julie; Chanson, Anne-Laure; Giddey, Marlyse; Le Roy, Didier; Calandra, Thierry

2013-01-15

The cytokine macrophage migration inhibitory factor (MIF) is an important component of the early proinflammatory response of the innate immune system. However, the antimicrobial defense mechanisms mediated by MIF remain fairly mysterious. In the present study, we examined whether MIF controls bacterial uptake and clearance by professional phagocytes, using wild-type and MIF-deficient macrophages. MIF deficiency did not affect bacterial phagocytosis, but it strongly impaired the killing of gram-negative bacteria by macrophages and host defenses against gram-negative bacterial infection, as shown by increased mortality in a Klebsiella pneumonia model. Consistent with MIF's regulatory role of Toll-like 4 expression in macrophages, MIF-deficient cells stimulated with lipopolysaccharide or Escherichia coli exhibited reduced nuclear factor κB activity and tumor necrosis factor (TNF) production. Addition of recombinant MIF or TNF corrected the killing defect of MIF-deficient macrophages. Together, these data show that MIF is a key mediator of host responses against gram-negative bacteria, acting in part via a modulation of bacterial killing by macrophages.

Risk factors of treatment failure and 30-day mortality in patients with bacteremia due to MRSA with reduced vancomycin susceptibility.

PubMed

Yang, Chien-Chang; Sy, Cheng-Len; Huang, Yhu-Chering; Shie, Shian-Sen; Shu, Jwu-Ching; Hsieh, Pang-Hsin; Hsiao, Ching-Hsi; Chen, Chih-Jung

2018-05-18

Bacteremia caused by MRSA with reduced vancomycin susceptibility (MRSA-RVS) frequently resulted in treatment failure and mortality. The relation of bacterial factors and unfavorable outcomes remains controversial. We retrospectively reviewed clinical data of patients with bacteremia caused by MRSA with vancomycin MIC = 2 mg/L from 2009 to 2012. The significance of bacterial genotypes, agr function and heterogeneous vancomycin-intermediate S. aureus (hIVSA) phenotype in predicting outcomes were determined after clinical covariates adjustment with multivariate analysis. A total of 147 patients with mean age of 63.5 (±18.1) years were included. Seventy-nine (53.7%) patients failed treatment. Forty-seven (31.9%) patients died within 30 days of onset of MRSA bacteremia. The Charlson index, Pitt bacteremia score and definitive antibiotic regimen were independent factors significantly associated with either treatment failure or mortality. The hVISA phenotype was a potential risk factor predicting treatment failure (adjusted odds ratio 2.420, 95% confidence interval 0.946-6.191, P = 0.0652). No bacterial factors were significantly associated with 30-day mortality. In conclusion, the comorbidities, disease severity and antibiotic regimen remained the most relevant factors predicting treatment failure and 30-day mortality in patients with MRSA-RVS bacteremia. hIVSA phenotype was the only bacterial factor potentially associated with unfavorable outcome in this cohort.

Virulence and Immunomodulatory Roles of Bacterial Outer Membrane Vesicles

PubMed Central

Ellis, Terri N.; Kuehn, Meta J.

2010-01-01

Summary: Outer membrane (OM) vesicles are ubiquitously produced by Gram-negative bacteria during all stages of bacterial growth. OM vesicles are naturally secreted by both pathogenic and nonpathogenic bacteria. Strong experimental evidence exists to categorize OM vesicle production as a type of Gram-negative bacterial virulence factor. A growing body of data demonstrates an association of active virulence factors and toxins with vesicles, suggesting that they play a role in pathogenesis. One of the most popular and best-studied pathogenic functions for membrane vesicles is to serve as natural vehicles for the intercellular transport of virulence factors and other materials directly into host cells. The production of OM vesicles has been identified as an independent bacterial stress response pathway that is activated when bacteria encounter environmental stress, such as what might be experienced during the colonization of host tissues. Their detection in infected human tissues reinforces this theory. Various other virulence factors are also associated with OM vesicles, including adhesins and degradative enzymes. As a result, OM vesicles are heavily laden with pathogen-associated molecular patterns (PAMPs), virulence factors, and other OM components that can impact the course of infection by having toxigenic effects or by the activation of the innate immune response. However, infected hosts can also benefit from OM vesicle production by stimulating their ability to mount an effective defense. Vesicles display antigens and can elicit potent inflammatory and immune responses. In sum, OM vesicles are likely to play a significant role in the virulence of Gram-negative bacterial pathogens. PMID:20197500

Evidence of major genes affecting resistance to bacterial cold water disease in rainbow trout using Bayesian methods of segregation analysis

USDA-ARS?s Scientific Manuscript database

Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. We previously detected genetic variation for BCWD resistance in our rainbow trout population, and a family-based selection program to improve resistance was initiated at the National Center for Cool and Col...

Evidence of major genes affecting bacterial cold water disease resistance in rainbow trout using Bayesian methods of complex segregation analysis

USDA-ARS?s Scientific Manuscript database

Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture. We previously detected genetic variation for BCWD resistance in our rainbow trout population, and a family-based selection program to improve resistance was initiated at the NCCCWA in 2005. The main objec...

Changes in Vaginal Microbiota and Immune Mediators in HIV-1-Seronegative Kenyan Women Initiating Depot Medroxyprogesterone Acetate.

PubMed

Roxby, Alison C; Fredricks, David N; Odem-Davis, Katherine; Ásbjörnsdóttir, Kristjana; Masese, Linnet; Fiedler, Tina L; De Rosa, Stephen; Jaoko, Walter; Kiarie, James N; Overbaugh, Julie; McClelland, R Scott

2016-04-01

Depot medroxyprogesterone acetate (DMPA) is associated with HIV acquisition. We studied changes in vaginal microbiota and inflammatory milieu after DMPA initiation. In a cohort of HIV-negative Kenyan women, we collected monthly vaginal swabs over 1 year before and after DMPA. Using quantitative polymerase chain reaction, we compared quantities of Lactobacillus crispatus, Lactobacillus jensenii, Lactobacillus iners, Gardnerella vaginalis, and total bacterial load (16S ribosomal RNA gene levels). Six vaginal immune mediators were measured with enzyme-linked immunosorbent assay. Trends in the detection and quantity of bacteria were estimated by logistic and linear mixed-effects regression. From 2010 to 2012, 15 HIV-seronegative women initiated DMPA, contributing 85 visits (median, 6 visits/woman; range, 3-8 visits/woman). The median time of DMPA-exposed follow-up was 8.4 months (range, 1.5-11.6 months). Seven women (46%) had bacterial vaginosis within 70 days before DMPA start. L. iners was detected in 13 women (87%) before DMPA start, but other lactobacilli were rarely detected. Gardnerella vaginalis decreased by 0.21 log10 copies per swab per month after DMPA exposure (P = 0.01). Total bacterial load decreased by 0.08 log10 copies per swab per month of DMPA (P = 0.02). Sustained decreases in interleukin (IL)-6 (P = 0.03), IL-8 (P = 0.04), and IL-1 receptor antagonist (P < 0.001) were also noted. Nine women (60%) had L. crispatus detected post-DMPA, which significantly correlated with reduced IL-6 (P < 0.01) and IL-8 (P = 0.02). Initiation of DMPA led to sustained shifts in vaginal bacterial concentrations and levels of inflammatory mediators. Further studies are warranted to outline components of the vaginal microbiota influenced by DMPA use and impact on HIV susceptibility.

Microbial Successions and Metabolite Changes during Fermentation of Salted Shrimp (Saeu-Jeot) with Different Salt Concentrations

PubMed Central

Lee, Se Hee; Jung, Ji Young; Jeon, Che Ok

2014-01-01

To investigate the effects of salt concentration on saeu-jeot (salted shrimp) fermentation, four sets of saeu-jeot samples with 20%, 24%, 28%, and 32% salt concentrations were prepared, and the pH, bacterial and archaeal abundances, bacterial communities, and metabolites were monitored during the entire fermentation period. Quantitative PCR showed that Bacteria were much more abundant than Archaea in all saeu-jeot samples, suggesting that bacterial populations play more important roles than archaeal populations even in highly salted samples. Community analysis indicated that Vibrio, Photobacterium, Psychrobacter, Pseudoalteromonas, and Enterovibrio were identified as the initially dominant genera, and the bacterial successions were significantly different depending on the salt concentration. During the early fermentation period, Salinivibrio predominated in the 20% salted samples, whereas Staphylococcus, Halomonas, and Salimicrobium predominated in the 24% salted samples; eventually, Halanaerobium predominated in the 20% and 24% salted samples. The initially dominant genera gradually decreased as the fermentation progressed in the 28% and 32% salted samples, and eventually Salimicrobium became predominant in the 28% salted samples. However, the initially dominant genera still remained until the end of fermentation in the 32% salted samples. Metabolite analysis showed that the amino acid profile and the initial glycerol increase were similar in all saeu-jeot samples regardless of the salt concentration. After 30–80 days of fermentation, the levels of acetate, butyrate, and methylamines in the 20% and 24% salted samples increased with the growth of Halanaerobium, even though the amino acid concentrations steadily increased until approximately 80–107 days of fermentation. This study suggests that a range of 24–28% salt concentration in saeu-jeot fermentation is appropriate for the production of safe and tasty saeu-jeot. PMID:24587230

Stochasticity of bacterial attachment and its predictability by the extended derjaguin-landau-verwey-overbeek theory.

PubMed

Chia, Teck Wah R; Nguyen, Vu Tuan; McMeekin, Thomas; Fegan, Narelle; Dykes, Gary A

2011-06-01

Bacterial attachment onto materials has been suggested to be stochastic by some authors but nonstochastic and based on surface properties by others. We investigated this by attaching pairwise combinations of two Salmonella enterica serovar Sofia (S. Sofia) strains (with different physicochemical and attachment properties) with one strain each of S. enterica serovar Typhimurium, S. enterica serovar Infantis, or S. enterica serovar Virchow (all with similar physicochemical and attachment abilities) in ratios of 0.428, 1, and 2.333 onto glass, stainless steel, Teflon, and polysulfone. Attached bacterial cells were recovered and counted. If the ratio of attached cells of each Salmonella serovar pair recovered was the same as the initial inoculum ratio, the attachment process was deemed stochastic. Experimental outcomes from the study were compared to those predicted by the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory. Significant differences (P < 0.05) between the initial and the attached ratios for serovar pairs containing S. Sofia S1296a for all different ratios were apparent for all materials. For S. Sofia S1635-containing pairs, 7 out of 12 combinations of serovar pairs and materials had attachment ratios not significantly different (P > 0.05) from the initial ratio of 0.428. Five out of 12 and 10 out of 12 samples had attachment ratios not significantly different (P > 0.05) from the initial ratios of 1 and 2.333, respectively. These results demonstrate that bacterial attachment to different materials is likely to be nonstochastic only when the key physicochemical properties of the bacteria were significantly different (P < 0.05) from each other. XDLVO theory could successfully predict the attachment of some individual isolates to particular materials but could not be used to predict the likelihood of stochasticity in pairwise attachment experiments.

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta

PubMed Central

Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X.; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing

2016-01-01

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems. PMID:27824160

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta.

PubMed

Lv, Xiaofei; Ma, Bin; Yu, Junbao; Chang, Scott X; Xu, Jianming; Li, Yunzhao; Wang, Guangmei; Han, Guangxuan; Bo, Guan; Chu, Xiaojing

2016-11-08

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.

Bacterial vaginosis in pregnancy and the risk of prematurity: a meta-analysis.

PubMed

Flynn, C A; Helwig, A L; Meurer, L N

1999-11-01

We conducted this meta-analysis to determine the magnitude of risk conferred by bacterial vaginosis during pregnancy on preterm delivery. We selected articles from a combination of the results of a MEDLINE search (1966-1996), a manual search of bibliographies, and contact with leading researchers. We included case control and cohort studies evaluating the risk of preterm delivery, low birth weight, preterm premature rupture of membranes, or preterm labor for pregnant women who had bacterial vaginosis and those who did not. DATA COLLECTION AND ANALYSIS. Two investigators independently conducted literature searches, applied inclusion criteria, performed data extraction, and critically appraised included studies. Summary estimates of risk were calculated as odds ratios (ORs) using the fixed and random effects models. We included 19 studies in the final analysis. Bacterial vaginosis during pregnancy was associated with a statistically significant increased risk for all outcomes evaluated. In the subanalyses for preterm delivery, bacterial vaginosis remained a significant risk factor. Pooling adjusted ORs yielded a 60% increased risk of preterm delivery given the presence of bacterial vaginosis. Bacterial vaginosis is an important risk factor for prematurity and pregnancy morbidity. Further studies will help clarify the benefits of treating bacterial vaginosis and the potential role of screening during pregnancy.

Importance of inoculum properties on the structure and growth of bacterial communities during Recolonisation of humus soil with different pH.

PubMed

Pettersson, Marie; Bååth, Erland

2013-08-01

The relationship between community structure and growth and pH tolerance of a soil bacterial community was studied after liming in a reciprocal inoculum study. An unlimed (UL) humus soil with a pH of 4.0 was fumigated with chloroform for 4 h, after which < 1 % of the initial bacterial activity remained. Half of the fumigated soil was experimentally limed (EL) to a pH of 7.6. Both the UL and the EL soil were then reciprocally inoculated with UL soil or field limed (FL) soil with a pH of 6.2. The FL soil was from a 15-year-old experiment. The structural changes were measured on both bacteria in soil and on bacteria able to grow on agar plates using phospholipids fatty acid (PLFA) and denaturing gradient gel electrophoresis (DGGE) analysis. The developing community pH tolerance and bacterial growth were also monitored over time using thymidine incorporation. The inoculum source had a significant impact on both growth and pH tolerance of the bacterial community in the EL soil. These differences between the EL soil inoculated with UL soil and FL soil were correlated to structural changes, as evidenced by both PLFA and DGGE analyses on the soil. Similar correlations were seen to the fraction of the community growing on agar plates. There were, however, no differences between the soil bacterial communities in the unlimed soils with different inocula. This study showed the connection between the development of function (growth), community properties (pH tolerance) and the structure of the bacterial community. It also highlighted the importance of both the initial properties of the community and the selection pressure after environmental changes in shaping the resulting microbial community.

The Living Dead: Bacterial Community Structure of a Cadaver at the Onset and End of the Bloat Stage of Decomposition

PubMed Central

Hyde, Embriette R.; Haarmann, Daniel P.; Lynne, Aaron M.; Bucheli, Sibyl R.; Petrosino, Joseph F.

2013-01-01

Human decomposition is a mosaic system with an intimate association between biotic and abiotic factors. Despite the integral role of bacteria in the decomposition process, few studies have catalogued bacterial biodiversity for terrestrial scenarios. To explore the microbiome of decomposition, two cadavers were placed at the Southeast Texas Applied Forensic Science facility and allowed to decompose under natural conditions. The bloat stage of decomposition, a stage easily identified in taphonomy and readily attributed to microbial physiology, was targeted. Each cadaver was sampled at two time points, at the onset and end of the bloat stage, from various body sites including internal locations. Bacterial samples were analyzed by pyrosequencing of the 16S rRNA gene. Our data show a shift from aerobic bacteria to anaerobic bacteria in all body sites sampled and demonstrate variation in community structure between bodies, between sample sites within a body, and between initial and end points of the bloat stage within a sample site. These data are best not viewed as points of comparison but rather additive data sets. While some species recovered are the same as those observed in culture-based studies, many are novel. Our results are preliminary and add to a larger emerging data set; a more comprehensive study is needed to further dissect the role of bacteria in human decomposition. PMID:24204941

The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition.

PubMed

Hyde, Embriette R; Haarmann, Daniel P; Lynne, Aaron M; Bucheli, Sibyl R; Petrosino, Joseph F

2013-01-01

Human decomposition is a mosaic system with an intimate association between biotic and abiotic factors. Despite the integral role of bacteria in the decomposition process, few studies have catalogued bacterial biodiversity for terrestrial scenarios. To explore the microbiome of decomposition, two cadavers were placed at the Southeast Texas Applied Forensic Science facility and allowed to decompose under natural conditions. The bloat stage of decomposition, a stage easily identified in taphonomy and readily attributed to microbial physiology, was targeted. Each cadaver was sampled at two time points, at the onset and end of the bloat stage, from various body sites including internal locations. Bacterial samples were analyzed by pyrosequencing of the 16S rRNA gene. Our data show a shift from aerobic bacteria to anaerobic bacteria in all body sites sampled and demonstrate variation in community structure between bodies, between sample sites within a body, and between initial and end points of the bloat stage within a sample site. These data are best not viewed as points of comparison but rather additive data sets. While some species recovered are the same as those observed in culture-based studies, many are novel. Our results are preliminary and add to a larger emerging data set; a more comprehensive study is needed to further dissect the role of bacteria in human decomposition.

Effects of assimilable organic carbon and free chlorine on bacterial growth in drinking water.

PubMed

Liu, Xiaolu; Wang, Jingqi; Liu, Tingting; Kong, Weiwen; He, Xiaoqing; Jin, Yi; Zhang, Bolin

2015-01-01

Assimilable organic carbon (AOC) is one of the most important factors affecting the re-growth of microorganisms in drinking water. High AOC concentrations result in biological instability, but disinfection kills microbes to ensure the safety of drinking water. Free chlorine is an important oxidizing agent used during the disinfection process. Therefore, we explored the combined effects of AOC and free chlorine on bacterial growth in drinking water using flow cytometry (FCM). The initial AOC concentration was 168 μg.L(-1) in all water samples. Without free chlorine, the concentrations of intact bacteria increased but the level of AOC decreased. The addition of sodium hypochlorite caused an increase and fluctuation in AOC due to the oxidation of organic carbon. The concentrations of intact bacteria decreased from 1.1 × 10(5) cells.mL(-1) to 2.6 × 10(4) cells.mL(-1) at an initial free chlorine dose of 0.6 mg.L(-1) to 4.8 × 10(4) cells.mL(-1) at an initial free chlorine dose of 0.3 mg.L(-1) due to free chlorine originating from sodium hypochlorite. Additionally, free chlorine might be more obviously affected AOC concentrations than microbial growth did. These results suggested that AOC and free chlorine might have combined effects on microbial growth. In this study, our results showed concentrations determined by FCM were higher than those by HPC, which indicated that some E. coli detected by FCM might not be detected using HPC in drinking water. The level of free chlorine might restrain the consumption of AOC by inhibiting the growth of E. coli; on the other hand, chlorination might increase the level of AOC, thereby increase the potential for microbial growth in the drinking water network.

Effects of Assimilable Organic Carbon and Free Chlorine on Bacterial Growth in Drinking Water

PubMed Central

Liu, Tingting; Kong, Weiwen; He, Xiaoqing; Jin, Yi; Zhang, Bolin

2015-01-01

Assimilable organic carbon (AOC) is one of the most important factors affecting the re-growth of microorganisms in drinking water. High AOC concentrations result in biological instability, but disinfection kills microbes to ensure the safety of drinking water. Free chlorine is an important oxidizing agent used during the disinfection process. Therefore, we explored the combined effects of AOC and free chlorine on bacterial growth in drinking water using flow cytometry (FCM). The initial AOC concentration was 168 μg.L-1 in all water samples. Without free chlorine, the concentrations of intact bacteria increased but the level of AOC decreased. The addition of sodium hypochlorite caused an increase and fluctuation in AOC due to the oxidation of organic carbon. The concentrations of intact bacteria decreased from 1.1×105 cells.mL-1 to 2.6×104 cells.mL-1 at an initial free chlorine dose of 0.6 mg.L-1 to 4.8×104 cells.mL-1 at an initial free chlorine dose of 0.3 mg.L-1 due to free chlorine originating from sodium hypochlorite. Additionally, free chlorine might be more obviously affected AOC concentrations than microbial growth did. These results suggested that AOC and free chlorine might have combined effects on microbial growth. In this study, our results showed concentrations determined by FCM were higher than those by HPC, which indicated that some E. coli detected by FCM might not be detected using HPC in drinking water. The level of free chlorine might restrain the consumption of AOC by inhibiting the growth of E. coli; on the other hand, chlorination might increase the level of AOC, thereby increase the potential for microbial growth in the drinking water network. PMID:26034988

The physicochemical process of bacterial attachment to abiotic surfaces: Challenges for mechanistic studies, predictability and the development of control strategies.

PubMed

Wang, Yi; Lee, Sui Mae; Dykes, Gary

2015-01-01

Bacterial attachment to abiotic surfaces can be explained as a physicochemical process. Mechanisms of the process have been widely studied but are not yet well understood due to their complexity. Physicochemical processes can be influenced by various interactions and factors in attachment systems, including, but not limited to, hydrophobic interactions, electrostatic interactions and substratum surface roughness. Mechanistic models and control strategies for bacterial attachment to abiotic surfaces have been established based on the current understanding of the attachment process and the interactions involved. Due to a lack of process control and standardization in the methodologies used to study the mechanisms of bacterial attachment, however, various challenges are apparent in the development of models and control strategies. In this review, the physicochemical mechanisms, interactions and factors affecting the process of bacterial attachment to abiotic surfaces are described. Mechanistic models established based on these parameters are discussed in terms of their limitations. Currently employed methods to study these parameters and bacterial attachment are critically compared. The roles of these parameters in the development of control strategies for bacterial attachment are reviewed, and the challenges that arise in developing mechanistic models and control strategies are assessed.

Determinants of bacterial communities in Canadian agroforestry systems.

PubMed

Banerjee, Samiran; Baah-Acheamfour, Mark; Carlyle, Cameron N; Bissett, Andrew; Richardson, Alan E; Siddique, Tariq; Bork, Edward W; Chang, Scott X

2016-06-01

Land-use change is one of the most important factors influencing soil microbial communities, which play a pivotal role in most biogeochemical and ecological processes. Using agroforestry systems as a model, this study examined the effects of land uses and edaphic properties on bacterial communities in three agroforestry types covering a 270 km soil-climate gradient in Alberta, Canada. Our results demonstrate that land-use patterns exert stronger effects on soil bacterial communities than soil zones in these agroforestry systems. Plots with trees in agroforestry systems promoted greater bacterial abundance and to some extent species richness, which was associated with more nutrient-rich soil resources. While Acidobacteria, Actinobacteria and Alphaproteobacteria were the dominant bacterial phyla and subphyla across land uses, Arthrobacter, Acidobacteria_Gp16, Burkholderia, Rhodanobacter and Rhizobium were the keystone taxa in these agroforestry systems. Soil pH and carbon contents emerged as the major determinants of bacterial community characteristics. We found non-random co-occurrence and modular patterns of soil bacterial communities, and these patterns were controlled by edaphic factors and not their taxonomy. Overall, this study highlights the drivers and co-occurrence patterns of soil microbial communities in agroforestry systems. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Membrane rafts in host-pathogen interactions.

PubMed

Riethmüller, Joachim; Riehle, Andrea; Grassmé, Heike; Gulbins, Erich

2006-12-01

Central elements in the infection of mammalian cells with viral, bacterial and parasitic pathogens include the adhesion of the pathogen to surface receptors of the cell, recruitment of additional receptor proteins to the infection-site, a re-organization of the membrane and, in particular, the intracellular signalosome. Internalization of the pathogen results in the formation of a phagosome that is supposed to fuse with lysosomes to form phagolysosomes, which serve the degradation of the pathogen, an event actively prevented by some pathogens. In summary, these changes in the infected cell permit pathogens to trigger apoptosis (for instance of macrophages paralysing the initial immune response), to invade the cell and/or to survive in the cell, but they also serve the mammalian cell to defeat the infection, for instance by activation of transcription factors and the release of cytokines. Distinct membrane domains in the plasma membrane and intracellular vesicles that are mainly composed of sphingolipids and cholesterol or enriched with the sphingolipid ceramide, are critically involved in all of these events occurring during the infection. These membrane structures are therefore very attractive targets for novel drugs to interfere with bacterial, viral and parasitic infections.

Menaquinone analogs inhibit growth of bacterial pathogens.

PubMed

Schlievert, Patrick M; Merriman, Joseph A; Salgado-Pabón, Wilmara; Mueller, Elizabeth A; Spaulding, Adam R; Vu, Bao G; Chuang-Smith, Olivia N; Kohler, Petra L; Kirby, John R

2013-11-01

Gram-positive bacteria cause serious human illnesses through combinations of cell surface and secreted virulence factors. We initiated studies with four of these organisms to develop novel topical antibacterial agents that interfere with growth and exotoxin production, focusing on menaquinone analogs. Menadione, 1,4-naphthoquinone, and coenzymes Q1 to Q3 but not menaquinone, phylloquinone, or coenzyme Q10 inhibited the growth and to a greater extent exotoxin production of Staphylococcus aureus, Bacillus anthracis, Streptococcus pyogenes, and Streptococcus agalactiae at concentrations of 10 to 200 μg/ml. Coenzyme Q1 reduced the ability of S. aureus to cause toxic shock syndrome in a rabbit model, inhibited the growth of four Gram-negative bacteria, and synergized with another antimicrobial agent, glycerol monolaurate, to inhibit S. aureus growth. The staphylococcal two-component system SrrA/B was shown to be an antibacterial target of coenzyme Q1. We hypothesize that menaquinone analogs both induce toxic reactive oxygen species and affect bacterial plasma membranes and biosynthetic machinery to interfere with two-component systems, respiration, and macromolecular synthesis. These compounds represent a novel class of potential topical therapeutic agents.

Enterobacter Strains Might Promote Colon Cancer.

PubMed

Yurdakul, Dilşad; Yazgan-Karataş, Ayten; Şahin, Fikrettin

2015-09-01

Many studies have been performed to determine the interaction between bacterial species and cancer. However, there has been no attempts to demonstrate a possible relationship between Enterobacter spp. and colon cancer so far. Therefore, in the present study, it is aimed to investigate the effects of Enterobacter strains on colon cancer. Bacterial proteins were isolated from 11 Enterobacter spp., one Morganella morganii, and one Escherichia coli strains, and applied onto NCM460 (Incell) and CRL1790 (ATCC) cell lines. Cell viability and proliferation were determined in MTS assay. Flow Cytometry was used to detect CD24 level and apoptosis. Real-Time PCR studies were performed to determine NFKB and Bcl2 expression. Graphpad Software was used for statistical analysis. The results showed that proteins, isolated from the Enterobacter spp., have significantly increased cell viability and proliferation, while decreasing the apoptosis of the cell lines tested. The data in the present study indicated that Enterobacter strains might promote colon cancer. Moreover, Enterobacter spp. could be a clinically important factor for colon cancer initiation and progression. Studies can be extended on animal models in order to develop new strategies for treatment.

Structure of the LPS O-chain from Fusobacterium nucleatum strain 10953, containing sialic acid

PubMed Central

Vinogradov, Evgeny; St. Michael, Frank; Homma, Kiyonobu; Sharma, Ashu; Cox, Andrew D.

2017-01-01

Fusobacterium nucleatum is an anaerobic bacterium found in the human mouth where it causes periodontitis. Recently, it has been gaining attention as a potential causative agent for colorectal cancer and is strongly linked with pregnancy complications including pre-term and still births. Little is known about virulence factors of this organism and thus we have initiated studies to examine the bacterial surface glycochemistry. Consistent with a recent paper suggesting that F. nucleatum strain 10593 can synthesize sialic acid, a staining technique identified sialic acid on the bacterial surface. We isolated lipopolysaccharide from this F. nucleatum strain and performed structural analysis on the O-antigen. Our studies identified a trisaccharide repeating unit of the O-antigen with the following structure: -[→4)-α-Neup5Ac-(2→4)-β-D-Galp-(1→3)-α-D-FucpNAc4NAc-(1-]-where Ac indicates 4-N-acetylation of ∼30% FucNAc4N residues. The presence of sialic acid as a constituent of the O-antigen is consistent with recent data identifying de novo sialic acid synthesis in this strain. PMID:28199859

Bacterial lung sepsis in patients with febrile neutropenia.

PubMed

Lanoix, Jean-Philippe; Schmit, Jean-Luc; Douadi, Youcef

2012-05-01

This review provides an update on microbiological and therapeutic data in febrile neutropenic patients in general and those with bacterial lung sepsis in particular. Although the Infectious Diseases Society of America updated its guidelines on febrile neutropenia in 2010, changing epidemiological factors and the spread of new drug resistance constitutes challenges for initial treatment of this condition. Lung sepsis stands out because of the frequent absence of microbiological identification. We review the use of newly available, novel, broad-spectrum antibiotics (linezolid, tigecycline, daptomycin, etc.) in this indication. Although the incidence of Gram-negative infections in neutropenic fever is leveling off, there is a worrying increase in resistance. New drugs are available but not well studied in febrile neutropenia; daptomycin and tigecycline should not be used in suspected lung sepsis in these patients. New diagnostic tools (such as the procalcitonin assay and the LightCycler SeptiFast assay, Roche Molecular Systems) appear to be unhelpful in febrile neutropenia, although more data on fungal sepsis are required. There are no specific features of the treatment of pneumonia or septic shock in neutropenic fever, but both conditions increase the mortality rate.

Recent advances in recurrent urinary tract infection from pathogenesis and biomarkers to prevention

PubMed Central

Jhang, Jia-Fong; Kuo, Hann-Chorng

2017-01-01

Recurrent urinary tract infection (UTI) might be one of the most common problems in urological clinics. Recent research has revealed novel evidence about recurrent UTI and it should be considered a different disease from the first infection. The pathogenesis of recurrent UTI might include two mechanisms, bacterial factors and deficiencies in host defense. Bacterial survival in the urinary bladder after antibiotic treatment and progression to form intracellular bacterial communities might be the most important bacterial factors. In host defense deficiency, a defect in pathogen recognition and urothelial barrier function impairment play the most important roles. Immunodeficiency and urogenital tract anatomical abnormalities have been considered the essential risk factors for recurrent UTI. In healthy women, voiding dysfunction and behavioral factors also increase the risk of recurrent UTI. Sexual intercourse and estrogen deficiency in postmenopausal women might have the strongest association with recurrent UTI. Traditional lifestyle factors such as fluid intake and diet are not considered independent risk factors now. Serum and urine biomarkers to predict recurrent UTI from the first infection have also attracted a wide attention recently. Current clinical evidence suggests that serum macrophage colony-stimulating factor and urinary nerve growth factor have potential predictive value for recurrent UTI. Clinical trials have proven the efficacy of the oral immunoactive agent OM-89 for the prevention of UTI. Vaccines for recurrent UTI are recommended by the latest guidelines and are available on the market. PMID:28974905

Diagnosis of Meningococcal Meningitis by Broad-Range Bacterial PCR with Cerebrospinal Fluid

PubMed Central

Kotilainen, Pirkko; Jalava, Jari; Meurman, Olli; Lehtonen, Olli-Pekka; Rintala, Esa; Seppälä, Olli-Pekka; Eerola, Erkki; Nikkari, Simo

1998-01-01

We used broad-range bacterial PCR combined with DNA sequencing to examine prospectively cerebrospinal fluid (CSF) samples from patients with suspected meningitis. Fifty-six CSF samples from 46 patients were studied during the year 1995. Genes coding for bacterial 16S and/or 23S rRNA genes could be amplified from the CSF samples from five patients with a clinical picture consistent with acute bacterial meningitis. For these patients, the sequenced PCR product shared 98.3 to 100% homology with the Neisseria meningitidis sequence. For one patient, the diagnosis was initially made by PCR alone. Of the remaining 51 CSF samples, for 50 (98.0%) samples the negative PCR findings were in accordance with the negative findings by bacterial culture and Gram staining, as well as with the eventual clinical diagnosis for the patient. However, the PCR test failed to detect the bacterial rRNA gene in one CSF sample, the culture of which yielded Listeria monocytogenes. These results invite new research efforts to be focused on the application of PCR with broad-range bacterial primers to improve the etiologic diagnosis of bacterial meningitis. In a clinical setting, Gram staining and bacterial culture still remain the cornerstones of diagnosis. PMID:9665992

Bacterial α2-macroglobulins: colonization factors acquired by horizontal gene transfer from the metazoan genome?

PubMed Central

Budd, Aidan; Blandin, Stephanie; Levashina, Elena A; Gibson, Toby J

2004-01-01

Background Invasive bacteria are known to have captured and adapted eukaryotic host genes. They also readily acquire colonizing genes from other bacteria by horizontal gene transfer. Closely related species such as Helicobacter pylori and Helicobacter hepaticus, which exploit different host tissues, share almost none of their colonization genes. The protease inhibitor α2-macroglobulin provides a major metazoan defense against invasive bacteria, trapping attacking proteases required by parasites for successful invasion. Results Database searches with metazoan α2-macroglobulin sequences revealed homologous sequences in bacterial proteomes. The bacterial α2-macroglobulin phylogenetic distribution is patchy and violates the vertical descent model. Bacterial α2-macroglobulin genes are found in diverse clades, including purple bacteria (proteobacteria), fusobacteria, spirochetes, bacteroidetes, deinococcids, cyanobacteria, planctomycetes and thermotogae. Most bacterial species with bacterial α2-macroglobulin genes exploit higher eukaryotes (multicellular plants and animals) as hosts. Both pathogenically invasive and saprophytically colonizing species possess bacterial α2-macroglobulins, indicating that bacterial α2-macroglobulin is a colonization rather than a virulence factor. Conclusions Metazoan α2-macroglobulins inhibit proteases of pathogens. The bacterial homologs may function in reverse to block host antimicrobial defenses. α2-macroglobulin was probably acquired one or more times from metazoan hosts and has then spread widely through other colonizing bacterial species by more than 10 independent horizontal gene transfers. yfhM-like bacterial α2-macroglobulin genes are often found tightly linked with pbpC, encoding an atypical peptidoglycan transglycosylase, PBP1C, that does not function in vegetative peptidoglycan synthesis. We suggest that YfhM and PBP1C are coupled together as a periplasmic defense and repair system. Bacterial α2-macroglobulins might provide useful targets for enhancing vaccine efficacy in combating infections. PMID:15186489

Treatment of bacterial meningitis: an update.

PubMed

Shin, Seon Hee; Kim, Kwang Sik

2012-10-01

The introduction of protein conjugate vaccines for Haemophilus influenzae type b (Hib), Streptococcus pneumoniae (S. pneumoniae) and Neisseria meningitidis (N. menigitidis) has changed the epidemiology of bacterial meningitis. Bacterial meningitis continues to be an important cause of mortality and morbidity, and our incomplete knowledge of its pathogenesis and emergence of antimicrobial resistant bacteria contribute to such mortality and morbidity. An early empiric antibiotic treatment is critical for the management of patients with bacterial meningitis. This article gives an overview on optimal treatment strategies of bacterial meningitis, along with considerations of new insights on epidemiology, clinical and laboratory findings supportive of bacterial meningitis, chemoprophylaxis, selection of initial antimicrobial agents for suspected bacterial meningitis, antimicrobial resistance and utility of new antibiotics, status on anti-inflammatory agents and adjunctive therapy, and pathogenesis of bacterial meningitis. Prompt treatment of bacterial meningitis with an appropriate antibiotic is essential. Optimal antimicrobial treatment of bacterial meningitis requires bactericidal agents able to penetrate the blood-brain barrier (BBB), with efficacy in cerebrospinal fluid (CSF). Several new antibiotics have been introduced for the treatment of meningitis caused by resistant bacteria, but their use in human studies has been limited. More complete understanding of the microbial and host interactions that are involved in the pathogenesis of bacterial meningitis and associated neurologic sequelae is likely to help in developing new strategies for the prevention and therapy of bacterial meningitis.

Sample dilution and bacterial community composition influence empirical leucine-to-carbon conversion factors in surface waters of the world's oceans.

PubMed

Teira, Eva; Hernando-Morales, Víctor; Cornejo-Castillo, Francisco M; Alonso-Sáez, Laura; Sarmento, Hugo; Valencia-Vila, Joaquín; Serrano Catalá, Teresa; Hernández-Ruiz, Marta; Varela, Marta M; Ferrera, Isabel; Gutiérrez Morán, Xosé Anxelu; Gasol, Josep M

2015-12-01

The transformation of leucine incorporation rates to prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world's oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e., removal of grazers [F treatment]) or filtration combined with dilution (i.e., also relieving resource competition [FD treatment]). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu(-1) and were significantly lower in the FD than in the F samples. Also, changes in bacterial community composition during the incubations, as assessed by automated ribosomal intergenic spacer analysis (ARISA), were more pronounced in the FD than in the F treatments, compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCF determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus), and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCF variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts, although this results in relatively low carbon production rates in the oligotrophic ocean. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Sample Dilution and Bacterial Community Composition Influence Empirical Leucine-to-Carbon Conversion Factors in Surface Waters of the World's Oceans

PubMed Central

Hernando-Morales, Víctor; Cornejo-Castillo, Francisco M.; Alonso-Sáez, Laura; Sarmento, Hugo; Valencia-Vila, Joaquín; Serrano Catalá, Teresa; Hernández-Ruiz, Marta; Varela, Marta M.; Ferrera, Isabel; Gutiérrez Morán, Xosé Anxelu; Gasol, Josep M.

2015-01-01

The transformation of leucine incorporation rates to prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world's oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e., removal of grazers [F treatment]) or filtration combined with dilution (i.e., also relieving resource competition [FD treatment]). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu−1 and were significantly lower in the FD than in the F samples. Also, changes in bacterial community composition during the incubations, as assessed by automated ribosomal intergenic spacer analysis (ARISA), were more pronounced in the FD than in the F treatments, compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCF determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus), and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCF variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts, although this results in relatively low carbon production rates in the oligotrophic ocean. PMID:26407885

Aspect has a greater impact on alpine soil bacterial community structure than elevation.

PubMed

Wu, Jieyun; Anderson, Barbara J; Buckley, Hannah L; Lewis, Gillian; Lear, Gavin

2017-03-01

Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a 'natural laboratory' to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structure suggest that they are driven by various interacting factors at different spatial scales. Here, we investigated the relative impacts of non-resource (e.g. soil temperature, pH) and resource conditions (e.g. soil carbon and nitrogen) on the biogeography of soil bacterial communities across broad (i.e. along a 1500 m mountain elevation gradient) and fine sampling scales (i.e. along sunny and shady aspects of a mountain ridge). Our analysis of 16S rRNA gene data confirmed that when sampling across distances of < 1000 m, bacterial community composition was more closely related to the aspect of a site than its elevation. However, despite large differences in climate and resource-availability factors across elevation- and aspect-related gradients, bacterial community composition and richness were most strongly correlated with soil pH. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Bacterial community profile of contaminated soils in a typical antimony mining site.

PubMed

Wang, Ningning; Zhang, Suhuan; He, Mengchang

2018-01-01

The soils around the world's largest antimony mine have been contaminated by high concentrations of Sb and As, which might influence microbial diversity in the surrounding soils. The ecological effects of bioavailable Sb and As on the composition and diversity of microbial community in soils remain unknown. In this study, the relative abundance, taxonomic diversity and composition of bacterial community in soils from a typical Sb mine area, and the relationship between the bacterial community and bioavailable concentrations as well as environmental factors have been investigated comprehensively using high-throughput sequencing (HTS) and diffusive gradients in thin films (DGT). The results indicated that Proteobacteria, Acidobacteria, Chloroflexi, Bacteroidetes, Actinobacteria, Gemmatimonadetes, and Cyanobacteria were the dominant bacterial populations at phylum level in all soil samples, accounting for more than 80% of the bacteria sequenced. The abundance and diversity of bacterial community vary along a metal contamination gradient. Redundancy discriminate analysis (RDA) revealed that 74.74% of bacterial community variation in the contaminated soils was explained by six environmental factors (pH, Sb DGT , As DGT , potential ecological risk index (RI), TC, TN), among which pH, Sb DGT , and As DGT were dominant factors influencing the composition and diversity of bacteria. This study contributes to our understanding of microbial diversity in a local ecosystem and introduces the option of studying bioavailable Sb and As using DGT.

Soil bacterial communities are shaped by temporal and environmental filtering: evidence from a long-term chronosequence.

PubMed

Freedman, Zachary; Zak, Donald R

2015-09-01

Soil microbial communities are abundant, hyper-diverse and mediate global biogeochemical cycles, but we do not yet understand the processes mediating their assembly. Current hypothetical frameworks suggest temporal (e.g. dispersal limitation) and environmental (e.g. soil pH) filters shape microbial community composition; however, there is limited empirical evidence supporting this framework in the hyper-diverse soil environment, particularly at large spatial (i.e. regional to continental) and temporal (i.e. 100 to 1000 years) scales. Here, we present evidence from a long-term chronosequence (4000 years) that temporal and environmental filters do indeed shape soil bacterial community composition. Furthermore, nearly 20 years of environmental monitoring allowed us to control for potentially confounding environmental variation. Soil bacterial communities were phylogenetically distinct across the chronosequence. We determined that temporal and environmental factors accounted for significant portions of bacterial phylogenetic structure using distance-based linear models. Environmental factors together accounted for the majority of phylogenetic structure, namely, soil temperature (19%), pH (17%) and litter carbon:nitrogen (C:N; 17%). However, of all individual factors, time since deglaciation accounted for the greatest proportion of bacterial phylogenetic structure (20%). Taken together, our results provide empirical evidence that temporal and environmental filters act together to structure soil bacterial communities across large spatial and long-term temporal scales. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Confinement regulates complex biochemical networks: initiation of blood clotting by "diffusion acting".

PubMed

Shen, Feng; Pompano, Rebecca R; Kastrup, Christian J; Ismagilov, Rustem F

2009-10-21

This study shows that environmental confinement strongly affects the activation of nonlinear reaction networks, such as blood coagulation (clotting), by small quantities of activators. Blood coagulation is sensitive to the local concentration of soluble activators, initiating only when the activators surpass a threshold concentration, and therefore is regulated by mass transport phenomena such as flow and diffusion. Here, diffusion was limited by decreasing the size of microfluidic chambers, and it was found that microparticles carrying either the classical stimulus, tissue factor, or a bacterial stimulus, Bacillus cereus, initiated coagulation of human platelet-poor plasma only when confined. A simple analytical argument and numerical model were used to describe the mechanism for this phenomenon: confinement causes diffusible activators to accumulate locally and surpass the threshold concentration. To interpret the results, a dimensionless confinement number, Cn, was used to describe whether a stimulus was confined, and a Damköhler number, Da(2), was used to describe whether a subthreshold stimulus could initiate coagulation. In the context of initiation of coagulation by bacteria, this mechanism can be thought of as "diffusion acting", which is distinct from "diffusion sensing". The ability of confinement and diffusion acting to change the outcome of coagulation suggests that confinement should also regulate other biological "on" and "off" processes that are controlled by thresholds.

Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes

PubMed Central

Duchi, Diego; Gryte, Kristofer; Robb, Nicole C; Morichaud, Zakia; Sheppard, Carol; Wigneshweraraj, Sivaramesh

2018-01-01

Abstract Transcription initiation is a major step in gene regulation for all organisms. In bacteria, the promoter DNA is first recognized by RNA polymerase (RNAP) to yield an initial closed complex. This complex subsequently undergoes conformational changes resulting in DNA strand separation to form a transcription bubble and an RNAP-promoter open complex; however, the series and sequence of conformational changes, and the factors that influence them are unclear. To address the conformational landscape and transitions in transcription initiation, we applied single-molecule Förster resonance energy transfer (smFRET) on immobilized Escherichia coli transcription open complexes. Our results revealed the existence of two stable states within RNAP–DNA complexes in which the promoter DNA appears to adopt closed and partially open conformations, and we observed large-scale transitions in which the transcription bubble fluctuated between open and closed states; these transitions, which occur roughly on the 0.1 s timescale, are distinct from the millisecond-timescale dynamics previously observed within diffusing open complexes. Mutational studies indicated that the σ70 region 3.2 of the RNAP significantly affected the bubble dynamics. Our results have implications for many steps of transcription initiation, and support a bend-load-open model for the sequence of transitions leading to bubble opening during open complex formation. PMID:29177430

ANALYSIS OF BACTERIAL COMMUNITIES IN SEAGRASS BED SEDIMENTS BY DOUBLE-GRADIENT DENATURING GRADIENT GEL ELECTROPHORESIS OF PCR-AMPLIFIED 16SRRNA GENES

EPA Science Inventory

Bacterial communities associated with seagrass bed sediments are not well studied. The work presented here investigated several factors, including the presence or absence of vegetation, depth into sediment, and season, and their impact on bacterial community diversity. Double gra...

Structures of RNA Polymerase Closed and Intermediate Complexes Reveal Mechanisms of DNA Opening and Transcription Initiation.

PubMed

Glyde, Robert; Ye, Fuzhou; Darbari, Vidya Chandran; Zhang, Nan; Buck, Martin; Zhang, Xiaodong

2017-07-06

Gene transcription is carried out by RNA polymerases (RNAPs). For transcription to occur, the closed promoter complex (RPc), where DNA is double stranded, must isomerize into an open promoter complex (RPo), where the DNA is melted out into a transcription bubble and the single-stranded template DNA is delivered to the RNAP active site. Using a bacterial RNAP containing the alternative σ 54 factor and cryoelectron microscopy, we determined structures of RPc and the activator-bound intermediate complex en route to RPo at 3.8 and 5.8 Å. Our structures show how RNAP-σ 54 interacts with promoter DNA to initiate the DNA distortions required for transcription bubble formation, and how the activator interacts with RPc, leading to significant conformational changes in RNAP and σ 54 that promote RPo formation. We propose that DNA melting is an active process initiated in RPc and that the RNAP conformations of intermediates are significantly different from that of RPc and RPo. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Pathophysiology and Genetics of Bronchiectasis Unrelated to Cystic Fibrosis.

PubMed

Nikolic, Aleksandra

2018-05-12

Bronchiectasis is characterized by deregulated inflammatory response and recurrent bacterial infection resulting in progressive lung damage and an irreversible dilatation of bronchi and bronchioles. Generally accepted model of the development of bronchiectasis is the "vicious cycle hypothesis" that proposes compromising of the mucociliary clearance by an initial event, which leads to the infection of the respiratory tract followed by further impairment of mucociliary function, bacterial proliferation, and more inflammation. Bronchiectasis is a very common symptom in patients with cystic fibrosis (CF), while bronchiectasis unrelated to CF is heterogeneous pathology of unknown cause with a large number of potential contributory factors and poorly understood pathogenesis. It is presumed that bronchiectasis unrelated to CF is a multifactorial condition predisposed by genetic factors. Different molecules have been implicated in the onset and development of idiopathic bronchiectasis, as well as modulation of the disease severity and response to therapy. Most of these molecules are involved in the processes that contribute to the homeostasis of the lung tissue, especially mucociliary clearance, protease-antiprotease balance, and immunomodulation. Evaluation of the studies performed towards investigation of the role these molecules play in bronchiectasis identifies genetic variants that may be of potential importance for clinical management of the disease, and also of interest for future research efforts. This review focuses on the molecules with major roles in lung homeostasis and their involvement in bronchiectasis unrelated to CF.

Lipopolysaccharide O-Antigen Prevents Phagocytosis of Vibrio anguillarum by Rainbow Trout (Oncorhynchus mykiss) Skin Epithelial Cells

PubMed Central

Lindell, Kristoffer; Fahlgren, Anna; Hjerde, Erik; Willassen, Nils-Peder; Fällman, Maria; Milton, Debra L.

2012-01-01

Colonization of host tissues is a first step taken by many pathogens during the initial stages of infection. Despite the impact of bacterial disease on wild and farmed fish, only a few direct studies have characterized bacterial factors required for colonization of fish tissues. In this study, using live-cell and confocal microscopy, rainbow trout skin epithelial cells, the main structural component of the skin epidermis, were demonstrated to phagocytize bacteria. Mutant analyses showed that the fish pathogen Vibrio anguillarum required the lipopolysaccharide O-antigen to evade phagocytosis and that O-antigen transport required the putative wzm-wzt-wbhA operon, which encodes two ABC polysaccharide transporter proteins and a methyltransferase. Pretreatment of the epithelial cells with mannose prevented phagocytosis of V. anguillarum suggesting that a mannose receptor is involved in the uptake process. In addition, the O-antigen transport mutants could not colonize the skin but they did colonize the intestines of rainbow trout. The O-antigen polysaccharides were also shown to aid resistance to the antimicrobial factors, lysozyme and polymyxin B. In summary, rainbow trout skin epithelial cells play a role in the fish innate immunity by clearing bacteria from the skin epidermis. In defense, V. anguillarum utilizes O-antigen polysaccharides to evade phagocytosis by the epithelial cells allowing it to colonize rapidly fish skin tissues. PMID:22662189

Chronic oral infection with major periodontal bacteria Tannerella forsythia modulates systemic atherosclerosis risk factors and inflammatory markers.

PubMed

Chukkapalli, Sasanka S; Rivera-Kweh, Mercedes F; Velsko, Irina M; Chen, Hao; Zheng, Donghang; Bhattacharyya, Indraneel; Gangula, Pandu R; Lucas, Alexandra R; Kesavalu, Lakshmyya

2015-04-01

Tannerella forsythia is a Gram-negative anaerobic organism that inhabits the subgingival cavity and initiates connective tissue destruction and alveolar bone resorption in periodontal disease (PD). PD is a chronic immunoinflammatory disease and has been linked to several systemic diseases including atherosclerosis. This study evaluated the effects of a chronic oral infection with T. forsythia ATCC 43037 on the induction of PD, inflammatory markers and atherosclerosis risk factors in hyperlipidemic ApoE(null) mice. Mice were orally infected for 12 and 24 weeks prior to euthanasia. Bacterial colonization of the oral cavity and bacteremia was confirmed via isolation of genomic DNA from oral plaque and tissues. Oral infection elicited significantly elevated levels of serum IgG and IgM antibodies and alveolar bone resorption compared to control mice. Tannerella forsythia-infected mice had increased serum amyloid A, and significantly reduced serum nitric oxide when compared to controls. Tannerella forsythia chronic infection also significantly increased serum lipoproteins suggesting altered cholesterol metabolism and potential for aortic inflammation. Despite enhanced acute phase reactants and altered lipid profiles, T. forsythia infection was associated with decreased aortic plaque. This study investigates the potential of a known periodontal bacterial pathogen found in atherosclerotic plaque in humans to accelerate atherosclerosis in hyperlipdemic mice. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Kinetics of Coinfection with Influenza A Virus and Streptococcus pneumoniae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Amber M.; Adler, Frederick R.; Ribeiro, Ruy M.

Secondary bacterial infections are a leading cause of illness and death during epidemic and pandemic influenza. Experimental studies suggest a lethal synergism between influenza and certain bacteria, particularly Streptococcus pneumoniae, but the precise processes involved are unclear. In this paper, to address the mechanisms and determine the influences of pathogen dose and strain on disease, we infected groups of mice with either the H1N1 subtype influenza A virus A/Puerto Rico/8/34 (PR8) or a version expressing the 1918 PB1-F2 protein (PR8-PB1-F2(1918)), followed seven days later with one of two S. pneumoniae strains, type 2 D39 or type 3 A66.1. We determinedmore » that, following bacterial infection, viral titers initially rebound and then decline slowly. Bacterial titers rapidly rise to high levels and remain elevated. We used a kinetic model to explore the coupled interactions and study the dominant controlling mechanisms. We hypothesize that viral titers rebound in the presence of bacteria due to enhanced viral release from infected cells, and that bacterial titers increase due to alveolar macrophage impairment. Dynamics are affected by initial bacterial dose but not by the expression of the influenza 1918 PB1-F2 protein. Finally, our model provides a framework to investigate pathogen interaction during coinfections and to uncover dynamical differences based on inoculum size and strain.« less

Origins of carbonate spherulites: Implications for Brazilian Aptian pre-salt reservoir

NASA Astrophysics Data System (ADS)

Chafetz, Henry; Barth, Jennifer; Cook, Megan; Guo, Xuan; Zhou, Jie

2018-03-01

Spherulites, spherical to elliptical allochems composed of crystals radiating from a common core, investigated from a variety of depositional settings, e.g., hot springs, ambient water temperature geyser, tufa, and caliche, are all composed of a fine-grained nucleus made-up of carbonate encrusted bacterial bodies, biofilms, and/or EPS and surrounded by a cortex of radiating crystals of either aragonite or calcite. The microbes and their by-products in the nucleus induced the precipitation of carbonate, overcoming the inhibition to initiate crystal formation. The enveloping radiating crystals comprising aragonitic cortices tended to grow abiotically producing well-formed euhedral crystals with a paucity of included bacterial fossils. Whereas those cortical crystals made-up of calcite commonly contained bacterial fossils, indicating that the bacterial colonies contributed to the calcitic cortical crystal precipitation. Similar spherulites form a thick, widespread accumulation in the Aptian Pre-Salt lacustrine deposits in the Campos Basin, offshore Brazil. As with the travertine, tufa, and caliche spherulites, the Pre-Salt spherulites most likely initiated carbonate precipitation around bacterial colonies and/or their bioproducts, probably while afloat in a lacustrine water column before settling to the water-sediment interface. Absence of inter-spherulite sediment and the spherulite-to-spherulite compaction indicate that cortical crystal growth continued while the spherulites were at the sediment-water interface rather than displacively within a sediment.

Kinetics of Coinfection with Influenza A Virus and Streptococcus pneumoniae

DOE PAGES

Smith, Amber M.; Adler, Frederick R.; Ribeiro, Ruy M.; ...

2013-03-21

Secondary bacterial infections are a leading cause of illness and death during epidemic and pandemic influenza. Experimental studies suggest a lethal synergism between influenza and certain bacteria, particularly Streptococcus pneumoniae, but the precise processes involved are unclear. In this paper, to address the mechanisms and determine the influences of pathogen dose and strain on disease, we infected groups of mice with either the H1N1 subtype influenza A virus A/Puerto Rico/8/34 (PR8) or a version expressing the 1918 PB1-F2 protein (PR8-PB1-F2(1918)), followed seven days later with one of two S. pneumoniae strains, type 2 D39 or type 3 A66.1. We determinedmore » that, following bacterial infection, viral titers initially rebound and then decline slowly. Bacterial titers rapidly rise to high levels and remain elevated. We used a kinetic model to explore the coupled interactions and study the dominant controlling mechanisms. We hypothesize that viral titers rebound in the presence of bacteria due to enhanced viral release from infected cells, and that bacterial titers increase due to alveolar macrophage impairment. Dynamics are affected by initial bacterial dose but not by the expression of the influenza 1918 PB1-F2 protein. Finally, our model provides a framework to investigate pathogen interaction during coinfections and to uncover dynamical differences based on inoculum size and strain.« less

Factors shaping bacterial phylogenetic and functional diversity in coastal waters of the NW Mediterranean Sea

NASA Astrophysics Data System (ADS)

Boras, Julia A.; Vaqué, Dolors; Maynou, Francesc; Sà, Elisabet L.; Weinbauer, Markus G.; Sala, Maria Montserrat

2015-03-01

To evaluate the main factors shaping bacterioplankton phylogenetic and functional diversity in marine coastal waters, we carried out a two-year study based on a monthly sampling in Blanes Bay (NW Mediterranean). We expected the key factors driving bacterial diversity to be (1) temperature and nutrient concentration, together with chlorophyll a concentration as an indicator of phytoplankton biomass and, hence, a carbon source for bacteria (here called bottom-up factors), and (2) top-down pressure (virus- and protist-mediated mortality of bacteria). Phylogenetic diversity was analyzed by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA. Functional diversity was assessed by using monomeric carbon sources in Biolog EcoPlates and by determining the activity of six extracellular enzymes. Our results indicate that the bacterial phylogenetic and functional diversity in this coastal system is shaped mainly by bottom-up factors. A dendrogram analysis of the DGGE banding patterns revealed three main sample clusters. Two clusters differed significantly in temperature, nitrate and chlorophyll a concentration, and the third was characterized by the highest losses of bacterial production due to viral lysis detected over the whole study period. Protistan grazing had no effect on bacterial functional diversity, since there were no correlations between protist-mediated mortality (PMM) and extracellular enzyme activities, and utilization of only two out of the 31 carbon sources (N-acetyl-D-glucosamine and α-cyclodextrin) was correlated with PMM. In contrast, virus-mediated mortality correlated with changes in the percentage of use of four carbon sources, and also with specific leu-aminopeptidase and β-glucosidase activity. This suggests that viral lysate provides a pool of labile carbon sources, presumably including amino acids and glucose, which may inhibit proteolytic and glucosidic activity. Our results indicate that bottom-up factors play a more important role than top-down factors (i.e. viral lysis and protistan grazing) in shaping bacterial community structure and activity. Furthermore, they suggest that viruses play a more important role than protists in modifying community structure and functional diversity of bacteria in oligotrophic marine coastal waters.

Contingent interactions among biofilm-forming bacteria determine preservation or decay in the first steps toward fossilization of marine embryos.

PubMed

Raff, Elizabeth C; Andrews, Mary E; Turner, F Rudolf; Toh, Evelyn; Nelson, David E; Raff, Rudolf A

2013-01-01

Fossils of soft tissues provide important records of early animals and embryos, and there is substantial evidence for a role for microbes in soft tissue fossilization. We are investigating the initial events in interactions of bacteria with freshly dead tissue, using marine embryos as a model system. We previously found that microbial invasion can stabilize embryo tissue that would otherwise disintegrate in hours or days by generating a bacterial pseudomorph, a three dimensional biofilm that both replaces the tissue and replicates its morphology. In this study, we sampled seawater at different times and places near Sydney, Australia, and determined the range and frequency of different taphonomic outcomes. Although destruction was most common, bacteria in 35% of seawater samples yielded morphology‐preserving biofilms. We could replicate the taphonomic pathways seen with seawater bacterial communities using single cultured strains of marine gammaproteobacteria. Each given species reproducibly generated a consistent taphonomic outcome and we identified species that yielded each of the distinct pathways produced by seawater bacterial communities. Once formed,bacterial pseudomorphs are stable for over a year and resist attack by other bacteria and destruction by proteases and other lytic enzymes. Competition studies showed that the initial action of a pseudomorphing strain can be blocked by a strain that destroys tissues. Thus embryo preservation in nature may depend on contingent interactions among bacterial species that determine if pseudomorphing occurs.We used Artemia nauplius larvae to show that bacterial biofilm replacement of tissue is not restricted to embryos, but is relevant for preservation of small multicellular organisms. We present a model for bacterial self‐assembly of large‐scale three‐dimensional tissue pseudomorphs, based on smallscaleinteractions among individual bacterial cells to form local biofilms at structural boundaries within the tissue. Localbiofilms then conjoin to generate the pseudomorph.

Evidence of major genes for resistance to bacterial cold-water disease in rainbow trout using mixed inheritance multiple-threshold models and Bayesian segregation analysis

USDA-ARS?s Scientific Manuscript database

PURPOSE: Bacterial cold water disease (BCWD) causes significant economic loss in salmonid aquaculture, and in 2005, a rainbow trout breeding program was initiated at the NCCCWA to select for increased disease survival. The main objectives of this study were to determine the mode of inheritance of di...

The Synthetic Peroxisome Proliferator-Activated Receptor-γ Agonist Ciglitazone Attenuates Neuroinflammation and Accelerates Encapsulation in Bacterial Brain Abscesses1

PubMed Central

Kielian, Tammy; Md. Syed, Mohsin; Liu, Shuliang; Phulwani, Nirmal K.; Phillips, Napoleon; Wagoner, Gail; Drew, Paul D.; Esen, Nilufer

2008-01-01

Brain abscesses result from a pyogenic parenchymal infection commonly initiated by Gram-positive bacteria such as Staphylococcus aureus. Although the host immune response elicited following infection is essential for effective bacterial containment, this response also contributes to the significant loss of brain parenchyma by necrosis that may be reduced by modulating the inflammatory response. Ciglitazone, a PPAR-γ agonist with anti-inflammatory properties, was evaluated for its ability to influence the course of brain abscess development when treatment was initiated 3 days following infection. Interestingly, abscess-associated bacterial burdens were significantly lower following ciglitazone administration, which could be explained, in part, by the finding that ciglitazone enhanced S. aureus phagocytosis by microglia. In addition, ciglitazone attenuated the expression of select inflammatory mediators during brain abscess development including inducible NO synthase, TNF-α, IL-1β, CXCL2, and CCL3. Unexpectedly, ciglitazone also accelerated brain abscess encapsulation, which was typified by the heightened expression of fibronectin and α-smooth muscle actin-positive myofibroblasts. Collectively, through its ability to attenuate excessive inflammation and accelerate abscess encapsulation, ciglitazone may effectively sequester brain abscesses and limit bacterial dissemination. PMID:18354226

Reagent-free bacterial identification using multivariate analysis of transmission spectra

NASA Astrophysics Data System (ADS)

Smith, Jennifer M.; Huffman, Debra E.; Acosta, Dayanis; Serebrennikova, Yulia; García-Rubio, Luis; Leparc, German F.

2012-10-01

The identification of bacterial pathogens from culture is critical to the proper administration of antibiotics and patient treatment. Many of the tests currently used in the clinical microbiology laboratory for bacterial identification today can be highly sensitive and specific; however, they have the additional burdens of complexity, cost, and the need for specialized reagents. We present an innovative, reagent-free method for the identification of pathogens from culture. A clinical study has been initiated to evaluate the sensitivity and specificity of this approach. Multiwavelength transmission spectra were generated from a set of clinical isolates including Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus. Spectra of an initial training set of these target organisms were used to create identification models representing the spectral variability of each species using multivariate statistical techniques. Next, the spectra of the blinded isolates of targeted species were identified using the model achieving >94% sensitivity and >98% specificity, with 100% accuracy for P. aeruginosa and S. aureus. The results from this on-going clinical study indicate this approach is a powerful and exciting technique for identification of pathogens. The menu of models is being expanded to include other bacterial genera and species of clinical significance.

Clinical appearances, healing patterns, risk factors, and outcomes of horses with fungal keratitis: 53 cases (1978-1996)

PubMed

Gaarder, J E; Rebhun, W C; Ball, M A; Patten, V; Shin, S; Erb, H

1998-07-01

To compare initial clinical appearances, healing mechanisms, risk factors, and outcomes of horses with fungal keratitis. Retrospective analysis. 52 horses (53 eyes) with fungal keratitis. Medical records and clinical photographs of eyes were reviewed. Keratomycoses were categorized on the basis of clinical appearance at initial examination and pattern of healing. Five distinct forms of mycotic keratitis were recognized. Of 53 affected eyes, 34 (64%) retained sight and had varying degrees of corneal scarring after treatment, 6 (11%) had a cosmetic appearance but were blind, and 13 (25%) were enucleated. Bacterial-like ulcers were the most frequent type and the most difficult for predicting outcome. Eyes affected by superficial fungal keratitis were likely to be chronically infected and to require debridement and extended treatment but usually healed with minimal scarring. Keratomycosis with a surrounding furrow resulted in a grave prognosis. Aspergillus organisms were isolated from 9 of 10 such eyes. Cake-frosting material was a positive prognostic sign. Fungal corneal stromal abscesses tended to be caused by yeast. This information will aid practitioners in recognizing various forms of fungal keratitis and guide them when making therapeutic decisions and prognoses for affected horses.

Serum lipopolysaccharide-binding protein prediction of severe bacterial infection in cirrhotic patients with ascites.

PubMed

Albillos, Agustín; de-la-Hera, Antonio; Alvarez-Mon, Melchor

2004-05-15

Serum lipopolysaccharide-binding protein is increased in a subset of non-infected ascitic cirrhotic patients, a finding previously related to bacterial passage from the gut to the circulation without overt infection. We prospectively analysed the risk factors associated with a first episode of severe bacterial infection in 84 ascitic cirrhotics, followed up for a median of 46 weeks. The cumulative probability of such infection in patients with raised and normal lipopolysaccharide-binding protein was 32.4% and 8.0% (p=0.004), respectively. Increased lipopolysaccharide-binding protein was the only factor independently associated with severe bacterial infection in a multivariate analysis (relative risk 4.49, 95% CI 1.42-14.1). Monitoring of serum lipopolysaccharide-binding protein could, therefore, help to target cirrhotic patients with ascites for antibiotic prophylaxis.

[Biofilm: set-up and organization of a bacterial community].

PubMed

Filloux, Alain; Vallet, Isabelle

2003-01-01

Bacterial attachment on various surfaces mostly takes place in the form of specialised bacterial communities, referred to as biofilm. The biofilm is formed through series of interactions between cells and adherence to surface, resulting in an organised structure. In this review we have been using Pseudomonas aeruginosa as a model microorganism to describe the series of events that occurred during this developmental process. P. aeruginosa is an opportunistic pathogen that has a wide variety of hosts and infectious sites. In addition to biofilm formation in certain tissues, inert surfaces, such as catheters, are also target for bacterial biofilm development. The use of convenient genetic screens has made possible the identification of numerous biofilm-defective mutants, which have been characterised further. These studies have allowed the proposal for a global model, in which key events are described for the different stages of biofilm formation. Briefly, flagellar mobility is crucial for approaching the surface, whereas type IV pili motility is preponderant for surface colonisation and microcolonies formation. These microcolonies are finally packed together and buried in an exopolysaccharide matrix to form the differentiated bio-film. It is obvious that the different stages of biofilm formation also involved perception of environmental stimuli. These stimuli, and their associated complex regulatory networks, have still to be fully characterised to understand the bacterial strategy, which initiates biofilm formation. One such regulatory system, called Quorum sensing, is one of the key player in the initial differentiation of biofilm. Finally, a better understanding, at the molecular level, of biofilm establishment and persistence should help for the design of antimicrobials that prevent bacterial infections.

Transformation of organo-ferric peat colloids by a heterotrophic bacterium

NASA Astrophysics Data System (ADS)

Oleinikova, Olga V.; Shirokova, Liudmila S.; Gérard, Emmanuele; Drozdova, Olga Yu.; Lapitskiy, Sergey A.; Bychkov, Andrey Yu.; Pokrovsky, Oleg S.

2017-05-01

Bacterial mineralization of allochthonous (soil) dissolved organic matter (DOM) in boreal waters governs the CO2 flux from the lakes and rivers to the atmosphere, which is one of the main factor of carbon balance in high latitudes. However, the fate of colloidal trace element (TE) during bacterial processing of DOM remains poorly constrained. We separated monoculture of Pseudomonas saponiphila from a boreal creek and allowed it to react with boreal Fe-rich peat leachate of approximate colloidal (3 kDa-0.45 μm) composition C1000Fe12Al3.3Mg2Ca3.7P1.2Mn0.1Ba0.5 in nutrient-free media. The total net decrease of Dissolved Organic Carbon (DOC) concentration over 4 day of exposure was within 5% of the initial value, whereas the low molecular weight fraction of Corg (LMW<3 kDa) yielded a 16%-decrease due to long-term bio-uptake or coagulation. There was a relative depletion in Fe over Corg of 0.45 μm, colloidal and LMW fraction in the course of peat leachate interaction with P. saponiphila. Al, Mn, Ni, Cu, Ga, REEs, Y, U were mostly affected by bacterial presence and exhibited essentially the adsorption at the cell surface over first hours of reaction, in contrast to Fe, Ti, Zr, and Nb that showed both short-term adsorption and long-term removal by physical coagulation/coprecipitation with Fe hydroxide. The low molecular weight fraction (LMW<3 kDa) of most TE was a factor of 2-5 less affected by microbial presence via adsorption or removal than the high molecular weight (HMW) colloidal fractions (<0.45 μm and <50 kDa). The climate change-induced acceleration of heterotrophic bacterial activity in boreal and subarctic waters may lead to preferential removal of Fe over DOC from conventionally dissolved fraction and the decrease of the proportion of LMW < 3 kDa fraction and the increase of HMW colloids. Enhanced heterotrophic mineralization of organo-ferric colloids under climate warming scenario may compensate for on-going "browning" of surface waters.

Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica.

PubMed

Mesa, Victoria; Navazas, Alejandro; González-Gil, Ricardo; González, Aida; Weyens, Nele; Lauga, Béatrice; Gallego, Jose Luis R; Sánchez, Jesús; Peláez, Ana Isabel

2017-04-15

The aim of this study was to investigate the potential of indigenous arsenic-tolerant bacteria to enhance arsenic phytoremediation by the autochthonous pseudometallophyte Betula celtiberica The first goal was to perform an initial analysis of the entire rhizosphere and endophytic bacterial communities of the above-named accumulator plant, including the cultivable bacterial species. B. celtiberica 's microbiome was dominated by taxa related to Flavobacteriales , Burkholderiales , and Pseudomonadales , especially the Pseudomonas and Flavobacterium genera. A total of 54 cultivable rhizobacteria and 41 root endophytes, mainly affiliated with the phyla Proteobacteria , Bacteroidetes , Firmicutes , and Actinobacteria , were isolated and characterized with respect to several potentially useful features for metal plant accumulation, such as the ability to promote plant growth, metal chelation, and/or mitigation of heavy-metal stress. Seven bacterial isolates were further selected and tested for in vitro accumulation of arsenic in plants; four of them were finally assayed in field-scale bioaugmentation experiments. The exposure to arsenic in vitro caused an increase in the total nonprotein thiol compound content in roots, suggesting a detoxification mechanism through phytochelatin complexation. In the contaminated field, the siderophore and indole-3-acetic acid producers of the endophytic bacterial consortium enhanced arsenic accumulation in the leaves and roots of Betula celtiberica , whereas the rhizosphere isolate Ensifer adhaerens strain 91R mainly promoted plant growth. Field experimentation showed that additional factors, such as soil arsenic content and pH, influenced arsenic uptake in the plant, attesting to the relevance of field conditions in the success of phytoextraction strategies. IMPORTANCE Microorganisms and plants have developed several ways of dealing with arsenic, allowing them to resist and metabolize this metalloid. These properties form the basis of phytoremediation treatments and the understanding that the interactions of plants with soil bacteria are crucial for the optimization of arsenic uptake. To address this in our work, we initially performed a microbiome analysis of the autochthonous Betula celtiberica plants growing in arsenic-contaminated soils, including endosphere and rhizosphere bacterial communities. We then proceeded to isolate and characterize the cultivable bacteria that were potentially better suited to enhance phytoextraction efficiency. Eventually, we went to the field application stage. Our results corroborated the idea that recovery of pseudometallophyte-associated bacteria adapted to a large historically contaminated site and their use in bioaugmentation technologies are affordable experimental approaches and potentially very useful for implementing effective phytoremediation strategies with plants and their indigenous bacteria. Copyright © 2017 American Society for Microbiology.

Use of Endophytic and Rhizosphere Bacteria To Improve Phytoremediation of Arsenic-Contaminated Industrial Soils by Autochthonous Betula celtiberica

PubMed Central

Navazas, Alejandro; González-Gil, Ricardo; González, Aida; Weyens, Nele; Lauga, Béatrice; Gallego, Jose Luis R.; Sánchez, Jesús; Peláez, Ana Isabel

2017-01-01

ABSTRACT The aim of this study was to investigate the potential of indigenous arsenic-tolerant bacteria to enhance arsenic phytoremediation by the autochthonous pseudometallophyte Betula celtiberica. The first goal was to perform an initial analysis of the entire rhizosphere and endophytic bacterial communities of the above-named accumulator plant, including the cultivable bacterial species. B. celtiberica's microbiome was dominated by taxa related to Flavobacteriales, Burkholderiales, and Pseudomonadales, especially the Pseudomonas and Flavobacterium genera. A total of 54 cultivable rhizobacteria and 41 root endophytes, mainly affiliated with the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria, were isolated and characterized with respect to several potentially useful features for metal plant accumulation, such as the ability to promote plant growth, metal chelation, and/or mitigation of heavy-metal stress. Seven bacterial isolates were further selected and tested for in vitro accumulation of arsenic in plants; four of them were finally assayed in field-scale bioaugmentation experiments. The exposure to arsenic in vitro caused an increase in the total nonprotein thiol compound content in roots, suggesting a detoxification mechanism through phytochelatin complexation. In the contaminated field, the siderophore and indole-3-acetic acid producers of the endophytic bacterial consortium enhanced arsenic accumulation in the leaves and roots of Betula celtiberica, whereas the rhizosphere isolate Ensifer adhaerens strain 91R mainly promoted plant growth. Field experimentation showed that additional factors, such as soil arsenic content and pH, influenced arsenic uptake in the plant, attesting to the relevance of field conditions in the success of phytoextraction strategies. IMPORTANCE Microorganisms and plants have developed several ways of dealing with arsenic, allowing them to resist and metabolize this metalloid. These properties form the basis of phytoremediation treatments and the understanding that the interactions of plants with soil bacteria are crucial for the optimization of arsenic uptake. To address this in our work, we initially performed a microbiome analysis of the autochthonous Betula celtiberica plants growing in arsenic-contaminated soils, including endosphere and rhizosphere bacterial communities. We then proceeded to isolate and characterize the cultivable bacteria that were potentially better suited to enhance phytoextraction efficiency. Eventually, we went to the field application stage. Our results corroborated the idea that recovery of pseudometallophyte-associated bacteria adapted to a large historically contaminated site and their use in bioaugmentation technologies are affordable experimental approaches and potentially very useful for implementing effective phytoremediation strategies with plants and their indigenous bacteria. PMID:28188207

Consider a source: Microplastic in rivers is abundant, mobile, and selects for unique bacterial assemblages

NASA Astrophysics Data System (ADS)

Hoellein, T. J.; Kelly, J. J.; McCormick, A.; London, M.

2016-02-01

Microplastic particles (< 5mm) in oceans are an emerging ecological concern. While rivers are considered a major source of microplastic to oceans, little is known about microplastic abundance, transport, and biological interactions in rivers. Our initial research an urban river showed microplastic collected downstream of a wastewater treatment plant (WWTP) was more abundant than upstream, more abundant than many marine sites, and had higher occurrences of bacterial taxa associated with plastic decomposition and gastrointestinal pathogens than natural habitats (e.g., seston and water column). Based on these data, we conducted follow-up projects to measure 1) the role of WWTPs on microplastic abundance in 10 rivers, 2) microplastic concentrations in WWTP influent, sludge, and effluent, and 3) deposition rates of microplastic downstream of a WWTP point source. In each project, we characterized bacterial community composition on microplastic and natural habitats using next-generation Illumina sequencing. Although maximum concentrations varied among 10 sites, microplastic concentration was significantly higher downstream of WWTPs than upstream. WWTPs retained a significant component of microplastic in two activated sludge plants (>90%). Microplastic deposition length in an urban river was >2 km, and concentrations were orders of magnitude higher in the sediment than water column. Finally, bacterial communities were distinct on microplastic in water column and sediment habitats, yet communities became more similar with increasing distance from WWTP effluent sites. These data support the role of rivers as sources of microplastic to downstream ecosystems, but also illustrate that rivers are active sites of microplastic retention and bacterial colonization. Results will inform policies and engineering advances for mitigating microplastic inputs and redistribution. We advocate for research on plastic in the environment which synthesizes data from freshwater and marine disciplines. This approach is needed to facilitate quantitative analyses of the physical and biological factors driving the `life cycle' of plastic at a global scale.

Recurrent Urinary Tract Infections Management in Women

PubMed Central

Al-Badr, Ahmed; Al-Shaikh, Ghadeer

2013-01-01

Urinary tract infections (UTIs) are one of the most frequent clinical bacterial infections in women, accounting for nearly 25% of all infections. Around 50–60% of women will develop UTIs in their lifetimes. Escherichia coli is the organism that causes UTIs in most patients. Recurrent UTIs (RUTI) are mainly caused by reinfection by the same pathogen. Having frequent sexual intercourse is one of the greatest risk factors for RUTIs. In a subgroup of individuals with coexisting morbid conditions, complicated RUTIs can lead to upper tract infections or urosepsis. Although the initial treatment is antimicrobial therapy, use of different prophylactic regimens and alternative strategies are available to reduce exposure to antibiotics. PMID:23984019

Is intestinal inflammation linking dysbiosis to gut barrier dysfunction during liver disease?

PubMed Central

Brandl, Katharina

2016-01-01

Changes in the intestinal microbiota composition contribute to the pathogenesis of many disorders including gastrointestinal and liver diseases. Recent studies have broadened our understanding of the “gut-liver” axis. Dietary changes, other environmental and genetic factors can lead to alterations in the microbiota. Dysbiosis can further disrupt the integrity of the intestinal barrier leading to pathological bacterial translocation and the initiation of an inflammatory response in the liver. In this article, the authors dissect the different steps involved in disease pathogenesis to further refine approaches for the medical management of liver diseases. The authors will specifically discuss the role of dysbiosis in inducing intestinal inflammation and increasing intestinal permeability. PMID:26088524

Improving Conduct and Feasibility of Clinical Trials to Evaluate Antibacterial Drugs to Treat Hospital-Acquired Bacterial Pneumonia and Ventilator-Associated Bacterial Pneumonia: Recommendations of the Clinical Trials Transformation Initiative Antibacterial Drug Development Project Team.

PubMed

Knirsch, Charles; Alemayehu, Demissie; Botgros, Radu; Comic-Savic, Sabrina; Friedland, David; Holland, Thomas L; Merchant, Kunal; Noel, Gary J; Pelfrene, Eric; Reith, Christina; Santiago, Jonas; Tiernan, Rosemary; Tenearts, Pamela; Goldsack, Jennifer C; Fowler, Vance G

2016-08-15

The etiology of hospital-acquired or ventilator-associated bacterial pneumonia (HABP/VABP) is often multidrug-resistant infections. The evaluation of new antibacterial drugs for efficacy in this population is important, as many antibacterial drugs have demonstrated limitations when studied in this population. HABP/VABP trials are expensive and challenging to conduct due to protocol complexity and low patient enrollment, among other factors. The Clinical Trials Transformation Initiative (CTTI) seeks to advance antibacterial drug development by streamlining HABP/VABP clinical trials to improve efficiency and feasibility while maintaining ethical rigor, patient safety, information value, and scientific validity. In 2013, CTTI engaged a multidisciplinary group of experts to discuss challenges impeding the conduct of HABP/VABP trials. Separate workstreams identified challenges associated with HABP/VABP protocol complexity. The Project Team developed potential solutions to streamline HABP/VABP trials using a Quality by Design approach. CTTI recommendations focus on 4 key areas to improve HABP/VABP trials: informed consent processes/practices, protocol design, choice of an institutional review board (IRB), and trial outcomes. Informed consent processes should include legally authorized representatives. Protocol design decisions should focus on eligibility criteria, prestudy antibacterial therapy considerations, use of new diagnostics, and sample size. CTTI recommends that sponsors use a central IRB and discuss trial endpoints with regulators, including defining a clinical failure and evaluating the impact of concomitant antibacterial drugs. Streamlining HABP/VABP trials by addressing key protocol elements can improve trial startup and patient recruitment/retention, reduce trial complexity and costs, and ensure patient safety while advancing antibacterial drug development. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

Procalcitonin as a potential predicting factor for prognosis in bacterial meningitis.

PubMed

Park, Bong Soo; Kim, Si Eun; Park, Si Hyung; Kim, Jinseung; Shin, Kyong Jin; Ha, Sam Yeol; Park, JinSe; Kim, Sung Eun; Lee, Byung In; Park, Kang Min

2017-02-01

We investigated the potential role of serum procalcitonin in differentiating bacterial meningitis from viral meningitis, and in predicting the prognosis in patients with bacterial meningitis. This was a retrospective study of 80 patients with bacterial meningitis (13 patients died). In addition, 58 patients with viral meningitis were included as the disease control groups for comparison. The serum procalcitonin level was measured in all patients at admission. Differences in demographic and laboratory data, including the procalcitonin level, were analyzed between the groups. We used the mortality rate during hospitalization as a marker of prognosis in patients with bacterial meningitis. Multiple logistic regression analysis showed that high serum levels of procalcitonin (>0.12ng/mL) were an independently significant variable for differentiating bacterial meningitis from viral meningitis. The risk of having bacterial meningitis with high serum levels of procalcitonin was at least 6 times higher than the risk of having viral meningitis (OR=6.76, 95% CI: 1.84-24.90, p=0.004). In addition, we found that high levels of procalcitonin (>7.26ng/mL) in the blood were an independently significant predictor for death in patients with bacterial meningitis. The risk of death in patients with bacterial meningitis with high serum levels of procalcitonin may be at least 9 times higher than those without death (OR=9.09, 95% CI: 1.74-47.12, p=0.016). We found that serum procalcitonin is a useful marker for differentiating bacterial meningitis from viral meningitis, and it is also a potential predicting factor for prognosis in patients with bacterial meningitis. Copyright © 2016 Elsevier Ltd. All rights reserved.

Porphyromonas gingivalis: An Overview of Periodontopathic Pathogen below the Gum Line

PubMed Central

How, Kah Yan; Song, Keang Peng; Chan, Kok Gan

2016-01-01

Periodontal disease represents a group of oral inflammatory infections initiated by oral pathogens which exist as a complex biofilms on the tooth surface and cause destruction to tooth supporting tissues. The severity of this disease ranges from mild and reversible inflammation of the gingiva (gingivitis) to chronic destruction of connective tissues, the formation of periodontal pocket and ultimately result in loss of teeth. While human subgingival plaque harbors more than 500 bacterial species, considerable research has shown that Porphyromonas gingivalis, a Gram-negative anaerobic bacterium, is the major etiologic agent which contributes to chronic periodontitis. This black-pigmented bacterium produces a myriad of virulence factors that cause destruction to periodontal tissues either directly or indirectly by modulating the host inflammatory response. Here, this review provides an overview of P. gingivalis and how its virulence factors contribute to the pathogenesis with other microbiome consortium in oral cavity. PMID:26903954

Quorum Sensing Attenuates Virulence in Sodalis praecaptivus.

PubMed

Enomoto, Shinichiro; Chari, Abhishek; Clayton, Adam Larsen; Dale, Colin

2017-05-10

Sodalis praecaptivus is a close relative and putative environmental progenitor of the widely distributed, insect-associated, Sodalis-allied symbionts. Here we show that mutant strains of S. praecaptivus that lack genetic components of a quorum-sensing (QS) apparatus have a rapid and potent killing phenotype following microinjection into an insect host. Transcriptomic and genetic analyses indicate that insect killing occurs as a consequence of virulence factors, including insecticidal toxins and enzymes that degrade the insect integument, which are normally repressed by QS at high infection densities. This method of regulation suggests that virulence factors are only utilized in early infection to initiate the insect-bacterial association. Once bacteria reach sufficient density in host tissues, the QS circuit represses expression of these harmful genes, facilitating a long-lasting and benign association. We discuss the implications of the functionality of this QS system in the context of establishment and evolution of mutualistic relationships involving these bacteria. Published by Elsevier Inc.

Systemic sclerosis and infections.

PubMed

Randone, Silvia Bellando; Guiducci, Serena; Cerinic, Marco Matucci

2008-10-01

Systemic sclerosis (SSc) is an autoimmune disease characterized by vascular obliteration, excessive extracellular matrix deposition and fibrosis of the connective tissues of the skin, lungs, gastrointestinal tract, heart, and kidneys. Numerous infectious agents (bacterial and viral) have been proposed as possible triggering factors (Parvovirus B19, Cytomegalovirus, Epstein-Barr virus, Retroviruses). Homology between viruses and autoantibody targets suggests that molecular mimicry may have a role in initiating antibody response in different disorders characterized by diffuse vascular disease, including SSc. Endothelial cell may be infected bacteria or viruses that play a particular role in inducing vasculitis. The pathogenic hypothesis include: a mechanism of molecular mimicry, the role played by endothelial cell damage, the presence of superantigens and the role of microchimeric cells. Although several studies provide important information linking infectious agents to SSc, a direct casual association between infections and SSc is still missing. In SSc viral products could synergize with other factors in the microenvironment predisposing to SSc development.

Crosstalk between the microbiome and cancer cells by quorum sensing peptides.

PubMed

Wynendaele, Evelien; Verbeke, Frederick; D'Hondt, Matthias; Hendrix, An; Van De Wiele, Christophe; Burvenich, Christian; Peremans, Kathelijne; De Wever, Olivier; Bracke, Marc; De Spiegeleer, Bart

2015-02-01

To date, the precise role of the human microbiome in health and disease states remains largely undefined. Complex and selective crosstalk systems between the microbiome and mammalian cells are also not yet reported. Research up till now mainly focused on bacterial synthesis of virulence factors, reactive oxygen/nitrogen species (ROS/RNS) and hydrogen sulphide, as well as on the activation of exogenous mutagen precursors by intestinal bacteria. We discovered that certain quorum sensing peptides, produced by bacteria, interact with mammalian cells, in casu cancer cells: Phr0662 (Bacillus sp.), EntF-metabolite (Enterococcus faecium) and EDF-derived (Escherichia coli) peptides initiate HCT-8/E11 colon cancer cell invasion, with Phr0662 also promoting angiogenesis. Our findings thus indicate that the human microbiome, through their quorum sensing peptides, may be one of the factors responsible for cancer metastasis. Copyright © 2014 Elsevier Inc. All rights reserved.

Role of biomarkers in the management of antibiotic therapy: an expert panel review II: clinical use of biomarkers for initiation or discontinuation of antibiotic therapy

PubMed Central

2013-01-01

Biomarker-guided initiation of antibiotic therapy has been studied in four conditions: acute pancreatitis, lower respiratory tract infection (LRTI), meningitis, and sepsis in the ICU. In pancreatitis with suspected infected necrosis, initiating antibiotics best relies on fine-needle aspiration and demonstration of infected material. We suggest that PCT be measured to help predict infection; however, available data are insufficient to decide on initiating antibiotics based on PCT levels. In adult patients suspected of community-acquired LRTI, we suggest withholding antibiotic therapy when the serum PCT level is low (<0.25 ng/mL); in patients having nosocomial LRTI, data are insufficient to recommend initiating therapy based on a single PCT level or even repeated measurements. For children with suspected bacterial meningitis, we recommend using a decision rule as an aid to therapeutic decisions, such as the Bacterial Meningitis Score or the Meningitest®; a single PCT level ≥0.5 ng/mL also may be used, but false-negatives may occur. In adults with suspected bacterial meningitis, we suggest integrating serum PCT measurements in a clinical decision rule to help distinguish between viral and bacterial meningitis, using a 0.5 ng/mL threshold. For ICU patients suspected of community-acquired infection, we do not recommend using a threshold serum PCT value to help the decision to initiate antibiotic therapy; data are insufficient to recommend using PCT serum kinetics for the decision to initiate antibiotic therapy in patients suspected of ICU-acquired infection. In children, CRP can probably be used to help discontinue therapy, although the evidence is limited. In adults, antibiotic discontinuation can be based on an algorithm using repeated PCT measurements. In non-immunocompromised out- or in- patients treated for RTI, antibiotics can be discontinued if the PCT level at day 3 is < 0.25 ng/mL or has decreased by >80-90%, whether or not microbiological documentation has been obtained. For ICU patients who have nonbacteremic sepsis from a known site of infection, antibiotics can be stopped if the PCT level at day 3 is < 0.5 ng/mL or has decreased by >80% relative to the highest level recorded, irrespective of the severity of the infectious episode; in bacteremic patients, a minimal duration of therapy of 5 days is recommended. PMID:23830525

Polysaccharides as Bacterial Antiadhesive Agents and "Smart" Constituents for Improved Drug Delivery Systems Against Helicobacter pylori Infection.

PubMed

Menchicchi, Bianca; Hensel, Andreas; Goycoolea, Francisco M

2015-01-01

The standard eradication treatment of the hostile Helicobacter pylori (H. pylori) stomach infection is facing increasing alarming antibiotic resistance worldwide and calls for alternative strategies to the use of antibiotics. One new perspective in this direction is cytoprotective compounds for targeted prevention of the adhesion of the bacteria to the stomach host cell and to inhibit the bacterial cell-cell communication via quorum sensing by specific inhibitors. Bacterial adhesion of H. pylori to the host cells is mainly mediated by carbohydrate-protein interactions. Therefore, the use of polyvalent carbohydrates, (e.g. plant-derived polysaccharides), as potential antiadhesive compounds, seems to be a promising tool to prevent the initial docking of the bacterium to the stomach cells. Polysaccharides are common constituents of daily food, either as starch or as dietary fiber and often also function as excipients for galenic drug-delivery formulations. In addition, polysaccharides with defined pharmacodynamics action against bacterial outer membrane proteins can have potential as therapeutic tools in the treatment of bacterial infections. Some polysaccharides are known to possess antibacterial properties against gram-positive bacteria, others to inhibit bacterial colonization by blocking specific carbohydrate receptors involved in host-bacteria interaction. This mode of action is advocated as alternative antiadhesion therapy. Ongoing research is also seeking for polysaccharide-based nanoformulations with potential for local drug delivery at the stomach as novel H. pylori therapies. These approaches pose challenges concerned with the stability of the nanomaterials in the harsh conditions of the gastric environment and their capacity to adhere to the stomach mucosa. In a global scenario, geographical diversity and social habits, namely lifestyle and dietary factors, influence the prevalence of the H. pylori-associated diseases and their severity. In this context, the exploration of the biological activity of plant-derived products or polysaccharides commonly present in foods is increasingly becoming more and more attractive. This review aims to present the current state-of-the-art on the antiadhesive capacity of different polysaccharide families, on polysaccharide-based nanosystems and the proof-of-concept evidence of their potential use as alternative medicines against H. pylori.

Identification and structural analysis of an L-asparaginase enzyme from guinea pig with putative tumor cell killing properties.

PubMed

Schalk, Amanda M; Nguyen, Hien-Anh; Rigouin, Coraline; Lavie, Arnon

2014-11-28

The initial observation that guinea pig serum kills lymphoma cells marks the serendipitous discovery of a new class of anti-cancer agents. The serum cell killing factor was shown to be an enzyme with L-asparaginase (ASNase) activity. As a direct result of this observation, several bacterial L-asparaginases were developed and are currently approved by the Food and Drug Administration for the treatment of the subset of hematological malignancies that are dependent on the extracellular pool of the amino acid asparagine. As drugs, these enzymes act to hydrolyze asparagine to aspartate, thereby starving the cancer cells of this amino acid. Prior to the work presented here, the precise identity of this guinea pig enzyme has not been reported in the peer-reviewed literature. We discovered that the guinea pig enzyme annotated as H0W0T5_CAVPO, which we refer to as gpASNase1, has the required low Km property consistent with that possessed by the cell-killing guinea pig serum enzyme. Elucidation of the ligand-free and aspartate complex gpASNase1 crystal structures allows a direct comparison with the bacterial enzymes and serves to explain the lack of L-glutaminase activity in the guinea pig enzyme. The structures were also used to generate a homology model for the human homolog hASNase1 and to help explain its vastly different kinetic properties compared with gpASNase1, despite a 70% sequence identity. Given that the bacterial enzymes frequently present immunogenic and other toxic side effects, this work suggests that gpASNase1 could be a promising alternative to these bacterial enzymes. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

High density growth of T7 expression strains with auto-induction option

DOEpatents

Studier, F William [Stony Brook, NY

2009-07-14

Disclosed is a method for promoting auto-induction of transcription of cloned DNA in cultures of bacterial cells grown batchwise, the transcription being under the control of a promoter whose activity can be induced by an exogenous inducer whose ability to induce said promoter is dependent on the metabolic state of said bacterial cells. Initially, a culture media is provided which includes: i) an inducer that causes induction of transcription from said promoter in said bacterial cells; and ii) a metabolite that prevents induction by said inducer, the concentration of said metabolite being adjusted so as to substantially preclude induction by said inducer in the early stages of growth of the bacterial culture, but such that said metabolite is depleted to a level that allows induction by said inducer at a later stage of growth. The culture medium is inoculated with a bacterial inoculum, the inoculum comprising bacterial cells containing cloned DNA, the transcription of which is induced by said inducer. The culture is then incubated under conditions appropriate for growth of the bacterial cells.

The significance of oral streptococci in patients with pneumonia with risk factors for aspiration: the bacterial floral analysis of 16S ribosomal RNA gene using bronchoalveolar lavage fluid.

PubMed

Akata, Kentaro; Yatera, Kazuhiro; Yamasaki, Kei; Kawanami, Toshinori; Naito, Keisuke; Noguchi, Shingo; Fukuda, Kazumasa; Ishimoto, Hiroshi; Taniguchi, Hatsumi; Mukae, Hiroshi

2016-05-11

Aspiration pneumonia has been a growing interest in an aging population. Anaerobes are important pathogens, however, the etiology of aspiration pneumonia is not fully understood. In addition, the relationship between the patient clinical characteristics and the causative pathogens in pneumonia patients with aspiration risk factors are unclear. To evaluate the relationship between the patient clinical characteristics with risk factors for aspiration and bacterial flora in bronchoalveolar lavage fluid (BALF) in pneumonia patients, the bacterial floral analysis of 16S ribosomal RNA gene was applied in addition to cultivation methods in BALF samples. From April 2010 to February 2014, BALF samples were obtained from the affected lesions of pneumonia via bronchoscopy, and were evaluated by the bacterial floral analysis of 16S rRNA gene in addition to cultivation methods in patients with community-acquired pneumonia (CAP) and healthcare-associated pneumonia (HCAP). Factors associated with aspiration risks in these patients were analyzed. A total of 177 (CAP 83, HCAP 94) patients were enrolled. According to the results of the bacterial floral analysis, detection rate of oral streptococci as the most detected bacterial phylotypes in BALF was significantly higher in patients with aspiration risks (31.0 %) than in patients without aspiration risks (14.7 %) (P = 0.009). In addition, the percentages of oral streptococci in each BALF sample were significantly higher in patients with aspiration risks (26.6 ± 32.0 %) than in patients without aspiration risks (13.8 ± 25.3 %) (P = 0.002). A multiple linear regression analysis showed that an Eastern Cooperative Oncology Group (ECOG) performance status (PS) of ≥3, the presence of comorbidities, and a history of pneumonia within a previous year were significantly associated with a detection of oral streptococci in BALF. The bacterial floral analysis of 16S rRNA gene revealed that oral streptococci were mostly detected as the most detected bacterial phylotypes in BALF samples in CAP and HCAP patients with aspiration risks, especially in those with a poor ECOG-PS or a history of pneumonia.

The impact of bacterial and viral co‐infection in severe influenza

PubMed Central

Blyth, Christopher C.; Webb, Steve A. R.; Kok, Jen; Dwyer, Dominic E.; van Hal, Sebastiaan J.; Foo, Hong; Ginn, Andrew N.; Kesson, Alison M.; Seppelt, Ian; Iredell, Jonathan R.

2013-01-01

Please cite this paper as: Blyth et al. (2013) The impact of bacterial and viral co‐infection in severe influenza. Influenza and Other Respiratory Viruses 7(2) 168–176. Background  Many questions remain concerning the burden, risk factors and impact of bacterial and viral co‐infection in patients with pandemic influenza admitted to the intensive care unit (ICU). Objectives  To examine the burden, risk factors and impact of bacterial and viral co‐infection in Australian patients with severe influenza. Patients/Methods  A cohort study conducted in 14 ICUs was performed. Patients with proven influenza A during the 2009 influenza season were eligible for inclusion. Demographics, risk factors, clinical data, microbiological data, complications and outcomes were collected. Polymerase chain reaction for additional bacterial and viral respiratory pathogens was performed on stored respiratory samples. Results  Co‐infection was identified in 23·3–26·9% of patients with severe influenza A infection: viral co‐infection, 3·2–3·4% and bacterial co‐infection, 20·5–24·7%. Staphylococcus aureus was the most frequent bacterial co‐infection followed by Streptococcus pneumoniae and Haemophilus influenzae. Patients with co‐infection were younger [mean difference in age = 8·46 years (95% CI: 0·18–16·74 years)], less likely to have significant co‐morbidities (32·0% versus 66·2%, P = 0·004) and less frequently obese [mean difference in body mass index = 6·86 (95% CI: 1·77–11·96)] compared to those without co‐infection. Conclusions  Bacterial or viral co‐infection complicated one in four patients admitted to ICU with severe influenza A infection. Despite the co‐infected patients being younger and with fewer co‐morbidities, no significant difference in outcomes was observed. It is likely that co‐infection contributed to a need for ICU admission in those without other risk factors for severe influenza disease. Empiric antibiotics with staphylococcal activity should be strongly considered in all patients with severe influenza A infection. PMID:22487223

Demonstration of bacterial biofilms in culture-negative silicone stent and jones tube.

PubMed

Parsa, Kami; Schaudinn, Christoph; Gorur, Amita; Sedghizadeh, Parish P; Johnson, Thomas; Tse, David T; Costerton, John W

2010-01-01

To demonstrate the presence of bacterial biofilms on a dacryocystorhinostomy silicone stent and a Jones tube. One dacryocystorhinostomy silicone stent and one Jones tube were removed from 2 patients who presented with an infection of their respective nasolacrimal system. Cultures were obtained, and the implants were processed for scanning electron microscopy and confocal laser scanning microscopy, advanced microscopic methods that are applicable for detection of uncultivable biofilm organisms. Routine bacterial cultures revealed no growth, but bacterial biofilms on outer and inner surfaces of both implants were confirmed by advanced microscopic techniques. To the authors' knowledge, this is the first article that documents the presence of biofilms on a Crawford stent or a Jones tube on patients who presented with infections involving the nasolacrimal system. Although initial cultures revealed absence of any bacterial growth, confocal laser scanning microscopy and scanning electron microscopy documented bacterial colonization. Clinicians should consider the role of biofilms and the limitation of our standard culturing techniques while treating patients with device- or implant-related infections.

Relationship between bacterial diversity and environmental parameters during composting of different raw materials.

PubMed

Wang, Xueqin; Cui, Hongyang; Shi, Jianhong; Zhao, Xinyu; Zhao, Yue; Wei, Zimin

2015-12-01

The aim of this study was to compare the bacterial structure of seven different composts. The primary environmental factors affecting bacterial species were identified, and a strategy to enhance the abundance of uncultured bacteria through controlling relevant environmental parameters was proposed. The results showed that the physical-chemical parameters of each different pile changed in its own manner during composting, which affected the structure and succession of bacteria in different ways. DGGE profiles showed that there were 10 prominent species during composting. Among them, four species existed in all compost types, two species existed in several piles and four species were detected in a single material. Redundancy analysis results showed that bacterial species compositions were significantly influenced by C/N and moisture (p<0.05). The optimal range of C/N was 14-27. Based on these results, the primary environmental factors affecting a certain species were further identified as a potential control of bacterial diversity. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion

PubMed Central

Brüssow, Harald; Canchaya, Carlos; Hardt, Wolf-Dietrich

2004-01-01

Comparative genomics demonstrated that the chromosomes from bacteria and their viruses (bacteriophages) are coevolving. This process is most evident for bacterial pathogens where the majority contain prophages or phage remnants integrated into the bacterial DNA. Many prophages from bacterial pathogens encode virulence factors. Two situations can be distinguished: Vibrio cholerae, Shiga toxin-producing Escherichia coli, Corynebacterium diphtheriae, and Clostridium botulinum depend on a specific prophage-encoded toxin for causing a specific disease, whereas Staphylococcus aureus, Streptococcus pyogenes, and Salmonella enterica serovar Typhimurium harbor a multitude of prophages and each phage-encoded virulence or fitness factor makes an incremental contribution to the fitness of the lysogen. These prophages behave like “swarms” of related prophages. Prophage diversification seems to be fueled by the frequent transfer of phage material by recombination with superinfecting phages, resident prophages, or occasional acquisition of other mobile DNA elements or bacterial chromosomal genes. Prophages also contribute to the diversification of the bacterial genome architecture. In many cases, they actually represent a large fraction of the strain-specific DNA sequences. In addition, they can serve as anchoring points for genome inversions. The current review presents the available genomics and biological data on prophages from bacterial pathogens in an evolutionary framework. PMID:15353570

Prevalence and Risk Factors for Bacterial Vaginosis and Other Vulvovaginitis in a Population of Sexually Active Adolescents from Salvador, Bahia, Brazil

PubMed Central

Moreira Mascarenhas, Rita Elizabeth; Sacramento Cunha Machado, Márcia; Borges da Costa e Silva, Bruno Fernando; Fernandes Weyll Pimentel, Rodrigo; Teixeira Ferreira, Tatiana; Silva Leoni, Fernanda Maria; Grassi, Maria Fernanda Rios

2012-01-01

Bacterial vaginosis, trichomoniasis, and genital candidiasis are considered the main etiologies of vulvovaginitis. Few studies estimate the prevalence of vulvovaginitis among adolescents, especially in Brazil. This study aimed to determine the prevalence and main risk factors associated with bacterial vaginosis and genital infection by C. albicans and Trichomonas vaginalis among a group of adolescents from Salvador, Bahia, Brazil. One hundred sexually active adolescents followed at an adolescent gynecology clinic were included. Endocervical and vaginal samples were obtained during gynecological examination. Nugent criteria were applied for the diagnosis of bacterial vaginosis. For Candida albicans and Trichomonas vaginalis detection, culture in Sabouraud agar plates and Papanicolaou cytology were used, respectively. The mean age of participants was 16.6 ± 1.6 years. The prevalence of bacterial vaginosis was 20% (95% CI 12–28) and of genital infection by Candida was 22% (95% CI 14–30). Vaginal cytology detected Trichomonas vaginalis in one patient. Alcohol, tobacco, and illegal drug use (P = 0.02) and multiple lifetime partners were statistically related to bacterial vaginosis (P = 0.01). The prevalence of bacterial vaginosis and genital candidiasis was similar to other studies carried out among adolescents worldwide. PMID:23133306

Characteristics of aquatic bacterial community and the influencing factors in an urban river.

PubMed

Wang, Peng; Chen, Bo; Yuan, Ruiqiang; Li, Chuangqiong; Li, Yan

2016-11-01

Bacteria play a critical role in environmental and ecological processes in river ecosystems. We studied the bacterial community in the Ganjiang River, a major tributary of the Yangtze River, as it flowed through Nanchang, the largest city in the Ganjiang River basin. Water was sampled at five sites monthly during the wet season, and the bacterial community was characterized using Illumina high-throughput sequencing. A total of 811 operational taxonomic units (OTUs) were observed for all samples, ranging from 321 to 519 for each sample. The bacterial communities were maintained by a core of OTUs that persisted longitudinally and monthly. Actinobacteria (41.17% of total sequences) and Proteobacteria (31.80%) were the dominant phyla, while Firmicutes (mostly genus Lactococcus) became most abundant during flooding. Temperature and flow rate, rather than water chemistry, were the main factors influencing the bacterial community in river water. Temperature was the best individual parameter explaining the variations in OTU abundance, while flow rate was the best individual parameter explaining the variations in phylum abundance. Except for Proteobacteria, the relative abundance of bacterial phyla did not differ significantly between sites, and the degrees of influence of urban landscape on the bacterial community were estimated to be 17%-34%. Copyright © 2016 Elsevier B.V. All rights reserved.

Spontaneous bacterial peritonitis caused by Listeria monocytogenes: a case report and literature review.

PubMed

Cardoso, Cláudia; Cremers, Isabelle; Oliveira, Ana Paula

2012-01-01

Spontaneous bacterial peritonitis (SBP) is a common and often serious complication of long standing ascites in the presence of advanced liver disease.1 We report a case of a 51- year-old man with alcoholic cirrhosis admitted to our department with jaundice, ascitis and lower limbs edema. A diagnosis of spontaneous bacterial peritonitis was made and empiric therapy with cefotaxime was prescribed with no response. Three days later Listeria monocytogenes was detected in peritoneal fluid culture and amoxicillin was initiated according to in vitro sensibility test. Despite adequate antibiotic therapy, the patient died one week later.

[Results of conservative treatment for regressive vesicoureteral reflux in childhood].

PubMed

Popadiuk, S; Korzon, M; Plata, K

1995-09-01

The study involved 112 children with 169 confirmed vesicoureteric reflux grades I, II, III. During anti-bacterial treatment which lasted at last two years, spontaneous regression occurred in 82% of the vesicoureteral reflux. Renal scars were observed in 8% of the cases. Initially urinary tract infection was diagnosed in 84% of the children. This figure was reduced to 8% after anti-bacterial treatment. 54% of the observed children had associated diseases (anaemia, chronic enteropathy, bronchitis and pneumonia). The results confirmed the efficiency of anti-bacterial treatment in children with vesicoureteral reflux grades I, II, III.

Formation and dissolution of bacterial colonies.

PubMed

Weber, Christoph A; Lin, Yen Ting; Biais, Nicolas; Zaburdaev, Vasily

2015-09-01

Many organisms form colonies for a transient period of time to withstand environmental pressure. Bacterial biofilms are a prototypical example of such behavior. Despite significant interest across disciplines, physical mechanisms governing the formation and dissolution of bacterial colonies are still poorly understood. Starting from a kinetic description of motile and interacting cells we derive a hydrodynamic equation for their density on a surface, where most of the kinetic coefficients are estimated from experimental data for N. gonorrhoeae bacteria. We use it to describe the formation of multiple colonies with sizes consistent with experimental observations. Finally, we show how the changes in the cell-to-cell interactions lead to the dissolution of the bacterial colonies. The successful application of kinetic theory to a complex far from equilibrium system such as formation and dissolution of living bacterial colonies potentially paves the way for the physical quantification of the initial stages of biofilm formation.

Comparative study of Gram-negative bacteria response to solar photocatalytic inactivation.

PubMed

Achouri, Faouzi; BenSaid, Myriam; Bousselmi, Latifa; Corbel, Serge; Schneider, Raphaël; Ghrabi, Ahmed

2018-06-03

Solar photocatalytic inactivation of Gram-negative bacteria with immobilized TiO 2 -P25 in a fixed-bed reactor was modeled with simplified kinetic equations. The kinetic parameters are the following: the photocatalytic inactivation coefficient (k d,QUV ), the initial bacterial reduction rate (A) in the contact with the disinfecting agent, and the threshold level of damage (n) were determined to report the effect of Q UV /TiO 2 -P25 on bacterial cultivability and viability and to compare the response of bacterial strains to photocatalytic treatment. In addition, the integration of the reactivation coefficient (C r ) in the photocatalytic inactivation equation allowed evaluating the ability of bacterial reactivation after photocatalytic stress. Results showed different responses of the bacteria strains to photocatalytic stress and the ability of certain bacterial strains such as Escherichia coli ATCC25922 and Pseudomonas aeruginosa ATCC4114 to resuscitate after photocatalytic treatment.

Emergence of Competitive Dominant Ammonia-Oxidizing Bacterial Populations in a Full-Scale Industrial Wastewater Treatment Plant

PubMed Central

Layton, Alice C.; Dionisi, Hebe; Kuo, H.-W.; Robinson, Kevin G.; Garrett, Victoria M.; Meyers, Arthur; Sayler, Gary S.

2005-01-01

Ammonia-oxidizing bacterial populations in an industrial wastewater treatment plant were investigated with amoA and 16S rRNA gene real-time PCR assays. Nitrosomonas nitrosa initially dominated, but over time RI-27-type ammonia oxidizers, also within the Nitrosomonas communis lineage, increased from below detection to codominance. This shift occurred even though nitrification remained constant. PMID:15691975

Efficacy of a commercial probiotic relative to oxytetracycline as Gram-negative bacterial control agents in a rotifer (Brachionus plicatilis) batch culture

USDA-ARS?s Scientific Manuscript database

Two trials were conducted to evaluate two gram-negative bacterial control strategies in batch cultures of the rotifer Brachionus plicatilis. In the first trial, rotifers at an initial density of 47/mL were cultured for 5 d and dosed with a 10-mg/L solution of either oxytetracycline or a commercial p...

Aerobic cyanide degradation by bacterial isolates from cassava factory wastewater

PubMed Central

Kandasamy, Sujatha; Dananjeyan, Balachandar; Krishnamurthy, Kumar; Benckiser, Gero

2015-01-01

Ten bacterial strains that utilize cyanide (CN) as a nitrogen source were isolated from cassava factory wastewater after enrichment in a liquid media containing sodium cyanide (1 mM) and glucose (0.2% w/v). The strains could tolerate and grow in cyanide concentrations of up to 5 mM. Increased cyanide levels in the media caused an extension of lag phase in the bacterial growth indicating that they need some period of acclimatisation. The rate of cyanide removal by the strains depends on the initial cyanide and glucose concentrations. When initial cyanide and glucose concentrations were increased up to 5 mM, cyanide removal rate increased up to 63 and 61 per cent by Bacillus pumilus and Pseudomonas putida. Metabolic products such as ammonia and formate were detected in culture supernatants, suggesting a direct hydrolytic pathway without an intermediate formamide. The study clearly demonstrates the potential of aerobic treatment with cyanide degrading bacteria for cyanide removal in cassava factory wastewaters. PMID:26413045

Cellulosic hydrogen production with a sequencing bacterial hydrolysis and dark fermentation strategy.

PubMed

Lo, Yung-Chung; Bai, Ming-Der; Chen, Wen-Ming; Chang, Jo-Shu

2008-11-01

In this study, cellulose hydrolysis activity of two mixed bacterial consortia (NS and QS) was investigated. Combination of NS culture and BHM medium exhibited better hydrolytic activity under the optimal condition of 35 degrees C, initial pH 7.0, and 100rpm agitation. The NS culture could hydrolyze carboxymethyl cellulose (CMC), rice husk, bagasse and filter paper, among which CMC gave the best hydrolysis performance. The CMC hydrolysis efficiency increased with increasing CMC concentration from 5 to 50g/l. With a CMC concentration of 10g/l, the total reducing sugar (RS) production and the RS producing rate reached 5531.0mg/l and 92.9mg/l/h, respectively. Furthermore, seven H2-producing bacterial isolates (mainly Clostridium species) were used to convert the cellulose hydrolysate into H2 energy. With an initial RS concentration of 0.8g/l, the H2 production and yield was approximately 23.8ml/l and 1.21mmol H2/g RS (0.097mmol H2/g cellulose), respectively.

Aerobic cyanide degradation by bacterial isolates from cassava factory wastewater.

PubMed

Kandasamy, Sujatha; Dananjeyan, Balachandar; Krishnamurthy, Kumar; Benckiser, Gero

2015-01-01

Ten bacterial strains that utilize cyanide (CN) as a nitrogen source were isolated from cassava factory wastewater after enrichment in a liquid media containing sodium cyanide (1 mM) and glucose (0.2% w/v). The strains could tolerate and grow in cyanide concentrations of up to 5 mM. Increased cyanide levels in the media caused an extension of lag phase in the bacterial growth indicating that they need some period of acclimatisation. The rate of cyanide removal by the strains depends on the initial cyanide and glucose concentrations. When initial cyanide and glucose concentrations were increased up to 5 mM, cyanide removal rate increased up to 63 and 61 per cent by Bacillus pumilus and Pseudomonas putida. Metabolic products such as ammonia and formate were detected in culture supernatants, suggesting a direct hydrolytic pathway without an intermediate formamide. The study clearly demonstrates the potential of aerobic treatment with cyanide degrading bacteria for cyanide removal in cassava factory wastewaters.

The Date Palm Tree Rhizosphere Is a Niche for Plant Growth Promoting Bacteria in the Oasis Ecosystem

PubMed Central

Gtari, Maher; Boudabous, Abdellatif; Daffonchio, Daniele; Ouzari, Hadda-Imene

2015-01-01

In arid ecosystems environmental factors such as geoclimatic conditions and agricultural practices are of major importance in shaping the diversity and functionality of plant-associated bacterial communities. Assessing the influence of such factors is a key to understand (i) the driving forces determining the shape of root-associated bacterial communities and (ii) the plant growth promoting (PGP) services they provide. Desert oasis environment was chosen as model ecosystem where agriculture is possible by the microclimate determined by the date palm cultivation. The bacterial communities in the soil fractions associated with the root system of date palms cultivated in seven oases in Tunisia were assessed by culture-independent and dependent approaches. According to 16S rRNA gene PCR-DGGE fingerprinting, the shapes of the date palm rhizosphere bacterial communities correlate with geoclimatic features along a north-south aridity transect. Despite the fact that the date palm root bacterial community structure was strongly influenced by macroecological factors, the potential rhizosphere services reflected in the PGP traits of isolates screened in vitro were conserved among the different oases. Such services were exerted by the 83% of the screened isolates. The comparable numbers and types of PGP traits indicate their importance in maintaining the plant functional homeostasis despite the different environmental selection pressures. PMID:25866759

The date palm tree rhizosphere is a niche for plant growth promoting bacteria in the oasis ecosystem.

PubMed

Ferjani, Raoudha; Marasco, Ramona; Rolli, Eleonora; Cherif, Hanene; Cherif, Ameur; Gtari, Maher; Boudabous, Abdellatif; Daffonchio, Daniele; Ouzari, Hadda-Imene

2015-01-01

In arid ecosystems environmental factors such as geoclimatic conditions and agricultural practices are of major importance in shaping the diversity and functionality of plant-associated bacterial communities. Assessing the influence of such factors is a key to understand (i) the driving forces determining the shape of root-associated bacterial communities and (ii) the plant growth promoting (PGP) services they provide. Desert oasis environment was chosen as model ecosystem where agriculture is possible by the microclimate determined by the date palm cultivation. The bacterial communities in the soil fractions associated with the root system of date palms cultivated in seven oases in Tunisia were assessed by culture-independent and dependent approaches. According to 16S rRNA gene PCR-DGGE fingerprinting, the shapes of the date palm rhizosphere bacterial communities correlate with geoclimatic features along a north-south aridity transect. Despite the fact that the date palm root bacterial community structure was strongly influenced by macroecological factors, the potential rhizosphere services reflected in the PGP traits of isolates screened in vitro were conserved among the different oases. Such services were exerted by the 83% of the screened isolates. The comparable numbers and types of PGP traits indicate their importance in maintaining the plant functional homeostasis despite the different environmental selection pressures.

Fibrinogen Is at the Interface of Host Defense and Pathogen Virulence in Staphylococcus aureus Infection

PubMed Central

Ko, Ya-Ping; Flick, Matthew J.

2017-01-01

Fibrinogen not only plays a pivotal role in hemostasis but also serves key roles in antimicrobial host defense. As a rapidly assembled provisional matrix protein, fibrin(ogen) can function as an early line of host protection by limiting bacterial growth, suppressing dissemination of microbes to distant sites, and mediating host bacterial killing. Fibrinogen-mediated host antimicrobial activity occurs predominantly through two general mechanisms, namely, fibrin matrices functioning as a protective barrier and fibrin(ogen) directly or indirectly driving host protective immune function. The potential of fibrin to limit bacterial infection and disease has been countered by numerous bacterial species evolving and maintaining virulence factors that engage hemostatic system components within vertebrate hosts. Bacterial factors have been isolated that simply bind fibrinogen or fibrin, promote fibrin polymer formation, or promote fibrin dissolution. Staphylococcus aureus is an opportunistic gram-positive bacterium, the causative agent of a wide range of human infectious diseases, and a prime example of a pathogen exquisitely sensitive to host fibrinogen. Indeed, current data suggest fibrinogen serves as a context-dependent determinant of host defense or pathogen virulence in Staphylococcus infection whose ultimate contribution is dictated by the expression of S. aureus virulence factors, the path of infection, and the tissue microenvironment. PMID:27056151

Paroxysmal Sympathetic Hyperactivity in Critically Ill Children with Encephalitis and Meningoencephalitis.

PubMed

Farias-Moeller, Raquel; Carpenter, Jessica L; Dean, Nathan; Wells, Elizabeth M

2015-12-01

Autonomic dysfunction in pediatric patients with acquired brain injury is often encountered and greatly understudied. We sought to identify the incidence of Paroxysmal Sympathetic Hyperactivity (PSH) in critically ill pediatric patients with meningoencephalitis and encephalitis, associated risk factors and influence on outcome. Children admitted to the pediatric intensive care unit (PICU) with a diagnosis of meningoencephalitis and/or encephalitis were identified from a single institution Neurocritical Care database. The patients were stratified as having a bacterial or non-bacterial cause of their meningoencephalitis/encephalitis. Data from their hospitalization was supplemented with a retrospective review of the electronic medical record. PSH was defined as episodic lability in heart rate and/or blood pressure, hyperthermia, diaphoresis, dystonic posturing, tachypnea and/or agitation without any other cause. Statistical analysis was performed using t-test and chi-squared to compare outcomes and risk factors between patients with PSH and without. PSH was found in 41 % of children studied. Subgroup analysis revealed patients with non-bacterial encephalitis were more likely to experience PSH (51 %) as compared to those with bacterial causes (27 %). Fever and/or seizures on presentation and female gender were associated with higher occurrence of PSH but only in the non-bacterial etiology group. There were trends toward increased length of PICU and overall hospital stay for patients with PSH. PSH was found in a high percentage of our patients with significant variation in risk factors and outcome noted between patients with bacterial and nonbacterial causes of their meningoencephalitis/encephalitis.

Host Genetic and Environmental Effects on Mouse Cecum Microbiota

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, James H; Foster, Carmen M; Vishnivetskaya, Tatiana A

2012-01-01

The mammalian gut harbors complex and variable microbial communities, across both host phylogenetic space and conspecific individuals. A synergy of host genetic and environmental factors shape these communities and account for their variability, but their individual contributions and the selective pressures involved are still not well understood. We employed barcoded pyrosequencing of V1-2 and V4 regions of bacterial small subunit ribosomal RNA genes to characterize the effects of host genetics and environment on cecum assemblages in 10 genetically distinct, inbred mouse strains. Eight of these strains are the foundation of the Collaborative Cross (CC), a panel of mice derived frommore » a genetically diverse set of inbred founder strains, designed specifically for complex trait analysis. Diversity of gut microbiota was characterized by complementing phylogenetic and distance-based, sequence-clustering approaches. Significant correlations were found between the mouse strains and their gut microbiota, reflected by distinct bacterial communities. Cohabitation and litter had a reduced, although detectable effect, and the microbiota response to these factors varied by strain. We identified bacterial phylotypes that appear to be discriminative and strain-specific to each mouse line used. Cohabitation of different strains of mice revealed an interaction of host genetic and environmental factors in shaping gut bacterial consortia, in which bacterial communities became more similar but retained strain specificity. This study provides a baseline analysis of intestinal bacterial communities in the eight CC progenitor strains and will be linked to integrated host genotype, phenotype and microbiota research on the resulting CC panel.« less

Immunoproteomic identification of immunogenic proteins in Cronobacter sakazakii strain BAA-894.

PubMed

Wang, Jian; Du, Xin-Jun; Lu, Xiao-Nan; Wang, Shuo

2013-03-01

Cronobacter spp. are emerging opportunistic pathogens. Cronobacter sakazakii is considered as the predominant species in all infections. So far, our understanding of the species' immunogens and potential virulence factors of Cronobacter spp. remains limited. In this study, an immunoproteomic approach was used to investigate soluble and insoluble proteins from the genome-sequenced strain C. sakazakii ATCC BAA-894. Proteins were separated using two-dimensional electrophoresis, detected by Western blotting with polyclonal antibodies of C. sakazakii BAA-894, and identified using tandem mass spectrometry (MALDI-MS and MALDI-MS/MS, MS/MSMS). A total of 11 immunoreactive proteins were initially identified in C. sakazakii BAA-894, including two outer membrane proteins, four periplasmic proteins, and five cytoplasmic proteins. In silico functional analysis of the 11 identified proteins indicated three proteins that were initially described as immunogens of pathogenic bacteria. For the remaining eight proteins, one protein was categorized as a potential virulence factor involved in protection against reactive oxygen species, and seven proteins were considered to play potential roles in adhesion, invasion, and biofilm formation. To our knowledge, this is the first time that immunogenic proteins of C. sakazakii BAA-894 have been identified as immunogens and potential virulence factors by an immunoproteomics approach. Future studies should investigate the roles of these proteins in bacterial pathogenesis and modulation of host immune responses during infection to identify their potential as molecular therapeutic targets.

Orbital abscess bacterial isolates and in vitro antimicrobial susceptibility patterns in dogs and cats.

PubMed

Wang, Annie L; Ledbetter, Eric C; Kern, Thomas J

2009-01-01

To determine bacterial populations, in vitro antimicrobial susceptibility patterns, and sources of microorganisms for dogs and cats with orbital abscess. In total, 34 dogs and 7 cats with orbital abscess participated in the study. Medical records of dogs and cats with a clinical diagnosis of orbital abscess, confirmed by cytologic or histopathologic evaluation of orbital specimens, were reviewed from the years 1990 to 2007. Animal signalment, presumptive source of microorganisms and mechanism of orbital introduction, bacterial isolates, and aerobic bacterial in vitro antimicrobial susceptibility test results were recorded. Percentages of susceptible aerobic bacterial isolates were compared among antimicrobials. Twenty dogs and five cats had positive culture results. The most frequent bacterial genera isolated from dogs were Staphylococcus, Escherichia, Bacteroides, Clostridium and Pasteurella. The most frequent bacterial genera isolated from cats were Pasteurella and Bacteroides. Aerobic bacterial isolates from dogs had the highest percentage of susceptibility to amikacin, ceftiofur, gentamicin, imipenem, ticarcillin and trimethoprim-sulfamethoxazole. Aerobic bacterial isolates from dogs had the lowest percentage of susceptibility to ampicillin, clindamycin, erythromycin and penicillin. Antimicrobial resistance was uncommon among feline aerobic bacterial isolates. The most commonly identified routes of orbital bacteria introduction were extension from adjacent anatomical structures, penetrating exogenous trauma, and foreign bodies. Mixed aerobic and anaerobic bacterial infections of the orbit occur commonly in dogs and cats. On the basis of aerobic and anaerobic bacterial isolates and in vitro susceptibility testing of aerobic bacterial isolates, cephalosporins, extended-spectrum penicillins, potentiated-penicillins and carbapenems are recommended for initial antimicrobial therapy of orbital abscess in dogs and cats.

Empirical treatment of bacterial keratitis: an international survey of corneal specialists.

PubMed

Austin, Ariana; Schallhorn, Julie; Geske, Mike; Mannis, Mark; Lietman, Tom; Rose-Nussbaumer, Jennifer

2017-08-01

New antibiotic agents and changing susceptibility patterns may have changed the empirical treatment of bacterial keratitis. Our objective in this study was to survey cornea specialists' practice patterns in the initial treatment of bacterial ulcers. This study consisted of a short online survey emailed to members of the Cornea Society listserv for an international sample of cornea specialists. Data collection began July 2014 and ended October 2014. A total of 1009 surveys were emailed, and we received 140 (14%) responses. The majority of US clinicians surveyed (n=83, 80%) chose fortified antibiotics empirically, with 55% (n=57) selecting fortified vancomycin and 16% (n=17) using fluoroquinolone alone. International respondents were twice as likely to use fluoroquinolone monotherapy (31%, n=11, p=0.07) and less likely to use fortified vancomycin (33%, n=12, p=0.03). Forty-five per cent (n=46) of US respondents reported that their initial antibiotic choice covered methicillin-resistant Staphylococcus aureus , compared with 22% (n=8) of international respondents (p<0.01). Overall, respondents who were concerned about availability of antibiotics and toxicity were 20.86 (p<0.001) and 7.48 (p<0.001) times more likely to choose fluoroquinolone monotherapy, respectively. If respondents' primary considerations were broad spectrum coverage or antibiotic resistance they had 7.10 (p<0.001) and 12.51 (p<0.001) times the odds of using fortified vancomycin, respectively. Practice patterns for the initial treatment of bacterial keratitis vary with clinicians in the USA being more likely to use fortified antibiotics versus fluoroquinolone monotherapy and more concerned with resistant organisms than their international peers.

Measurement of the incorporation rates of four amino acids into proteins for estimating bacterial production.

PubMed

Servais, P

1995-03-01

In aquatic ecosystems, [(3)H]thymidine incorporation into bacterial DNA and [(3)H]leucine incorporation into proteins are usually used to estimate bacterial production. The incorporation rates of four amino acids (leucine, tyrosine, lysine, alanine) into proteins of bacteria were measured in parallel on natural freshwater samples from the basin of the river Meuse (Belgium). Comparison of the incorporation into proteins and into the total macromolecular fraction showed that these different amino acids were incorporated at more than 90% into proteins. From incorporation measurements at four subsaturated concentrations (range, 2-77 nm), the maximum incorporation rates were determined. Strong correlations (r > 0.91 for all the calculated correlations) were found between the maximum incorporation rates of the different tested amino acids over a range of two orders of magnitude of bacterial activity. Bacterial production estimates were calculated using theoretical and experimental conversion factors. The productions calculated from the incorporation rates of the four amino acids were in good concordance, especially when the experimental conversion factors were used (slope range, 0.91-1.11, and r > 0.91). This study suggests that the incorporation of various amino acids into proteins can be used to estimate bacterial production.

Pilot- and bench-scale testing of faecal indicator bacteria survival in marine beach sand near point sources

USGS Publications Warehouse

Mika, K.B.; Imamura, G.; Chang, C.; Conway, V.; Fernandez, G.; Griffith, J.F.; Kampalath, R.A.; Lee, C.M.; Lin, C.-C.; Moreno, R.; Thompson, S.; Whitman, R.L.; Jay, J.A.

2009-01-01

Aim: Factors affecting faecal indicator bacteria (FIB) and pathogen survival/persistence in sand remain largely unstudied. This work elucidates how biological and physical factors affect die-off in beach sand following sewage spills. Methods and Results: Solar disinfection with mechanical mixing was pilot-tested as a disinfection procedure after a large sewage spill in Los Angeles. Effects of solar exposure, mechanical mixing, predation and/or competition, season, and moisture were tested at bench scale. First-order decay constants for Escherichia coli ranged between -0??23 and -1??02 per day, and for enterococci between -0??5 and -1??0 per day. Desiccation was a dominant factor for E. coli but not enterococci inactivation. Effects of season were investigated through a comparison of experimental results from winter, spring, and fall. Conclusions: Moisture was the dominant factor controlling E. coli inactivation kinetics. Initial microbial community and sand temperature were also important factors. Mechanical mixing, common in beach grooming, did not consistently reduce bacterial levels. Significance and Impact of the Study: Inactivation rates are mainly dependent on moisture and high sand temperature. Chlorination was an effective disinfection treatment in sand microcosms inoculated with raw influent. ?? 2009 The Society for Applied Microbiology.

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape

PubMed Central

Constancias, Florentin; Saby, Nicolas P A; Terrat, Sébastien; Dequiedt, Samuel; Horrigue, Wallid; Nowak, Virginie; Guillemin, Jean-Philippe; Biju-Duval, Luc; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

2015-01-01

Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km2, by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships) according to phyla. Altogether, this study provided valuable clues about the ecological behavior of soil bacterial and archaeal taxa at an agricultural landscape scale and could be useful for developing sustainable strategies of land management. PMID:25922908

The Population Biology of Bacterial Plasmids: A PRIORI Conditions for the Existence of Conjugationally Transmitted Factors

PubMed Central

Stewart, Frank M.; Levin, Bruce R.

1977-01-01

A mathematical model for the population dynamics of conjugationally transmitted plasmids in bacterial populations is presented and its properties analyzed. Consideration is given to nonbacteriocinogenic factors that are incapable of incorporation into the chromosome of their host cells, and to bacterial populations maintained in either continuous (chemostat) or discrete (serial transfer) culture. The conditions for the establishment and maintenance of these infectious extrachromosomal elements and equilibrium frequencies of cells carrying them are presented for different values of the biological parameters: population growth functions, conjugational transfer and segregation rate constants. With these parameters in a biologically realistic range, the theory predicts a broad set of physical conditions, resource concentrations and dilution rates, where conjugationally transmitted plasmids can become established and where cells carrying them will maintain high frequencies in bacterial populations. This can occur even when plasmid-bearing cells are much less fit (i.e., have substantially lower growth rates) than cells free of these factors. The implications of these results and the reality and limitations of the model are discussed and the values of its parameters in natural populations speculated upon. PMID:17248761

Preclinical Investigations Reveal the Broad-Spectrum Neutralizing Activity of Peptide Pep19-2.5 on Bacterial Pathogenicity Factors

PubMed Central

Sánchez-Gómez, Susana; Martinez de Tejada, Guillermo; Dömming, Sabine; Brandenburg, Julius; Kaconis, Yani; Hornef, Mathias; Dupont, Aline; Marwitz, Sebastian; Goldmann, Torsten; Ernst, Martin; Gutsmann, Thomas; Schürholz, Tobias

2013-01-01

Bacterial infections are known to cause severe health-threatening conditions, including sepsis. All attempts to get this disease under control failed in the past, and especially in times of increasing antibiotic resistance, this leads to one of the most urgent medical challenges of our times. We designed a peptide to bind with high affinity to endotoxins, one of the most potent pathogenicity factors involved in triggering sepsis. The peptide Pep19-2.5 reveals high endotoxin neutralization efficiency in vitro, and here, we demonstrate its antiseptic/anti-inflammatory effects in vivo in the mouse models of endotoxemia, bacteremia, and cecal ligation and puncture, as well as in an ex vivo model of human tissue. Furthermore, we show that Pep19-2.5 can bind and neutralize not only endotoxins but also other bacterial pathogenicity factors, such as those from the Gram-positive bacterium Staphylococcus aureus. This broad neutralization efficiency and the additive action of the peptide with common antibiotics makes it an exceptionally appropriate drug candidate against bacterial sepsis and also offers multiple other medication opportunities. PMID:23318793

Tailoring the Immune Response via Customization of Pathogen Gene Expression.

PubMed

Runco, Lisa M; Stauft, Charles B; Coleman, J Robert

2014-01-01

The majority of studies focused on the construction and reengineering of bacterial pathogens have mainly relied on the knocking out of virulence factors or deletion/mutation of amino acid residues to then observe the microbe's phenotype and the resulting effect on the host immune response. These knockout bacterial strains have also been proposed as vaccines to combat bacterial disease. Theoretically, knockout strains would be unable to cause disease since their virulence factors have been removed, yet they could induce a protective memory response. While knockout strains have been valuable tools to discern the role of virulence factors in host immunity and bacterial pathogenesis, they have been unable to yield clinically relevant vaccines. The advent of synthetic biology and enhanced user-directed gene customization has altered this binary process of knockout, followed by observation. Recent studies have shown that a researcher can now tailor and customize a given microbe's gene expression to produce a desired immune response. In this commentary, we highlight these studies as a new avenue for controlling the inflammatory response as well as vaccine development.

Tailoring the Immune Response via Customization of Pathogen Gene Expression

PubMed Central

Runco, Lisa M.; Stauft, Charles B.

2014-01-01

The majority of studies focused on the construction and reengineering of bacterial pathogens have mainly relied on the knocking out of virulence factors or deletion/mutation of amino acid residues to then observe the microbe's phenotype and the resulting effect on the host immune response. These knockout bacterial strains have also been proposed as vaccines to combat bacterial disease. Theoretically, knockout strains would be unable to cause disease since their virulence factors have been removed, yet they could induce a protective memory response. While knockout strains have been valuable tools to discern the role of virulence factors in host immunity and bacterial pathogenesis, they have been unable to yield clinically relevant vaccines. The advent of synthetic biology and enhanced user-directed gene customization has altered this binary process of knockout, followed by observation. Recent studies have shown that a researcher can now tailor and customize a given microbe's gene expression to produce a desired immune response. In this commentary, we highlight these studies as a new avenue for controlling the inflammatory response as well as vaccine development. PMID:24719769

Solubility and bacterial sealing ability of MTA and root-end filling materials.

PubMed

Espir, Camila Galletti; Guerreiro-Tanomaru, Juliane Maria; Spin-Neto, Rubens; Chávez-Andrade, Gisselle Moraima; Berbert, Fabio Luiz Camargo Villela; Tanomaru-Filho, Mario

2016-04-01

Objective To evaluate solubility and sealing ability of Mineral Trioxide Aggregate (MTA) and root-end filling materials. Material and Methods The materials evaluated were: MTA, Calcium Silicate Cement with zirconium oxide (CSC/ZrO2), and zinc oxide/eugenol (ZOE). Solubility test was performed according to ANSI/ADA. The difference between initial and final mass of the materials was analyzed after immersion in distilled water for 7 and 30 days. Retrograde cavities in human teeth with single straight root canal were performed by using ultrasonic tip CVD 9.5107-8. The cavities were filled with the evaluated materials to evaluate sealing ability using the bacterial leakage test with Enterococcus faecalis. Bacterial leakage was evaluated every 24 hours for six weeks observing the turbidity of Brain Heart infusion (BHI) medium in contact with root apex. Data were submitted to ANOVA followed by Tukey tests (solubility), and Kruskal-Wallis and Dunn tests (sealing ability) at a 5% significance level. Results For the 7-day period, ZOE presented highest solubility when compared with the other groups (p<0.05). For the 30-day period, no difference was observed among the materials. Lower bacterial leakage was observed for MTA and CSC/ZrO2, and both presented better results than ZOE (p<0.05). Conclusion MTA and CSC/ZrO2 presented better bacterial sealing capacity, which may be related to lower initial solubility observed for these materials in relation to ZOE.

Influence of environmental variation on the bacterioplankton community and its loss to viral lysis in the Curonian Lagoon

NASA Astrophysics Data System (ADS)

Šulčius, Sigitas; Reunamo, Anna; Paškauskas, Ričardas; Leskinen, Piia

2018-05-01

Coastal lagoons are continuously exposed to strong environmental gradients that determine the distribution and trophic interactions of microbial communities. Therefore, in this study we assessed whether and how environmental changes influence the bacterial community and its vulnerability to viral infection and lysis along the major environmental gradient in the Curonian Lagoon. We found significant differences in bacterial community profiles, their richness and evenness between the riverine, freshwater southern part and the Baltic Sea water intrusion-influenced northern part of the lagoon, suggesting strong environmental control of the structure of bacterial communities. Viruses were found to be play an important role in bacterial mortality in the Curonian Lagoon, being responsible for the removal of 20-50% of the bacterial standing stock. We observed differences in virioplankton decay rates and virus burst sizes between the northern and southern parts of the lagoon. However, no relationships were found between viral activity and bacterial communities within the lagoon ecosystem. The frequency of infected cells and virus-mediated bacterial mortality (VMBM) remained constant among the sampling sites irrespective of differences in bacteria community assemblages and environmental conditions. The results indicate that factors determining changes in bacterial diversity are different from the factors limiting their vulnerability to viral infection and lysis. This study also suggests that under changing environmental conditions, virus-bacteria interactions are more stable than the interacting viral and bacterial communities themselves. These findings are important for understanding the functioning of the coastal ecosystems under the rapidly changing local (spatial and temporal) and global (e.g. eutrophication, climate change) conditions.

Distinct bacterial communities across a gradient of vegetation from a preserved Brazilian Cerrado.

PubMed

de Araujo, Ademir Sergio Ferreira; Bezerra, Walderly Melgaço; Dos Santos, Vilma Maria; Rocha, Sandra Mara Barbosa; Carvalho, Nilza da Silva; de Lyra, Maria do Carmo Catanho Pereira; Figueiredo, Marcia do Vale Barreto; de Almeida Lopes, Ângela Celis; Melo, Vania Maria Maciel

2017-04-01

The Cerrado biome in the Sete Cidades National Park, an Ecological Reserve in Northeastern Brazil, has conserved its native biodiversity and presents a variety of plants found in other savannas in Brazil. Despite this finding the soil microbial diversity and community structure are poorly understood. Therefore, we described soil bacterial diversity and distribution along a savanna vegetation gradient taking into account the prevailing environmental factors. The bacterial composition was retrieved by sequencing a fragment of the 16S ribosomal RNA gene. The bacterial operational taxonomic units (OTUs) were assigned to 37 different phyla, 96 classes, and 83 genera. At the phylum level, a core comprised by Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, Verrucomicrobia and Planctomycetes, was detected in all areas of Cerrado. 'Cerrado stricto sensu' and 'Cerradao' share more similarities between edaphic properties and vegetation and also present more similar bacterial communities, while 'Floresta decidual' and 'Campo graminoide' show the largest environmental differences and also more distinct bacterial communities. Proteobacteria (26%), Acidobacteria (21%) and Actinobacteria (21%) were the most abundant phyla within the four areas. All the samples present similar bacteria richness (alpha diversity) and the observed differences among them (beta diversity) were more related to the abundance of specific taxon OTUs compared to their presence or absence. Total organic C, N and P are the main abiotic factors structuring the bacterial communities. In summary, our findings show the bacterial community structure was clearly different across the Cerrado gradient, but that these environments share a bacterial phylum-core comprising Proteobacteria, Acidobacteria, Actinobacteria, Verrucomicrobia and Planctomycetes with other Brazilian savannas.

Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges.

PubMed

Prest, Emmanuelle I; Hammes, Frederik; van Loosdrecht, Mark C M; Vrouwenvelder, Johannes S

2016-01-01

Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order to maintain good drinking water microbial quality up to consumer's tap. A new definition and methodological approach for biological stability is proposed.

Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges

PubMed Central

Prest, Emmanuelle I.; Hammes, Frederik; van Loosdrecht, Mark C. M.; Vrouwenvelder, Johannes S.

2016-01-01

Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order to maintain good drinking water microbial quality up to consumer’s tap. A new definition and methodological approach for biological stability is proposed. PMID:26870010

Bacterial Community Dynamics in Full-Scale Activated Sludge Bioreactors: Operational and Ecological Factors Driving Community Assembly and Performance

PubMed Central

Valentín-Vargas, Alexis; Toro-Labrador, Gladys; Massol-Deyá, Arturo A.

2012-01-01

The assembling of bacterial communities in conventional activated sludge (CAS) bioreactors was thought, until recently, to be chaotic and mostly unpredictable. Studies done over the last decade have shown that specific, and often, predictable random and non-random factors could be responsible for that process. These studies have also motivated a “structure–function” paradigm that is yet to be resolved. Thus, elucidating the factors that affect community assembly in the bioreactors is necessary for predicting fluctuations in community structure and function. For this study activated sludge samples were collected during a one-year period from two geographically distant CAS bioreactors of different size. Combining community fingerprinting analysis and operational parameters data with a robust statistical analysis, we aimed to identify relevant links between system performance and bacterial community diversity and dynamics. In addition to revealing a significant β-diversity between the bioreactors’ communities, results showed that the largest bioreactor had a less dynamic but more efficient and diverse bacterial community throughout the study. The statistical analysis also suggests that deterministic factors, as opposed to stochastic factors, may have a bigger impact on the community structure in the largest bioreactor. Furthermore, the community seems to rely mainly on mechanisms of resistance and functional redundancy to maintain functional stability. We suggest that the ecological theories behind the Island Biogeography model and the species-area relationship were appropriate to predict the assembly of bacterial communities in these CAS bioreactors. These results are of great importance for engineers and ecologists as they reveal critical aspects of CAS systems that could be applied towards improving bioreactor design and operation. PMID:22880016

Development and validation of a whole-cell inhibition assay for bacterial methionine aminopeptidase by surface-enhanced laser desorption ionization-time of flight mass spectrometry.

PubMed

Greis, Kenneth D; Zhou, Songtao; Siehnel, Richard; Klanke, Chuck; Curnow, Alan; Howard, Jeremy; Layh-Schmitt, Gerlinde

2005-08-01

Bacterial methionine aminopeptidase (MAP) is a protease that removes methionine from the N termini of newly synthesized bacterial proteins after the peptide deformylase enzyme cleaves the formyl group from the initiator formylmethionine. MAP is an essential bacterial gene product and thus represents a potential target for therapeutic intervention. A fundamental challenge in the antibacterial drug discovery field is demonstrating conclusively that compounds with in vitro enzyme inhibition activity produce the desired antibacterial effect by interfering with the same target in whole bacterial cells. One way to address the activity of inhibitor compounds is by profiling cellular biomarkers in whole bacterial cells using compounds that are known inhibitors of a particular target. However, in the case of MAP, no specific inhibitors were available for such studies. Instead, a genetically attenuated MAP strain was generated in which MAP expression was placed under the control of an inducible arabinose promoter. Thus, MAP inhibition in whole cells could be mimicked by growth in the absence of arabinose. This genetically attenuated strain was used as a benchmark for MAP inhibition by profiling whole-cell lysates for unprocessed proteins using surface-enhanced laser desorption ionization-time of flight mass spectrometry (MS). Eight proteins between 4 and 14 kDa were confirmed as being unprocessed and containing the initiator methionine by adding back purified MAP to the preparations prior to MS analysis. Upon establishing these unprocessed proteins as biomarkers for MAP inhibition, the assay was used to screen small-molecule chemical inhibitors of purified MAP for whole-cell activity. Fifteen compound classes yielded three classes of compound with whole-cell activity for further optimization by chemical expansion. This report presents the development, validation, and implementation of a whole-cell inhibition assay for MAP.

Reproducible Biofilm Cultivation of Chemostat-Grown Escherichia coli and Investigation of Bacterial Adhesion on Biomaterials Using a Non-Constant-Depth Film Fermenter

PubMed Central

Lüdecke, Claudia; Jandt, Klaus D.; Siegismund, Daniel; Kujau, Marian J.; Zang, Emerson; Rettenmayr, Markus; Bossert, Jörg; Roth, Martin

2014-01-01

Biomaterials-associated infections are primarily initiated by the adhesion of microorganisms on the biomaterial surfaces and subsequent biofilm formation. Understanding the fundamental microbial adhesion mechanisms and biofilm development is crucial for developing strategies to prevent such infections. Suitable in vitro systems for biofilm cultivation and bacterial adhesion at controllable, constant and reproducible conditions are indispensable. This study aimed (i) to modify the previously described constant-depth film fermenter for the reproducible cultivation of biofilms at non-depth-restricted, constant and low shear conditions and (ii) to use this system to elucidate bacterial adhesion kinetics on different biomaterials, focusing on biomaterials surface nanoroughness and hydrophobicity. Chemostat-grown Escherichia coli were used for biofilm cultivation on titanium oxide and investigating bacterial adhesion over time on titanium oxide, poly(styrene), poly(tetrafluoroethylene) and glass. Using chemostat-grown microbial cells (single-species continuous culture) minimized variations between the biofilms cultivated during different experimental runs. Bacterial adhesion on biomaterials comprised an initial lag-phase I followed by a fast adhesion phase II and a phase of saturation III. With increasing biomaterials surface nanoroughness and increasing hydrophobicity, adhesion rates increased during phases I and II. The influence of materials surface hydrophobicity seemed to exceed that of nanoroughness during the lag-phase I, whereas it was vice versa during adhesion phase II. This study introduces the non-constant-depth film fermenter in combination with a chemostat culture to allow for a controlled approach to reproducibly cultivate biofilms and to investigate bacterial adhesion kinetics at constant and low shear conditions. The findings will support developing and adequate testing of biomaterials surface modifications eventually preventing biomaterial-associated infections. PMID:24404192

Melanization and Pathogenicity in the Insect, Tenebrio molitor, and the Crustacean, Pacifastacus leniusculus, by Aeromonas hydrophila AH-3

PubMed Central

Noonin, Chadanat; Jiravanichpaisal, Pikul; Söderhäll, Irene; Merino, Susana; Tomás, Juan M.; Söderhäll, Kenneth

2010-01-01

Aeromonas hydrophila is the most common Aeromonas species causing infections in human and other animals such as amphibians, reptiles, fish and crustaceans. Pathogenesis of Aeromonas species have been reported to be associated with virulence factors such as lipopolysaccharides (LPS), bacterial toxins, bacterial secretion systems, flagella, and other surface molecules. Several mutant strains of A. hydrophila AH-3 were initially used to study their virulence in two animal species, Pacifastacus leniusculus (crayfish) and Tenebrio molitor larvae (mealworm). The AH-3 strains used in this study have mutations in genes involving the synthesis of flagella, LPS structures, secretion systems, and some other factors, which have been reported to be involved in A. hydrophila pathogenicity. Our study shows that the LPS (O-antigen and external core) is the most determinant A. hydrophila AH-3 virulence factor in both animals. Furthermore, we studied the immune responses of these hosts to infection of virulent or non-virulent strains of A. hydrophila AH-3. The AH-3 wild type (WT) containing the complete LPS core is highly virulent and this bacterium strongly stimulated the prophenoloxidase activating system resulting in melanization in both crayfish and mealworm. In contrast, the ΔwaaE mutant which has LPS without O-antigen and external core was non-virulent and lost ability to stimulate this system and melanization in these two animals. The high phenoloxidase activity found in WT infected crayfish appears to result from a low expression of pacifastin, a prophenoloxidase activating enzyme inhibitor, and this gene expression was not changed in the ΔwaaE mutant infected animal and consequently phenoloxidase activity was not altered as compared to non-infected animals. Therefore we show that the virulence factors of A. hydrophila are the same regardless whether an insect or a crustacean is infected and the O-antigen and external core is essential for activation of the proPO system and as virulence factors for this bacterium. PMID:21206752

Bacterial pneumonia as an influenza complication.

PubMed

Martin-Loeches, Ignacio; van Someren Gréve, Frank; Schultz, Marcus J

2017-04-01

The pathogenesis and impact of coinfection, in particular bacterial coinfection, in influenza are incompletely understood. This review summarizes results from studies on bacterial coinfection in the recent pandemic influenza outbreak. Systemic immune mechanisms play a key role in the development of coinfection based on the complexity of the interaction of the host and the viral and bacterial pathogens. Several studies were performed to determine the point prevalence of bacterial coinfection in influenza. Coinfection in influenza is frequent in critically ill patients with Streptococcus pneumoniae being the most frequent bacterial pathogen and higher rates of potentially resistant pathogens over the years. Bacterial pneumonia is certainly an influenza complication. The recent epidemiology findings have helped to partially resolve the contribution of different pathogens. Immunosuppression is a risk factor for bacterial coinfection in influenza, and the epidemiology of coinfection has changed over the years during the last influenza pandemic, and these recent findings should be taken into account during present outbreaks.

A uniform bacterial growth potential assay for different water types.

PubMed

Farhat, Nadia; Hammes, Frederik; Prest, Emmanuelle; Vrouwenvelder, Johannes

2018-06-06

The bacterial growth potential is important to understand and manage bacterial regrowth-related water quality concerns. Bacterial growth potential depends on growth promoting/limiting compounds, therefore, nutrient availability is the key factor governing bacterial growth potential. Selecting proper tools for bacterial growth measurement is essential for routine implementation of the growth potential measurement. This study proposes a growth potential assay that is universal and can be used for different water types and soil extract without restrictions of pure culture or cultivability of the bacterial strain. The proposed assay measures the sample bacterial growth potential by using the indigenous community as inocula. Flow cytometry (FCM) and adenosine tri-phosphate (ATP) were used to evaluate the growth potential of six different microbial communities indigenous to the sample being analyzed, with increasing carbon concentrations. Bottled mineral water, non-chlorinated tap water, seawater, river water, wastewater effluent and a soil organic carbon extract were analyzed. Results showed that indigenous bacterial communities followed normal batch growth kinetics when grown on naturally present organic carbon. Indigenous bacterial growth could detect spiked organic carbon concentrations as low as 10 μg/L. The indigenous community in all samples responded proportionally to the increase in acetate-carbon and proportional growth could be measured with both FCM and ATP. Bacterial growth was proportional to the carbon concentration but not the same proportion factor for the different water samples tested. The effect of inoculating the same water with different indigenous microbial communities on the growth potential was also examined. The FCM results showed that the highest increase in total bacterial cell concentration was obtained with bacteria indigenous to the water sample. The growth potential assay using indigenous bacterial community revealed consistent results of bacterial growth in all the different samples tested and therefore providing a fast, more stable, and accurate approach for monitoring the biological stability of waters compared to the previously developed assays. The growth potential assay can be used to aid in detecting growth limitations by compounds other than organic carbon. Copyright © 2018 Elsevier Ltd. All rights reserved.

[Identification of hexavalent chromium reducing bacteria Cr4-1 and optimization of its reduction conditions].

PubMed

Zhu, Peilei; Jiao, Shilin; Jiang, Pu; Zeng, Xin; Luo, Qifang; Wang, Lin

2015-03-01

To identify the hexavalent chromium reduction Cr4-1, and to study the better conditions of the bacterial growth and its Cr(VI) reduction. The physiological and biochemical methods and 16s rDNA sequencing were used for identification of bacteria Cr4-1. The influence of temperature, pH, initial Cr (VI) concentration and shaking speed on bacterial growth and Cr (VI) reduction were studied. Mass balance analysis was used to analyze the end products of the reduction reaction. A Cr(VI) reducing bacteria Cr4-1, screened from acclimated activated sludge, was identified as Bacillus cereus. The appropriate conditions of bacterial growth was 25 °C, pH 7 to 8, shaking speed 150 r/min, while the suitable conditions for Cr(VI) reduction was 35 °C, pH 8 to 9. When the initial Cr(VI) concentration increased from 20 mg/L to 60 mg/L, the reduction rate decreased gradually. Under the suitable reducing conditions, when the initial concentration of Cr (VI) was 30 mg/L, the reduction rate could up to 100% in 9 h. The end product was soluble trivalent chromium. Strain Cr4-1 had a good effect on Cr (VI) reduction and the final product was soluble trivalent chromium.

Protozoan, Bacterial, and Volatile Fatty Acid Changes Associated with Feeding Tylosin

PubMed Central

Satapathy, N.; Purser, D. B.

1967-01-01

Tylosin was fed to two of six wethers for 79 days, to a second two for only 28 days, and not at all to a third pair (controls). The addition of tylosin to the daily feed resulted in a rapid twofold increase in protozoal concentration and a change in the composition or characteristics, or both, of the bacterial population. The results indicate that the bacterial population was modified to the extent of about 80%. Total acid concentrations were initially depressed but appeared to be greater than those in control animals at the termination of the experiment. Deletion of tylosin from the ration resulted in a rapid decrease in protozoal concentrations, whereas changes in the bacterial population did not occur for a further 30 days. PMID:16349756

The TLR2 Antagonist Staphylococcal Superantigen-Like Protein 3 Acts as a Virulence Factor to Promote Bacterial Pathogenicity in vivo.

PubMed

Koymans, Kirsten J; Goldmann, Oliver; Karlsson, Christofer A Q; Sital, Wiedjai; Thänert, Robert; Bisschop, Adinda; Vrieling, Manouk; Malmström, Johan; van Kessel, Kok P M; de Haas, Carla J C; van Strijp, Jos A G; Medina, Eva

2017-01-01

Toll-like receptor (TLR) signaling is important in the initiation of immune responses and subsequent instigation of adaptive immunity. TLR2 recognizes bacterial lipoproteins and plays a central role in the host defense against bacterial infections, including those caused by Staphylococcus aureus. Many studies have demonstrated the importance of TLR2 in murine S. aureus infection. S. aureus evades TLR2 activation by secreting two proteins, staphylococcal superantigen-like protein 3 (SSL3) and 4 (SSL4). In this study, we demonstrate that antibodies against SSL3 and SSL4 are found in healthy individuals, indicating that humans are exposed to these proteins during S. aureus colonization or infection. To investigate the TLR2-antagonistic properties of SSL3 and SSL4, we compared the infection with wild-type and SSL3/4 knockout S. aureus strains in an intravenous murine infection model. Direct evaluation of the contribution of SSL3/4 to infection pathogenesis was hindered by the fact that the SSLs were not expressed in the murine system. To circumvent this limitation, an SSL3-overproducing strain (pLukM-SSL3) was generated, resulting in constitutive expression of SSL3. pLukM-SSL3 exhibited increased virulence compared to the parental strain in a murine model that was found to be TLR2 dependent. Altogether, these data indicate that SSL3 contributes to S. aureus virulence in vivo. © 2017 S. Karger AG, Basel.

Stability of the rhizosphere and endophytic bacterial communities associated with Arabidopsis thaliana (L.) Heynh under impact of cosmic factors

NASA Astrophysics Data System (ADS)

Kordium, V. A.; Adamchuk-Chala, N. I.; Moshinec, H. V.

The orbital experiment will involve a growing of Arabidopsis plant seed to seed in the presence of a plant probiotic bacteria consortium introduced into the system The purpose of experiment is to characterize microbial community associated with Arabidopsis thaliana and determine how consortium of introduced bacteria along with the endemic plant-associated bacteria influences the plant development reproductive system and seed formation in spaceflight conditions The first study will be an examination of the survival of model bacteria in on the inoculated plant The second complex study is to examine the plant traits in particular the ultrastructure of root statocytes in order to determine whether the plant development proceeds normally under microgravity conditions on background of introduced bacteria and to assess the structural changes occurring in the cotyledons generative organs and seeds The third set of observations will concern studies of the structure of microbial community associated with Arabidopsis plants with traditional and molecular tools The fourth part of the work will be an examination of mobile genetic elements that can play a role in adaptation of bacteria to the spaceflight conditions however they may affect the stability of bacterial endo- and rhizosphere communities The final part of the proposal initiates the study of possible risk of the bacterial consortium use for a plant inoculation in spaceflight conditions An evaluation of this risk will be performed via examination of expression of the Klebsiella

Sulfur diagenesis in marine sediments

NASA Technical Reports Server (NTRS)

Goldhaber, M.

1985-01-01

Bacterial sulfate reduction occurs in all marine sediments that contain organic matter. Aqueous sulfide (HS-, H2S), one of the initial products of bacterial sulfide reduction, is extremely reactive with iron bearing minerals: sulfur is fixed into sediments as iron sulfide (first FeS and then Fe2S2). A working definition is given of sulfur diagenesis in marine sediments. Controls and consequences of sulfate reduction rates in marine sediments are examined.

Antibacterial activity of dilute povidone-iodine solutions used for ocular surface disinfection in dogs.

PubMed

Roberts, S M; Severin, G A; Lavach, J D

1986-06-01

Bacterial cultures of specimens from healthy canine eyelids and ocular surfaces were found to demonstrate bacterial growth in 69.7% (53/76) of the eyes sampled. Organisms most commonly isolated included: Staphylococcus aureus, alpha-hemolytic Streptococcus sp, S epidermidis, and Escherichia coli. Evaluation of dilute povidone-iodine solutions for effectiveness as ocular surface disinfectants was conducted. Bacterial growth initially detected in 32 of 46 eyes was not detected after disinfection with a 2-minute scrub and 2-minute soaking procedure, using 1:2, 1:10, or 1:50 dilutions of a povidone-iodine solution that contained 1% available iodine. The eyelid and ocular surfaces of 16 eyes were disinfected with 1:100 povidone-iodine solution. Bacterial growth initially present in 10 of 16 eyes was present in 1 eye after disinfection and consisted of a single colony of E coli. After eyes were disinfected with 1:10, 1:50, or 1:100 povidone-iodine solutions, there was no evidence of corneal epithelial edema or sloughing. In 15 eyes subjected to disinfection with the 1:2 dilution, one instance of epithelial corneal edema was noticed. A 1:50 dilution of povidone-iodine is recommended as an ocular surface disinfectant for use in presurgical situations.

Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function.

PubMed

Ruiz-González, Clara; Archambault, Esther; Laforest-Lapointe, Isabelle; Del Giorgio, Paul A; Kembel, Steven W; Messier, Christian; Nock, Charles A; Beisner, Beatrix E

2018-06-14

Freshwater bacterioplankton communities are influenced by the inputs of material and bacteria from the surrounding landscape, yet few studies have investigated how different terrestrial inputs affect bacterioplankton. We examined whether the addition of soils collected under various tree species combinations differentially influences lake bacterial communities. Lake water was incubated for 6 days following addition of five different soils. We assessed the taxonomic composition (16S rRNA gene sequencing) and metabolic activity (Biolog Ecoplates) of lake bacteria with and without soil addition, and compared these to initial soil communities. Soil bacterial assemblages showed a strong influence of tree composition, but such community differences were not reflected in the structure of lake communities that developed during the experiment. Bacterial taxa showing the largest abundance increases during incubation were initially present in both lake water and across most soils, and were related to Cytophagales, Burkholderiales and Rhizobiales. No clear metabolic profiles based on inoculum source were found, yet soil-amended communities used 60% more substrate than non-inoculated communities. Overall, we show that terrestrial inputs influence aquatic communities by stimulating the growth and activity of certain ubiquitous taxa distributed across the terrestrial-aquatic continuum, yet different forest soils did not cause predictable changes in lake bacterioplankton assemblages.

Bacterial diversity and composition during rain events with and without Saharan dust influence reaching a high mountain lake in the Alps.

PubMed

Peter, Hannes; Hörtnagl, Paul; Reche, Isabel; Sommaruga, Ruben

2014-12-01

The diversity of airborne microorganisms that potentially reach aquatic ecosystems during rain events is poorly explored. Here, we used a culture-independent approach to characterize bacterial assemblages during rain events with and without Saharan dust influence arriving to a high mountain lake in the Austrian Alps. Bacterial assemblage composition differed significantly between samples with and without Saharan dust influence. Although alpha diversity indices were within the same range in both sample categories, rain events with Atlantic or continental origins were dominated by Betaproteobacteria, whereas those with Saharan dust intrusions were dominated by Gammaproteobacteria. The high diversity and evenness observed in all samples suggests that different sources of bacteria contributed to the airborne assemblage collected at the lake shore. During experiments with bacterial assemblages collected during rain events with Saharan dust influence, cell numbers rapidly increased in sterile lake water from initially ∼3 × 103 cell ml-1 to 3.6-11.1 x105 cells ml-1 within 4-5 days, and initially, rare taxa dominated at the end of the experiment. Our study documents the dispersal of viable bacteria associated to Saharan dust intrusions travelling northwards as far as 47° latitude.

Proteus mirabilis fimbriae- and urease-dependent clusters assemble in an extracellular niche to initiate bladder stone formation

PubMed Central

Schaffer, Jessica N.; Norsworthy, Allison N.; Sun, Tung-Tien

2016-01-01

The catheter-associated uropathogen Proteus mirabilis frequently causes urinary stones, but little has been known about the initial stages of bladder colonization and stone formation. We found that P. mirabilis rapidly invades the bladder urothelium, but generally fails to establish an intracellular niche. Instead, it forms extracellular clusters in the bladder lumen, which form foci of mineral deposition consistent with development of urinary stones. These clusters elicit a robust neutrophil response, and we present evidence of neutrophil extracellular trap generation during experimental urinary tract infection. We identified two virulence factors required for cluster development: urease, which is required for urolithiasis, and mannose-resistant Proteus-like fimbriae. The extracellular cluster formation by P. mirabilis stands in direct contrast to uropathogenic Escherichia coli, which readily formed intracellular bacterial communities but not luminal clusters or urinary stones. We propose that extracellular clusters are a key mechanism of P. mirabilis survival and virulence in the bladder. PMID:27044107

A substantial fraction of phytoplankton-derived DON is resistant to degradation by a metabolically versatile, widely distributed marine bacterium

PubMed Central

Kimmance, Susan; McCormack, Paul

2017-01-01

The capacity of bacteria for degrading dissolved organic nitrogen (DON) and remineralising ammonium is of importance for marine ecosystems, as nitrogen availability frequently limits productivity. Here, we assess the capacity of a widely distributed and metabolically versatile marine bacterium to degrade phytoplankton-derived dissolved organic carbon (DOC) and nitrogen. To achieve this, we lysed exponentially growing diatoms and used the derived dissolved organic matter (DOM) to support an axenic culture of Alteromonas sp.. Bacterial biomass (as particulate carbon and nitrogen) was monitored for 70 days while growth dynamics (cell count), DOM (DOC, DON) and dissolved nutrient concentrations were monitored for up to 208 days. Bacterial biomass increased rapidly within the first 7 days prior to a period of growth/death cycles potentially linked to rapid nutrient recycling. We found that ≈75% of the initial DOC and ≈35% of the initial DON were consumed by bacteria within 40 and 4 days respectively, leaving a significant fraction of DOM resilient to degradation by this bacterial species. The different rates and extents to which DOC and DON were accessed resulted in changes in DOM stoichiometry and the iterative relationship between DOM quality and bacterial growth over time influenced bacterial cell C:N molar ratio. C:N values increased to 10 during the growth phase before decreasing to values of ≈5, indicating a change from relative N-limitation/C-sufficiency to relative C-limitation/N-sufficiency. Consequently, despite its reported metabolic versatility, we demonstrate that Alteromonas sp. was unable to access all phytoplankton derived DOM and that a bacterial community is likely to be required. By making the relatively simple assumption that an experimentally derived fraction of DOM remains resilient to bacterial degradation, these experimental results were corroborated by numerical simulations using a previously published model describing the interaction between DOM and bacteria in marine systems, thus supporting our hypothesis. PMID:28158278

A substantial fraction of phytoplankton-derived DON is resistant to degradation by a metabolically versatile, widely distributed marine bacterium.

PubMed

Polimene, Luca; Clark, Darren; Kimmance, Susan; McCormack, Paul

2017-01-01

The capacity of bacteria for degrading dissolved organic nitrogen (DON) and remineralising ammonium is of importance for marine ecosystems, as nitrogen availability frequently limits productivity. Here, we assess the capacity of a widely distributed and metabolically versatile marine bacterium to degrade phytoplankton-derived dissolved organic carbon (DOC) and nitrogen. To achieve this, we lysed exponentially growing diatoms and used the derived dissolved organic matter (DOM) to support an axenic culture of Alteromonas sp.. Bacterial biomass (as particulate carbon and nitrogen) was monitored for 70 days while growth dynamics (cell count), DOM (DOC, DON) and dissolved nutrient concentrations were monitored for up to 208 days. Bacterial biomass increased rapidly within the first 7 days prior to a period of growth/death cycles potentially linked to rapid nutrient recycling. We found that ≈75% of the initial DOC and ≈35% of the initial DON were consumed by bacteria within 40 and 4 days respectively, leaving a significant fraction of DOM resilient to degradation by this bacterial species. The different rates and extents to which DOC and DON were accessed resulted in changes in DOM stoichiometry and the iterative relationship between DOM quality and bacterial growth over time influenced bacterial cell C:N molar ratio. C:N values increased to 10 during the growth phase before decreasing to values of ≈5, indicating a change from relative N-limitation/C-sufficiency to relative C-limitation/N-sufficiency. Consequently, despite its reported metabolic versatility, we demonstrate that Alteromonas sp. was unable to access all phytoplankton derived DOM and that a bacterial community is likely to be required. By making the relatively simple assumption that an experimentally derived fraction of DOM remains resilient to bacterial degradation, these experimental results were corroborated by numerical simulations using a previously published model describing the interaction between DOM and bacteria in marine systems, thus supporting our hypothesis.

Antibiotic-induced changes in the microbiota disrupt redox dynamics in the gut

PubMed Central

Reese, Aspen T; Cho, Eugenia H; Klitzman, Bruce; Nichols, Scott P; Wisniewski, Natalie A; Villa, Max M; Durand, Heather K; Jiang, Sharon; Midani, Firas S; Nimmagadda, Sai N; O'Connell, Thomas M; Wright, Justin P; Deshusses, Marc A

2018-01-01

How host and microbial factors combine to structure gut microbial communities remains incompletely understood. Redox potential is an important environmental feature affected by both host and microbial actions. We assessed how antibiotics, which can impact host and microbial function, change redox state and how this contributes to post-antibiotic succession. We showed gut redox potential increased within hours of an antibiotic dose in mice. Host and microbial functioning changed under treatment, but shifts in redox potentials could be attributed specifically to bacterial suppression in a host-free ex vivo human gut microbiota model. Redox dynamics were linked to blooms of the bacterial family Enterobacteriaceae. Ecological succession to pre-treatment composition was associated with recovery of gut redox, but also required dispersal from unaffected gut communities. As bacterial competition for electron acceptors can be a key ecological factor structuring gut communities, these results support the potential for manipulating gut microbiota through managing bacterial respiration. PMID:29916366

Bacterial effectors target the plant cell nucleus to subvert host transcription.

PubMed

Canonne, Joanne; Rivas, Susana

2012-02-01

In order to promote virulence, Gram-negative bacteria have evolved the ability to inject so-called type III effector proteins into host cells. The plant cell nucleus appears to be a subcellular compartment repeatedly targeted by bacterial effectors. In agreement with this observation, mounting evidence suggests that manipulation of host transcription is a major strategy developed by bacteria to counteract plant defense responses. It has been suggested that bacterial effectors may adopt at least three alternative, although not mutually exclusive, strategies to subvert host transcription. T3Es may (1) act as transcription factors that directly activate transcription in host cells, (2) affect histone packing and chromatin configuration, and/or (3) target host transcription factor activity. Here, we provide an overview on how all these strategies may lead to host transcriptional re-programming and, as a result, to improved bacterial multiplication inside plant cells.

Antagonism and antibiotic resistance drive a species-specific plant microbiota differentiation in Echinacea spp.

PubMed

Maggini, Valentina; Miceli, Elisangela; Fagorzi, Camilla; Maida, Isabel; Fondi, Marco; Perrin, Elena; Mengoni, Alessio; Bogani, Patrizia; Chiellini, Carolina; Mocali, Stefano; Fabiani, Arturo; Decorosi, Francesca; Giovannetti, Luciana; Firenzuoli, Fabio; Fani, Renato

2018-06-14

A key factor in the study of plant-microbes interaction is the composition of plant microbiota, but little is known about the factors determining its functional and taxonomic organization. Here we investigated the possible forces driving the assemblage of bacterial endophytic and rhizospheric communities, isolated from two congeneric medicinal plants, Echinacea purpurea (L.) Moench and Echinacea angustifolia (DC) Heller, grown in the same soil, by analyzing bacterial strains (isolated from three different compartments, i.e. rhizospheric soil, roots, and stem/leaves) for phenotypic features such as antibiotic resistance, extracellular enzymatic activity, siderophore, and indole 3-acetic acid production, as well as cross antagonistic activities. Data obtained highlighted that bacteria from different plant compartments were characterized by specific antibiotic resistance phenotypes and antibiotic production, suggesting that the bacterial communities themselves could be responsible for structuring their own communities by the production of antimicrobial molecules selecting bacterial adaptive phenotypes for plant tissue colonization.

The effects of commensal bacteria on innate immune responses in the female genital tract

PubMed Central

Mirmonsef, P; Gilbert, D; Zariffard, MR; Hamaker, BR; Kaur, A; Landay, AL; Spear, GT

2013-01-01

The innate and adaptive immune systems are important mechanisms for resistance to pathogens in the female lower genital tract. Lactobacilli at this site help maintain a healthy vagina by producing several factors including lactic acid. Indeed, bacterial vaginosis, a condition in which the genital microbiota is altered, is strongly associated with increased rates of a number of infections including HIV. However, the precise factors that contribute to increased rates of microbial and viral infections in bacterial vaginosis remain to be elucidated. We have studied the effects of bacterial microbiota in the lower genital tract on innate immunity and have found that Toll-like receptor ligands and short chain fatty acids, produced by bacterial microbiota, have dramatic effects on immune function. In this review, we will discuss these results, in addition to some recent articles that we believe will enhance our understanding of how microbes might interact with the immune system. PMID:21143335

[Combination therapy of chronic bacterial prostatitis].

PubMed

Khryanin, A A; Reshetnikov, O V

2016-08-01

The article discusses the possible etiological factors in the development of chronic bacterial prostatitis. The authors presented a comparative long-term analysis of morbidity from non-viral sexually transmitted infections (STIs) in Russia. Against the background of general decline in STIs incidence, a significant percentage of them is made up by urogenital trichomoniasis. The findings substantiated the advantages of combination therapy (ornidazole and ofloxacin) for bacterial urinary tract infections.

Factors affecting the bacterial community composition and heterotrophic production of Columbia River estuarine turbidity maxima.

PubMed

Herfort, Lydie; Crump, Byron C; Fortunato, Caroline S; McCue, Lee Ann; Campbell, Victoria; Simon, Holly M; Baptista, António M; Zuber, Peter

2017-12-01

Estuarine turbidity maxima (ETM) function as hotspots of microbial activity and diversity in estuaries, yet, little is known about the temporal and spatial variability in ETM bacterial community composition. To determine which environmental factors affect ETM bacterial populations in the Columbia River estuary, we analyzed ETM bacterial community composition (Sanger sequencing and amplicon pyrosequencing of 16S rRNA gene) and bulk heterotrophic production ( 3 H-leucine incorporation rates). We collected water 20 times to cover five ETM events and obtained 42 samples characterized by different salinities, turbidities, seasons, coastal regimes (upwelling vs. downwelling), locations, and particle size. Spring and summer populations were distinct. All May samples had similar bacterial community composition despite having different salinities (1-24 PSU), but summer non-ETM bacteria separated into marine, freshwater, and brackish assemblages. Summer ETM bacterial communities varied depending on coastal upwelling or downwelling conditions and on the sampling site location with respect to tidal intrusion during the previous neap tide. In contrast to ETM, whole (>0.2 μm) and free-living (0.2-3 μm) assemblages of non-ETM waters were similar to each other, indicating that particle-attached (>3 μm) non-ETM bacteria do not develop a distinct community. Brackish water type (ETM or non-ETM) is thus a major factor affecting particle-attached bacterial communities. Heterotrophic production was higher in particle-attached than free-living fractions in all brackish waters collected throughout the water column during the rise to decline of turbidity through an ETM event (i.e., ETM-impacted waters). However, free-living communities showed higher productivity prior to or after an ETM event (i.e., non-ETM-impacted waters). This study has thus found that Columbia River ETM bacterial communities vary based on seasons, salinity, sampling location, and particle size, with the existence of three particle types characterized by different bacterial communities in ETM, ETM-impacted, and non-ETM-impacted brackish waters. Taxonomic analysis suggests that ETM key biological function is to remineralize organic matter. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

PubMed

Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

2013-03-01

We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Response of soil bacterial communities to lead and zinc pollution revealed by Illumina MiSeq sequencing investigation.

PubMed

Xu, Xihui; Zhang, Zhou; Hu, Shunli; Ruan, Zhepu; Jiang, Jiandong; Chen, Chen; Shen, Zhenguo

2017-01-01

Soil provides a critical environment for microbial community development. However, microorganisms may be sensitive to substances such as heavy metals (HMs), which are common soil contaminants. This study investigated bacterial communities using 16S ribosomal RNA (rRNA) gene fragment sequencing in geographic regions with and without HM pollution to elucidate the effects of soil properties and HMs on bacterial communities. No obvious changes in the richness or diversity of bacterial communities were observed between samples from mining and control areas. Significant differences in bacterial richness and diversity were detected between samples from different geographic regions, indicating that the basic soil characteristics were the most important factors affecting bacterial communities other than HMs. However, the abundances of several phyla and genera differed significantly between mining and control samples, suggesting that Zn and Pb pollution may impact the soil bacterial community composition. Moreover, regression analyses showed that the relative abundances of these phyla and genera were correlated significantly with the soil-available Zn and Pb contents. Redundancy analysis indicated that the soil K, ammoniacal nitrogen (NH 4 + -N), total Cu, and available Zn and Cu contents were the most important factors. Our results not only suggested that the soil bacteria were sensitive to HM stresses but also indicated that other soil properties may affect soil microorganisms to a greater extent.

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review.

PubMed

Fujiyoshi, So; Tanaka, Daisuke; Maruyama, Fumito

2017-01-01

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using four factors: temperature, relative humidity (RH), air exchange rate, and occupant density, as a minimum requirement. We also summarize the relevant legislation by country. Choice of factors to measure remain controversial are discussed.

Transmission of Airborne Bacteria across Built Environments and Its Measurement Standards: A Review

PubMed Central

Fujiyoshi, So; Tanaka, Daisuke; Maruyama, Fumito

2017-01-01

Human health is influenced by various factors including microorganisms present in built environments where people spend most of their lives (approximately 90%). It is therefore necessary to monitor and control indoor airborne microbes for occupational safety and public health. Most studies concerning airborne microorganisms have focused on fungi, with scant data available concerning bacteria. The present review considers papers published from 2010 to 2017 approximately and factors affecting properties of indoor airborne bacteria (communities and concentration) with respect to temporal perspective and to multiscale interaction viewpoint. From a temporal perspective, bacterial concentrations in built environments change depending on numbers of human occupancy, while properties of bacterial communities tend to remain stable. Similarly, the bacteria found in social and community spaces such as offices, classrooms and hospitals are mainly associated with human occupancy. Other major sources of indoor airborne bacteria are (i) outdoor environments, and (ii) the building materials themselves. Indoor bacterial communities and concentrations are varied with varying interferences by outdoor environment. Airborne bacteria from the outdoor environment enter an indoor space through open doors and windows, while indoor bacteria are simultaneously released to the outer environment. Outdoor bacterial communities and their concentrations are also affected by geographical factors such as types of land use and their spatial distribution. The bacteria found in built environments therefore originate from any of the natural and man-made surroundings around humans. Therefore, to better understand the factors influencing bacterial concentrations and communities in built environments, we should study all the environments that humans contact as a single ecosystem. In this review, we propose the establishment of a standard procedure for assessing properties of indoor airborne bacteria using four factors: temperature, relative humidity (RH), air exchange rate, and occupant density, as a minimum requirement. We also summarize the relevant legislation by country. Choice of factors to measure remain controversial are discussed. PMID:29238327

Confinement Regulates Complex Biochemical Networks: Initiation of Blood Clotting by “Diffusion Acting”

PubMed Central

Shen, Feng; Pompano, Rebecca R.; Kastrup, Christian J.; Ismagilov, Rustem F.

2009-01-01

Abstract This study shows that environmental confinement strongly affects the activation of nonlinear reaction networks, such as blood coagulation (clotting), by small quantities of activators. Blood coagulation is sensitive to the local concentration of soluble activators, initiating only when the activators surpass a threshold concentration, and therefore is regulated by mass transport phenomena such as flow and diffusion. Here, diffusion was limited by decreasing the size of microfluidic chambers, and it was found that microparticles carrying either the classical stimulus, tissue factor, or a bacterial stimulus, Bacillus cereus, initiated coagulation of human platelet-poor plasma only when confined. A simple analytical argument and numerical model were used to describe the mechanism for this phenomenon: confinement causes diffusible activators to accumulate locally and surpass the threshold concentration. To interpret the results, a dimensionless confinement number, Cn, was used to describe whether a stimulus was confined, and a Damköhler number, Da2, was used to describe whether a subthreshold stimulus could initiate coagulation. In the context of initiation of coagulation by bacteria, this mechanism can be thought of as “diffusion acting”, which is distinct from “diffusion sensing”. The ability of confinement and diffusion acting to change the outcome of coagulation suggests that confinement should also regulate other biological “on” and “off” processes that are controlled by thresholds. PMID:19843446

Symbiosis initiation in the bacterially luminous sea urchin cardinalfish Siphamia versicolor.

PubMed

Dunlap, P V; Gould, A L; Wittenrich, M L; Nakamura, M

2012-09-01

To determine how each new generation of the sea urchin cardinalfish Siphamia versicolor acquires the symbiotic luminous bacterium Photobacterium mandapamensis, and when in its development the S. versicolor initiates the symbiosis, procedures were established for rearing S. versicolor larvae in an aposymbiotic state. Under the conditions provided, larvae survived and developed for 28 days after their release from the mouths of males. Notochord flexion began at 8 days post release (dpr). By 28 dpr, squamation was evident and the caudal complex was complete. The light organ remained free of bacteria but increased in size and complexity during development of the larvae. Thus, aposymbiotic larvae of the fish can survive and develop for extended periods, major components of the luminescence system develop in the absence of the bacteria and the bacteria are not acquired directly from a parent, via the egg or during mouth brooding. Presentation of the symbiotic bacteria to aposymbiotic larvae at 8-10 dpr, but not earlier, led to initiation of the symbiosis. Upon colonization of the light organ, the bacterial population increased rapidly and cells forming the light-organ chambers exhibited a differentiated appearance. Therefore, the light organ apparently first becomes receptive to colonization after 1 week post-release development, the symbiosis is initiated by bacteria acquired from the environment and bacterial colonization induces morphological changes in the nascent light organ. The abilities to culture larvae of S. versicolor for extended periods and to initiate the symbiosis in aposymbiotic larvae are key steps in establishing the experimental tractability of this highly specific vertebrate and microbe mutualism. © 2012 The Authors. Journal of Fish Biology © 2012 The Fisheries Society of the British Isles.

Bacterial and fungal endophthalmitis in upper Egypt: related species and risk factors.

PubMed

Gharamah, A A; Moharram, A M; Ismail, M A; Al-Hussaini, A K

2012-08-01

To study risk factors, contributing factors of bacterial and fungal endophthalmitis in Upper Egypt, test the isolated species sensitive to some therapeutic agents, and to investigate the air-borne bacteria and fungi in opthalmology operating rooms. Thirty one cases of endophthalmitis were clinically diagnosed and microbiologically studied. Indoor air-borne bacteria and fungi inside four air-conditioned operating rooms in the Ophthalmology Department at Assiut University Hospitals were also investigated. The isolated microbes from endophthalmitis cases were tested for their ability to produce some extracellular enzymes including protease, lipase, urease, phosphatase and catalase. Also the ability of 5 fungal isolates from endophthalmitis origin to produce mycotoxins and their sensitivity to some therapeutic agents were studied. Results showed that bacteria and fungi were responsihle for infection in 10 and 6 cases of endophthalmitis, respectively and only 2 cases produced a mixture of bacteria and fungi. Trauma was the most prevalent risk factor of endophthalmitis where 58.1% of the 31 cases were due to trauma. In ophthalmology operating rooms, different bacterial and fungal species were isolated. 8 bacterial and 5 fungal isolates showed their ability to produce enzymes while only 3 fungal isolates were able to produce mycotoxins. Terbinafine showed the highest effect against most isolates in vitro. The ability of bacterial and fungal isolates to produce extracellular enzymes and mycotoxins may be aid in the invasion and destruction of eye tissues. Microbial contamination of operating rooms with air-borne bacteria and fungi in the present work may be a source of postoperative endophthalmitis.

Prognostic factors of liver cirrhosis mortality after a first episode of spontaneous bacterial peritonitis. A multicenter study.

PubMed

Melcarne, Luigi; Sopeña, Julia; Martínez-Cerezo, Francisco José; Vergara, Mercedes; Miquel, Mireia; Sánchez-Delgado, Jordi; Dalmau, Blai; Machlab, Salvador; Portilla, Dustin; González-Padrón, Yonaisy; Real Álvarez, Mónica; Carpintero, Chantal; Casas, Meritxell

2018-02-01

Spontaneous bacterial peritonitis is an infectious complication with a negative impact on survival of patients with cirrhosis. To analyze the short- and long-term survival after a first episode of bacterial peritonitis and the associated prognostic factors. This was a retrospective, multicenter study of patients admitted to hospital for spontaneous bacterial peritonitis between 2008 and 2013. Independent variables related to mortality were analyzed by logistic regression. The prognostic power of the Child Pugh Score, the Model for End-Stage Liver Disease (MELD) and the Charlson index was analyzed by ROC curve. A total of 159 patients were enrolled, 72% were males with a mean age of 63.5 years and a mean MELD score of 19 (SD ± 9.5). Mortality at 30 and 90 days and one and two years was 21%, 31%, 55% and 69%, respectively. Hepatic encephalopathy (p = 0.008, OR 3.5, 95% CI 1.4-8.8) and kidney function (p = 0.026, OR 2.7, 95% CI 1.13-16.7) were independent factors for short- and long-term mortality. MELD was a good marker of short- and long-term survival (area under the curve [AUC] 0.7: 95% CI 1.02-1.4). The Charlson index was related to long-term mortality (AUC 0.68: 95% CI 0.6-0.77). Short- and long-term mortality of spontaneous bacterial peritonitis is still high. The main prognostic factors for mortality are impairment of liver and kidney function. MELD and the Charlson index are good markers of survival.

Inhibition of bacterial and leukocyte adhesion under shear stress conditions by material surface chemistry.

PubMed

Patel, Jasmine D; Ebert, Michael; Stokes, Ken; Ward, Robert; Anderson, James M

2003-01-01

Biomaterial-centered infections, initiated by bacterial adhesion, persist due to a compromised host immune response. Altering implant materials with surface modifying endgroups (SMEs) may enhance their biocompatibility by reducing bacterial and inflammatory cell adhesion. A rotating disc model, which generates shear stress within physiological ranges, was used to characterize adhesion of leukocytes and Staphylococcus epidermidis on polycarbonate-urethanes and polyetherurethanes modified with SMEs (polyethylene oxide, fluorocarbon and dimethylsiloxane) under dynamic flow conditions. Bacterial adhesion in the absence of serum was found to be mediated by shear stress and surface chemistry, with reduced adhesion exhibited on materials modified with polydimethylsiloxane and polyethylene oxide SMEs. In contrast, bacterial adhesion was enhanced on materials modified with fluorocarbon SMEs. In the presence of serum, bacterial adhesion was primarily neither material nor shear dependent. However, bacterial adhesion in serum was significantly reduced to < or = 10% compared to adhesion in serum-free media. Leukocyte adhesion in serum exhibited a shear dependency with increased adhesion occurring in regions exposed to lower shear-stress levels of < or = 7 dyne/cm2. Additionally, polydimethylsiloxane and polyethylene oxide SMEs reduced leukocyte adhesion on polyether-urethanes. In conclusion, these results suggest that surface chemistry and shear stress can mediate bacterial and cellular adhesion. Furthermore, materials modified with polyethylene oxide SMEs are capable of inhibiting bacterial adhesion, consequently minimizing the probability of biomaterial-centered infections.

Bacterial Infections in Children With Acute Myeloid Leukemia Receiving Ciprofloxacin Prophylaxis.

PubMed

Al Omar, Suha; Anabtawi, Nadine; Al Qasem, Wiam; Rihani, Rawad

2017-04-01

The aim of the study was to describe the incidence and type of bacterial infections associated with the use of ciprofloxacin prophylaxis as single agent in pediatric patients with acute myeloid leukemia (AML). This was a retrospective review of all patients with AML, who were treated according to the AML02 protocol between 2011 and 2015. The medical records were reviewed for any positive cultures from the initiation of the protocol until death or protocol discontinuation. Patient demographics, type of infections, type of isolated bacteria, and intensive care unit admissions were recorded. A total of 50 patients were evaluated, who were of a mean age of 8 years±5.1 (SD). We identified 77 episodes of bacterial infections in 42 (84%) patients. Among those bacterial infections, 73 episodes were with bacteremia and included 45 (62%) gram-positive bacterial infections, 24 (33%) gram-negative bacterial infections, and 4 (6%) mixed gram-negative and gram-positive bacterial infections. Coagulase-negative Staphylococcus and Viridans streptococci were the most commonly isolated bacteria in 33% and 30% of the episodes, respectively. Seventeen (45%) patients with bacteremia required intensive care unit admission. A high rate of bacterial infection was detected in patients who received the AML02 protocol, mainly gram-positive bacterial infections. The prophylactic regimen should be reconsidered for its efficacy, and other antibacterial prophylaxis may be used.

Bacterial Pneumonia in Patients with Cancer: Novel Risk Factors and Management.

PubMed

Wong, Justin L; Evans, Scott E

2017-06-01

Bacterial pneumonias exact unacceptable morbidity on patients with cancer. Although the risk is often most pronounced among patients with treatment-induced cytopenias, the numerous contributors to life-threatening pneumonias in cancer populations range from derangements of lung architecture and swallow function to complex immune defects associated with cytotoxic therapies and graft-versus-host disease. These structural and immunologic abnormalities often make the diagnosis of pneumonia challenging in patients with cancer and impact the composition and duration of therapy. This article addresses host factors that contribute to pneumonia susceptibility, summarizes diagnostic recommendations, and reviews current guidelines for management of bacterial pneumonia in patients with cancer. Copyright © 2016 Elsevier Inc. All rights reserved.

Stream microbial diversity in response to environmental changes: review and synthesis of existing research

PubMed Central

Zeglin, Lydia H.

2015-01-01

The importance of microbial activity to ecosystem function in aquatic ecosystems is well established, but microbial diversity has been less frequently addressed. This review and synthesis of 100s of published studies on stream microbial diversity shows that factors known to drive ecosystem processes, such as nutrient availability, hydrology, metal contamination, contrasting land-use and temperature, also cause heterogeneity in bacterial diversity. Temporal heterogeneity in stream bacterial diversity was frequently observed, reflecting the dynamic nature of both stream ecosystems and microbial community composition. However, within-stream spatial differences in stream bacterial diversity were more commonly observed, driven specifically by different organic matter (OM) compartments. Bacterial phyla showed similar patterns in relative abundance with regard to compartment type across different streams. For example, surface water contained the highest relative abundance of Actinobacteria, while epilithon contained the highest relative abundance of Cyanobacteria and Bacteroidetes. This suggests that contrasting physical and/or nutritional habitats characterized by different stream OM compartment types may select for certain bacterial lineages. When comparing the prevalence of physicochemical effects on stream bacterial diversity, effects of changing metal concentrations were most, while effects of differences in nutrient concentrations were least frequently observed. This may indicate that although changing nutrient concentrations do tend to affect microbial diversity, other environmental factors are more likely to alter stream microbial diversity and function. The common observation of connections between ecosystem process drivers and microbial diversity suggests that microbial taxonomic turnover could mediate ecosystem-scale responses to changing environmental conditions, including both microbial habitat distribution and physicochemical factors. PMID:26042102

Structure and dynamics of the gut bacterial microbiota of the bark beetle, Dendroctonus rhizophagus (Curculionidae: Scolytinae) across their life stages

PubMed Central

2017-01-01

Bark beetles play an important role as agents of natural renovation and regeneration in coniferous forests. Several studies have documented the metabolic capacity of bacteria associated with the gut, body surface, and oral secretions of these insects; however, little is known about how the bacterial community structure changes during the life cycle of the beetles. This study represents the first comprehensive analysis of the bacterial community of the gut of the bark beetle D. rhizophagus during the insect’s life cycle using 454 pyrosequencing. A total of 4 bacterial phyla, 7 classes, 15 families and 23 genera were identified. The α-diversity was low, as demonstrated in previous studies. The dominant bacterial taxa belonged to the Enterobacteriaceae and Pseudomonadaceae families. This low α-diversity can be attributed to the presence of defensive chemical compounds in conifers or due to different morpho-physiological factors in the gut of these insects acting as strong selective factors. Members of the genera Rahnella, Serratia, Pseudomonas and Propionibacterium were found at all life stages, and the first three genera, particularly Rahnella, were predominant suggesting the presence of a core microbiome in the gut. Significant differences in β-diversity were observed, mainly due to bacterial taxa present at low frequencies and only in certain life stages. The predictive functional profiling indicated metabolic pathways related to metabolism of amino acids and carbohydrates, and membrane transport as the most significant in the community. These differences in the community structure might be due to several selective factors, such as gut compartmentalization, physicochemical conditions, and microbial interactions. PMID:28406998

[Diagnostic value of serum procalcitonin in identifying the etiology of non-responding community-acquired pneumonia after initial antibiotic therapy].

PubMed

Wang, Zheng; Zhang, Xiaoju; Wu, Jizhen; Zhang, Wenping; Kuang, Hongyan; Li, Xiao; Xuan, Weixia; Wang, Kai; Ma, Lijun

2014-11-01

This study was to investigate the diagnostic value of serum procalcitonin(PCT) in identifying the etiology of non-responding community-acquired pneumonia (CAP) after initial antibiotic therapy. A retrospective analysis was performed for 232 hospitalized CAP patients admitted to the People's Hospital of Zhengzhou University during June 2013 and January 2014. Early treatment failure was defined as the presence of persistent fever (>38 °C) and/or clinical symptoms (malaise, cough, expectoration, dyspnea) or deterioration after at least 72 h of initial antimicrobial treatment, or development of respiratory failure requiring mechanical ventilation, or septic shock. Bronchoscopy or transthoracic lung biopsy was performed in case of early treatment failure when indicated. Serum level of PCT was detected by double antibody sandwich method. The differences between 2 or more groups were compared using 2-independent student t test, one-way ANOVA; Mann-Whitney U test, Kruskal-Wallis rank sum test, or χ(2) test. Risk factors and odds ratios for nonresponsiveness were analyzed by setting up a Logistic regression model. The diagnostic values of PCT were determined by receiver operating characteristic curves (ROC curves). Of the 232 CAP patients enrolled, 124 were male and 108 were female, with an average age of (46 ± 20) years. Thirty-six patients failed to respond to the initial antibiotic therapy. As shown by Logistic regression analysis, the risk factors for treatment failure included hypoalbuminemia, type 2 diabetes, previous history of splenectomy , PSI 4-5 grade, and lung infiltration ≥ 3 lobes. The most common causes of non-responsiveness were antimicrobial insufficiency (n = 23), and misdiagnosis of noninfectious mimics of pneumonia (n = 11), with 2 cases of unidentified etiology. The serum PCT level in admission was 0.19 (0.07-0.66) µg/L in the antimicrobial insufficiency subgroup, which was significantly higher than that in the misdiagnosis subgroup [0.06(0.05-0.08)µg/L; P < 0.01]. The antimicrobial insufficiency subgroup included 11 cases of bacterial infection (5 of G(+) cocci and 6 of G(-) bacilli) and 12 cases of nonbacterial infection; their PCT levels were 0.66(0.19-5.80) µg/L and 0.08(0.05-0.20) µg/L, respectively (P < 0.01). There was no statistically significant difference among PCT levels of the 4 subgroups of nonbacterial infections (4 tuberculosis, 3 fungi, 3 atypical pathogens, 2 viruses) (F = 3.025, P = 0.094). The cut-off values of PCT were >0.13 µg/L and >0.115 µg/L for differentiating non-responsiveness originated from bacterial infection or other causes, and infection vs non-infection, which yielded a sensitivity of 100% (11/11) and 65% (14/23) , specificity of 83% (19/23) and 91% (10/11) , and AUC of 0.955 and 0.802, respectively. Antibiotic failure to cover the microbial pathogens, infectious complications and misdiagnosis are the most common causes of early treatment failure in patients with CAP. Serum PCT level fails to predict non-responsiveness, but is suggestive of bacterial infections in hospitalized CAP patients with early treatment failure.

Biogenic synthesis of silver nanoparticles using Piper betle aqueous extract and evaluation of its anti-quorum sensing and antibiofilm potential against uropathogens with cytotoxic effects: an in vitro and in vivo approach.

PubMed

Srinivasan, Ramanathan; Vigneshwari, Loganathan; Rajavel, Tamilselvam; Durgadevi, Ravindran; Kannappan, Arunachalam; Balamurugan, Krishnaswamy; Pandima Devi, Kasi; Veera Ravi, Arumugam

2018-04-01

Urinary tract infections are the utmost common bacterial infections caused by Proteus mirabilis, Pseudomonas aeruginosa, Escherichia coli, and Serratia marcescens. These uropathogens resist the action of several antibiotics due to their ability to form biofilms. Most of these bacterial pathogens use the quorum sensing (QS) machinery to co-ordinate their cells and regulate several virulence factors and biofilm formation. On the other hand, the anti-quorum sensing (anti-QS) and antibiofilm potential of silver nanoparticles have been well reported against certain bacterial pathogens, but to the best of our knowledge, no report is available against the pathogenicity of uropathogens in particular S. marcescens and P. mirabilis. Therefore, the present study is primarily focused on the anti-QS and antibiofilm potential of Piper betle-based synthesized silver nanoparticles (PbAgNPs) against S. marcescens and P. mirabilis. Initially, the silver nanoparticles were synthesized by the aqueous extract of P. betle and characterized by UV-absorbance spectroscopy, XRD, FT-IR, SEM, TEM, and DLS. The synthesized silver nanoparticles were assessed for their anti-QS activity and the obtained results revealed that the PbAgNPs inhibited the QS-mediated virulence factors such as prodigiosin, protease, biofilm formation, exopolysaccharides and hydrophobicity productions in uropathogens. The gene expression analysis divulged the downregulation of fimA, fimC, flhD, and bsmB genes in S. marcescens and flhB, flhD, and rsbA genes in P. mirabilis, respectively. The in vivo Caenorhabditis elegans assays revealed the non-toxic and anti-adherence efficiency of PbAgNPs. Furthermore, the non-toxic effect of PbAgNPs was also confirmed through peripheral blood mononuclear cells and normal lung epithelial cells. Therefore, the contemporary study demonstrates the use of PbAgNPs as a possible alternative toward conventional antibiotics in controlling QS and biofilm-related uropathogen infections.

The Effect of Elevated Intra-Abdominal Pressure on TLR4 Signaling in Intestinal Mucosa and on Intestinal Bacterial Translocation in a Rat.

PubMed

Strier, Adam; Kravarusic, Dragan; Coran, Arnold G; Srugo, Isaac; Bitterman, Nir; Dorfman, Tatiana; Pollak, Yulia; Matter, Ibrahim; Sukhotnik, Igor

2017-02-01

Recent evidence suggests that elevated intra-abdominal pressure (IAP) may adversely affect the intestinal barrier function. Toll-like receptor 4 (TLR-4) is responsible for the recognition of bacterial endotoxin or lipopolysaccharide and for initiation of the Gram-negative septic shock syndrome. The objective of the current study was to determine the effects of elevated IAP on intestinal bacterial translocation (BT) and TLR-4 signaling in intestinal mucosa in a rat model. Male Sprague-Dawley rats were randomly assigned to one of two experimental groups: sham animals (Sham) and IAP animals who were subjected to a 15 mmHg pressure pneumoperitoneum for 30 minutes. Rats were sacrificed 24 hours later. BT to mesenteric lymph nodes, liver, portal vein blood, and peripheral blood was determined at sacrifice. TLR4-related gene and protein expression (TLR-4; myeloid differentiation factor 88 [Myd88] and TNF-α receptor-associated factor 6 [TRAF6]) expression were determined using real-time PCR, western blotting, and immunohistochemistry. Thirty percent of sham rats developed BT in the mesenteric lymph nodes (level I) and 20% of control rats developed BT in the liver and portal vein (level II). abdominal compartment syndrome (ACS) rats demonstrated an 80% BT in the lymph nodes (Level I) and 40% BT in the liver and portal vein (Level II). Elevated BT was accompanied by a significant increase in TLR-4 immunostaining in jejunum (51%) and ileum (35.9%), and in a number of TRAF6-positive cells in jejunum (2.1%) and ileum (24.01%) compared to control animals. ACS rats demonstrated a significant increase in TLR4 and MYD88 protein levels compared to control animals. Twenty-four hours after the induction of elevated IAP in a rat model, increased BT rates were associated with increased TLR4 signaling in intestinal mucosa.

Minocycline enhances the mesenchymal stromal/stem cell pro-healing phenotype in triple antimicrobial-loaded hydrogels.

PubMed

Guerra, Alberto Daniel; Rose, Warren E; Hematti, Peiman; Kao, W John

2017-03-15

Mesenchymal stromal/stem cells (MSCs) have demonstrated pro-healing properties including an anti-inflammatory cytokine profile and the promotion of angiogenesis via expression of growth factors in pre-clinical models. MSCs encapsulated in poly(ethylene glycol) diacrylate (PEGdA) and thiolated gelatin poly(ethylene glycol) (Gel-PEG-Cys) crosslinked hydrogels have led to controlled cellular presentation at wound sites with favorable wound healing outcomes. However, the therapeutic potential of MSC-loaded hydrogels may be limited by non-specific protein adsorption on the delivery matrix that could facilitate the initial adhesion of microorganisms and subsequent virulent biofilm formation. Antimicrobials loaded concurrently in the hydrogels with MSCs could reduce microbial bioburden and promote healing, but the antimicrobial effect on the MSC wound healing capacity and the antibacterial efficacy of the hydrogels is unknown. We demonstrate that minocycline specifically induces a favorable change in MSC migration capacity, proliferation, gene expression, extracellular matrix (ECM) attachment, and adhesion molecule and growth factor release with subsequent increased angiogenesis. We then demonstrate that hydrogels loaded with MSCs, minocycline, vancomycin, and linezolid can significantly decrease bacterial bioburden. Our study suggests that minocycline can serve as a dual mechanism for the regenerative capacity of MSCs and the reduction of bioburden in triple antimicrobial-loaded hydrogels. Wound healing is a complex biological process that can be hindered by bacterial infection, excessive inflammation, and inadequate microvasculature. In this study, we develop a new formulation of poly(ethylene glycol) diacrylate and thiolated gelatin poly(ethylene glycol) crosslinked hydrogels loaded with minocycline, vancomycin, linezolid, and mesenchymal stromal/stem cells that induces a favorable wound healing phenotype in mesenchymal stromal/stem cells and prevents bacterial bioburden on the hydrogel. This combinatorial approach to biomaterial development has the potential to impact wound healing for contaminated full thickness cutaneous wounds. Copyright © 2017. Published by Elsevier Ltd.

Uropathogenic E. coli Induce Different Immune Response in Testicular and Peritoneal Macrophages: Implications for Testicular Immune Privilege

PubMed Central

Bhushan, Sudhanshu; Hossain, Hamid; Lu, Yongning; Geisler, Andreas; Tchatalbachev, Svetlin; Mikulski, Zbigniew; Schuler, Gerhard; Klug, Jörg; Pilatz, Adrian; Wagenlehner, Florian; Chakraborty, Trinad; Meinhardt, Andreas

2011-01-01

Infertility affects one in seven couples and ascending bacterial infections of the male genitourinary tract by Escherichia coli are an important cause of male factor infertility. Thus understanding mechanisms by which immunocompetent cells such as testicular macrophages (TM) respond to infection and how bacterial pathogens manipulate defense pathways is of importance. Whole genome expression profiling of TM and peritoneal macrophages (PM) infected with uropathogenic E. coli (UPEC) revealed major differences in regulated genes. However, a multitude of genes implicated in calcium signaling pathways was a common feature which indicated a role of calcium-dependent nuclear factor of activated T cells (NFAT) signaling. UPEC-dependent NFAT activation was confirmed in both cultured TM and in TM in an in vivo UPEC infectious rat orchitis model. Elevated expression of NFATC2-regulated anti-inflammatory cytokines was found in TM (IL-4, IL-13) and PM (IL-3, IL-4, IL-13). NFATC2 is activated by rapid influx of calcium, an activity delineated to the pore forming toxin alpha-hemolysin by bacterial mutant analysis. Alpha-hemolysin suppressed IL-6 and TNF-α cytokine release from PM and caused differential activation of MAP kinase and AP-1 signaling pathways in TM and PM leading to reciprocal expression of key pro-inflammatory cytokines in PM (IL-1α, IL-1β, IL-6 downregulated) and TM (IL-1β, IL-6 upregulated). In addition, unlike PM, LPS-treated TM were refractory to NFκB activation shown by the absence of degradation of IκBα and lack of pro-inflammatory cytokine secretion (IL-6, TNF-α). Taken together, these results suggest a mechanism to the conundrum by which TM initiate immune responses to bacteria, while maintaining testicular immune privilege with its ability to tolerate neo-autoantigens expressed on developing spermatogenic cells. PMID:22164293

Incidence of bacterial diseases associated with irrigation methods on onions (Allium cepa).

PubMed

Chorolque, A; Pozzo Ardizzi, C; Pellejero, G; Aschkar, G; García Navarro, F J; Jiménez Ballesta, R

2018-04-24

In the last decade, diseases of bacterial origin in onions have increased and this has led to significant losses in production. These diseases are currently observed in both the Old and New Worlds. The aim of the experimental work reported here was to evaluate whether the irrigation method influences the incidence of diseases of bacterial origin. In cases where the inoculum was natural, the initial incidence of Soft Bacterial Rot was not manifested in any treatment in the first year, whereas at the end of the conservation period all treatments had increased incidences of infection. Sprinkler irrigation (8%) was statistically differentiated from the other treatments, for which the final incidence was similar (4.5%). For all irrigation treatments, the final incidence of Bacterial Soft Rot decreased or remained stable towards the end of the cycle, with the exception of sprinkler irrigation in 2015, which increased. It can be inferred from the results that the irrigation method does have an influence on the incidence of diseases of bacterial origin in the post-harvest stage for onions. This article is protected by copyright. All rights reserved.

Atmospheric pressure argon surface discharges propagated in long tubes: physical characterization and application to bio-decontamination

NASA Astrophysics Data System (ADS)

Kovalova, Zuzana; Leroy, Magali; Jacobs, Carolyn; Kirkpatrick, Michael J.; Machala, Zdenko; Lopes, Filipa; Laux, Christophe O.; DuBow, Michael S.; Odic, Emmanuel

2015-11-01

Pulsed corona discharges propagated in argon (or in argon with added water vapor) at atmospheric pressure on the interior surface of a 49 cm long quartz tube were investigated for the application of surface bio-decontamination. H2O molecule dissociation in the argon plasma generated reactive species (i.e. OH in ground and excited states) and UV emission, which both directly affected bacterial cells. In order to facilitate the evaluation of the contribution of UV radiation, a DNA damage repair defective bacterial strain, Escherichia coli DH-1, was used. Discharge characteristics, including propagation velocity and plasma temperature, were measured. Up to ~5.5 and ~5 log10 reductions were observed for E. coli DH-1 bacteria (from 106 initial load) exposed 2 cm and 44 cm away from the charged electrode, respectively, for a 20 min plasma treatment. The factors contributing to the observed bactericidal effect include desiccation, reactive oxygen species (OH) plus H2O2 accumulation in the liquid phase, and UV-B (and possibly VUV) emission in dry argon. The steady state temperature measured on the quartz tube wall did not exceeded 29 °C the contribution of heating, along with that of H2O2 accumulation, was estimated to be low. The effect of UV-B emission alone or in combination with the other stress factors of the plasma process was examined for different operating conditions.

Gram Positive Bacterial Superantigen Outside-In Signaling Causes Toxic Shock Syndrome

PubMed Central

Brosnahan, Amanda J.; Schlievert, Patrick M.

2011-01-01

Staphylococcus aureus and Streptococcus pyogenes (group A streptococci) are gram-positive pathogens capable of producing a variety of bacterial exotoxins known as superantigens. Superantigens interact with antigen-presenting cells (APCs) and T cells to induce T cell proliferation and massive cytokine production, which leads to fever, rash, capillary leak, and subsequent hypotension, the major symptoms of toxic shock syndrome. Both S. aureus and group A streptococci colonize mucosal surfaces, including the anterior nares and vagina for S. aureus, and the oropharynx and less commonly the vagina for group A streptococci. However, due to their abilities to secrete a variety of virulence factors, the organisms can also cause illnesses from the mucosa. This review provides an updated discussion of the biochemical and structural features of one group of secreted virulence factors, the staphylococcal and group A streptococcal superantigens, and their abilities to cause toxic shock syndrome from a mucosal surface. The main focus of this review, however, is the abilities of superantigens to induce cytokines and chemokines from epithelial cells, which has been linked to a dodecapeptide region that is relatively conserved among all superantigens and is distinct from the binding sites required for interactions with APCs and T cells. This phenomenon, termed outside-in signaling, acts to recruit adaptive immune cells to the submucosa, where the superantigens can then interact with those cells to initiate the final cytokine cascades that lead to toxic shock syndrome. PMID:21535475

Gram-positive bacterial superantigen outside-in signaling causes toxic shock syndrome.

PubMed

Brosnahan, Amanda J; Schlievert, Patrick M

2011-12-01

Staphylococcus aureus and Streptococcus pyogenes (group A streptococci) are Gram-positive pathogens capable of producing a variety of bacterial exotoxins known as superantigens. Superantigens interact with antigen-presenting cells (APCs) and T cells to induce T cell proliferation and massive cytokine production, which leads to fever, rash, capillary leak and subsequent hypotension, the major symptoms of toxic shock syndrome. Both S. aureus and group A streptococci colonize mucosal surfaces, including the anterior nares and vagina for S. aureus, and the oropharynx and less commonly the vagina for group A streptococci. However, due to their abilities to secrete a variety of virulence factors, the organisms can also cause illnesses from the mucosa. This review provides an updated discussion of the biochemical and structural features of one group of secreted virulence factors, the staphylococcal and group A streptococcal superantigens, and their abilities to cause toxic shock syndrome from a mucosal surface. The main focus of this review, however, is the abilities of superantigens to induce cytokines and chemokines from epithelial cells, which has been linked to a dodecapeptide region that is relatively conserved among all superantigens and is distinct from the binding sites required for interactions with APCs and T cells. This phenomenon, termed outside-in signaling, acts to recruit adaptive immune cells to the submucosa, where the superantigens can then interact with those cells to initiate the final cytokine cascades that lead to toxic shock syndrome. © 2011 The Authors Journal compilation © 2011 FEBS.

Electroactive Mg2+-Hydroxyapatite Nanostructured Networks against Drug-Resistant Bone Infection Strains.

PubMed

Andrés, Nancy C; Sieben, Juan M; Baldini, Mónica; Rodríguez, Carlos H; Famiglietti, Ángela; Messina, Paula V

2018-06-13

Surface colonization competition between bacteria and host cells is one of the critical factors involved in tissue/implant integration. Current biomaterials are evaluated for their ability both of withstanding favorable responses of host tissue cells and of resisting bacterial contamination. In this work, the antibacterial ability of biocompatible Mg 2+ -substituted nanostructured hydroxyapatite (HA) was investigated. The densities of Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli strains were significantly decreased after culture in the presence of Mg-substituted HA materials in direct correlation with Mg 2+ -Ca 2+ switch in the HA lattice. It was noticed that this decrease was accompanied by a minimal alteration of bacterial environments; therefore, the Mg 2+ -HA antibacterial effect was associated with the material surface topography and it electroactive behavior. It was observed that 2.23 wt % Mg 2+ -HA samples exhibited the best antibacterial performance; it decreased 2-fold the initial population of E. coli, P. aeruginosa, and S. aureus at the intermediate concentration (50 mg mL -1 of broth). Our results reinforce the potential of Mg-HA nanostructured materials to be used in antibacterial coatings for implantable devices and/or medicinal materials to prevent bone infection and to promote wound healing.

Mg isotope fractionation during microbe-mineral interactions

NASA Astrophysics Data System (ADS)

Kim, Insu; Ryu, Jong-sik; Lee, Kwang-sik; Lee, Dongho

2014-05-01

Magnesium is involved in various biogeochemical processes important to the global climate change over geological time-scale. Mg isotopes allow us to directly trace the Mg cycle in the Earth's surface but the factors controlling Mg isotopic compositions have not fully understood yet. Here, we conducted a batch experiment using two bacterial species (Shewanella putrefaciens and Burkholderia fungorum) and three major Mg-bearing minerals (biotite, dolomite and hornblende). All elemental concentrations increased by 336 h and then reached to steady-state values, of which Mg concentrations varied depending on minerals and bacterial species. This result indicates that the mineral dissolution is affect by the presence of microbes, which either provide organic acids or attach onto mineral surface. The Mg isotopic compositions of initial minerals biotite, dolomite and hornblende are -0.35o of biotite, -0.99o of dolomite, and -0.24o of hornblende, in δ26Mg. Similarly, δ26Mg values increased by 336 h and reached to steady-state values, which also varied with minerals and microbes. During dissolution of three minerals, the light isotope of Mg is preferentially incorporated into the dissolved phases and then the dissolved δ26Mg values become consistent with those of minerals with the time.

Determinants of acquisition and carriage of Staphylococcus aureus in infancy.

PubMed

Peacock, Sharon J; Justice, Anita; Griffiths, D; de Silva, G D I; Kantzanou, M N; Crook, Derrick; Sleeman, Karen; Day, Nicholas P J

2003-12-01

Nasal carriage of Staphylococcus aureus is a major risk factor for invasive S. aureus disease. The aim of this study was to define factors associated with carriage. We conducted a prospective, longitudinal community-based study of infants and their mothers for a period of 6 months following delivery. The epidemiology of carriage was examined for 100 infant-mother pairs. Infant carriage varied significantly with age, falling from 40 to 50% during the first 8 weeks to 21% by 6 months. Determinants of infant S. aureus carriage included maternal carriage, breastfeeding, and number of siblings. Bacterial typing of S. aureus was performed by pulsed-field gel electrophoresis and multilocus sequence typing. The majority of individuals carried a single strain of S. aureus over time, and the mother was the usual source for colonizing isolates in infants. The effect of other components of the normal nasal flora on the development of S. aureus carriage was examined in 157 consecutive infants. Negative associations (putative bacterial interference) between S. aureus and other species occurred early in infancy but were not sustained. An increasing antistaphylococcal effect observed over time was not attributable to bacterial interference. S. aureus carriage in infants is likely to be determined by a combination of host, environmental, and bacterial factors, but bacterial interference does not appear to be an ultimate determinant of carrier status.

Expression of virulence factors by Staphylococcus aureus grown in serum.

PubMed

Oogai, Yuichi; Matsuo, Miki; Hashimoto, Masahito; Kato, Fuminori; Sugai, Motoyuki; Komatsuzawa, Hitoshi

2011-11-01

Staphylococcus aureus produces many virulence factors, including toxins, immune-modulatory factors, and exoenzymes. Previous studies involving the analysis of virulence expression were mainly performed by in vitro experiments using bacterial medium. However, when S. aureus infects a host, the bacterial growth conditions are quite different from those in a medium, which may be related to the different expression of virulence factors in the host. In this study, we investigated the expression of virulence factors in S. aureus grown in calf serum. The expression of many virulence factors, including hemolysins, enterotoxins, proteases, and iron acquisition factors, was significantly increased compared with that in bacterial medium. In addition, the expression of RNA III, a global regulon for virulence expression, was significantly increased. This effect was partially restored by the addition of 300 μM FeCl₃ into serum, suggesting that iron depletion is associated with the increased expression of virulence factors in serum. In chemically defined medium without iron, a similar effect was observed. In a mutant with agr inactivated grown in serum, the expression of RNA III, psm, and sec4 was not increased, while other factors were still induced in the mutant, suggesting that another regulatory factor(s) is involved. In addition, we found that serum albumin is a major factor for the capture of free iron to prevent the supply of iron to bacteria grown in serum. These results indicate that S. aureus expresses virulence factors in adaptation to the host environment.

Coupled effects of chemotaxis and growth on traveling bacterial waves.

PubMed

Yan, Zhifeng; Bouwer, Edward J; Hilpert, Markus

2014-08-01

Traveling bacterial waves are capable of improving contaminant remediation in the subsurface. It is fairly well understood how bacterial chemotaxis and growth separately affect the formation and propagation of such waves. However, their interaction is not well understood. We therefore perform a modeling study to investigate the coupled effects of chemotaxis and growth on bacterial migration, and examine their effects on contaminant remediation. We study the waves by using different initial electron acceptor concentrations for different bacteria and substrate systems. Three types of traveling waves can occur: a chemotactic wave due to the biased movement of chemotactic bacteria resulting from metabolism-generated substrate concentration gradients; a growth/decay/motility wave due to a dynamic equilibrium between bacterial growth, decay and random motility; and an integrated wave due to the interaction between bacterial chemotaxis and growth. Chemotaxis hardly enhances the bacterial propagation if it is too weak to form a chemotactic wave or its wave speed is less than half of the growth/decay/motility wave speed. However, chemotaxis significantly accelerates bacterial propagation once its wave speed exceeds the growth/decay/motility wave speed. When convection occurs, it speeds up the growth/decay/motility wave but slows down or even eliminates the chemotactic wave due to the dispersion. Bacterial survival proves particularly important for bacterial propagation. Therefore we develop a conceptual model to estimate the speed of growth/decay/motility waves. Copyright © 2014 Elsevier B.V. All rights reserved.

To Study the Incidence, Predictive Factors and Clinical Outcome of Spontaneous Bacterial Peritonitis in Patients of Cirrhosis with Ascites.

PubMed

Paul, Kavita; Kaur, Jasmine; Kazal, Harbans Lal

2015-07-01

To study the prevalence and predictive factors of spontaneous bacterial peritonitis (SBP) in patients of cirrhosis with ascites and to study the clinical characteristics and prognosis of patients with SBP. The present study was conducted on 122 cases admitted in Department of Medicine, through emergency, in Guru Gobind Singh Medical College and Hospital, Faridkot, Punjab, India. Cases of cirrhosis (irrespective of aetiology) with ascites between the ages of 18-75 years were included in this study. Ascitic fluid of every patient was aspirated under all aseptic measures, before initiation of antibiotic therapy and was sent for biochemical analysis, culture and cytological analysis. Mean age of patients enrolled was 50.30± 10.98 years. 85% were male and 15% were female. Alcohol (73.8%) was the leading cause of cirrhosis followed by HCV (37.7%) and HBV (4.9%). Of the 122 patients studied, 27 (20.4%) patients were diagnosed as having SBP and its variants. Monomicrobial Bacterascites (BA) was present in 5 patients and Culture Negative Neutrocytic Ascites (CNNA) was present in 22 patients. Escherichia coli were the most common isolated organism followed by Klebsiella. The various factors that predispose to development of SBP include low ascitic fluid protein concentration, a high level of serum bilirubin, deranged serum creatinine, high Child-Pugh score and high MELD score. Ascitic fluid analysis remains the single most important test for identifying and assessing a course of SBP. Bedside inoculation of 10-20ml of ascitic fluid into culture bottle at patient bedside will yield better results. Early diagnosis and treatment will reduce the mortality rate in these patients.

Effect of reclamation of abandoned salinized farmland on soil bacterial communities in arid northwest China.

PubMed

Cheng, Zhibo; Chen, Yun; Zhang, Fenghua

2018-07-15

Understanding the impact of reclamation of abandoned salinized farmland on soil bacterial community is of great importance for maintaining soil health and sustainability in arid regions. In this study, we used field sampling and 454 pyrosequencing methods to investigate the effects of 5-year reclamation treatments on soil properties, bacterial community composition and diversity. The four reclamation treatments are: abandoned salinized farmland (CK), cropland (CL), grassland (GL) and woodland (WL). We have found soil properties are significantly altered by abandoned salinized farmland reclamation. In particular, the lowest soil pH and electrical conductivity (EC) values are observed in CL (P<0.05). The dominant phyla are Firmicutes, Proteobacteria, Chloroflexi, Actinobacteria and Acidobacteria in all treatments. At the genus levels, the relative abundance of Bacillus, Lactococcus, Streptococcus and Enterococcus in CK, GL and WL is significantly higher than in CL. Bacterial diversity indices (i.e. ACE, Chao and Shannon) dramatically increase after the reclamation, with the highest in CL. Similar patterns of bacterial communities have been observed in CK, GL and WL soils, but significantly different from CL. Regression analyses indicate that the relative abundance of these phyla are significantly correlated with soil Fe, pH and EC. Results from non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) indicate that soil Fe content, EC and pH are the most important factors in shaping soil bacterial communities. Overall, results indicate that abandoned salinized farmland reclaimed for CL significantly decrease soil pH and EC, and increase soil bacterial community diversity. Soil Fe concentration, EC and pH are the dominant environmental factors affecting soil bacterial community composition. The important role of Fe concentration in shaping bacterial community composition is a new discovery among the similar studies. Copyright © 2018. Published by Elsevier B.V.

Changes in soil physicochemical properties and soil bacterial community in mulberry (Morus alba L.)/alfalfa (Medicago sativa L.) intercropping system.

PubMed

Zhang, Meng-Meng; Wang, Ning; Hu, Yan-Bo; Sun, Guang-Yu

2018-04-01

A better understanding of tree-based intercropping effects on soil physicochemical properties and bacterial community has a potential contribution to improvement of agroforestry productivity and sustainability. In this study, we investigated the effects of mulberry/alfalfa intercropping on soil physicochemical properties and soil bacterial community by MiSeq sequencing of bacterial 16S rRNA gene. The results showed a significant increase in the contents of available nitrogen, available phosphate, available potassium, and total carbon in the rhizosphere soil of the intercropped alfalfa. Sequencing results showed that intercropping improved bacterial richness and diversity of mulberry and alfalfa based on richness estimates and diversity indices. The relative abundances of Proteobacteria, Actinobacteria, and Firmicutes were significantly higher in intercropping mulberry than in monoculture mulberry; and the abundances of Proteobacteria, Bacteroidetes, and Gemmatimonadetes in the intercropping alfalfa were markedly higher than that in monoculture alfalfa. Bacterial taxa with soil nutrients cycling were enriched in the intercropping system. There were higher relative abundances of Bacillus (0.32%), Pseudomonas (0.14%), and Microbacterium (0.07%) in intercropping mulberry soil, and Bradyrhizobium (1.0%), Sphingomonas (0.56%), Pseudomonas (0.18%), Microbacterium (0.15%), Rhizobium (0.09%), Neorhizobium (0.08%), Rhodococcus (0.06%), and Burkholderia (0.04%) in intercropping alfalfa soil. Variance partition analysis showed that planting pattern contributed 26.7% of the total variation of bacterial community, and soil environmental factors explained approximately 56.5% of the total variation. This result indicated that the soil environmental factors were more important than the planting pattern in shaping the bacterial community in the field soil. Overall, mulberry/alfalfa intercropping changed soil bacterial community, which was related to changes in soil total carbon, available phosphate, and available potassium. © 2018 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Impact of bacterial coinfection on clinical outcomes in pneumococcal pneumonia.

PubMed

Kumagai, S; Ishida, T; Tachibana, H; Ito, Y; Ito, A; Hashimoto, T

2015-09-01

The aim of this study was to investigate the influence of bacterial coinfection on patients with pneumococcal pneumonia. We retrospectively analyzed the incidence, clinical features, microbial distributions, and outcomes of patients with bacterial coinfection in a cohort of 433 hospitalized patients with pneumococcal pneumonia. Eighty-five patients (19.6 %) were diagnosed with bacterial coinfection; the most frequent pathogens were Haemophilus influenzae (25 patients, 33.3 %), methicillin-susceptible Staphylococcus aureus (MSSA) (15 patients, 20.0 %), and Moraxella catarrhalis (13 patients, 17.3 %). The CURB-65 score and pneumonia severity index (PSI) were significantly higher in patients with bacterial coinfection (both P < 0.001). In addition, the proportion of patients with bacterial coinfection who met the Infectious Disease Society of America (IDSA)/American Thoracic Society (ATS) severe pneumonia criteria was significantly higher (P < 0.001). Multivariate logistic regression analysis identified three risk factors for bacterial coinfection in patients with pneumococcal pneumonia: alcoholism (odds ratio [OR], 5.12; 95 % confidence interval (95 % CI), 1.60-16.4; P = 0.006), hospitalization for 2 days or more within 90 days preceding admission (OR, 2.02; 95 % CI, 1.03-3.98; P = 0.041), and residence in a nursing home or extended care facility (OR, 3.22; 95 % CI, 1.48-6.97; P = 0.003). Multivariate analysis for 30-day mortality showed that bacterial coinfection was a significant adverse prognostic factor (OR, 2.50; 95 % CI, 1.13-5.53; P = 0.023), independent of IDSA/ATS severe pneumonia, PSI, or healthcare-associated pneumonia. In conclusion, bacterial coinfection may have an adverse impact on severity and outcomes of pneumococcal pneumonia.

The effects of light, primary production, and temperature on bacterial production at Station ALOHA

NASA Astrophysics Data System (ADS)

Viviani, D. A.; Church, M. J.

2016-02-01

In the open oceans, bacterial metabolism is responsible for a large fraction of the movement of reduced carbon through these ecosystems. While broad meta-analyses suggest that factors such as temperature or primary production control rates of bacterial production over large geographic scales, to date little is known about how these factors influence variability in bacterial production in the open sea. Here we present two years of measurements of 3H-leucine incorporation, a proxy for bacterial production, at the open ocean field site of the Hawaii Ocean Time-series, Station ALOHA (22° 45'N, 158° 00'W). By examining 3H-leucine incorporation over monthly, daily, and hourly scales, this work provides insight into processes controlling bacterial growth in this persistently oligotrophic habitat. Rates of 3H-leucine incorporation were consistently 60% greater when measured in the light than in the dark, highlighting the importance of sunlight in fueling bacterial metabolism in this ecosystem. Over diel time scales, rates of 3H-leucine incorporation were quasi-sinusoidal, with rates in the light higher near midday, while rates in the dark were greatest after sunset. Depth-integrated (0 -125 m) rates of 3H-leucine incorporation in both light and dark were more variable ( 5- and 4-fold, respectively) than coincident measurements of primary production ( 2-fold). On average, rates of bacterial production averaged 2 and 4% of primary production (in the dark and light, respectively). At near-monthly time scales, rates of 3H-leucine incorporation in both light and dark were significantly related to temperature. Our results suggest that in the subtropical oligotrophic Pacific, bacterial production appears decoupled from primary production as a result of seasonal-scale variations in temperature and light.

Global analysis of bacterial transcription factors to predict cellular target processes.

PubMed

Doerks, Tobias; Andrade, Miguel A; Lathe, Warren; von Mering, Christian; Bork, Peer

2004-03-01

Whole-genome sequences are now available for >100 bacterial species, giving unprecedented power to comparative genomics approaches. We have applied genome-context methods to predict target processes that are regulated by transcription factors (TFs). Of 128 orthologous groups of proteins annotated as TFs, to date, 36 are functionally uncharacterized; in our analysis we predict a probable cellular target process or biochemical pathway for half of these functionally uncharacterized TFs.

Socioeconomic and Behavioral Factors Leading to Acquired Bacterial Resistance to Antibiotics in Developing Countries

PubMed Central

Okeke, Iruka N.; Lamikanra, Adebayo

1999-01-01

In developing countries, acquired bacterial resistance to antimicrobial agents is common in isolates from healthy persons and from persons with community-acquired infections. Complex socioeconomic and behavioral factors associated with antibiotic resistance, particularly regarding diarrheal and respiratory pathogens, in developing tropical countries, include misuse of antibiotics by health professionals, unskilled practitioners, and laypersons; poor drug quality; unhygienic conditions accounting for spread of resistant bacteria; and inadequate surveillance. PMID:10081668

Characterizing the Bacterial Communities in Retail Stores in the United States

DTIC Science & Technology

2015-01-01

community or the factors that affect it. To our knowledge, only one study to date has investigated the indoor bacterial microbiome of retail stores...type of store affects the microbial community present, the impact of store type on the bacterial community was investigated by comparing the bacteria...genes analysis (Figure 2). Additionally, Leff and Fierer (2013) observed a high relative abundance of Enterobacteriaceae on fruits and vegetables but

Evaluation and optimization of ethanol production from carob pod extract by Zymomonas mobilis using response surface methodology.

PubMed

Vaheed, Hossein; Shojaosadati, Seyed Abbas; Galip, Hasan

2011-01-01

In this research, ethanol production from carob pod extract (extract) using Zymomonas mobilis with medium optimized by Plackett-Burman (P-B) and response surface methodologies (RSM) was studied. Z. mobilis was recognized as useful for ethanol production from carob pod extract. The effects of initial concentrations of sugar, peptone, and yeast extract as well as agitation rate (rpm), pH, and culture time in nonhydrolyzed carob pod extract were investigated. Significantly affecting variables (P = 0.05) in the model obtained from RSM studies were: weights of bacterial inoculum, initial sugar, peptone, and yeast extract. Acid hydrolysis was useful to complete conversion of sugars to glucose and fructose. Nonhydrolyzed extract showed higher ethanol yield and residual sugar compared with hydrolyzed extract. Ethanol produced (g g(-1) initial sugar, as the response) was not significantly different (P = 0.05) when Z. mobilis performance was compared in hydrolyzed and nonhydrolyzed extract. The maximum ethanol of 0.34 ± 0.02 g g(-1) initial sugar was obtained at 30°C, initial pH 5.2, and 80 rpm, using concentrations (g per 50 mL culture media) of: inoculum bacterial dry weight, 0.017; initial sugar, 5.78; peptone, 0.43; yeast extract, 0.43; and culture time of 36 h.

Production and purification of anti-bacterial biometabolite from wild-type Lactobacillus, isolated from fermented bamboo shoot: future suggestions and a proposed system for secondary metabolite onsite recovery during continuous fermentation.

PubMed

Badwaik, Laxmikant S; Borah, Pallab Kumar; Deka, Sankar C

2015-02-01

Wild-type lactobacillus isolated form Khorisa, a fermented bamboo shoot product of Assam, India were evaluated for production anti-bacterial secondary biometabolites, against Staphylococcus aureus. Submerged fermentation technique was used for the production of secondary anti-microbial biometabolite by a single wild-type lactobacillus strain, which tested positive for the release of anti-bacterial factor(s). Crude cell-free supernatant was obtained, followed by extraction in water-immiscible solvents viz., chloroform, hexane, petroleum ether. Chloroform extract of cell-free crude supernatant showed maximum yield (0.054 g/ml) and inhibited all indicator bacterial strains viz., Escherichia coli, Staphylococcus aureus, and Bacillus cereus. Yields of hexane and petroleum ether extract were 0.052 and 0.026 g/ml, respectively. Minimum lethal dose concentration assay of the chloroform extract showed LDmin values at 27, 1.68, and 1.68 mg/ml for E. coli, S. aureus, and B. cereus, respectively. Kill time for all the indicator bacterial strains were less than 12 h. The efficacy of the anti-bacterial substance seemed to depend on the presence of organic acids, particularly lactic acid. Conceptual-based suggestion for the development of an onsite secondary metabolites recovery system during continuous fermentation has also been attempted.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing.

PubMed

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-09

Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing's built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

Emerging bacterial pathogens: the past and beyond.

PubMed

Vouga, M; Greub, G

2016-01-01

Since the 1950s, medical communities have been facing with emerging and reemerging infectious diseases, and emerging pathogens are now considered to be a major microbiologic public health threat. In this review, we focus on bacterial emerging diseases and explore factors involved in their emergence as well as future challenges. We identified 26 major emerging and reemerging infectious diseases of bacterial origin; most of them originated either from an animal and are considered to be zoonoses or from water sources. Major contributing factors in the emergence of these bacterial infections are: (1) development of new diagnostic tools, such as improvements in culture methods, development of molecular techniques and implementation of mass spectrometry in microbiology; (2) increase in human exposure to bacterial pathogens as a result of sociodemographic and environmental changes; and (3) emergence of more virulent bacterial strains and opportunistic infections, especially affecting immunocompromised populations. A precise definition of their implications in human disease is challenging and requires the comprehensive integration of microbiological, clinical and epidemiologic aspects as well as the use of experimental models. It is now urgent to allocate financial resources to gather international data to provide a better understanding of the clinical relevance of these waterborne and zoonotic emerging diseases. Copyright © 2015. Published by Elsevier Ltd.

Estimating bacterial production in marine waters from the simultaneous incorporation of thymidine and leucine.

PubMed

Chin-Leo, G; Kirchman, D L

1988-08-01

We examined the simultaneous incorporation of [H]thymidine and [C]leucine to obtain two independent indices of bacterial production (DNA and protein syntheses) in a single incubation. Incorporation rates of leucine estimated by the dual-label method were generally higher than those obtained by the single-label method, but the differences were small (dual/single = 1.1 +/- 0.2 [mean +/- standard deviation]) and were probably due to the presence of labeled leucyl-tRNA in the cold trichloroacetic acid-insoluble fraction. There were no significant differences in thymidine incorporation between dual- and single-label incubations (dual/ single = 1.03 +/- 0.13). Addition of the two substrates in relatively large amounts (25 nM) did not apparently increase bacterial activity during short incubations (<5 h). With the dual-label method we found that thymidine and leucine incorporation rates covaried over depth profiles of the Chesapeake Bay. Estimates of bacterial production based on thymidine and leucine differed by less than 25%. Although the need for appropriate conversion factors has not been eliminated, the dual-label approach can be used to examine the variation in bacterial production while ensuring that the observed variation in incorporation rates is due to real changes in bacterial production rather than changes in conversion factors or introduction of other artifacts.

Urban-development-induced Changes in the Diversity and Composition of the Soil Bacterial Community in Beijing

NASA Astrophysics Data System (ADS)

Yan, Bing; Li, Junsheng; Xiao, Nengwen; Qi, Yue; Fu, Gang; Liu, Gaohui; Qiao, Mengping

2016-12-01

Numerous studies have implicated urbanization as a major cause of loss of biodiversity. Most of them have focused on plants and animals, even though soil microorganisms make up a large proportion of that biodiversity. However, it is unclear how the soil bacterial community is affected by urban development. Here, paired-end Illumina sequencing of the 16 S rRNA gene at V4 region was performed to study the soil microbial community across Beijing’s built-up area. Proteobacteria, Acidobacteria, Bacteroidetes, Actinobacteria, Gemmatimonadetes, Verrucomicrobia, Planctomycetes, and Chloroflexi were the dominant phyla in all samples, but the relative abundance of these phyla differed significantly across these concentric zones. The diversity and composition of the soil bacterial community were found to be closely correlated with soil pH. Variance partitioning analysis suggested that urban ring roads contributed 5.95% of the bacterial community variation, and soil environmental factors explained 17.65% of the variation. The results of the current work indicate that urban development can alter the composition and diversity of the soil microbial community, and showed pH to be a key factor in the shaping of the composition of the soil bacterial community. Urban development did have a strong impact on the bacterial community of urban soil in Beijing.

Apoptosis in HEp-2 cells infected with Ureaplasma diversum.

PubMed

Amorim, Aline Teixeira; Marques, Lucas Miranda; Santos, Angelita Maria Oliveira Gusmão; Martins, Hellen Braga; Barbosa, Maysa Santos; Rezende, Izadora Souza; Andrade, Ewerton Ferraz; Campos, Guilherme Barreto; Lobão, Tássia Neves; Cortez, Beatriz Araujo; Monezi, Telma Alvez; Machado-Santelli, Glaucia Maria; Timenetsky, Jorge

2014-09-04

Bacterial pathogens have many strategies for infecting and persisting in host cells. Adhesion, invasion and intracellular life are important features in the biology of mollicutes. The intracellular location of Ureaplasma diversum may trigger disturbances in the host cell. This includes activation or inhibition of pro and anti-apoptotic factors, which facilitate the development of host damage. The aim of the present study was to associate U. diversum infection in HEp-2 cells and apoptosis induction. Cells were infected for 72hs with four U. diversum clinical isolates and an ATCC strain. The U. diversum invasion was analyzed by Confocal Laser Scanning Microscopy and gentamicin invasion assay. The apoptosis was evaluated using pro-apoptotic and anti-apoptotic gene expression, and FITC Annexin V/Dead Cell Apoptosis Kit. The number of internalized ureaplasma in HEp-2 cells increased significantly throughout the infection. The flow cytometry analysis with fluorochromes to detect membrane depolarization and gene expression for caspase 2, 3 and 9 increased in infected cells after 24 hours. However, after 72 hours a considerable decrease of apoptotic cells was observed. The data suggests that apoptosis may be initially induced by some isolates in association with HEp-2 cells, but over time, there was no evidence of apoptosis in the presence of ureaplasma and HEp-2 cells. The initial increase and then decrease in apoptosis could be related to bacterial pathogen-associated molecular pattern (PAMPS). Moreover, the isolates of U. diversum presented differences in the studied parameters for apoptosis. It was also observed that the amount of microorganisms was not proportional to the induction of apoptosis in HEp-2 cells.

Culture-dependent and culture-independent assessment of spoilage community growth on VP lamb meat from packaging to past end of shelf-life.

PubMed

Kaur, Mandeep; Shang, Hongshan; Tamplin, Mark; Ross, Tom; Bowman, John P

2017-12-01

Packaging and storage temperature are important factors that influence the shelf-life of vacuum packed (VP) meat. In this study the shelf-life of VP bone-in lamb hind shanks stored at 8 °C and -1.2 °C was determined in parallel to analyses of starting and eventual spoilage bacterial communities via Illumina MiSeq based 16S rRNA amplicon sequencing. The mean total viable counts (TVC) and lactic acid bacterial viable counts (LAB) were observed to increase to log 7.5 CFU/cm 2 and 7 CFU/cm 2 after 6 and 42 days at 8 °C and -1.2 °C and stayed stable until shelf-life termination after 13 and 124 days, respectively. The sequence data showed initial communities were patchily distributed and were mainly derived from skin microbiome taxa likely prevalent within the abattoir. A broad diversity of VP meat associated specific spoilage organisms (SSO) were comparatively abundant in this initial population. Overtime meat spoilage communities developed a distinctive and stable microbiome. At -1.2 °C SSO included mainly Carnobacterium, Yersinia and Clostridium spp. while at 8 °C SSO expanded to include Hafnia, Lactococcus, Providencia spp. Growth curves inferred from the sequence data after taking into account rRNA copy number suggested that SSO growth rates were consistent with overall growth rates determined from TVC and LAB data and are predictable. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Bacterial DNA induces pulmonary damage via TLR-9 through cross-talk with neutrophils.

PubMed

Itagaki, Kiyoshi; Adibnia, Yasaman; Sun, Shiqin; Zhao, Cong; Sursal, Tolga; Chen, Yu; Junger, Wolfgang; Hauser, Carl J

2011-12-01

Bacterial DNA (bDNA) contains hypomethylated "CpG" repeats that can be recognized by Toll-like receptor 9 (TLR-9) as a pathogen-associated molecular pattern. The ability of bDNA to initiate lung injury via TLR-9 has been inferred on the basis of studies using artificial CpG DNA. But the role of authentic bDNA in lung injury is still unknown. Moreover, the mechanisms by which CpG DNA species can lead to pulmonary injury are unknown, although neutrophils (PMNs) are thought to play a key role in the genesis of septic acute lung injury. We evaluated the effects of bDNA on PMN-endothelial cell (EC) interactions thought critical for initiation of acute lung injury. Using a biocapacitance system to monitor real-time changes in endothelial permeability, we demonstrate here that bDNA causes EC permeability in a dose-dependent manner uniquely in the presence of PMNs. These permeability changes are inhibited by chloroquine, suggesting TLR-9 dependency. When PMNs were preincubated with bDNA and applied to ECs or when bDNA was applied to ECs without PMNs, no permeability changes were detected. To study the underlying mechanisms, we evaluated the effects of bDNA on PMN-EC adherence. Bacterial DNA significantly increased PMN adherence to ECs in association with upregulated adhesion molecules in both cell types. Taken together, our results strongly support the conclusion that bDNA can initiate lung injury by stimulating PMN-EC adhesive interactions predisposing to endothelial permeability. Bacterial DNA stimulation of TLR-9 appears to promote enhanced gene expression of adhesion molecules in both cell types. This leads to PMN-EC cross-talk, which is required for injury to occur.

The Response of Heterotrophic Prokaryote and Viral Communities to Labile Organic Carbon Inputs Is Controlled by the Predator Food Chain Structure.

PubMed

Sandaa, Ruth-Anne; Pree, Bernadette; Larsen, Aud; Våge, Selina; Töpper, Birte; Töpper, Joachim P; Thyrhaug, Runar; Thingstad, Tron Frede

2017-08-23

Factors controlling the community composition of marine heterotrophic prokaryotes include organic-C, mineral nutrients, predation, and viral lysis. Two mesocosm experiments, performed at an Arctic location and bottom-up manipulated with organic-C, had very different results in community composition for both prokaryotes and viruses. Previously, we showed how a simple mathematical model could reproduce food web level dynamics observed in these mesocosms, demonstrating strong top-down control through the predator chain from copepods via ciliates and heterotrophic nanoflagellates. Here, we use a steady-state analysis to connect ciliate biomass to bacterial carbon demand. This gives a coupling of top-down and bottom-up factors whereby low initial densities of ciliates are associated with mineral nutrient-limited heterotrophic prokaryotes that do not respond to external supply of labile organic-C. In contrast, high initial densities of ciliates give carbon-limited growth and high responsiveness to organic-C. The differences observed in ciliate abundance, and in prokaryote abundance and community composition in the two experiments were in accordance with these predictions. Responsiveness in the viral community followed a pattern similar to that of prokaryotes. Our study provides a unique link between the structure of the predator chain in the microbial food web and viral abundance and diversity.

Differential compartmentalization of Streptococcus pyogenes virulence factors and host protein binding properties as a mechanism for host adaptation.

PubMed

Kilsgård, Ola; Karlsson, Christofer; Malmström, Erik; Malmström, Johan

2016-11-01

Streptococcus pyogenes is an important human pathogen responsible for substantial morbidity and mortality worldwide. Although S. pyogenes is a strictly human pathogen with no other known animal reservoir, several murine infection models exist to explore different aspects of the bacterial pathogenesis. Inoculating mice with wild-type S. pyogenes strains can result in the generation of new bacterial phenotypes that are hypervirulent compared to the original inoculum. In this study, we used a serial mass spectrometry based proteomics strategy to investigate if these hypervirulent strains have an altered distribution of virulence proteins across the intracellular, surface associated and secreted bacterial compartments and if any change in compartmentalization can alter the protein-protein interaction network between bacteria and host proteins. Quantitative analysis of the S. pyogenes surface and secreted proteomes revealed that animal passaged strains are associated with significantly higher amount of virulence factors on the bacterial surface and in the media. This altered virulence factor compartmentalization results in increased binding of several mouse plasma proteins to the bacterial surface, a trend that was consistent for mouse plasma from several different mouse strains. In general, both the wild-type strain and animal passaged strain were capable of binding high amounts of human plasma proteins. However, compared to the non-passaged strains, the animal passaged strains displayed an increased ability to bind mouse plasma proteins, in particular for M protein binders, indicating that the increased affinity for mouse blood plasma proteins is a consequence of host adaptation of this pathogen to a new host. In conclusion, plotting the total amount of virulence factors against the total amount of plasma proteins associated to the bacterial surface could clearly separate out animal passaged strains from wild type strains indicating a virulence model that could predict the virulence of a S. pyogenes strain in mice and which could be used to identify key aspects of this bacteria's pathogenesis. Copyright © 2016 Elsevier GmbH. All rights reserved.

Spatial and species variations in bacterial communities associated with corals from the Red Sea as revealed by pyrosequencing.

PubMed

Lee, On On; Yang, Jiangke; Bougouffa, Salim; Wang, Yong; Batang, Zenon; Tian, Renmao; Al-Suwailem, Abdulaziz; Qian, Pei-Yuan

2012-10-01

Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals.

Time- and sediment depth-related variations in bacterial diversity and community structure in subtidal sands.

PubMed

Böer, Simone I; Hedtkamp, Stefanie I C; van Beusekom, Justus E E; Fuhrman, Jed A; Boetius, Antje; Ramette, Alban

2009-07-01

Bacterial community structure and microbial activity were determined together with a large number of contextual environmental parameters over 2 years in subtidal sands of the German Wadden Sea in order to identify the main factors shaping microbial community structure and activity in this habitat. Seasonal changes in temperature were directly reflected in bacterial activities and total community respiration, but could not explain variations in the community structure. Strong sediment depth-related patterns were observed for bacterial abundances, carbon production rates and extracellular enzymatic activities. Bacterial community structure also showed a clear vertical variation with higher operational taxonomic unit (OTU) numbers at 10-15 cm depth than in the top 10 cm, probably because of the decreasing disturbance by hydrodynamic forces with sediment depth. The depth-related variations in bacterial community structure could be attributed to vertical changes in bacterial abundances, chlorophyll a and NO(3)(-), indicating that spatial patterns of microbes are partially environmentally controlled. Time was the most important single factor affecting microbial community structure with an OTU replacement of up to 47% over 2 years and a contribution of 34% to the total variation. A large part of this variation was not related to any environmental parameters, suggesting that temporal variations in bacterial community structure are caused by yet unknown environmental drivers and/or by stochastic events in coastal sand habitats. Principal ecosystem functions such as benthic oxygen consumption and extracellular hydrolysis of organic matter were, however, at a high level at all times, indicating functional redundancy in the microbial communities.

Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

PubMed Central

Lee, On On; Yang, Jiangke; Bougouffa, Salim; Wang, Yong; Batang, Zenon; Tian, Renmao; Al-Suwailem, Abdulaziz

2012-01-01

Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals. PMID:22865078

Beneficial role of hydrophytes in removing Cr(VI) from wastewater in association with chromate-reducing bacterial strains Ochrobactrum intermedium and Brevibacterium.

PubMed

Faisal, Muhammad; Hasnain, Shahida

2005-01-01

This study deals with the use of three chromium-resistant bacterial strains (Ochrobactrum intermedium CrT-1, Brevibacterium CrT-13, and CrM-1) in conjunction with Eichornia crassipes for the removal of toxic chromium from wastewater. Bacterial strains resulted in reduced uptake of chromate into inoculated plants as compared to noninoculated control plants. In the presence of different heavy metals, chromium uptake into the plants was 28.7 and 7.15% less at an initial K2CrO4 concentration of 100 and 500 microg ml(-1) in comparison to a metal free chromium solution. K2CrO4 uptake into the plant occurred at different pHs tested, but maximum uptake was observed at pH 5. Nevertheless, the bacterial strains caused some decrease in chromate uptake into the plants, but the combined effect of plants and bacterial strains conduce more removal of Cr(VI) from the solution.

Structure, Function, and Assembly of Type 1 Fimbriae

NASA Astrophysics Data System (ADS)

Knight, Stefan D.; Bouckaert, Julie

Bacterial infections constitute a major global health problem, acutely accentuated by the rapid spread of antibiotic resistant bacterial strains. The widespread need for bacteria to attach - adhere - to target cells before they can initiate an infection may be used to advantage by targeting the bacterial adhesion tools such as pili and fimbriae for development of novel anti-bacterial vaccines and drugs. Type 1 fimbriae are widely expressed by Escherichia coli. and are used by uropathogenic strains to mediate attachment to specific niches in the urinary tract. These fimbriae belong to a class of fibrillar adhesion organelles assembled through the chaperone/usher pathway, one of the terminal branches of the general secretion pathway in Gram-negative bacteria. Our understanding of the assembly, structure and function of these structures has evolved significantly over the last decade. Here, we summarize current understanding of the function and biogenesis of fibrillar adhesion organelles, and provide some examples of recent progress towards interfering with bacterial adhesion as a means to prevent infection.

Isolation and identification of efficient Egyptian malathion-degrading bacterial isolates.

PubMed

Hamouda, S A; Marzouk, M A; Abbassy, M A; Abd-El-Haleem, D A; Shamseldin, Abdelaal

2015-03-01

Bacterial isolates degrading malathion were isolated from the soil and agricultural waste water due to their ability to grow on minimal salt media amended with malathion as a sole carbon source. Efficiencies of native Egyptian bacterial malathion-degrading isolates were investigated and the study generated nine highly effective malathion-degrading bacterial strains among 40. Strains were identified by partial sequencing of 16S rDNA analysis. Comparative analysis of 16S rDNA sequences revealed that these bacteria are similar with the genus Acinetobacter and Bacillus spp. and RFLP based PCR of 16S rDNA gave four different RFLP patterns among strains with enzyme HinfI while with enzyme HaeI they gave two RFLP profiles. The degradation rate of malathion in liquid culture was estimated using gas chromatography. Bacterial strains could degrade more than 90% of the initial malathion concentration (1000 ppm) within 4 days. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Isolated cell behavior drives the evolution of antibiotic resistance

PubMed Central

Artemova, Tatiana; Gerardin, Ylaine; Dudley, Carmel; Vega, Nicole M; Gore, Jeff

2015-01-01

Bacterial antibiotic resistance is typically quantified by the minimum inhibitory concentration (MIC), which is defined as the minimal concentration of antibiotic that inhibits bacterial growth starting from a standard cell density. However, when antibiotic resistance is mediated by degradation, the collective inactivation of antibiotic by the bacterial population can cause the measured MIC to depend strongly on the initial cell density. In cases where this inoculum effect is strong, the relationship between MIC and bacterial fitness in the antibiotic is not well defined. Here, we demonstrate that the resistance of a single, isolated cell—which we call the single-cell MIC (scMIC)—provides a superior metric for quantifying antibiotic resistance. Unlike the MIC, we find that the scMIC predicts the direction of selection and also specifies the antibiotic concentration at which selection begins to favor new mutants. Understanding the cooperative nature of bacterial growth in antibiotics is therefore essential in predicting the evolution of antibiotic resistance. PMID:26227664

Bacteria Facilitate Enteric Virus Co-infection of Mammalian Cells and Promote Genetic Recombination.

PubMed

Erickson, Andrea K; Jesudhasan, Palmy R; Mayer, Melinda J; Narbad, Arjan; Winter, Sebastian E; Pfeiffer, Julie K

2018-01-10

RNA viruses exist in genetically diverse populations due to high levels of mutations, many of which reduce viral fitness. Interestingly, intestinal bacteria can promote infection of several mammalian enteric RNA viruses, but the mechanisms and consequences are unclear. We screened a panel of 41 bacterial strains as a platform to determine how different bacteria impact infection of poliovirus, a model enteric virus. Most bacterial strains, including those extracted from cecal contents of mice, bound poliovirus, with each bacterium binding multiple virions. Certain bacterial strains increased viral co-infection of mammalian cells even at a low virus-to-host cell ratio. Bacteria-mediated viral co-infection correlated with bacterial adherence to cells. Importantly, bacterial strains that induced viral co-infection facilitated genetic recombination between two different viruses, thereby removing deleterious mutations and restoring viral fitness. Thus, bacteria-virus interactions may increase viral fitness through viral recombination at initial sites of infection, potentially limiting abortive infections. Copyright © 2017 Elsevier Inc. All rights reserved.

Detection of Streptococcus mutans Genomic DNA in Human DNA Samples Extracted from Saliva and Blood

PubMed Central

Vieira, Alexandre R.; Deeley, Kathleen B.; Callahan, Nicholas F.; Noel, Jacqueline B.; Anjomshoaa, Ida; Carricato, Wendy M.; Schulhof, Louise P.; DeSensi, Rebecca S.; Gandhi, Pooja; Resick, Judith M.; Brandon, Carla A.; Rozhon, Christopher; Patir, Asli; Yildirim, Mine; Poletta, Fernando A.; Mereb, Juan C.; Letra, Ariadne; Menezes, Renato; Wendell, Steven; Lopez-Camelo, Jorge S.; Castilla, Eduardo E.; Orioli, Iêda M.; Seymen, Figen; Weyant, Robert J.; Crout, Richard; McNeil, Daniel W.; Modesto, Adriana; Marazita, Mary L.

2011-01-01

Caries is a multifactorial disease, and studies aiming to unravel the factors modulating its etiology must consider all known predisposing factors. One major factor is bacterial colonization, and Streptococcus mutans is the main microorganism associated with the initiation of the disease. In our studies, we have access to DNA samples extracted from human saliva and blood. In this report, we tested a real-time PCR assay developed to detect copies of genomic DNA from Streptococcus mutans in 1,424 DNA samples from humans. Our results suggest that we can determine the presence of genomic DNA copies of Streptococcus mutans in both DNA samples from caries-free and caries-affected individuals. However, we were not able to detect the presence of genomic DNA copies of Streptococcus mutans in any DNA samples extracted from peripheral blood, which suggests the assay may not be sensitive enough for this goal. Values of the threshold cycle of the real-time PCR reaction correlate with higher levels of caries experience in children, but this correlation could not be detected for adults. PMID:21731912

The Pathogenesis of Staphylococcus aureus Eye Infections

PubMed Central

2018-01-01

Staphylococcus aureus is a major pathogen of the eye able to infect the tear duct, eyelid, conjunctiva, cornea, anterior and posterior chambers, and the vitreous chamber. Of these infections, those involving the cornea (keratitis) or the inner chambers of the eye (endophthalmitis) are the most threatening because of their potential to cause a loss in visual acuity or even blindness. Each of these ocular sites is protected by the constitutive expression of a variety of antimicrobial factors and these defenses are augmented by a protective host response to the organism. Such infections often involve a predisposing factor that weakens the defenses, such as the use of contact lenses prior to the development of bacterial keratitis or, for endophthalmitis, the trauma caused by cataract surgery or intravitreal injection. The structural carbohydrates of the bacterial surface induce an inflammatory response able to reduce the bacterial load, but contribute to the tissue damage. A variety of bacterial secreted proteins including alpha-toxin, beta-toxin, gamma-toxin, Panton-Valentine leukocidin and other two-component leukocidins mediate tissue damage and contribute to the induction of the inflammatory response. Quantitative animal models of keratitis and endophthalmitis have provided insights into the S. aureus virulence and host factors active in limiting such infections. PMID:29320451

Antimicrobial Nanoplexes meet Model Bacterial Membranes: the key role of Cardiolipin

NASA Astrophysics Data System (ADS)

Marín-Menéndez, Alejandro; Montis, Costanza; Díaz-Calvo, Teresa; Carta, Davide; Hatzixanthis, Kostas; Morris, Christopher J.; McArthur, Michael; Berti, Debora

2017-01-01

Antimicrobial resistance to traditional antibiotics is a crucial challenge of medical research. Oligonucleotide therapeutics, such as antisense or Transcription Factor Decoys (TFDs), have the potential to circumvent current resistance mechanisms by acting on novel targets. However, their full translation into clinical application requires efficient delivery strategies and fundamental comprehension of their interaction with target bacterial cells. To address these points, we employed a novel cationic bolaamphiphile that binds TFDs with high affinity to form self-assembled complexes (nanoplexes). Confocal microscopy revealed that nanoplexes efficiently transfect bacterial cells, consistently with biological efficacy on animal models. To understand the factors affecting the delivery process, liposomes with varying compositions, taken as model synthetic bilayers, were challenged with nanoplexes and investigated with Scattering and Fluorescence techniques. Thanks to the combination of results on bacteria and synthetic membrane models we demonstrate for the first time that the prokaryotic-enriched anionic lipid Cardiolipin (CL) plays a key-role in the TFDs delivery to bacteria. Moreover, we can hypothesize an overall TFD delivery mechanism, where bacterial membrane reorganization with permeability increase and release of the TFD from the nanoplexes are the main factors. These results will be of great benefit to boost the development of oligonucleotides-based antimicrobials of superior efficacy.

Isolation, identification, and algicidal activity of aerobic denitrifying bacterium R11 and its effect on Microcystis aeruginosa.

PubMed

Su, Jun-feng; Shao, Si-cheng; Huang, Ting-lin; Ma, Fang; Zhang, Kai; Wen, Gang; Zheng, Sheng-chen

2016-01-01

Recently, algicidal bacteria have attracted attention as possible agents for the inhibition of algal water blooms. In this study, an aerobic denitrifying bacterium, R11, with high algicidal activity against the toxic Microcystis aeruginosa was isolated from lake sediments. Based on its physiological characteristics and 16S rRNA gene sequence, it was identified as Raoultella, indicating that the bacterium R11 has a good denitrifying ability at 30 °C and can reduce the concentration of nitrate-N completely within 36 h. Additionally, different algicidal characteristics against Microcystis aeruginosa were tested. The results showed that the initial bacterial cell density and algal cell densities strongly influence the removal rates of chlorophyll a. Algicidal activity increased with an increase in the bacterial cell density. With densities of bacterial culture at over 2.4 × 10(5) cell/mL, algicidal activity of up to 80% was obtained in 4 days. We have demonstrated that, with the low initial algal cell density (OD680 less than 0.220), the algicidal activity reached was higher than 90% after 6 days.

Bacterial prostatitis.

PubMed

Gill, Bradley C; Shoskes, Daniel A

2016-02-01

The review provides the infectious disease community with a urologic perspective on bacterial prostatitis. Specifically, the article briefly reviews the categorization of prostatitis by type and provides a distillation of new findings published on bacterial prostatitis over the past year. It also highlights key points from the established literature. Cross-sectional prostate imaging is becoming more common and may lead to more incidental diagnoses of acute bacterial prostatitis. As drug resistance remains problematic in this condition, the reemergence of older antibiotics such as fosfomycin, has proven beneficial. With regard to chronic bacterial prostatitis, no clear clinical risk factors emerged in a large epidemiological study. However, bacterial biofilm formation has been associated with more severe cases. Surgery has a limited role in bacterial prostatitis and should be reserved for draining of a prostatic abscess or the removal of infected prostatic stones. Prostatitis remains a common and bothersome clinical condition. Antibiotic therapy remains the basis of treatment for both acute and chronic bacterial prostatitis. Further research into improving prostatitis treatment is indicated.

Distinct antimicrobial peptide expression determines host species-specific bacterial associations

PubMed Central

Franzenburg, Sören; Walter, Jonas; Künzel, Sven; Wang, Jun; Baines, John F.; Bosch, Thomas C. G.; Fraune, Sebastian

2013-01-01

Animals are colonized by coevolved bacterial communities, which contribute to the host’s health. This commensal microbiota is often highly specific to its host-species, inferring strong selective pressures on the associated microbes. Several factors, including diet, mucus composition, and the immune system have been proposed as putative determinants of host-associated bacterial communities. Here we report that species-specific antimicrobial peptides account for different bacterial communities associated with closely related species of the cnidarian Hydra. Gene family extensions for potent antimicrobial peptides, the arminins, were detected in four Hydra species, with each species possessing a unique composition and expression profile of arminins. For functional analysis, we inoculated arminin-deficient and control polyps with bacterial consortia characteristic for different Hydra species and compared their selective preferences by 454 pyrosequencing of the bacterial microbiota. In contrast to control polyps, arminin-deficient polyps displayed decreased potential to select for bacterial communities resembling their native microbiota. This finding indicates that species-specific antimicrobial peptides shape species-specific bacterial associations. PMID:24003149

Zoonotic bacterial meningitis in human adults.

PubMed

van Samkar, Anusha; Brouwer, Matthijs C; van der Ende, Arie; van de Beek, Diederik

2016-09-13

To describe the epidemiology, etiology, clinical characteristics, treatment, outcome, and prevention of zoonotic bacterial meningitis in human adults. We identified 16 zoonotic bacteria causing meningitis in adults. Zoonotic bacterial meningitis is uncommon compared to bacterial meningitis caused by human pathogens, and the incidence has a strong regional distribution. Zoonotic bacterial meningitis is mainly associated with animal contact, consumption of animal products, and an immunocompromised state of the patient. In a high proportion of zoonotic bacterial meningitis cases, CSF analysis showed only a mildly elevated leukocyte count. The recommended antibiotic therapy differs per pathogen, and the overall mortality is low. Zoonotic bacterial meningitis is uncommon but is associated with specific complications. The suspicion should be raised in patients with bacterial meningitis who have recreational or professional contact with animals and in patients living in regions endemic for specific zoonotic pathogens. An immunocompromised state is associated with a worse prognosis. Identification of risk factors and underlying disease is necessary to improve treatment. © 2016 American Academy of Neurology.

Human and riverine impacts on the dynamics of seawater nutrient and carbon parameters in Kwangyang Bay, South Korea

NASA Astrophysics Data System (ADS)

Kim, Tae-Wook; Kim, Dongseon; Baek, Seung Ho; Kim, Young Ok

2015-04-01

We investigated seawater nutrient and carbon parameters in Kwangyang Bay, South Korea, which has been exposed to significant human influences, in each core month of four seasons for between 2010 and 2012. The survey data were analyzed using multivariate statistics analysis (cluster and factor analysis). As a result, we found that the Seomjin River (the fifth largest river in South Korea) and biological activity, including phytoplankton photosynthesis and bacterial decomposition, were the main factors determining the overall water quality of the bay. However, the impacts of these factors varied both spatially and seasonally, because the factors were linked with the geographical environments and seasonal variations in freshwater discharge. In particular, the Seomjin River was primarily responsible for nitrate, silicate, total alkalinity, and dissolved inorganic carbon, and exhibited a significant impact in the summer. During the past 10 years, nutrient loads from the river and industrial complexes to the bay have decreased. The impacts of this decrease are visible in the phosphate concentration, which has fallen to a third of its initial value. We also examined the potential role of atmospheric nitrogen deposition in nitrogen cycling in the study area.

In Situ Hydrocarbon Degradation by Indigenous Nearshore Bacterial Populations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cherrier, J.

Potential episodic hydrocarbon inputs associated with oil mining and transportation together with chronic introduction of hydrocarbons via urban runoff into the relatively pristine coastal Florida waters poses a significant threat to Florida's fragile marine environment. It is therefore important to understand the extent to which indigenous bacterial populations are able to degrade hydrocarbon compounds and also determine factors that could potentially control and promote the rate at which these compounds are broken down in situ. Previous controlled laboratory experiments carried out by our research group demonstrated that separately both photo-oxidation and cometabolism stimulate bacterial hydrocarbon degradation by natural bacterial assemblagesmore » collected from a chronically petroleum contaminated site in Bayboro Bay, Florida. Additionally, we also demonstrated that stable carbon and radiocarbon abundances of respired CO{sub 2} could be used to trace in situ hydrocarbon degradation by indigenous bacterial populations at this same site. This current proposal had two main objectives: (a) to evaluate the cumulative impact of cometabolism and photo-oxidation on hydrocarbon degradation by natural bacterial assemblages collected the same site in Bayboro Bay, Florida and (b) to determine if in situ hydrocarbon degradation by indigenous bacterial populations this site could be traced using natural radiocarbon and stable carbon abundances of assimilated bacterial carbon. Funds were used for 2 years of full support for one ESI Ph.D. student, April Croxton. To address our first objective a series of closed system bacterial incubations were carried out using photo-oxidized petroleum and pinfish (i.e. cometabolite). Bacterial production of CO{sub 2} was used as the indicator of hydrocarbon degradation and {delta}{sup 13}C analysis of the resultant CO{sub 2} was used to evaluate the source of the respired CO{sub 2} (i.e. petroleum hydrocarbons or the pinfish cometabolite). Results from these time series experiments demonstrated that short-term exposure of petroleum to UV light enhanced hydrocarbon degradation by 48% over that observed for non-photo-oxidized petroleum. Despite the greater bio-availability of the photo-oxidized over the non-photo-oxidized petroleum, an initial lag in CO{sub 2} production was observed indicating potential phototoxicity of the photo- by-products. {delta}{sup 13}C analysis and mass balance calculations reveal that co-metabolism with pinfish resulted in increased hydrocarbon degradation for both photo-oxidized and non-photo-oxidized petroleum each by over 100%. These results demonstrate the cumulative effect of photo-oxidation and co-metabolism on petroleum hydrocarbon degradation by natural bacterial populations indigenous to systems chronically impacted by hydrocarbon input. To address the second objective of this proposal bacterial concentrates were collected from Bayboro Harbor in April 2001 for nucleic acid extraction and subsequent natural radiocarbon abundance analyses. Unfortunately, however, all of these samples were lost due to a faulty compressor in our -70 freezer. The freezer was subsequently repaired and samples were again collected from Bayboro Harbor in June 2002 and again December 2002. Several attempts were made to extract the nucleic acid samples--however, the student was not able to successfully extract and an adequate amount of uncontaminated nucleic acid samples for subsequent natural radiocarbon abundance measurements of the bacterial carbon by accelerator mass spectrometry (i.e. require at least 50 {micro}g carbon for AMS measurement). Consequently, we were not able to address the second objective of this proposed work.« less

Contrasting spatial patterns and ecological attributes of soil bacterial and archaeal taxa across a landscape.

PubMed

Constancias, Florentin; Saby, Nicolas P A; Terrat, Sébastien; Dequiedt, Samuel; Horrigue, Wallid; Nowak, Virginie; Guillemin, Jean-Philippe; Biju-Duval, Luc; Chemidlin Prévost-Bouré, Nicolas; Ranjard, Lionel

2015-06-01

Even though recent studies have clarified the influence and hierarchy of environmental filters on bacterial community structure, those constraining bacterial populations variations remain unclear. In consequence, our ability to understand to ecological attributes of soil bacteria and to predict microbial community response to environmental stress is therefore limited. Here, we characterized the bacterial community composition and the various bacterial taxonomic groups constituting the community across an agricultural landscape of 12 km(2) , by using a 215 × 215 m systematic grid representing 278 sites to precisely decipher their spatial distribution and drivers at this scale. The bacterial and Archaeal community composition was characterized by applying 16S rRNA gene pyrosequencing directly to soil DNA from samples. Geostatistics tools were used to reveal the heterogeneous distribution of bacterial composition at this scale. Soil physical parameters and land management explained a significant amount of variation, suggesting that environmental selection is the major process shaping bacterial composition. All taxa systematically displayed also a heterogeneous and particular distribution patterns. Different relative influences of soil characteristics, land use and space were observed, depending on the taxa, implying that selection and spatial processes might be differentially but not exclusively involved for each bacterial phylum. Soil pH was a major factor determining the distribution of most of the bacterial taxa and especially the most important factor explaining the spatial patterns of α-Proteobacteria and Planctomycetes. Soil texture, organic carbon content and quality were more specific to a few number of taxa (e.g., β-Proteobacteria and Chlorobi). Land management also influenced the distribution of bacterial taxa across the landscape and revealed different type of response to cropping intensity (positive, negative, neutral or hump-backed relationships) according to phyla. Altogether, this study provided valuable clues about the ecological behavior of soil bacterial and archaeal taxa at an agricultural landscape scale and could be useful for developing sustainable strategies of land management. © 2015 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Effects of initial moisture content of Korean traditional wheat-based fermentation starter nuruk on microbial abundance and diversity.

PubMed

Bal, Jyotiranjan; Yun, Suk-Hyun; Yeo, Soo-Hwan; Kim, Jung-Mi; Kim, Beom-Tae; Kim, Dae-Hyuk

2017-03-01

The brewing of makgeolli, one of Korea's most popular alcoholic beverages that is gaining popularity globally, is facilitated by nuruk, a traditional Korean cereal starter. The nuruk microbiome greatly influences the fermentation process as well as the nutritional, hygienic, and aromatic qualities of the product. This study is a continuation of our efforts to examine nuruk biodiversity at a depth previously unattainable. In this study, microfloral dynamics in wheat-based nuruk C, composed of traditional ingredients such as barley, green gram, and wheat and fermented under various internal moisture contents of 20% (C20), 26% (C26), and 30% (C30), was evaluated using 454 pyrosequencing during the 30-day fermentation process. Rarefaction analysis and alpha diversity parameters indicated adequate sampling. C20 showed the greatest fungal richness and diversity, C20 and C26 exhibited similar bacterial richness and diversity, while C30 had low fungal and bacterial richness. Fungal taxonomic assignments revealed that the initial moisture content caused selective enrichment of Aspergillus candidus with a decreasing trend during fermentation, whereas Saccharomycetales sp. exhibited increasing relative abundance with increasing moisture content from day 6 of the fermentation process. Depending on initial moisture level, changes in bacterial communities were also observed in the genera Streptomyces, Bacillus, and Staphylococcus, with decreasing trends whereas Saccharopolyspora exhibited a sigmoidal trend with the highest abundance in C26. These findings demonstrate the possible impact of initial moisture content of nuruk on microfloral richness, diversity, and dynamics; this study is thus a step toward our ultimate goal of enhancing the quality of nuruk.

Elucidation of Sigma Factor-Associated Networks in Pseudomonas aeruginosa Reveals a Modular Architecture with Limited and Function-Specific Crosstalk

PubMed Central

Schulz, Sebastian; Eckweiler, Denitsa; Bielecka, Agata; Nicolai, Tanja; Franke, Raimo; Dötsch, Andreas; Hornischer, Klaus; Bruchmann, Sebastian; Düvel, Juliane; Häussler, Susanne

2015-01-01

Sigma factors are essential global regulators of transcription initiation in bacteria which confer promoter recognition specificity to the RNA polymerase core enzyme. They provide effective mechanisms for simultaneously regulating expression of large numbers of genes in response to challenging conditions, and their presence has been linked to bacterial virulence and pathogenicity. In this study, we constructed nine his-tagged sigma factor expressing and/or deletion mutant strains in the opportunistic pathogen Pseudomonas aeruginosa. To uncover the direct and indirect sigma factor regulons, we performed mRNA profiling, as well as chromatin immunoprecipitation coupled to high-throughput sequencing. We furthermore elucidated the de novo binding motif of each sigma factor, and validated the RNA- and ChIP-seq results by global motif searches in the proximity of transcriptional start sites (TSS). Our integrated approach revealed a highly modular network architecture which is composed of insulated functional sigma factor modules. Analysis of the interconnectivity of the various sigma factor networks uncovered a limited, but highly function-specific, crosstalk which orchestrates complex cellular processes. Our data indicate that the modular structure of sigma factor networks enables P. aeruginosa to function adequately in its environment and at the same time is exploited to build up higher-level functions by specific interconnections that are dominated by a participation of RpoN. PMID:25780925

A novel host factor for integration of mycobacteriophage L5

PubMed Central

Pedulla, Marisa L.; Lee, Mong Hong; Lever, Dawn C.; Hatfull, Graham F.

1996-01-01

Bacterial integration host factors (IHFs) play central roles in the cellular processes of recombination, DNA replication, transcription, and bacterial pathogenesis. We describe here a novel mycobacterial IHF (mIHF) of Mycobacterium smegmatis and Mycobacterium tuberculosis that stimulates integration of mycobacteriophage L5. mIHF is the product of a single gene and is unrelated at the sequence level to other integration host factors. By itself, mIHF does not bind preferentially to attP DNA, although it significantly alters the pattern of integrase (Int) binding, promoting the formation of specific integrase–mIHF–attP intasome complexes. PMID:8986825

Two-Level factorial screening of new plasmid/strain combinations for prodution of recombinant-DNA products.

PubMed

Emborg, C; Jepsen, P K; Biedermann, K

1989-05-01

This article treats the basic problem of selection of experimental conditions for microbiological experiments for evaluation of newly isolated bacterial strains, mutants, or plasmid/strain combinations. For this purpose shake flask experiments in a 2(10-4)confounded factorial design at resolution IV with four blocks of 16 flasks were used. The design was used for testing of two new strain/plasmid combinations (E. coli MT 102/403-SD2 and W 3110/403-SD2) i.e., both strains with the same plasmid 403-SD2. Both strains were integrated in the design, so both strains were tested with nine factors (temperature, aeration, glucose, initial pH, pH regulation, reduced aeration, chloramphenicol, acetate, and glycerol). With both strains the interaction between initial pH and reduced aeration had a significant influence on the yield of the recombinant-DNA product nuclease. There was more than a factor of 10 between lowest and highest yield of product. In this interactive system the strains reacted differently. MT 102/403-SD2 had highest yields at high initial pH (8.4) and no reduction in aeration, whereas W 3110/403-SD2 had highest yields of nuclease at low initial pH (7.4) and reduced aeration (rubber stopper inserted after cultivation for 12 h). These data (and previous work) clearly demonstrate that it is impossible to suggest a simple set of experimental conditions for testing of new plasmid/strain combinations. It is clear that the exclusive application of a standardized growth technique e.g., LB-medium at 37 degrees C at an unspecified and uncontrolled aeration level, may lead to wrong conclusions on properties and potentials of now plasmid/strain combinations and may lead to rejection of useful strains or plasmids.

Bacterial Mercury Methylation At The Sediment-Water Interface Of Mercury Contaminated Sediments

EPA Science Inventory

Bench scale experiments were conducted to improve our understanding of bacterial mediation of mercury transformation (methylation), specifically those factors which govern the production of methyl mercury (MeHg) at the sediment-water interface. The greatest cause for concern re...

454 pyrosequencing analysis of bacterial diversity revealed by a comparative study of soils from mining subsidence and reclamation areas.

PubMed

Li, Yuanyuan; Chen, Longqian; Wen, Hongyu; Zhou, Tianjian; Zhang, Ting; Gao, Xiali

2014-03-28

Significant alteration in the microbial community can occur across reclamation areas suffering subsidence from mining. A reclamation site undergoing fertilization practices and an adjacent coal-excavated subsidence site (sites A and B, respectively) were examined to characterize the bacterial diversity using 454 high-throughput 16S rDNA sequencing. The dominant taxonomic groups in both the sites were Proteobacteria, Acidobacteria, Bacteroidetes, Betaproteobacteria, Actinobacteria, Gammaproteobacteria, Alphaproteobacteria, Deltaproteobacteria, Chloroflexi, and Firmicutes. However, the bacterial communities' abundance, diversity, and composition differed significantly between the sites. Site A presented higher bacterial diversity and more complex community structures than site B. The majority of sequences related to Proteobacteria, Gemmatimonadetes, Chloroflexi, Nitrospirae, Firmicutes, Betaproteobacteria, Deltaproteobacteria, and Anaerolineae were from site A; whereas those related to Actinobacteria, Planctomycetes, Bacteroidetes, Verrucomicrobia, Gammaproteobacteria, Nitriliruptoria, Alphaproteobacteria, and Phycisphaerae originated from site B. The distribution of some bacterial groups and subgroups in the two sites correlated with soil properties and vegetation due to reclamation practice. Site A exhibited enriched bacterial community, soil organic matter (SOM), and total nitrogen (TN), suggesting the presence of relatively diverse microorganisms. SOM and TN were important factors shaping the underlying microbial communities. Furthermore, the specific plant functional group (legumes) was also an important factor influencing soil microbial community composition. Thus, the effectiveness of 454 pyrosequencing in analyzing soil bacterial diversity was validated and an association between land ecological system restoration, mostly mediated by microbial communities, and an improvement in soil properties in coalmining reclamation areas was suggested.

Trimeric autotransporter adhesins contribute to Actinobacillus pleuropneumoniae pathogenicity in mice and regulate bacterial gene expression during interactions between bacteria and porcine primary alveolar macrophages.

PubMed

Qin, Wanhai; Wang, Lei; Zhai, Ruidong; Ma, Qiuyue; Liu, Jianfang; Bao, Chuntong; Zhang, Hu; Sun, Changjiang; Feng, Xin; Gu, Jingmin; Du, Chongtao; Han, Wenyu; Langford, P R; Lei, Liancheng

2016-01-01

Actinobacillus pleuropneumoniae is an important pathogen that causes respiratory disease in pigs. Trimeric autotransporter adhesin (TAA) is a recently discovered bacterial virulence factor that mediates bacterial adhesion and colonization. Two TAA coding genes have been found in the genome of A. pleuropneumoniae strain 5b L20, but whether they contribute to bacterial pathogenicity is unclear. In this study, we used homologous recombination to construct a double-gene deletion mutant, ΔTAA, in which both TAA coding genes were deleted and used it in in vivo and in vitro studies to confirm that TAAs participate in bacterial auto-aggregation, biofilm formation, cell adhesion and virulence in mice. A microarray analysis was used to determine whether TAAs can regulate other A. pleuropneumoniae genes during interactions with porcine primary alveolar macrophages. The results showed that deletion of both TAA coding genes up-regulated 36 genes, including ene1514, hofB and tbpB2, and simultaneously down-regulated 36 genes, including lgt, murF and ftsY. These data illustrate that TAAs help to maintain full bacterial virulence both directly, through their bioactivity, and indirectly by regulating the bacterial type II and IV secretion systems and regulating the synthesis or secretion of virulence factors. This study not only enhances our understanding of the role of TAAs but also has significance for those studying A. pleuropneumoniae pathogenesis.

Bacterial Prostatitis: Bacterial Virulence, Clinical Outcomes, and New Directions.

PubMed

Krieger, John N; Thumbikat, Praveen

2016-02-01

Four prostatitis syndromes are recognized clinically: acute bacterial prostatitis, chronic bacterial prostatitis, chronic prostatitis/chronic pelvic pain syndrome, and asymptomatic prostatitis. Because Escherichia coli represents the most common cause of bacterial prostatitis, we investigated the importance of bacterial virulence factors and antimicrobial resistance in E. coli strains causing prostatitis and the potential association of these characteristics with clinical outcomes. A structured literature review revealed that we have limited understanding of the virulence-associated characteristics of E. coli causing acute prostatitis. Therefore, we completed a comprehensive microbiological and molecular investigation of a unique strain collection isolated from healthy young men. We also considered new data from an animal model system suggesting certain E. coli might prove important in the etiology of chronic prostatitis/chronic pelvic pain syndrome. Our human data suggest that E. coli needs multiple pathogenicity-associated traits to overcome anatomic and immune responses in healthy young men without urological risk factors. The phylogenetic background and accumulation of an exceptional repertoire of extraintestinal pathogenic virulence-associated genes indicate that these E. coli strains belong to a highly virulent subset of uropathogenic variants. In contrast, antibiotic resistance confers little added advantage to E. coli strains in these healthy outpatients. Our animal model data also suggest that certain pathogenic E. coli may be important in the etiology of chronic prostatitis/chronic pelvic pain syndrome through mechanisms that are dependent on the host genetic background and the virulence of the bacterial strain.

Biogeography of planktonic and coral-associated microorganisms across the Hawaiian Archipelago.

PubMed

Salerno, Jennifer L; Bowen, Brian W; Rappé, Michael S

2016-08-01

Factors driving the distribution of marine microorganisms are widely debated and poorly understood. Recent studies show that free-living marine microbes exhibit geographical patterns indicative of limited dispersal. In contrast, host-associated microbes face a different set of dispersal challenges, and hosts may function as habitat 'islands' for resident microbial populations. Here, we examine the biogeographical distributions of planktonic and adjacent coral-associated bacterial communities across the Hawaiian Archipelago, Johnston Atoll (∼1400 km southwest of Hawaii) and American Samoa in the Pacific Ocean and investigate the potential underlying processes driving observed patterns. Statistical analyses of bacterial community structure, determined using a small-subunit ribosomal RNA gene-based approach, showed that bacterioplankton and coral-associated bacterial communities were distinct, and correlated with geographical distance between sites. In addition, biogeographical patterns of bacterial associates paralleled those of their host coral Porites lobata, highlighting the specificity of these associations and the impact that host dispersal may have on bacterial biogeography. Planktonic and coral-associated bacterial communities from distant Johnston Atoll were shown to be connected with communities from the center of the Hawaiian Archipelago, a pattern previously observed in fish and invertebrates. No significant correlations were detected with habitat type, temperature or depth. However, non-distance-based geographical groupings were detected, indicating that, in addition to dispersal, unidentified environmental factors also affected the distributions of bacterial communities investigated here. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Age-related risk factors for bacterial aetiology in community-acquired pneumonia.

PubMed

Sahuquillo-Arce, José M; Menéndez, Rosario; Méndez, Raúl; Amara-Elori, Isabel; Zalacain, Rafael; Capelastegui, Alberto; Aspa, Javier; Borderías, Luis; Martín-Villasclaras, Juan J; Bello, Salvador; Alfageme, Inmaculada; de Castro, Felipe Rodriguez; Rello, Jordi; Molinos, Luis; Ruiz-Manzano, Juan; Torres, Antoni

2016-11-01

The objective of this study was to evaluate the effect of age and comorbidities, smoking and alcohol use on microorganisms in patients with community-acquired pneumonia (CAP). A prospective multicentre study was performed with 4304 patients. We compared microbiological results, bacterial aetiology, smoking, alcohol abuse and comorbidities in three age groups: young adults (<45 years), adults (45-64 years) and seniors (>65 years). Bacterial aetiology was identified in 1522 (35.4%) patients. In seniors, liver disease was independently associated with Gram-negative bacteria (Haemophilus influenzae and Enterobacteriaceae), COPD with Pseudomonas aeruginosa (OR = 2.69 (1.46-4.97)) and Staphylococcus aureus (OR = 2.8 (1.24-6.3)) and neurological diseases with S. aureus. In adults, diabetes mellitus (DM) was a risk factor for Streptococcus pneumoniae and S. aureus, and COPD for H. influenzae (OR = 3.39 (1.06-10.83)). In young adults, DM was associated with S. aureus. Smoking was a risk factor for Legionella pneumophila regardless of age. Alcohol intake was associated with mixed aetiology and Coxiella burnetii in seniors, and with S. pneumoniae in young adults. It should be considered that the bacterial aetiology may differ according to the patient's age, comorbidities, smoking and alcohol abuse. More extensive microbiological testing is warranted in those with risk factors for infrequent microorganisms. © 2016 Asian Pacific Society of Respirology.

Bacterial bloodstream infections in the allogeneic hematopoietic cell transplant patient: new considerations for a persistent nemesis.

PubMed

Dandoy, C E; Ardura, M I; Papanicolaou, G A; Auletta, J J

2017-08-01

Bacterial bloodstream infections (BSI) cause significant transplant-related morbidity and mortality following allogeneic hematopoietic cell transplantation (allo-HCT). This manuscript reviews the risk factors for and the bacterial pathogens causing BSIs in allo-HCT recipients in the contemporary transplant period. In addition, it offers insight into emerging resistant pathogens and reviews clinical management considerations to treat and strategies to prevent BSIs in allo-HCT patients.

California Black Oak Drying Problems and the Bacterial Factor.

DTIC Science & Technology

1979-01-01

operations in Anderson area and to adjacent kilns by spacing stickers 18 inches apart and Georgia and wondered if bacterial tree drying softwood lumber at...on stickers in a weighted, volatile fatty acids which are the sapwood , and then from the outer, covered pile placed outdoors on the characteristic of...1. JT~~~ Figure 1 —Scanning electron micrographs of nonintected sapwood (A-B) and bacterially infected heartwood (C-D) from

The papain inhibitor (SPI) of Streptomyces mobaraensis inhibits bacterial cysteine proteases and is an antagonist of bacterial growth.

PubMed

Zindel, Stephan; Kaman, Wendy E; Fröls, Sabrina; Pfeifer, Felicitas; Peters, Anna; Hays, John P; Fuchsbauer, Hans-Lothar

2013-07-01

A novel papain inhibitory protein (SPI) from Streptomyces mobaraensis was studied to measure its inhibitory effect on bacterial cysteine protease activity (Staphylococcus aureus SspB) and culture supernatants (Porphyromonas gingivalis, Bacillus anthracis). Further, growth of Bacillus anthracis, Staphylococcus aureus, Pseudomonas aeruginosa, and Vibrio cholerae was completely inhibited by 10 μM SPI. At this concentration of SPI, no cytotoxicity was observed. We conclude that SPI inhibits bacterial virulence factors and has the potential to become a novel therapeutic treatment against a range of unrelated pathogenic bacteria.

Postviral Complications: Bacterial Pneumonia.

PubMed

Prasso, Jason E; Deng, Jane C

2017-03-01

Secondary bacterial pneumonia after viral respiratory infection remains a significant source of morbidity and mortality. Susceptibility is mediated by a variety of viral and bacterial factors, and complex interactions with the host immune system. Prevention and treatment strategies are limited to influenza vaccination and antibiotics/antivirals respectively. Novel approaches to identifying the individuals with influenza who are at increased risk for secondary bacterial pneumonias are urgently needed. Given the threat of further pandemics and the heightened prevalence of these viruses, more research into the immunologic mechanisms of this disease is warranted with the hope of discovering new potential therapies. Published by Elsevier Inc.

Procalcitonin guidance in patients with lower respiratory tract infections: a systematic review and meta-analysis.

PubMed

Hey, Juliane; Thompson-Leduc, Philippe; Kirson, Noam Y; Zimmer, Louise; Wilkins, Dana; Rice, Bernie; Iankova, Irena; Krause, Alexander; Schonfeld, Sophie A; DeBrase, Christopher R; Bozzette, Samuel; Schuetz, Philipp

2018-05-01

Although effective for bacterial lower respiratory tract infections (LRTIs), antibiotic treatment is often incorrectly prescribed for non-bacterial LRTIs. Procalcitonin has emerged as a promising biomarker to diagnose bacterial infections and guide antibiotic treatment decisions. As part of a regulatory submission to the U.S. Food and Drug Administration, this systematic review and meta-analysis summarizes the effects of procalcitonin-guided antibiotic stewardship on antibiotic use and clinical outcomes in adult LRTI patients. PubMed and the Cochrane Database of Systematic Reviews were searched for English-language randomized controlled trials published between January 2004 and May 2016. Random and fixed effects meta-analyses were performed to study efficacy (initiation of antibiotics, antibiotic use) and safety (mortality, length of hospital stay). Eleven trials were retained, comprising 4090 patients. Procalcitonin-guided patients had lower odds of antibiotic initiation (odds ratio: 0.26; 95% confidence interval [CI]: 0.13-0.52) and shorter mean antibiotic use (weighted mean difference: -2.15 days; 95% CI: -3.30 to -0.99) compared to patients treated with standard care. Procalcitonin use had no adverse impact on mortality (relative risk: 0.94; 95% CI: 0.69-1.28) and length of hospital stay (weighted mean difference: -0.15 days; 95% CI: -0.60 to 0.30). Procalcitonin guidance reduces antibiotic initiation and use among adults with LRTIs with no apparent adverse impact on length of hospital stay or mortality.

Associations between Ectomycorrhizal Fungi and Bacterial Needle Endophytes in Pinus radiata: Implications for Biotic Selection of Microbial Communities

PubMed Central

Rúa, Megan A.; Wilson, Emily C.; Steele, Sarah; Munters, Arielle R.; Hoeksema, Jason D.; Frank, Anna C.

2016-01-01

Studies of the ecological and evolutionary relationships between plants and their associated microbes have long been focused on single microbes, or single microbial guilds, but in reality, plants associate with a diverse array of microbes from a varied set of guilds. As such, multitrophic interactions among plant-associated microbes from multiple guilds represent an area of developing research, and can reveal how complex microbial communities are structured around plants. Interactions between coniferous plants and their associated microbes provide a good model system for such studies, as conifers host a suite of microorganisms including mutualistic ectomycorrhizal (ECM) fungi and foliar bacterial endophytes. To investigate the potential role ECM fungi play in structuring foliar bacterial endophyte communities, we sampled three isolated, native populations of Monterey pine (Pinus radiata), and used constrained analysis of principal coordinates to relate the community matrices of the ECM fungi and bacterial endophytes. Our results suggest that ECM fungi may be important factors for explaining variation in bacterial endophyte communities but this effect is influenced by population and environmental characteristics, emphasizing the potential importance of other factors — biotic or abiotic — in determining the composition of bacterial communities. We also classified ECM fungi into categories based on known fungal traits associated with substrate exploration and nutrient mobilization strategies since variation in these traits allows the fungi to acquire nutrients across a wide range of abiotic conditions and may influence the outcome of multi-species interactions. Across populations and environmental factors, none of the traits associated with fungal foraging strategy types significantly structured bacterial assemblages, suggesting these ECM fungal traits are not important for understanding endophyte-ECM interactions. Overall, our results suggest that both biotic species interactions and environmental filtering are important for structuring microbial communities but emphasize the need for more research into these interactions. PMID:27065966

Pan-Genomic Analysis Permits Differentiation of Virulent and Non-virulent Strains of Xanthomonas arboricola That Cohabit Prunus spp. and Elucidate Bacterial Virulence Factors

PubMed Central

Garita-Cambronero, Jerson; Palacio-Bielsa, Ana; López, María M.; Cubero, Jaime

2017-01-01

Xanthomonas arboricola is a plant-associated bacterial species that causes diseases on several plant hosts. One of the most virulent pathovars within this species is X. arboricola pv. pruni (Xap), the causal agent of bacterial spot disease of stone fruit trees and almond. Recently, a non-virulent Xap-look-a-like strain isolated from Prunus was characterized and its genome compared to pathogenic strains of Xap, revealing differences in the profile of virulence factors, such as the genes related to the type III secretion system (T3SS) and type III effectors (T3Es). The existence of this atypical strain arouses several questions associated with the abundance, the pathogenicity, and the evolutionary context of X. arboricola on Prunus hosts. After an initial characterization of a collection of Xanthomonas strains isolated from Prunus bacterial spot outbreaks in Spain during the past decade, six Xap-look-a-like strains, that did not clustered with the pathogenic strains of Xap according to a multi locus sequence analysis, were identified. Pathogenicity of these strains was analyzed and the genome sequences of two Xap-look-a-like strains, CITA 14 and CITA 124, non-virulent to Prunus spp., were obtained and compared to those available genomes of X. arboricola associated with this host plant. Differences were found among the genomes of the virulent and the Prunus non-virulent strains in several characters related to the pathogenesis process. Additionally, a pan-genomic analysis that included the available genomes of X. arboricola, revealed that the atypical strains associated with Prunus were related to a group of non-virulent or low virulent strains isolated from a wide host range. The repertoire of the genes related to T3SS and T3Es varied among the strains of this cluster and those strains related to the most virulent pathovars of the species, corylina, juglandis, and pruni. This variability provides information about the potential evolutionary process associated to the acquisition of pathogenicity and host specificity in X. arboricola. Finally, based in the genomic differences observed between the virulent and the non-virulent strains isolated from Prunus, a sensitive and specific real-time PCR protocol was designed to detect and identify Xap strains. This method avoids miss-identifications due to atypical strains of X. arboricola that can cohabit Prunus. PMID:28450852

RNA-Seq Links the Transcription Factors AINTEGUMENTA and AINTEGUMENTA-LIKE6 to Cell Wall Remodeling and Plant Defense Pathways1[OPEN

PubMed Central

Bequette, Carlton J.; Fu, Zheng Qing; Loraine, Ann E.

2016-01-01

AINTEGUMENTA (ANT) and AINTEGUMENTA-LIKE6 (AIL6) are two related transcription factors in Arabidopsis (Arabidopsis thaliana) that have partially overlapping roles in several aspects of flower development, including floral organ initiation, identity specification, growth, and patterning. To better understand the biological processes regulated by these two transcription factors, we performed RNA sequencing (RNA-Seq) on ant ail6 double mutants. We identified thousands of genes that are differentially expressed in the double mutant compared with the wild type. Analyses of these genes suggest that ANT and AIL6 regulate floral organ initiation and growth through modifications to the cell wall polysaccharide pectin. We found reduced levels of demethylesterified homogalacturonan and altered patterns of auxin accumulation in early stages of ant ail6 flower development. The RNA-Seq experiment also revealed cross-regulation of AIL gene expression at the transcriptional level. The presence of a number of overrepresented Gene Ontology terms related to plant defense in the set of genes differentially expressed in ant ail6 suggest that ANT and AIL6 also regulate plant defense pathways. Furthermore, we found that ant ail6 plants have elevated levels of two defense hormones: salicylic acid and jasmonic acid, and show increased resistance to the bacterial pathogen Pseudomonas syringae. These results suggest that ANT and AIL6 regulate biological pathways that are critical for both development and defense. PMID:27208279

Responses of benthic bacteria to experimental drying in sediments from Mediterranean temporary rivers.

PubMed

Amalfitano, Stefano; Fazi, Stefano; Zoppini, Annamaria; Barra Caracciolo, Anna; Grenni, Paola; Puddu, Alberto

2008-02-01

In the semiarid Mediterranean regions, water scarcity represents a common physiological stress for microbial communities residing in river sediments. However, the effect of drying has not yet adequately been evaluated when analyzing riverine microbiological processes. The bacterial community structure (abundance, biomass, composition) and functioning (carbon production, live cell percentage) were assessed during experimental desiccation in microcosms with sediments from different Mediterranean temporary rivers (Tagliamento, Krathis, Mulargia, Pardiela). Our results showed that the overall responses to drying of the bacterial community were independent from sediment origin and strictly related to water content. During desiccation, a prompt decline (up to 100%) of the initial bacterial carbon production was followed by a slower decrease in abundance and biomass, with an overall reduction of 74% and 78%, respectively. By the end of the experiment, live cells were still abundant but depressed in their main metabolic functions, thus resulting in a drastic increase in the community turnover time. Only 14% of the initial live cell biomass was available in dry sediments to immediately start the reactivation of the aquatic microbial food web after the arrival of new water. Community composition analysis showed a relative increase in alpha- and beta-Proteobacteria, when passing from wet to dry conditions. Our results suggest that the occurrence of drought events could affect carbon cycling through the freshwater microbial compartment, by temporarily limiting microbial mineralization and altering bacterial community structure.

Transcriptome analysis of Lactococcus lactis subsp. lactis during milk acidification as affected by dissolved oxygen and the redox potential.

PubMed

Larsen, Nadja; Moslehi-Jenabian, Saloomeh; Werner, Birgit Brøsted; Jensen, Maiken Lund; Garrigues, Christel; Vogensen, Finn Kvist; Jespersen, Lene

2016-06-02

Performance of Lactococcus lactis as a starter culture in dairy fermentations depends on the levels of dissolved oxygen and the redox state of milk. In this study the microarray analysis was used to investigate the global gene expression of L. lactis subsp. lactis DSM20481(T) during milk acidification as affected by oxygen depletion and the decrease of redox potential. Fermentations were carried out at different initial levels of dissolved oxygen (dO2) obtained by milk sparging with oxygen (high dO2, 63%) or nitrogen (low dO2, 6%). Bacterial exposure to high initial oxygen resulted in overexpression of genes involved in detoxification of reactive oxygen species (ROS), oxidation-reduction processes, biosynthesis of trehalose and down-regulation of genes involved in purine nucleotide biosynthesis, indicating that several factors, among them trehalose and GTP, were implicated in bacterial adaptation to oxidative stress. Generally, transcriptional changes were more pronounced during fermentation of oxygen sparged milk. Genes up-regulated in response to oxygen depletion were implicated in biosynthesis and transport of pyrimidine nucleotides, branched chain amino acids and in arginine catabolic pathways; whereas genes involved in salvage of nucleotides and cysteine pathways were repressed. Expression pattern of genes involved in pyruvate metabolism indicated shifts towards mixed acid fermentation after oxygen depletion with production of specific end-products, depending on milk treatment. Differential expression of genes, involved in amino acid and pyruvate pathways, suggested that initial oxygen might influence the release of flavor compounds and, thereby, flavor development in dairy fermentations. The knowledge of molecular responses involved in adaptation of L. lactis to the shifts of redox state and pH during milk fermentations is important for the dairy industry to ensure better control of cheese production. Copyright © 2016 Elsevier B.V. All rights reserved.

A Repeating Sulfated Galactan Motif Resuscitates Dormant Micrococcus luteus Bacteria.

PubMed

Böttcher, Thomas; Szamosvári, Dávid; Clardy, Jon

2018-07-01

Only a small fraction of bacteria can autonomously initiate growth on agar plates. Nongrowing bacteria typically enter a metabolically inactive dormant state and require specific chemical trigger factors or signals to exit this state and to resume growth. Micrococcus luteus has become a model organism for this important yet poorly understood phenomenon. Only a few resuscitation signals have been described to date, and all of them are produced endogenously by bacterial species. We report the discovery of a novel type of resuscitation signal that allows M. luteus to grow on agar but not agarose plates. Fractionation of the agar polysaccharide complex and sulfation of agarose allowed us to identify the signal as highly sulfated saccharides found in agar or carrageenans. Purification of hydrolyzed κ-carrageenan ultimately led to the identification of the signal as a small fragment of a large linear polysaccharide, i.e., an oligosaccharide of five or more sugars with a repeating disaccharide motif containing d-galactose-4-sulfate (G4S) 1,4-linked to 3,6-anhydro-α-d-galactose (DA), G4S-(DA-G4S) n ≥2 IMPORTANCE Most environmental bacteria cannot initiate growth on agar plates, but they can flourish on the same plates once growth is initiated. While there are a number of names for and manifestations of this phenomenon, the underlying cause appears to be the requirement for a molecular signal indicating safe growing conditions. Micrococcus luteus has become a model organism for studying this growth initiation process, often called resuscitation, because of its apparent connection with the persistent or dormant form of Mycobacterium tuberculosis , an important human pathogen. In this report, we identify a highly sulfated saccharide from agar or carrageenans that robustly resuscitates dormant M. luteus on agarose plates. We identified and characterized the signal as a small repeating disaccharide motif. Our results indicate that signals inherent in or absent from the polysaccharide composition of solid growth media can have major effects on bacterial growth. Copyright © 2018 American Society for Microbiology.

Phyllosphere bacterial community of floating macrophytes in paddy soil environments as revealed by illumina high-throughput sequencing.

PubMed

Xie, Wan-Ying; Su, Jian-Qiang; Zhu, Yong-Guan

2015-01-01

The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took Wolffia australiana as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

PubMed Central

Xie, Wan-Ying

2014-01-01

The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took Wolffia australiana as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of W. australiana harbored considerably rich communities of bacteria, with Proteobacteria and Bacteroidetes as the predominant phyla. The core microbiome in the phyllosphere contained genera such as Acidovorax, Asticcacaulis, Methylibium, and Methylophilus. Complexity of the phyllosphere bacterial communities in terms of class number and α-diversity was reduced compared to those in corresponding water and soil. Furthermore, the bacterial communities exhibited structures significantly different from those in water and soil. These findings and the following redundancy analysis (RDA) suggest that species sorting played an important role in the recruitment of bacterial species in the phyllosphere. The compositional structures of the phyllosphere bacterial communities were modulated predominantly by water physicochemical properties, while the initial soil bacterial communities had limited impact. Taken together, the findings from this study reveal the diversity and uniqueness of the phyllosphere bacterial communities associated with the floating macrophytes in paddy soil environments. PMID:25362067

Bacterial Cellulose Production from Industrial Waste and by-Product Streams

PubMed Central

Tsouko, Erminda; Kourmentza, Constantina; Ladakis, Dimitrios; Kopsahelis, Nikolaos; Mandala, Ioanna; Papanikolaou, Seraphim; Paloukis, Fotis; Alves, Vitor; Koutinas, Apostolis

2015-01-01

The utilization of fermentation media derived from waste and by-product streams from biodiesel and confectionery industries could lead to highly efficient production of bacterial cellulose. Batch fermentations with the bacterial strain Komagataeibacter sucrofermentans DSM (Deutsche Sammlung von Mikroorganismen) 15973 were initially carried out in synthetic media using commercial sugars and crude glycerol. The highest bacterial cellulose concentration was achieved when crude glycerol (3.2 g/L) and commercial sucrose (4.9 g/L) were used. The combination of crude glycerol and sunflower meal hydrolysates as the sole fermentation media resulted in bacterial cellulose production of 13.3 g/L. Similar results (13 g/L) were obtained when flour-rich hydrolysates produced from confectionery industry waste streams were used. The properties of bacterial celluloses developed when different fermentation media were used showed water holding capacities of 102–138 g·water/g·dry bacterial cellulose, viscosities of 4.7–9.3 dL/g, degree of polymerization of 1889.1–2672.8, stress at break of 72.3–139.5 MPa and Young’s modulus of 0.97–1.64 GPa. This study demonstrated that by-product streams from the biodiesel industry and waste streams from confectionery industries could be used as the sole sources of nutrients for the production of bacterial cellulose with similar properties as those produced with commercial sources of nutrients. PMID:26140376

Bacterial Cellulose Production from Industrial Waste and by-Product Streams.

PubMed

Tsouko, Erminda; Kourmentza, Constantina; Ladakis, Dimitrios; Kopsahelis, Nikolaos; Mandala, Ioanna; Papanikolaou, Seraphim; Paloukis, Fotis; Alves, Vitor; Koutinas, Apostolis

2015-07-01

The utilization of fermentation media derived from waste and by-product streams from biodiesel and confectionery industries could lead to highly efficient production of bacterial cellulose. Batch fermentations with the bacterial strain Komagataeibacter sucrofermentans DSM (Deutsche Sammlung von Mikroorganismen) 15973 were initially carried out in synthetic media using commercial sugars and crude glycerol. The highest bacterial cellulose concentration was achieved when crude glycerol (3.2 g/L) and commercial sucrose (4.9 g/L) were used. The combination of crude glycerol and sunflower meal hydrolysates as the sole fermentation media resulted in bacterial cellulose production of 13.3 g/L. Similar results (13 g/L) were obtained when flour-rich hydrolysates produced from confectionery industry waste streams were used. The properties of bacterial celluloses developed when different fermentation media were used showed water holding capacities of 102-138 g · water/g · dry bacterial cellulose, viscosities of 4.7-9.3 dL/g, degree of polymerization of 1889.1-2672.8, stress at break of 72.3-139.5 MPa and Young's modulus of 0.97-1.64 GPa. This study demonstrated that by-product streams from the biodiesel industry and waste streams from confectionery industries could be used as the sole sources of nutrients for the production of bacterial cellulose with similar properties as those produced with commercial sources of nutrients.

The effect of different growth regimes on the endophytic bacterial communities of the fern, Dicksonia sellowiana hook (Dicksoniaceae).

PubMed

de Araújo Barros, Irene; Luiz Araújo, Welington; Lúcio Azevedo, João

2010-10-01

Endophytic bacteria associated with the fern Dicksonia sellowiana were investigated. The bacterial communities from the surface-sterilized pinnae and rachis segments of the plants from the Brazilian Atlantic Rainforest that grew in native field conditions were compared with the bacterial communities from plants grown in greenhouses and plants that were initially grown in greenhouses and then transferred to the forest. From 540 pinnae and 540 rachis segments, 163 (30.2%) and 346 (64.2%) were colonized by bacteria, respectively. The main bacterial genera and species that were isolated included Bacillus spp. ( B. cereus, B. megaterium, B. pumilus and B. subtilis ) , Paenibacillus sp. , Amphibacillus sp. , Gracilibacillus sp. , Micrococcus sp. and Stenotrophomonas spp. ( S. maltophilia and S. nitroreducens ). B. pumilus was the most frequently isolated bacterial species . Amphibacillus and Gracilibacillus were reported as endophytes for the first time. Other commonly found bacterial genera were not observed in D. sellowiana , which may reflect preferences of specific bacterial communities inside this fern or detection limitations due to the isolation procedures. Plants that were grown in greenhouses and plants that were reintroduced into the forest displayed more bacterial genera and species diversity than native field plants, suggesting that reintroduction shifts the bacterial diversity. Endophytic bacteria that displayed antagonistic properties against different microorganisms were detected, but no obvious correlation was found between their frequencies with plant tissues or with plants from different growth regimes. This paper reports the first isolation of endophytic bacteria from a fern.

The effect of different growth regimes on the endophytic bacterial communities of the fern, Dicksonia sellowiana hook (Dicksoniaceae)

PubMed Central

de Araújo Barros, Irene; Luiz Araújo, Welington; Lúcio Azevedo, João

2010-01-01

Endophytic bacteria associated with the fern Dicksonia sellowiana were investigated. The bacterial communities from the surface-sterilized pinnae and rachis segments of the plants from the Brazilian Atlantic Rainforest that grew in native field conditions were compared with the bacterial communities from plants grown in greenhouses and plants that were initially grown in greenhouses and then transferred to the forest. From 540 pinnae and 540 rachis segments, 163 (30.2%) and 346 (64.2%) were colonized by bacteria, respectively. The main bacterial genera and species that were isolated included Bacillus spp. ( B. cereus, B. megaterium, B. pumilus and B. subtilis ) , Paenibacillus sp. , Amphibacillus sp. , Gracilibacillus sp. , Micrococcus sp. and Stenotrophomonas spp. ( S. maltophilia and S. nitroreducens ). B. pumilus was the most frequently isolated bacterial species . Amphibacillus and Gracilibacillus were reported as endophytes for the first time. Other commonly found bacterial genera were not observed in D. sellowiana , which may reflect preferences of specific bacterial communities inside this fern or detection limitations due to the isolation procedures. Plants that were grown in greenhouses and plants that were reintroduced into the forest displayed more bacterial genera and species diversity than native field plants, suggesting that reintroduction shifts the bacterial diversity. Endophytic bacteria that displayed antagonistic properties against different microorganisms were detected, but no obvious correlation was found between their frequencies with plant tissues or with plants from different growth regimes. This paper reports the first isolation of endophytic bacteria from a fern. PMID:24031575

Migration of Paraburkholderia terrae BS001 Along Old Fungal Hyphae in Soil at Various pH Levels.

PubMed

Yang, Pu; Oliveira da Rocha Calixto, Renata; van Elsas, Jan Dirk

2018-01-10

The movement of bacterial cells along with fungal hyphae in soil (the mycosphere) has been reported in several previous studies. However, how local soil conditions affect bacterial migration direction in the mycosphere has not been extensively studied. Here, we investigated the influence of two soil parameters, pH and soil moisture content, on the migration, and survival, of Paraburkholderia terrae BS001 in the mycosphere of Lyophyllum sp. strain Karsten in microcosms containing a loamy sand soil. The data showed that bacterial movement along the hyphal networks took place in both the "forward" and the "backward" directions. Low soil pH strongly restricted bacterial survival, as well as dispersal in both directions, in the mycosphere. The backward movement was weakly correlated with the amount of fungal tissue formed in the old mycelial network. The initial soil moisture content, set at 12 versus 17% (corresponding to 42 and 60% of the soil water holding capacity), also significantly affected the bacterial dispersal along the fungal hyphae. Overall, the presence of fungal hyphae was found to increase the soil pH (under conditions of acidity), which possibly exerted protective effects on the bacterial cells. Finally, we provide a refined model that describes the bacterial migration patterns with fungal hyphae based on the new findings in this study.

Self-Organization in High-Density Bacterial Colonies: Efficient Crowd Control

PubMed Central

Campbell, Kyle; Melke, Pontus; Williams, Joshua W; Jedynak, Bruno; Stevens, Ann M; Groisman, Alex; Levchenko, Andre

2007-01-01

Colonies of bacterial cells can display complex collective dynamics, frequently culminating in the formation of biofilms and other ordered super-structures. Recent studies suggest that to cope with local environmental challenges, bacterial cells can actively seek out small chambers or cavities and assemble there, engaging in quorum sensing behavior. By using a novel microfluidic device, we showed that within chambers of distinct shapes and sizes allowing continuous cell escape, bacterial colonies can gradually self-organize. The directions of orientation of cells, their growth, and collective motion are mutually correlated and dictated by the chamber walls and locations of chamber exits. The ultimate highly organized steady state is conducive to a more-organized escape of cells from the chambers and increased access of nutrients into and evacuation of waste out of the colonies. Using a computational model, we suggest that the lengths of the cells might be optimized to maximize self-organization while minimizing the potential for stampede-like exit blockage. The self-organization described here may be crucial for the early stage of the organization of high-density bacterial colonies populating small, physically confined growth niches. It suggests that this phenomenon can play a critical role in bacterial biofilm initiation and development of other complex multicellular bacterial super-structures, including those implicated in infectious diseases. PMID:18044986

Effect of UV-photofunctionalization on Oral Bacterial Attachment and Biofilm Formation to Titanium Implant Material

PubMed Central

de Avila, Erica Dorigatti; Lima, Bruno P.; Sekiya, Takeo; Torii, Yasuyoshi; Ogawa, Takahiro; Shi, Wenyuan; Lux, Renate

2015-01-01

Bacterial biofilm infections remain prevalent reasons for implant failure. Dental implant placement occurs in the oral environment, which harbors a plethora of biofilm-forming bacteria. Due to its trans-mucosal placement, part of the implant structure is exposed to oral cavity and there is no effective measure to prevent bacterial attachment to implant materials. Here, we demonstrated that UV treatment of titanium immediately prior to use (photofunctionalization) affects the ability of human polymicrobial oral biofilm communities to colonize in the presence of salivary and blood components. UV-treatment of machined titanium transformed the surface from hydrophobic to superhydrophilic. UV-treated surfaces exhibited a significant reduction in bacterial attachment as well as subsequent biofilm formation compared to untreated ones, even though overall bacterial viability was not affected. The function of reducing bacterial colonization was maintained on UV-treated titanium that had been stored in a liquid environment before use. Denaturing gradient gel-electrophoresis (DGGE) and DNA sequencing analyses revealed that while bacterial community profiles appeared different between UV-treated and untreated titanium in the initial attachment phase, this difference vanished as biofilm formation progressed. Our findings confirm that UV-photofunctionalization of titanium has a strong potential to improve outcome of implant placement by creating and maintaining antimicrobial surfaces. PMID:26210175

Illumina sequencing-based analyses of bacterial communities during short-chain fatty-acid production from food waste and sewage sludge fermentation at different pH values.

PubMed

Cheng, Weixiao; Chen, Hong; Yan, ShuHai; Su, Jianqiang

2014-09-01

Short-chain fatty acids (SCFAs) can be produced by primary and waste activated sludge anaerobic fermentation. The yield and product spectrum distribution of SCFAs can be significantly affected by different initial pH values. However, most studies have focused on the physical and chemical aspects of SCFA production by waste activated sludge fermentation at different pH values. Information on the bacterial community structures during acidogenic fermentation is limited. In this study, comparisons of the bacterial communities during the co-substrate fermentation of food wastes and sewage sludge at different pH values were performed using the barcoded Illumina paired-end sequencing method. The results showed that different pH environments harbored a characteristic bacterial community, including sequences related to Lactobacillus, Prevotella, Mitsuokella, Treponema, Clostridium, and Ureibacillus. The most abundant bacterial operational taxonomic units in the different pH environments were those related to carbohydrate-degrading bacteria, which are associated with constituents of co-substrate fermentation. Further analyses showed that during organic matter fermentation, a core microbiota composed of Firmicutes, Proteobacteria, and Bacteroidetes existed. Comparison analyses revealed that the bacterial community during fermentation was significantly affected by the pH, and that the diverse product distribution was related to the shift in bacterial communities.

Using host-pathogen protein interactions to identify and characterize Francisella tularensis virulence factors.

PubMed

Wallqvist, Anders; Memišević, Vesna; Zavaljevski, Nela; Pieper, Rembert; Rajagopala, Seesandra V; Kwon, Keehwan; Yu, Chenggang; Hoover, Timothy A; Reifman, Jaques

2015-12-29

Francisella tularensis is a select bio-threat agent and one of the most virulent intracellular pathogens known, requiring just a few organisms to establish an infection. Although several virulence factors are known, we lack an understanding of virulence factors that act through host-pathogen protein interactions to promote infection. To address these issues in the highly infectious F. tularensis subsp. tularensis Schu S4 strain, we deployed a combined in silico, in vitro, and in vivo analysis to identify virulence factors and their interactions with host proteins to characterize bacterial infection mechanisms. We initially used comparative genomics and literature to identify and select a set of 49 putative and known virulence factors for analysis. Each protein was then subjected to proteome-scale yeast two-hybrid (Y2H) screens with human and murine cDNA libraries to identify potential host-pathogen protein-protein interactions. Based on the bacterial protein interaction profile with both hosts, we selected seven novel putative virulence factors for mutant construction and animal validation experiments. We were able to create five transposon insertion mutants and used them in an intranasal BALB/c mouse challenge model to establish 50 % lethal dose estimates. Three of these, ΔFTT0482c, ΔFTT1538c, and ΔFTT1597, showed attenuation in lethality and can thus be considered novel F. tularensis virulence factors. The analysis of the accompanying Y2H data identified intracellular protein trafficking between the early endosome to the late endosome as an important component in virulence attenuation for these virulence factors. Furthermore, we also used the Y2H data to investigate host protein binding of two known virulence factors, showing that direct protein binding was a component in the modulation of the inflammatory response via activation of mitogen-activated protein kinases and in the oxidative stress response. Direct interactions with specific host proteins and the ability to influence interactions among host proteins are important components for F. tularensis to avoid host-cell defense mechanisms and successfully establish an infection. Although direct host-pathogen protein-protein binding is only one aspect of Francisella virulence, it is a critical component in directly manipulating and interfering with cellular processes in the host cell.

Metronidazole combined with nystatin (vagitories) in the prevention of bacterial vaginosis after initial treatment with oral metronidazole.

PubMed

Pulkkinen, P; Saranen, M; Kaaja, R

1993-01-01

In a double-blind trial comprising 66 patients we assessed the effect of metronidazole-nystatin vagitories on the prevention of bacterial vaginosis (BV) in women using IUD as a contraceptive method after an initial oral single dose of 2.0 g metronidazole and 7 days of intravaginal metronidazole-nystatin or placebo treatment. The prophylactic treatment consisted of metronidazole-nystatin or placebo vagitories applied at bedtime for 3 days after menstruation over 6 consecutive menstrual periods. The patients were randomized in two study groups: a treatment group of 32 patients (group A) and a placebo group of 34 patients (group B). The overall objective cure rate after the initial treatment was 97% in group A and 91% in group B. After 6 months of follow-up, the overall cumulative objective cure rate in group A was 100%, and 76% in group B. The single-dose oral treatment was well tolerated and no notable side effects were recorded.

Effects of CO[sub 2] and climate change on forest trees: Soil biology and enzymology

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moldenke, A.R.; Baumeister, N.; Caldwell, B.A.

1994-06-01

Samples of Teracosm soils were analyzed shortly after initial setup to determine whether initial conditions were equivalent and matched expected values for local soils. Total and active fungal biomass, active bacterial biomass and protozoan numbers were reduced, with greatest decreases occurring in the A horizon. No effect was observed on total bacterial biomass, nematode or anthropod densities, but changes in nematode and arthropod species composition occurred. Significant differences in total density and species composition occurred between the enclosed Teracosms and the open controls. Arthropod and nematode community structure in the three altitudinal field sites had significantly diverged. No significant differencesmore » in activities of key soil enzymes in C- and N-cycling (acid phosphatase, protease, B-glucosidase, phenol oxidase and peroxidase) were found between initial samples relative to treatment, but all levels were significantly difference relative to depth in soil profile. Activities were within ranges previously observed in forests of the Pacific Northwest.« less

Bacterial uptake of antibiotics in model unsaturated systems

NASA Astrophysics Data System (ADS)

Zhang, W.; Chen, Z.; Zhang, Y.; Zhao, Z.; Wang, G.; Gao, Y.; Boyd, S. A.; Zhu, D.; Li, H.

2016-12-01

Anthropogenic antibiotics are ubiquitously present in the environment due to large uses in human medicine and animal agriculture, and are causing unintended consequence to human and ecosystem health. Bacterial uptake of antibiotics could exert selection pressure on antibiotic resistance development among bacteria population. Therefore, understanding environmental factors controlling bioavailability of antibiotics to bacteria is critical to better assessing exposure risks and developing mitigation strategies. Nonetheless, conventional bioavailability assays are often performed in water-saturated systems that do not represent unsaturated soils where most bacteria live, therefore neglecting soil water as a controlling factor in determining the extent of antibiotic bacterial uptake. Therefore, we propose to study bacterial uptake of antibiotics in model unsaturated systems using GFP-tagged Escherichia coli bioreporter for tetracyclines. Our preliminary studies demonstrated the important role of water content (or water matric potential) in determining the bioavailability of antibiotics, and complex interactions of water potential, tetracycline diffusion, and E. coli growth. Therefore, unsaturated processes are important for understanding antibiotic resistance development and developing mitigation strategies.

Functional characteristics and influence factors of microbial community in sewage sludge composting with inorganic bulking agent.

PubMed

Wang, Ke; Mao, Hailong; Li, Xiangkun

2018-02-01

The metabolic function of microbial community dominated organics and nutrients transformation in aerobic composting process. In this study, the metabolic characteristics of bacterial and fungal communities were evaluated in 60 days composting of sludge and pumice by using FUNGuild and PICRUSt, respectively. The results showed that microbial community structure and metabolic characteristics were distinctively different at four composting periods. Bacterial genes related to carbohydrate metabolisms decreased during the first 30 days, but bacterial sequences associated with oxidative phosphorylation and fatty acids synthesis were enhanced in curing phase. Most of fungal animal pathogen and plant pathogen disappeared after treatment, and the abundance of saprotroph fungi increased from 44.3% to 97.8%. Oxidation reduction potential (ORP) significantly increased from -28 to 175 mV through incubation. RDA analysis showed that ORP was a crucial factor on the succession of both bacterial and fungal communities in sludge composting system. Copyright © 2017. Published by Elsevier Ltd.

Bacterial pathogens of the bovine respiratory disease complex.

PubMed

Griffin, Dee; Chengappa, M M; Kuszak, Jennifer; McVey, D Scott

2010-07-01

Pneumonia caused by the bacterial pathogens discussed in this article is the most significant cause of morbidity and mortality of the BRDC. Most of these infectious bacteria are not capable of inducing significant disease without the presence of other predisposing environmental factors, physiologic stressors, or concurrent infections. Mannheimia haemolytica is the most common and serious of these bacterial agents and is therefore also the most highly characterized. There are other important bacterial pathogens of BRD, such as Pasteurella multocida, Histophulus somni, and Mycoplasma bovis. Mixed infections with these organisms do occur. These pathogens have unique and common virulence factors but the resulting pneumonic lesions may be similar. Although the amount and quality of research associated with BRD has increased, vaccination and therapeutic practices are not fully successful. A greater understanding of the virulence mechanisms of the infecting bacteria and pathogenesis of pneumonia, as well as the characteristics of the organisms that allow tissue persistence, may lead to improved management, therapeutics, and vaccines. Copyright 2010 Elsevier Inc. All rights reserved.

Antibiotic-induced bacterial killing stimulates tumor necrosis factor-alpha release in whole blood.

PubMed

Arditi, M; Kabat, W; Yogev, R

1993-01-01

Rapid lysis of gram-negative bacteria is associated with considerable release of free endotoxin. Production of tumor necrosis factor (TNF) from adult whole blood ex vivo in response to bacterial products generated during antibiotic killing of Haemophilus influenzae type b (Hib) was investigated. Heparinized whole blood released TNF in a dose-dependent fashion in response to purified lipooligosaccharide of Hib. Bacteria (10(4)-10(7) cfu/mL) were placed into a Transwell filter insert (0.1 microns) and incubated with whole blood in the presence of various antibiotics. Exposure to ceftriaxone resulted in significantly greater release of TNF during killing of Hib than did exposure to imipenem, despite similar degrees of bacterial killing at 6 h. Polymyxin B inhibited the ceftriaxone-induced TNF release by 97%-99%, indicating that free endotoxin was the predominant stimulus for the increase in TNF release in this system. These observations suggest that ceftriaxone-induced killing of Hib results in bacterial cell wall products that are more proinflammatory than those produced by imipenem.

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits

PubMed Central

Hathaway, Jennifer J.M.; Kimble, Jason C.; Buecher, Debbie C.; Valdez, Ernest W.; Young, Jesse M.; Read, Kaitlyn J.H.; Northup, Diana E.

2017-01-01

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens. PMID:29093998

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits.

PubMed

Winter, Ara S; Hathaway, Jennifer J M; Kimble, Jason C; Buecher, Debbie C; Valdez, Ernest W; Porras-Alfaro, Andrea; Young, Jesse M; Read, Kaitlyn J H; Northup, Diana E

2017-01-01

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host's health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.

Environmental factors shaping cultured free-living amoebae and their associated bacterial community within drinking water network.

PubMed

Delafont, Vincent; Bouchon, Didier; Héchard, Yann; Moulin, Laurent

2016-09-01

Free-living amoebae (FLA) constitute an important part of eukaryotic populations colonising drinking water networks. However, little is known about the factors influencing their ecology in such environments. Because of their status as reservoir of potentially pathogenic bacteria, understanding environmental factors impacting FLA populations and their associated bacterial community is crucial. Through sampling of a large drinking water network, the diversity of cultivable FLA and their bacterial community were investigated by an amplicon sequencing approach, and their correlation with physicochemical parameters was studied. While FLA ubiquitously colonised the water network all year long, significant changes in population composition were observed. These changes were partially explained by several environmental parameters, namely water origin, temperature, pH and chlorine concentration. The characterisation of FLA associated bacterial community reflected a diverse but rather stable consortium composed of nearly 1400 OTUs. The definition of a core community highlighted the predominance of only few genera, majorly dominated by Pseudomonas and Stenotrophomonas. Co-occurrence analysis also showed significant patterns of FLA-bacteria association, and allowed uncovering potentially new FLA - bacteria interactions. From our knowledge, this study is the first that combines a large sampling scheme with high-throughput identification of FLA together with associated bacteria, along with their influencing environmental parameters. Our results demonstrate the importance of physicochemical parameters in the ecology of FLA and their bacterial community in water networks. Copyright © 2016 Elsevier Ltd. All rights reserved.

Skin and fur bacterial diversity and community structure on American southwestern bats: effects of habitat, geography and bat traits

USGS Publications Warehouse

Winter, Ara S.; Hathaway, Jennifer J. M.; Kimble, Jason C.; Buecher, Debbie C.; Valdez, Ernest W.; Porras-Alfaro, Andrea; Young, Jesse M.; Read, Kaitlyn J. H.; Northup, Diana E.

2017-01-01

Microorganisms that reside on and in mammals, such as bats, have the potential to influence their host’s health and to provide defenses against invading pathogens. However, we have little understanding of the skin and fur bacterial microbiota on bats, or factors that influence the structure of these communities. The southwestern United States offers excellent sites for the study of external bat bacterial microbiota due to the diversity of bat species, the variety of abiotic and biotic factors that may govern bat bacterial microbiota communities, and the lack of the newly emergent fungal disease in bats, white-nose syndrome (WNS), in the southwest. To test these variables, we used 16S rRNA gene 454 pyrosequencing from swabs of external skin and fur surfaces from 163 bats from 13 species sampled from southeastern New Mexico to northwestern Arizona. Community similarity patterns, random forest models, and generalized linear mixed-effects models show that factors such as location (e.g., cave-caught versus surface-netted) and ecoregion are major contributors to the structure of bacterial communities on bats. Bats caught in caves had a distinct microbial community compared to those that were netted on the surface. Our results provide a first insight into the distribution of skin and fur bat bacteria in the WNS-free environment of New Mexico and Arizona. More importantly, it provides a baseline of bat external microbiota that can be explored for potential natural defenses against pathogens.

Interlinkages between bacterial populations dynamics and the operational parameters in a moving bed membrane bioreactor treating urban sewage.

PubMed

Reboleiro-Rivas, P; Martín-Pascual, J; Morillo, J A; Juárez-Jiménez, B; Poyatos, J M; Rodelas, B; González-López, J

2016-01-01

Bacteria are key players in biological wastewater treatments (WWTs), thus a firm knowledge of the bacterial population dynamics is crucial to understand environmental/operational factors affecting the efficiency and stability of the biological depuration process. Unfortunately, little is known about the microbial ecology of the advanced biological WWTs combining suspended biomass (SB) and attached biofilms (AB). This study explored in depth the bacterial community structure and population dynamics in each biomass fraction from a pilot-scale moving bed membrane bioreactor (MBMBR) treating municipal sewage, by means of temperature-gradient gel electrophoresis (TGGE) and 454-pyrosequencing. Eight experimental phases were conducted, combining different carrier filling ratios, hydraulic retention times and concentrations of mixed liquor total suspended solids. The bacterial community, dominated by Proteobacteria (20.9-53.8%) and Actinobacteria (20.6-57.6%), was very similar in both biomass fractions and able to maintain its functional stability under all the operating conditions, ensuring a successful and steady depuration process. Multivariate statistical analysis demonstrated that solids concentration, carrier filling ratio, temperature and organic matter concentration in the influent were the significant factors explaining population dynamics. Bacterial diversity increased as carrier filling ratio increased (from 20% to 35%, v/v), and solids concentration was the main factor triggering the shifts of the community structure. These findings provide new insights on the influence of operational parameters on the biology of the innovative MBMBRs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Factors influencing bacterial adhesion to contact lenses.

PubMed

Dutta, Debarun; Cole, Nerida; Willcox, Mark

2012-01-01

The process of any contact lens related keratitis generally starts with the adhesion of opportunistic pathogens to contact lens surface. This article focuses on identifying the factors which have been reported to affect bacterial adhesion to contact lenses. Adhesion to lenses differs between various genera/species/strains of bacteria. Pseudomonas aeruginosa, which is the predominant causative organism, adheres in the highest numbers to both hydrogel and silicone hydrogel lenses in vitro. The adhesion of this strain reaches maximum numbers within 1h in most in vitro studies and a biofilm has generally formed within 24 h of cells adhering to the lens surface. Physical and chemical properties of contact lens material affect bacterial adhesion. The water content of hydroxyethylmethacrylate (HEMA)-based lenses and their iconicity affect the ability of bacteria to adhere. The higher hydrophobicity of silicone hydrogel lenses compared to HEMA-based lenses has been implicated in the higher numbers of bacteria that can adhere to their surfaces. Lens wear has different effects on bacterial adhesion, partly due to differences between wearers, responses of bacterial strains and the ability of certain tear film proteins when bound to a lens surface to kill certain types of bacteria.

Factors influencing bacterial adhesion to contact lenses

PubMed Central

Dutta, Debarun; Willcox, Mark

2012-01-01

The process of any contact lens related keratitis generally starts with the adhesion of opportunistic pathogens to contact lens surface. This article focuses on identifying the factors which have been reported to affect bacterial adhesion to contact lenses. Adhesion to lenses differs between various genera/species/strains of bacteria. Pseudomonas aeruginosa, which is the predominant causative organism, adheres in the highest numbers to both hydrogel and silicone hydrogel lenses in vitro. The adhesion of this strain reaches maximum numbers within 1h in most in vitro studies and a biofilm has generally formed within 24 h of cells adhering to the lens surface. Physical and chemical properties of contact lens material affect bacterial adhesion. The water content of hydroxyethylmethacrylate (HEMA)-based lenses and their iconicity affect the ability of bacteria to adhere. The higher hydrophobicity of silicone hydrogel lenses compared to HEMA-based lenses has been implicated in the higher numbers of bacteria that can adhere to their surfaces. Lens wear has different effects on bacterial adhesion, partly due to differences between wearers, responses of bacterial strains and the ability of certain tear film proteins when bound to a lens surface to kill certain types of bacteria. PMID:22259220

Proteolytic inactivation of tissue factor pathway inhibitor by bacterial omptins

PubMed Central

Yun, Thomas H.; Cott, Jessica E.; Tapping, Richard I.; Slauch, James M.

2009-01-01

The immune response to infection includes activation of the blood clotting system, leading to extravascular fibrin deposition to limit the spread of invasive microorganisms. Some bacteria have evolved mechanisms to counteract this host response. Pla, a member of the omptin family of Gram-negative bacterial proteases, promotes the invasiveness of the plague bacterium, Yersinia pestis, by activating plasminogen to plasmin to digest fibrin. We now show that the endogenous anticoagulant tissue factor pathway inhibitor (TFPI) is also highly sensitive to proteolysis by Pla and its orthologs OmpT in Escherichia coli and PgtE in Salmonella enterica serovar Typhimurium. Using gene deletions, we demonstrate that bacterial inactivation of TFPI requires omptin expression. TFPI inactivation is mediated by proteolysis since Western blot analysis showed that TFPI cleavage correlated with loss of anticoagulant function in clotting assays. Rates of TFPI inactivation were much higher than rates of plasminogen activation, indicating that TFPI is a better substrate for omptins. We hypothesize that TFPI has evolved sensitivity to proteolytic inactivation by bacterial omptins to potentiate procoagulant responses to bacterial infection. This may contribute to the hemostatic imbalance in disseminated intravascular coagulation and other coagulopathies accompanying severe sepsis. PMID:18988866

Bacterial translation elongation factor EF-Tu interacts and colocalizes with actin-like MreB protein.

PubMed

Defeu Soufo, Hervé Joël; Reimold, Christian; Linne, Uwe; Knust, Tobias; Gescher, Johannes; Graumann, Peter L

2010-02-16

We show that translation initiation factor EF-Tu plays a second important role in cell shape maintenance in the bacterium Bacillus subtilis. EF-Tu localizes in a helical pattern underneath the cell membrane and colocalizes with MreB, an actin-like cytoskeletal element setting up rod cell shape. The localization of MreB and of EF-Tu is interdependent, but in contrast to the dynamic MreB filaments, EF-Tu structures are more static and may serve as tracks for MreB filaments. In agreement with this idea, EF-Tu and MreB interact in vivo and in vitro. Lowering of the EF-Tu levels had a minor effect on translation but a strong effect on cell shape and on the localization of MreB, and blocking of the function of EF-Tu in translation did not interfere with the localization of MreB, showing that, directly or indirectly, EF-Tu affects the cytoskeletal MreB structure and thus serves two important functions in a bacterium.