Prebiotic and Probiotic Regulation of Bone Health: Role of the Intestine and its Microbiome

PubMed Central

McCabe, Laura; Britton, Robert A.; Parameswaran, Narayanan

2015-01-01

Recent advances in our understanding of how the intestinal microbiome contributes to health and disease have generated great interest in developing strategies for modulating the abundance of microbes and/or their activity to improve overall human health and prevent pathologies such as osteoporosis. Bone is an organ that the gut has long been known to regulate through absorption of calcium, the key bone mineral. However, it is clear that modulation of the gut and its microbiome can affect bone density and strength in a variety of animal models (zebra fish, rodents, chicken) and humans. This is demonstrated in studies ablating the microbiome through antibiotic treatment or using germ-free mouse conditions as well as in studies modulating the microbiome activity and composition through prebiotic and/or probiotic treatment. This review will discuss recent developments in this new and exciting area. PMID:26419466

Symbiosis-inspired approaches to antibiotic discovery.

PubMed

Adnani, Navid; Rajski, Scott R; Bugni, Tim S

2017-07-06

Covering: 2010 up to 2017Life on Earth is characterized by a remarkable abundance of symbiotic and highly refined relationships among life forms. Defined as any kind of close, long-term association between two organisms, symbioses can be mutualistic, commensalistic or parasitic. Historically speaking, selective pressures have shaped symbioses in which one organism (typically a bacterium or fungus) generates bioactive small molecules that impact the host (and possibly other symbionts); the symbiosis is driven fundamentally by the genetic machineries available to the small molecule producer. The human microbiome is now integral to the most recent chapter in animal-microbe symbiosis studies and plant-microbe symbioses have significantly advanced our understanding of natural products biosynthesis; this also is the case for studies of fungal-microbe symbioses. However, much less is known about microbe-microbe systems involving interspecies interactions. Microbe-derived small molecules (i.e. antibiotics and quorum sensing molecules, etc.) have been shown to regulate transcription in microbes within the same environmental niche, suggesting interspecies interactions whereas, intraspecies interactions, such as those that exploit autoinducing small molecules, also modulate gene expression based on environmental cues. We, and others, contend that symbioses provide almost unlimited opportunities for the discovery of new bioactive compounds whose activities and applications have been evolutionarily optimized. Particularly intriguing is the possibility that environmental effectors can guide laboratory expression of secondary metabolites from "orphan", or silent, biosynthetic gene clusters (BGCs). Notably, many of the studies summarized here result from advances in "omics" technologies and highlight how symbioses have given rise to new anti-bacterial and antifungal natural products now being discovered.

Lactobacillus rhamnosus GG and its SpaC pilus adhesin modulate inflammatory responsiveness and TLR-related gene expression in the fetal human gut

PubMed Central

Ganguli, Kriston; Collado, Maria Carmen; Rautava, Jaana; Lu, Lei; Satokari, Reetta; von Ossowski, Ingemar; Reunanen, Justus; de Vos, Willem M.; Palva, Airi; Isolauri, Erika; Salminen, Seppo; Walker, W. Allan; Rautava, Samuli

2015-01-01

Background Bacterial contact in utero modulates fetal and neonatal immune responses. Maternal probiotic supplementation reduces the risk of immune-mediated disease in the infant. We investigated the immunomodulatory properties of live Lactobacillus rhamnosus GG and its SpaC pilus adhesin in human fetal intestinal models. Methods TNF-α mRNA expression was measured by qPCR in a human fetal intestinal organ culture model exposed to live L. rhamnosus GG and proinflammatory stimuli. Binding of recombinant SpaC pilus protein to intestinal epithelial cells was assessed in human fetal intestinal organ culture and the human fetal intestinal epithelial cell line H4 by immunohistochemistry and immunofluorescence, respectively. TLR-related gene expression in fetal ileal organ culture after exposure to recombinant SpaC was assessed by qPCR. Results Live L. rhamnosus GG significantly attenuates pathogen-induced TNF-α mRNA expression in the human fetal gut. Recombinant SpaC protein was found to adhere to the fetal gut and to modulate varying levels of TLR-related gene expression. Conclusion The human fetal gut is responsive to luminal microbes. L. rhamnosus GG significantly attenuates fetal intestinal inflammatory responses to pathogenic bacteria. The L. rhamnosus GG pilus adhesin SpaC binds to immature human intestinal epithelial cells and directly modulates intestinal epithelial cell innate immune gene expression. PMID:25580735

Antimicrobial Decapeptide KSL-W Attenuates Candida albicans Virulence by Modulating Its Effects on Toll-Like Receptor, Human Beta-Defensin, and Cytokine Expression by Engineered human Oral Mucosa

DTIC Science & Technology

2011-02-02

against phytopathogenic fungi that cause postharvest decay in fruits . Mol Plant Microbe Interact 2000;13:837–46. [28] Montesinos E, Antimicrobial peptides...inactivated KSL-W did not affect epithelial cell proliferation (Fig. 2). 3.3. KSL-W pre-treatment reduced Candida growth in the infected oral mucosa tissue...against fungi , such as C. albi- cans, remains to be determined. Oral candidiasis is associatedwith gingival tissuewhere epithe- lial cells are the primary

Postnatal colonization with human "infant-type" Bifidobacterium species alters behavior of adult gnotobiotic mice.

PubMed

Luk, Berkley; Veeraragavan, Surabi; Engevik, Melinda; Balderas, Miriam; Major, Angela; Runge, Jessica; Luna, Ruth Ann; Versalovic, James

2018-01-01

Accumulating studies have defined a role for the intestinal microbiota in modulation of host behavior. Research using gnotobiotic mice emphasizes that early microbial colonization with a complex microbiota (conventionalization) can rescue some of the behavioral abnormalities observed in mice that grow to adulthood completely devoid of bacteria (germ-free mice). However, the human infant and adult microbiomes vary greatly, and effects of the neonatal microbiome on neurodevelopment are currently not well understood. Microbe-mediated modulation of neural circuit patterning in the brain during neurodevelopment may have significant long-term implications that we are only beginning to appreciate. Modulation of the host central nervous system by the early-life microbiota is predicted to have pervasive and lasting effects on brain function and behavior. We sought to replicate this early microbe-host interaction by colonizing gnotobiotic mice at the neonatal stage with a simplified model of the human infant gut microbiota. This model consortium consisted of four "infant-type" Bifidobacterium species known to be commensal members of the human infant microbiota present in high abundance during postnatal development. Germ-free mice and mice neonatally-colonized with a complex, conventional murine microbiota were used for comparison. Motor and non-motor behaviors of the mice were tested at 6-7 weeks of age, and colonization patterns were characterized by 16S ribosomal RNA gene sequencing. Adult germ-free mice were observed to have abnormal memory, sociability, anxiety-like behaviors, and motor performance. Conventionalization at the neonatal stage rescued these behavioral abnormalities, and mice colonized with Bifidobacterium spp. also exhibited important behavioral differences relative to the germ-free controls. The ability of Bifidobacterium spp. to improve the recognition memory of both male and female germ-free mice was a prominent finding. Together, these data demonstrate that the early-life gut microbiome, and human "infant-type" Bifidobacterium species, affect adult behavior in a strongly sex-dependent manner, and can selectively recapitulate the results observed when mice are colonized with a complex microbiota.

Safety of Novel Microbes for Human Consumption: Practical Examples of Assessment in the European Union

PubMed Central

Brodmann, Theodor; Endo, Akihito; Gueimonde, Miguel; Vinderola, Gabriel; Kneifel, Wolfgang; de Vos, Willem M.; Salminen, Seppo; Gómez-Gallego, Carlos

2017-01-01

Novel microbes are either newly isolated genera and species from natural sources or bacterial strains derived from existing bacteria. Novel microbes are gaining increasing attention for the general aims to preserve and modify foods and to modulate gut microbiota. The use of novel microbes to improve health outcomes is of particular interest because growing evidence points to the importance of gut microbiota in human health. As well, some recently isolated microorganisms have promise for use as probiotics, although in-depth assessment of their safety is necessary. Recent examples of microorganisms calling for more detailed evaluation include Bacteroides xylanisolvens, Akkermansia muciniphila, fructophilic lactic acid bacteria (FLAB), and Faecalibacterium prausnitzii. This paper discusses each candidate's safety evaluation for novel food or novel food ingredient approval according to European Union (EU) regulations. The factors evaluated include their beneficial properties, antibiotic resistance profiling, history of safe use (if available), publication of the genomic sequence, toxicological studies in agreement with novel food regulations, and the qualified presumptions of safety. Sufficient evidences have made possible to support and authorize the use of heat-inactivated B. xylanisolvens in the European Union. In the case of A. muciniphila, the discussion focuses on earlier safety studies and the strain's suitability. FLAB are also subjected to standard safety assessments, which, along with their proximity to lactic acid bacteria generally considered to be safe, may lead to novel food authorization in the future. Further research with F. prausnitzii will increase knowledge about its safety and probiotic properties and may lead to its future use as novel food. Upcoming changes in EUU Regulation 2015/2283 on novel food will facilitate the authorization of future novel products and might increase the presence of novel microbes in the food market. PMID:28955311

Engineered microbes and methods for microbial oil production

DOEpatents

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

2015-02-10

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis and storage properties.

A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases.

PubMed

Chen, Xing; Huang, Yu-An; You, Zhu-Hong; Yan, Gui-Ying; Wang, Xue-Song

2017-03-01

Accumulating clinical observations have indicated that microbes living in the human body are closely associated with a wide range of human noninfectious diseases, which provides promising insights into the complex disease mechanism understanding. Predicting microbe-disease associations could not only boost human disease diagnostic and prognostic, but also improve the new drug development. However, little efforts have been attempted to understand and predict human microbe-disease associations on a large scale until now. In this work, we constructed a microbe-human disease association network and further developed a novel computational model of KATZ measure for Human Microbe-Disease Association prediction (KATZHMDA) based on the assumption that functionally similar microbes tend to have similar interaction and non-interaction patterns with noninfectious diseases, and vice versa. To our knowledge, KATZHMDA is the first tool for microbe-disease association prediction. The reliable prediction performance could be attributed to the use of KATZ measurement, and the introduction of Gaussian interaction profile kernel similarity for microbes and diseases. LOOCV and k-fold cross validation were implemented to evaluate the effectiveness of this novel computational model based on known microbe-disease associations obtained from HMDAD database. As a result, KATZHMDA achieved reliable performance with average AUCs of 0.8130 ± 0.0054, 0.8301 ± 0.0033 and 0.8382 in 2-fold and 5-fold cross validation and LOOCV framework, respectively. It is anticipated that KATZHMDA could be used to obtain more novel microbes associated with important noninfectious human diseases and therefore benefit drug discovery and human medical improvement. Matlab codes and dataset explored in this work are available at http://dwz.cn/4oX5mS . xingchen@amss.ac.cn or zhuhongyou@gmail.com or wangxuesongcumt@163.com. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Modulation of host immunity by beneficial microbes.

PubMed

Zamioudis, Christos; Pieterse, Corné M J

2012-02-01

In nature, plants abundantly form beneficial associations with soilborne microbes that are important for plant survival and, as such, affect plant biodiversity and ecosystem functioning. Classical examples of symbiotic microbes are mycorrhizal fungi that aid in the uptake of water and minerals, and Rhizobium bacteria that fix atmospheric nitrogen for the plant. Several other types of beneficial soilborne microbes, such as plant-growth-promoting rhizobacteria and fungi with biological control activity, can stimulate plant growth by directly suppressing deleterious soilborne pathogens or by priming aboveground plant parts for enhanced defense against foliar pathogens or insect herbivores. The establishment of beneficial associations requires mutual recognition and substantial coordination of plant and microbial responses. A growing body of evidence suggests that beneficial microbes are initially recognized as potential invaders, after which an immune response is triggered, whereas, at later stages of the interaction, mutualists are able to short-circuit plant defense responses to enable successful colonization of host roots. Here, we review our current understanding of how symbiotic and nonsymbiotic beneficial soil microbes modulate the plant immune system and discuss the role of local and systemic defense responses in establishing the delicate balance between the two partners.

Engineered microbes and methods for microbial oil production

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

Stephanopoulos, Gregory; Tai, Mitchell; Chakraborty, Sagar

Some aspects of this invention provide engineered microbes for oil production. Methods for microbe engineering and for use of engineered microbes are also provided herein. In some embodiments, microbes are provided that are engineered to modulate a combination of rate-controlling steps of lipid synthesis, for example, a combination of a step generating metabolites, acetyl-CoA, ATP or NADPH for lipid synthesis (a push step), and a step sequestering a product or an intermediate of a lipid synthesis pathway that mediates feedback inhibition of lipid synthesis (a pull step). Such push-and-pull engineered microbes exhibit greatly enhanced conversion yields and TAG synthesis andmore » storage properties.« less

An Astrobiology Microbes Exhibit and Education Module

NASA Technical Reports Server (NTRS)

Lindstrom, Marilyn M.; Allen, Jaclyn S.; Stocco, Karen; Tobola, Kay; Olendzenski, Lorraine

2001-01-01

Telling the story of NASA-sponsored scientific research to the public in exhibits is best done by partnerships of scientists and museum professionals. Likewise, preparing classroom activities and training teachers to use them should be done by teams of teachers and scientists. Here we describe how we used such partnerships to develop a new astrobiology augmentation to the Microbes! traveling exhibit and a companion education module. "Additional information is contained in the original extended abstract."

Topological distortion and reorganized modular structure of gut microbial co-occurrence networks in inflammatory bowel disease

NASA Astrophysics Data System (ADS)

Baldassano, Steven N.; Bassett, Danielle S.

2016-05-01

The gut microbiome plays a key role in human health, and alterations of the normal gut flora are associated with a variety of distinct disease states. Yet, the natural dependencies between microbes in healthy and diseased individuals remain far from understood. Here we use a network-based approach to characterize microbial co-occurrence in individuals with inflammatory bowel disease (IBD) and healthy (non-IBD control) individuals. We find that microbial networks in patients with IBD differ in both global structure and local connectivity patterns. While a “core” microbiome is preserved, network topology of other densely interconnected microbe modules is distorted, with potent inflammation-mediating organisms assuming roles as integrative and highly connected inter-modular hubs. We show that while both networks display a rich-club organization, in which a small set of microbes commonly co-occur, the healthy network is more easily disrupted by elimination of a small number of key species. Further investigation of network alterations in disease might offer mechanistic insights into the specific pathogens responsible for microbiome-mediated inflammation in IBD.

Diversity and evolution of the primate skin microbiome

PubMed Central

Council, Sarah E.; Savage, Amy M.; Urban, Julie M.; Ehlers, Megan E.; Skene, J. H. Pate; Platt, Michael L.; Dunn, Robert R.; Horvath, Julie E.

2016-01-01

Skin microbes play a role in human body odour, health and disease. Compared with gut microbes, we know little about the changes in the composition of skin microbes in response to evolutionary changes in hosts, or more recent behavioural and cultural changes in humans. No studies have used sequence-based approaches to consider the skin microbe communities of gorillas and chimpanzees, for example. Comparison of the microbial associates of non-human primates with those of humans offers unique insights into both the ancient and modern features of our skin-associated microbes. Here we describe the microbes found on the skin of humans, chimpanzees, gorillas, rhesus macaques and baboons. We focus on the bacterial and archaeal residents in the axilla using high-throughput sequencing of the 16S rRNA gene. We find that human skin microbial communities are unique relative to those of other primates, in terms of both their diversity and their composition. These differences appear to reflect both ancient shifts during millions of years of primate evolution and more recent changes due to modern hygiene. PMID:26763711

The influence of the human microbiome and probiotics on cardiovascular health

PubMed Central

Ettinger, Grace; MacDonald, Kyle; Reid, Gregor; Burton, Jeremy P

2014-01-01

Cardiovascular disease (CVD) is a major cause of death worldwide. Of the many etiological factors, microorganisms constitute one. From the local impact of the gut microbiota on energy metabolism and obesity, to the distal association of periodontal disease with coronary heart disease, microbes have a significant impact on cardiovascular health. In terms of the ability to modulate or influence the microbes, probiotic applications have been considered. These are live microorganisms which when administered in adequate amounts confer a benefit on the host. While a number of reports have established the beneficial abilities of certain probiotic bacterial strains to reduce cholesterol and hypertension, recent research suggests that their use could be more widely applied. This review presents an up-to-date summary of the known associations of the microbiome with CVD, and potential applications of probiotic therapy. PMID:25529048

The influence of the human microbiome and probiotics on cardiovascular health.

PubMed

Ettinger, Grace; MacDonald, Kyle; Reid, Gregor; Burton, Jeremy P

2014-01-01

Cardiovascular disease (CVD) is a major cause of death worldwide. Of the many etiological factors, microorganisms constitute one. From the local impact of the gut microbiota on energy metabolism and obesity, to the distal association of periodontal disease with coronary heart disease, microbes have a significant impact on cardiovascular health. In terms of the ability to modulate or influence the microbes, probiotic applications have been considered. These are live microorganisms which when administered in adequate amounts confer a benefit on the host. While a number of reports have established the beneficial abilities of certain probiotic bacterial strains to reduce cholesterol and hypertension, recent research suggests that their use could be more widely applied. This review presents an up-to-date summary of the known associations of the microbiome with CVD, and potential applications of probiotic therapy.

Understanding and Modulating Mammalian-Microbial Communication for Improved Human Health

PubMed Central

Mani, Sridhar; Boelsterli, Urs A.; Redinbo, Matthew R.

2013-01-01

The fact that the bacteria in the human gastrointestinal (GI) tract play a symbiotic role was noted as early as 1885, well before we began to manage microbial infections using antibiotics. However, even with the first antimicrobial compounds used in humans, the sulfa drugs, microbes were recognized to be critically involved in the biotransformation of these therapeutics. Thus, the roles played by the microbiota in physiology and in the management of human health have long been appreciated. Detailed examinations of GI symbiotic bacteria that started in the early 2000s and the first phases of the Human Microbiome Project that were completed in 2012 have ushered in an exciting period of granularity with respect to the ecology, genetics, and chemistry of the mammalian-microbial axes of communication. Here we review aspects of the biochemical pathways at play between commensal GI bacteria and several mammalian systems, including both local-epithelia and nonlocal responses including inflammation, immunology, metabolism, and neurobiology. Finally, we discuss how the microbial biotransformation of therapeutic compounds, such as anticancer or nonsteroidal anti-inflammatory drugs, can be modulated to reduce toxicity and potentially improve therapeutic efficacy. PMID:24160697

Biodiversity and Functional Genomics in the Human Microbiome

PubMed Central

Morgan, Xochitl C.; Segata, Nicola; Huttenhower, Curtis

2012-01-01

Over the course of our lives, humans are colonized by a tremendous diversity of commensal microbes, which comprise the human microbiome. The collective genetic potential (metagenome) of the human microbiome is orders of magnitude more than the human genome, and it profoundly affects human health and disease in ways we are only beginning to understand. Advances in computing and high-throughput sequencing have enabled population-level surveys such as MetaHIT and the recently-released Human Microbiome Project, detailed investigations of the microbiome in human disease, and mechanistic studies employing gnotobiotic model organisms. The resulting knowledge of human microbiome composition, function, and range of variation across multiple body sites has begun to assemble a rich picture of commensal host-microbe and microbe- microbe interactions as well as their roles in human health and disease and their potential as diagnostic and therapeutic tools. PMID:23140990

The Human Microbiome: Our Second Genome*

PubMed Central

Grice, Elizabeth A.; Segre, Julia A.

2012-01-01

The human genome has been referred to as the blueprint of human biology. In this review we consider an essential but largely ignored overlay to that blueprint, the human microbiome, which is composed of those microbes that live in and on our bodies. The human microbiome is a source of genetic diversity, a modifier of disease, an essential component of immunity, and a functional entity that influences metabolism and modulates drug interactions. Characterization and analysis of the human microbiome have been greatly catalyzed by advances in genomic technologies. We discuss how these technologies have shaped this emerging field of study and advanced our understanding of the human microbiome. We also identify future challenges, many of which are common to human genetic studies, and predict that in the future, analyzing genetic variation and risk of human disease will sometimes necessitate the integration of human and microbial genomic data sets. PMID:22703178

Insights into teichoic acid biosynthesis by Bifidobacterium bifidum PRL2010.

PubMed

Colagiorgi, Angelo; Turroni, Francesca; Mancabelli, Leonardo; Serafini, Fausta; Secchi, Andrea; van Sinderen, Douwe; Ventura, Marco

2015-09-01

Bifidobacteria are colonizers of the human gut, where they are interacting with their host as well as with other members of the intestinal microbiota. Teichoic acids (TAs) have previously been shown to play an important role in modulating microbe-host interactions in the human gut. However, so far, there is a paucity of information regarding the presence of TAs in the cell envelope of bifidobacteria. In silico analyses targeting the chromosomes of all 48 (sub)species that currently represent the genus Bifidobacterium revealed the presence of genes responsible for TA biosynthesis, suggesting that bifidobacteria contain both wall TAs and lipoteichoic acids. Transcriptome analyses of the infant gut commensal Bifidobacterium bifidum PRL2010 highlighted that the transcription of the presumptive TA biosynthetic loci is modulated in response to environmental conditions reflecting those of the human gut. Furthermore, chemical characterization of TAs produced by PRL2010 indicates the presence of lipoteichoic acids. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Current state of coenzyme Q(10) production and its applications.

PubMed

Jeya, Marimuthu; Moon, Hee-Jung; Lee, Jeong-Lim; Kim, In-Won; Lee, Jung-Kul

2010-02-01

Coenzyme Q(10) (CoQ(10)), an obligatory cofactor in the aerobic respiratory electron transfer for energy generation, is formed from the conjugation of a benzoquinone ring with a hydrophobic isoprenoid chain. CoQ(10) is now used as a nutritional supplement because of its antioxidant properties and is beneficial in the treatment of several human diseases when administered orally. Bioprocesses have been developed for the commercial production of CoQ(10) because of its increased demand, and these bioprocesses depend on microbes that produce high levels of CoQ(10) naturally. However, as knowledge of the biosynthetic enzymes and the regulatory mechanisms modulating CoQ(10) production increases, approaches arise for the genetic engineering of CoQ(10) production in Escherichia coli and Agrobacterium tumefaciens. This review focused on approaches for CoQ(10) production, strategies used to engineer CoQ(10) production in microbes, and potential applications of CoQ(10).

The weapon potential of a microbe.

PubMed

Casadevall, Arturo; Pirofski, Liise-anne

2004-06-01

The designation of a microbe as a potential biological weapon poses the vexing question of how such a decision is made given the many pathogenic microbes that cause disease. Analysis of the properties of microbes that are currently considered biological weapons against humans revealed no obvious relationship to virulence, except that all are pathogenic for humans. Notably, the weapon potential of a microbe rather than its pathogenic properties or virulence appeared to be the major consideration when categorizing certain agents as biological weapons. In an effort to standardize the assessment of the risk that is posed by microbes as biological warfare agents using the basic principles of microbial communicability (defined here as a parameter of transmission) and virulence, a simple formula is proposed for estimating the weapon potential of a microbe.

A Perspective on the Interplay of Ultraviolet-Radiation, Skin Microbiome and Skin Resident Memory TCRαβ+ Cells.

PubMed

Patra, VijayKumar; Laoubi, Léo; Nicolas, Jean-François; Vocanson, Marc; Wolf, Peter

2018-01-01

The human skin is known to be inhabited by diverse microbes, including bacteria, fungi, viruses, archaea, and mites. This microbiome exerts a protective role against infections by promoting immune development and inhibiting pathogenic microbes to colonize skin. One of the factors having an intense effect on the skin and its resident microbes is ultraviolet-radiation (UV-R). UV-R can promote or inhibit the growth of microbes on the skin and modulate the immune system which can be either favorable or harmful. Among potential UV-R targets, skin resident memory T cells (T RM ) stand as well positioned immune cells at the forefront within the skin. Both CD4 + or CD8 + αβ T RM cells residing permanently in peripheral tissues have been shown to play prominent roles in providing accelerated and long-lived specific immunity, tissue homeostasis, wound repair. Nevertheless, their response upon UV-R exposure or signals from microbiome are poorly understood compared to resident TCRγδ cells. Skin T RM survive for long periods of time and are exposed to innumerable antigens during lifetime. The interplay of T RM with skin residing microbes may be crucial in pathophysiology of various diseases including psoriasis, atopic dermatitis and polymorphic light eruption. In this article, we share our perspective about how UV-R may directly shape the persistence, phenotype, specificity, and function of skin T RM ; and moreover, whether UV-R alters barrier function, leading to microbial-specific skin T RM , disrupting the healthy balance between skin microbiome and skin immune cells, and resulting in chronic inflammation and diseased skin.

The HMI™ module: a new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro.

PubMed

Marzorati, Massimo; Vanhoecke, Barbara; De Ryck, Tine; Sadaghian Sadabad, Mehdi; Pinheiro, Iris; Possemiers, Sam; Van den Abbeele, Pieter; Derycke, Lara; Bracke, Marc; Pieters, Jan; Hennebel, Tom; Harmsen, Hermie J; Verstraete, Willy; Van de Wiele, Tom

2014-05-22

Recent scientific developments have shed more light on the importance of the host-microbe interaction, particularly in the gut. However, the mechanistic study of the host-microbe interplay is complicated by the intrinsic limitations in reaching the different areas of the gastrointestinal tract (GIT) in vivo. In this paper, we present the technical validation of a new device--the Host-Microbiota Interaction (HMI) module--and the evidence that it can be used in combination with a gut dynamic simulator to evaluate the effect of a specific treatment at the level of the luminal microbial community and of the host surface colonization and signaling. The HMI module recreates conditions that are physiologically relevant for the GIT: i) a mucosal area to which bacteria can adhere under relevant shear stress (3 dynes cm(-2)); ii) the bilateral transport of low molecular weight metabolites (4 to 150 kDa) with permeation coefficients ranging from 2.4 × 10(-6) to 7.1 × 10(-9) cm sec(-1); and iii) microaerophilic conditions at the bottom of the growing biofilm (PmO2 = 2.5 × 10(-4) cm sec(-1)). In a long-term study, the host's cells in the HMI module were still viable after a 48-hour exposure to a complex microbial community. The dominant mucus-associated microbiota differed from the luminal one and its composition was influenced by the treatment with a dried product derived from yeast fermentation. The latter--with known anti-inflammatory properties--induced a decrease of pro-inflammatory IL-8 production between 24 and 48 h. The study of the in vivo functionality of adhering bacterial communities in the human GIT and of the localized effect on the host is frequently hindered by the complexity of reaching particular areas of the GIT. The HMI module offers the possibility of co-culturing a gut representative microbial community with enterocyte-like cells up to 48 h and may therefore contribute to the mechanistic understanding of host-microbiome interactions.

The HMI™ module: a new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro

PubMed Central

2014-01-01

Background Recent scientific developments have shed more light on the importance of the host-microbe interaction, particularly in the gut. However, the mechanistic study of the host-microbe interplay is complicated by the intrinsic limitations in reaching the different areas of the gastrointestinal tract (GIT) in vivo. In this paper, we present the technical validation of a new device - the Host-Microbiota Interaction (HMI) module - and the evidence that it can be used in combination with a gut dynamic simulator to evaluate the effect of a specific treatment at the level of the luminal microbial community and of the host surface colonization and signaling. Results The HMI module recreates conditions that are physiologically relevant for the GIT: i) a mucosal area to which bacteria can adhere under relevant shear stress (3 dynes cm−2); ii) the bilateral transport of low molecular weight metabolites (4 to 150 kDa) with permeation coefficients ranging from 2.4 × 10−6 to 7.1 × 10−9 cm sec−1; and iii) microaerophilic conditions at the bottom of the growing biofilm (PmO2 = 2.5 × 10−4 cm sec−1). In a long-term study, the host’s cells in the HMI module were still viable after a 48-hour exposure to a complex microbial community. The dominant mucus-associated microbiota differed from the luminal one and its composition was influenced by the treatment with a dried product derived from yeast fermentation. The latter - with known anti-inflammatory properties - induced a decrease of pro-inflammatory IL-8 production between 24 and 48 h. Conclusions The study of the in vivo functionality of adhering bacterial communities in the human GIT and of the localized effect on the host is frequently hindered by the complexity of reaching particular areas of the GIT. The HMI module offers the possibility of co-culturing a gut representative microbial community with enterocyte-like cells up to 48 h and may therefore contribute to the mechanistic understanding of host-microbiome interactions. PMID:24884540

Filthy lucre: A metagenomic pilot study of microbes found on circulating currency in New York City

PubMed Central

Maritz, Julia M.; Sullivan, Steven A.; Prill, Robert J.; Aksoy, Emre; Scheid, Paul; Carlton, Jane M.

2017-01-01

Background Paper currency by its very nature is frequently transferred from one person to another and represents an important medium for human contact with—and potential exchange of—microbes. In this pilot study, we swabbed circulating $1 bills obtained from a New York City bank in February (Winter) and June (Summer) 2013 and used shotgun metagenomic sequencing to profile the communities found on their surface. Using basic culture conditions, we also tested whether viable microbes could be recovered from bills. Results Shotgun metagenomics identified eukaryotes as the most abundant sequences on money, followed by bacteria, viruses and archaea. Eukaryotic assemblages were dominated by human, other metazoan and fungal taxa. The currency investigated harbored a diverse microbial population that was dominated by human skin and oral commensals, including Propionibacterium acnes, Staphylococcus epidermidis and Micrococcus luteus. Other taxa detected not associated with humans included Lactococcus lactis and Streptococcus thermophilus, microbes typically associated with dairy production and fermentation. Culturing results indicated that viable microbes can be isolated from paper currency. Conclusions We conducted the first metagenomic characterization of the surface of paper money in the United States, establishing a baseline for microbes found on $1 bills circulating in New York City. Our results suggest that money amalgamates DNA from sources inhabiting the human microbiome, food, and other environmental inputs, some of which can be recovered as viable organisms. These monetary communities may be maintained through contact with human skin, and DNA obtained from money may provide a record of human behavior and health. Understanding these microbial profiles is especially relevant to public health as money could potentially mediate interpersonal transfer of microbes. PMID:28384336

Intestinal microbiota composition modulates choline bioavailability from diet and accumulation of the proatherogenic metabolite trimethylamine-N-oxide.

PubMed

Romano, Kymberleigh A; Vivas, Eugenio I; Amador-Noguez, Daniel; Rey, Federico E

2015-03-17

Choline is a water-soluble nutrient essential for human life. Gut microbial metabolism of choline results in the production of trimethylamine (TMA), which upon absorption by the host is converted in the liver to trimethylamine-N-oxide (TMAO). Recent studies revealed that TMAO exacerbates atherosclerosis in mice and positively correlates with the severity of this disease in humans. However, which microbes contribute to TMA production in the human gut, the extent to which host factors (e.g., genotype) and diet affect TMA production and colonization of these microbes, and the effects TMA-producing microbes have on the bioavailability of dietary choline remain largely unknown. We screened a collection of 79 sequenced human intestinal isolates encompassing the major phyla found in the human gut and identified nine strains capable of producing TMA from choline in vitro. Gnotobiotic mouse studies showed that TMAO accumulates in the serum of animals colonized with TMA-producing species, but not in the serum of animals colonized with intestinal isolates that do not generate TMA from choline in vitro. Remarkably, low levels of colonization by TMA-producing bacteria significantly reduced choline levels available to the host. This effect was more pronounced as the abundance of TMA-producing bacteria increased. Our findings provide a framework for designing strategies aimed at changing the representation or activity of TMA-producing bacteria in the human gut and suggest that the TMA-producing status of the gut microbiota should be considered when making recommendations about choline intake requirements for humans. Cardiovascular disease (CVD) is the leading cause of death and disability worldwide, and increased trimethylamine N-oxide (TMAO) levels have been causally linked with CVD development. This work identifies members of the human gut microbiota responsible for both the accumulation of trimethylamine (TMA), the precursor of the proatherogenic compound TMAO, and subsequent decreased choline bioavailability to the host. Understanding how to manipulate the representation and function of choline-consuming, TMA-producing species in the intestinal microbiota could potentially lead to novel means for preventing or treating atherosclerosis and choline deficiency-associated diseases. Copyright © 2015 Romano et al.

Modulating bacterial and gut mucosal interactions with engineered biofilm matrix proteins.

PubMed

Duraj-Thatte, Anna M; Praveschotinunt, Pichet; Nash, Trevor R; Ward, Frederick R; Joshi, Neel S

2018-02-22

Extracellular appendages play a significant role in mediating communication between bacteria and their host. Curli fibers are a class of bacterial fimbria that is highly amenable to engineering. We demonstrate the use of engineered curli fibers to rationally program interactions between bacteria and components of the mucosal epithelium. Commensal E. coli strains were engineered to produce recombinant curli fibers fused to the trefoil family of human cytokines. Biofilms formed from these strains bound more mucins than those producing wild-type curli fibers, and modulated mucin rheology as well. When treated with bacteria producing the curli-trefoil fusions mammalian cells behaved identically in terms of their migration behavior as when they were treated with the corresponding soluble trefoil factors. Overall, this demonstrates the potential utility of curli fibers as a scaffold for the display of bioactive domains and an untapped approach to rationally modulating host-microbe interactions using bacterial matrix proteins.

Role of plant growth regulators as chemical signals in plant-microbe interactions: a double edged sword.

PubMed

Spence, Carla; Bais, Harsh

2015-10-01

Growth regulators act not only as chemicals that modulate plant growth but they also act as signal molecules under various biotic and abiotic stresses. Of all growth regulators, abscisic acid (ABA) is long known for its role in modulating plants response against both biotic and abiotic stress. Although the genetic information for ABA biosynthesis in plants is well documented, the knowledge about ABA biosynthesis in other organisms is still in its infancy. It is known that various microbes including bacteria produce and secrete ABA, but the overall functional significance of why ABA is synthesized by microbes is not known. Here we discuss the functional involvement of ABA biosynthesis by a pathogenic fungus. Furthermore, we propose that ABA biosynthesis in plant pathogenic fungi could be targeted for novel fungicidal discovery. Copyright © 2015 Elsevier Ltd. All rights reserved.

Gut microbes in correlation with mood: case study in a closed experimental human life support system.

PubMed

Li, L; Su, Q; Xie, B; Duan, L; Zhao, W; Hu, D; Wu, R; Liu, H

2016-08-01

Gut microbial community, which may influence our mood, can be shaped by modulating the gut ecosystem through dietary strategies. Understanding the gut-brain correlationship in healthy people is important for maintenance of mental health and prevention of mental illnesses. A case study on the correlation between gut microbial alternation and mood swing of healthy adults was conducted in a closed human life support system during a 105-day experiment. Gut microbial community structures were analyzed using high-throughput sequencing every 2 weeks. A profile of mood states questionnaire was used to record the mood swings. Correlation between gut microbes and mood were identified with partial least squares discrimination analysis. Microbial community structures in the three healthy adults were strongly correlated with mood states. Bacterial genera Roseburia, Phascolarctobacterium, Lachnospira, and Prevotella had potential positive correlation with positive mood, while genera Faecalibacterium, Bifidobacterium, Bacteroides, Parabacteroides, and Anaerostipes were correlated with negative mood. Among which, Faecalibacterium spp. had the highest abundance, and showed a significant negative correlation with mood. Our results indicated that the composition of microbial community could play a role in emotional change in mentally physically healthy adults. © 2016 John Wiley & Sons Ltd.

New developments in microbial interspecies signaling.

PubMed

Shank, Elizabeth Anne; Kolter, Roberto

2009-04-01

There is a growing appreciation that in addition to well-documented intraspecies quorum sensing systems, small molecules act as signals between microbes of different species. This review will focus on how bacterial small molecules modulate these interspecies interactions. We will particularly emphasize complex relationships such as those between microbes and insects, interactions resulting in non-antagonistic outcomes (i.e. developmental and morphological processes), how co-culture can lead to the discovery of new small molecules, and the use of known compounds to evoke unexpected responses and mediate crosstalk between microbes.

Can the gastrointestinal microbiota be modulated by dietary fibre to treat obesity?

PubMed

Davis, H C

2018-05-01

Recent research suggests that the human gastrointestinal microbiota is greatly involved in yielding, storing and expending energy from the diet; therefore, it may be a further factor in linking diet to obesity. The gut microbial composition is affected by diet throughout the human lifespan, and is highly dynamic and efficient in response to dietary alterations in particular to dietary fibre intake. Short-chained fatty acids (SCFA) are the bi-product of fibre fermentation and have both obesogenic and anti-obesogenic properties. The production of specific forms of SCFAs depends on the microbes available in the gut and the type of fibre ingested. The gut microbiome associated with healthy lean individuals has a higher microbial biodiversity and a greater Bacteroidete to Firmicute ratio compared to the obese individuals associated with microbiome. These gut microbial associations are similar to those seen in individuals with high and low dietary fibre intakes, respectively. Metabolites generated by Bacteroidetes and Firmicutes include the three main SCFA related to obesity, namely butyrate, acetate and propionate. However, neither Bacteroidetes nor Firmicutes is purely causative or purely preventative of obesity. More research is crucial in linking the various types of fibre with particular SCFA production and the microbiome it promotes before suggesting that dietary fibre modulation of the gut microbiome can treat obesity. However, the long-term dietary trend plays the principal role in assembling the diversity and abundance of gut microbes; thus, a sustained diet high in fibre may help prevent obesity by promoting a microbiome associated with a lean phenotype.

Soil biodiversity and human health

NASA Astrophysics Data System (ADS)

Six, Johan; Pereg, Lily; Brevik, Eric

2017-04-01

Biodiversity is important for the maintenance of soil quality. Healthy, biodiverse soils are crucial for human health and wellbeing from several reasons, for example: biodiversity has been shown to be important in controlling populations of pathogens; healthy, well-covered soils can reduce disease outbreaks; carbon-rich soils may also reduce outbreaks of human and animal parasites; exposure to soil microbes can reduce allergies; soils have provided many of our current antibiotics; soil organisms can provide biological disease and pest control agents, healthy soils mean healthier and more abundant foods; soil microbes can enhance crop plant resilience; healthy soils promote good clean air quality, less prone to wind and water erosion; and healthy soils provide clean and safe water through filtration, decontamination by microbes and removal of pollutants. Soil microbes and other biota provide many benefits to human health. Soil microbes are a source of medicines, such as antibiotics, anticancer drugs and many more. Organisms that affect soil health and thus human health include those involved in nutrient cycling, decomposition of organic matter and determining soil structure (e.g. aggregation). Again these are related to food security but also affect human health in other ways. Many beneficial organisms have been isolated from soil - plant growth promoting and disease suppressive microbes used as inoculants, foliar inoculants for improvement of ruminant digestion systems and inoculants used in bioremediation of toxic compounds in the environment. Soil biodiversity is highly recognised now as an important feature of healthy soil and imbalances have been shown to give advantage to harmful over beneficial organisms. This presentation will highlight the many connections of biodiversity to soil quality and human health.

Gut Microbiota: Modulation of Host Physiology in Obesity

PubMed Central

Allen, Jacob M.; Mailing, Lucy J.; Kashyap, Purna C.; Woods, Jeffrey A.

2016-01-01

Many factors are involved in weight gain and metabolic disturbances associated with obesity. The gut microbiota has been of particular interest in recent years, since both human and animal studies have increased our understanding of the delicate symbiosis between the trillions of microbes that reside in the GI tract and the host. It has been suggested that disruption of this mutual tolerance may play a significant role in modulating host physiology during obesity. Environmental influences such as diet, exercise, and early life exposures can significantly impact the composition of the microbiota, and this dysbiosis can in turn lead to increased host adiposity via a number of different mechanisms. The ability of the microbiota to regulate host fat deposition, metabolism, and immune function makes it an attractive target for achieving sustained weight loss. PMID:27511459

Plant Hormones: Key Players in Gut Microbiota and Human Diseases?

PubMed

Chanclud, Emilie; Lacombe, Benoît

2017-09-01

It is well established that plant hormones such as auxins, cytokinins (CKs), and abscisic acid (ABA) not only govern important plant physiological traits but are key players in plant-microbe interactions. A poorly appreciated fact, however, is that both microbes and animals produce and perceive plant hormones and their mimics. Moreover, dietary plant hormones impact on human physiological process such as glucose assimilation, inflammation, and cell division. This leads us to wonder whether plant hormones could ensure functions in microbes per se as well as in animal-microbe interactions. We propose here and explore the hypothesis that plant hormones play roles in animal-microbiota relationships, with consequences for human health. Copyright © 2017 Elsevier Ltd. All rights reserved.

The possible mechanisms of the human microbiome in allergic diseases.

PubMed

Ipci, Kagan; Altıntoprak, Niyazi; Muluk, Nuray Bayar; Senturk, Mehmet; Cingi, Cemal

2017-02-01

In the present paper, we discuss the importance of the microbiome in allergic disease. In this review paper, the data from the Medline (PubMed) and search engine of Kirikkale University were systematically searched for all relevant articles in June 15th, 2015 for the past 30 years. The keywords of "microbiome", "dysbiosis", "allergy", "allergic rhinitis", "allergic disease", "mechanisms" and "treatment" were used alone or together. In this paper, microbiomes were presented in terms of "Definition", "Influence of \\the human microbiome on health", "The microbiome and allergic diseases", and "Modulation of the gut microbiota in terms of treatment and prevention". Microbiological dysbiosis is also reviewed. The microbiome is the genetic material of all microbes (bacteria, fungi, protozoa, and viruses) that live on or in the human body. Microbes outnumber human cells in a 10:1 ratio. Most microbes live in the gut, particularly the large intestine. Changes in the immune function of the respiratory tract are (at least in theory) linked to the immunomodulatory activity of the gut microbiota via the concept of a "common mucosal response". The gut microbiota shapes systemic immunity, thus affecting the lung mucosa. Alternatively, changes in the gut microbiota may reflect alterations in the oropharyngeal microbiota, which may in turn directly affect the lung microbiota and host immune responses via microaspiration. Dysbiosis is defined as qualitative and quantitative changes in the intestinal flora; and modern diet and lifestyle, antibiotics, psychological and physical stress result in alterations in bacterial metabolism, as well as the overgrowth of potentially pathogenic microorganisms. All immune system components are directly or indirectly regulated by the microbiota. The nature of microbial exposure early in life appears to be important for the development of robust immune regulation; disruption of either the microbiota or the host response can trigger chronic inflammation. Dysbiosis is also an important clinical entity. Antibiotics, psychological and physical stress, and dietary factors contribute to intestinal dysbiosis.

Siderophore biosynthesis coordinately modulated the virulence-associated interactive metabolome of uropathogenic Escherichia coli and human urine

PubMed Central

Su, Qiao; Guan, Tianbing; Lv, Haitao

2016-01-01

Uropathogenic Escherichia coli (UPEC) growth in women’s bladders during urinary tract infection (UTI) incurs substantial chemical exchange, termed the “interactive metabolome”, which primarily accounts for the metabolic costs (utilized metabolome) and metabolic donations (excreted metabolome) between UPEC and human urine. Here, we attempted to identify the individualized interactive metabolome between UPEC and human urine. We were able to distinguish UPEC from non-UPEC by employing a combination of metabolomics and genetics. Our results revealed that the interactive metabolome between UPEC and human urine was markedly different from that between non-UPEC and human urine, and that UPEC triggered much stronger perturbations in the interactive metabolome in human urine. Furthermore, siderophore biosynthesis coordinately modulated the individualized interactive metabolome, which we found to be a critical component of UPEC virulence. The individualized virulence-associated interactive metabolome contained 31 different metabolites and 17 central metabolic pathways that were annotated to host these different metabolites, including energetic metabolism, amino acid metabolism, and gut microbe metabolism. Changes in the activities of these pathways mechanistically pinpointed the virulent capability of siderophore biosynthesis. Together, our findings provide novel insights into UPEC virulence, and we propose that siderophores are potential targets for further discovery of drugs to treat UPEC-induced UTI. PMID:27076285

Siderophore biosynthesis coordinately modulated the virulence-associated interactive metabolome of uropathogenic Escherichia coli and human urine.

PubMed

Su, Qiao; Guan, Tianbing; Lv, Haitao

2016-04-14

Uropathogenic Escherichia coli (UPEC) growth in women's bladders during urinary tract infection (UTI) incurs substantial chemical exchange, termed the "interactive metabolome", which primarily accounts for the metabolic costs (utilized metabolome) and metabolic donations (excreted metabolome) between UPEC and human urine. Here, we attempted to identify the individualized interactive metabolome between UPEC and human urine. We were able to distinguish UPEC from non-UPEC by employing a combination of metabolomics and genetics. Our results revealed that the interactive metabolome between UPEC and human urine was markedly different from that between non-UPEC and human urine, and that UPEC triggered much stronger perturbations in the interactive metabolome in human urine. Furthermore, siderophore biosynthesis coordinately modulated the individualized interactive metabolome, which we found to be a critical component of UPEC virulence. The individualized virulence-associated interactive metabolome contained 31 different metabolites and 17 central metabolic pathways that were annotated to host these different metabolites, including energetic metabolism, amino acid metabolism, and gut microbe metabolism. Changes in the activities of these pathways mechanistically pinpointed the virulent capability of siderophore biosynthesis. Together, our findings provide novel insights into UPEC virulence, and we propose that siderophores are potential targets for further discovery of drugs to treat UPEC-induced UTI.

Microbial modulation of bacoside A biosynthetic pathway and systemic defense mechanism in Bacopa monnieri under Meloidogyne incognita stress.

PubMed

Gupta, Rupali; Singh, Akanksha; Srivastava, Madhumita; Singh, Vivek; Gupta, M M; Pandey, Rakesh

2017-02-03

Plant-associated beneficial microbes have been explored to fulfill the imperative function for plant health. However, their impact on the host secondary metabolite production and nematode disease management remains elusive. Our present work has shown that chitinolytic microbes viz., Chitiniphilus sp. MTN22 and Streptomyces sp. MTN14 singly as well as in combination modulated the biosynthetic pathway of bacoside A and systemic defense mechanism against Meloidogyne incognita in Bacopa monnieri. Interestingly, expression of bacoside biosynthetic pathway genes (3-Hydroxy-3-methylglutaryl coenzyme A reductase, mevalonate diphosphate decarboxylase, and squalene synthase) were upregulated in plants treated with the microbial combination in the presence as well as in absence of M. incognita stress. These microbes not only augmented bacoside A production (1.5 fold) but also strengthened host resistance via enhancement in chlorophyll a, defense enzymes and phenolic compounds like gallic acid, syringic acid, ferulic acid and cinnamic acid. Furthermore, elevated lignification and callose deposition in the microbial combination treated plants corroborate well with the above findings. Overall, the results provide novel insights into the underlying mechanisms of priming by beneficial microbes and underscore their capacity to trigger bacoside A production in B. monnieri under biotic stress.

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.

PubMed

Levy, Roie; Carr, Rogan; Kreimer, Anat; Freilich, Shiri; Borenstein, Elhanan

2015-05-17

Host-microbe and microbe-microbe interactions are often governed by the complex exchange of metabolites. Such interactions play a key role in determining the way pathogenic and commensal species impact their host and in the assembly of complex microbial communities. Recently, several studies have demonstrated how such interactions are reflected in the organization of the metabolic networks of the interacting species, and introduced various graph theory-based methods to predict host-microbe and microbe-microbe interactions directly from network topology. Using these methods, such studies have revealed evolutionary and ecological processes that shape species interactions and community assembly, highlighting the potential of this reverse-ecology research paradigm. NetCooperate is a web-based tool and a software package for determining host-microbe and microbe-microbe cooperative potential. It specifically calculates two previously developed and validated metrics for species interaction: the Biosynthetic Support Score which quantifies the ability of a host species to supply the nutritional requirements of a parasitic or a commensal species, and the Metabolic Complementarity Index which quantifies the complementarity of a pair of microbial organisms' niches. NetCooperate takes as input a pair of metabolic networks, and returns the pairwise metrics as well as a list of potential syntrophic metabolic compounds. The Biosynthetic Support Score and Metabolic Complementarity Index provide insight into host-microbe and microbe-microbe metabolic interactions. NetCooperate determines these interaction indices from metabolic network topology, and can be used for small- or large-scale analyses. NetCooperate is provided as both a web-based tool and an open-source Python module; both are freely available online at http://elbo.gs.washington.edu/software_netcooperate.html.

Ticks and Tick-Borne Infections: Complex Ecology, Agents, and Host Interactions.

PubMed

Wikel, Stephen K

2018-06-20

Ticks transmit the most diverse array of infectious agents of any arthropod vector. Both ticks and the microbes they transmit are recognized as significant threats to human and veterinary public health. This article examines the potential impacts of climate change on the distribution of ticks and the infections they transmit; the emergence of novel tick-borne pathogens, increasing geographic range and incidence of tick-borne infections; and advances in the characterization of tick saliva mediated modulation of host defenses and the implications of those interactions for transmission, establishment, and control of tick infestation and tick-borne infectious agents.

The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation.

PubMed

Langdon, Amy; Crook, Nathan; Dantas, Gautam

2016-04-13

The widespread use of antibiotics in the past 80 years has saved millions of human lives, facilitated technological progress and killed incalculable numbers of microbes, both pathogenic and commensal. Human-associated microbes perform an array of important functions, and we are now just beginning to understand the ways in which antibiotics have reshaped their ecology and the functional consequences of these changes. Mounting evidence shows that antibiotics influence the function of the immune system, our ability to resist infection, and our capacity for processing food. Therefore, it is now more important than ever to revisit how we use antibiotics. This review summarizes current research on the short-term and long-term consequences of antibiotic use on the human microbiome, from early life to adulthood, and its effect on diseases such as malnutrition, obesity, diabetes, and Clostridium difficile infection. Motivated by the consequences of inappropriate antibiotic use, we explore recent progress in the development of antivirulence approaches for resisting infection while minimizing resistance to therapy. We close the article by discussing probiotics and fecal microbiota transplants, which promise to restore the microbiota after damage of the microbiome. Together, the results of studies in this field emphasize the importance of developing a mechanistic understanding of gut ecology to enable the development of new therapeutic strategies and to rationally limit the use of antibiotic compounds.

Skin microbiome: genomics-based insights into the diversity and role of skin microbes

PubMed Central

Kong, Heidi H.

2011-01-01

Recent advances in DNA sequencing methodology have enabled studies of human skin microbes that circumvent difficulties in isolating and characterizing fastidious microbes. Sequence-based approaches have identified greater diversity of cutaneous bacteria than studies using traditional cultivation techniques. However, improved sequencing technologies and analytical methods are needed to study all skin microbes, including bacteria, archaea, fungi, viruses, and mites, and how they interact with each other and their human hosts. This review discusses current skin microbiome research, with a primary focus on bacteria, and the challenges facing investigators striving to understand how skin micro-organisms contribute to health and disease. PMID:21376666

From evolutionary advantage to disease agents: forensic re-evaluation of host-microbe interactions and pathogenicity

PubMed Central

Rivera-Pérez, Jessica I.; González, Alfredo A.; Toranzos, Gary A.

2016-01-01

As the “human microbiome era” continues, there is an increasing awareness of our resident microbiota and its indispensable role in our increased fitness as holobionts. However, the host-microbe relationship is not so clearly defined for some human symbionts. Here we discuss examples of “accidental pathogens”, meaning previously non-pathogenic and/or environmental microbes thought to have inadvertently experienced an evolutionary shift towards pathogenicity. For instance, symbionts such as Helicobacter pylori and JC Polyomavirus have been shown to accompany humans since prehistoric times and are still abundant in extant populations as part of the microbiome. And yet, the relationship between a subgroup of these microbes and their human hosts seems to have changed with time, and they have recently gained notoriety as gastrointestinal and neuropathogens, respectively. On the other hand, environmental microbes such as Legionella spp. have recently experienced a shift in host range and are now a major problem in industrialized countries as a result of artificial ecosystems. Other variables involved in this accidental phenomenon could be the apparent change or reduction in the diversity of human-associated microbiota because of modern medicine and lifestyles. All of this could result in an increased prevalence of “accidental pathogens” in the form of emerging pathogens. PMID:28155809

Responses to Microbial Challenges by SLAMF Receptors

PubMed Central

van Driel, Boaz Job; Liao, Gongxian; Engel, Pablo; Terhorst, Cox

2016-01-01

The SLAMF family (SLAMF) of cell surface glycoproteins is comprised of nine glycoproteins and while SLAMF1, 3, 5, 6, 7, 8, and 9 are self-ligand receptors, SLAMF2 and SLAMF4 interact with each other. Their interactions induce signal transduction networks in trans, thereby shaping immune cell–cell communications. Collectively, these receptors modulate a wide range of functions, such as myeloid cell and lymphocyte development, and T and B cell responses to microbes and parasites. In addition, several SLAMF receptors serve as microbial sensors, which either positively or negatively modulate the function of macrophages, dendritic cells, neutrophils, and NK cells in response to microbial challenges. The SLAMF receptor–microbe interactions contribute both to intracellular microbicidal activity as well as to migration of phagocytes to the site of inflammation. In this review, we describe the current knowledge on how the SLAMF receptors and their specific adapters SLAM-associated protein and EAT-2 regulate innate and adaptive immune responses to microbes. PMID:26834746

Butyrate-producing bacteria, including mucin degraders, from the swine intestinal tract

USDA-ARS?s Scientific Manuscript database

Butyrate-producing microbes promote gastrointestinal health in the human gut, and similar benefits are likely derived from butyrate-producing microbes in other animal hosts. Consequently, there is considerable potential for butyrate-producing microbes to be utilized in health-promoting application...

Induction of Systemic Resistance against Insect Herbivores in Plants by Beneficial Soil Microbes

PubMed Central

Rashid, Md. Harun-Or; Chung, Young R.

2017-01-01

Soil microorganisms with growth-promoting activities in plants, including rhizobacteria and rhizofungi, can improve plant health in a variety of different ways. These beneficial microbes may confer broad-spectrum resistance to insect herbivores. Here, we provide evidence that beneficial microbes modulate plant defenses against insect herbivores. Beneficial soil microorganisms can regulate hormone signaling including the jasmonic acid, ethylene and salicylic acid pathways, thereby leading to gene expression, biosynthesis of secondary metabolites, plant defensive proteins and different enzymes and volatile compounds, that may induce defenses against leaf-chewing as well as phloem-feeding insects. In this review, we discuss how beneficial microbes trigger induced systemic resistance against insects by promoting plant growth and highlight changes in plant molecular mechanisms and biochemical profiles. PMID:29104585

The food-gut human axis: the effects of diet on gut microbiota and metabolome.

PubMed

De Angelis, Maria; Garruti, Gabriella; Minervini, Fabio; Bonfrate, Leonilde; Portincasa, Piero; Gobbetti, Marco

2017-04-27

Gut microbiota, the largest symbiont community hosted in human organism, is emerging as a pivotal player in the relationship between dietary habits and health. Oral and, especially, intestinal microbes metabolize dietary components, affecting human health by producing harmful or beneficial metabolites, which are involved in the incidence and progression of several intestinal related and non-related diseases. Habitual diet (Western, Agrarian and Mediterranean omnivore diets, vegetarian, vegan and gluten-free diets) drives the composition of the gut microbiota and metabolome. Within the dietary components, polymers (mainly fibers, proteins, fat and polyphenols) that are not hydrolyzed by human enzymes seem to be the main leads of the metabolic pathways of gut microbiota, which in turn directly influences the human metabolome. Specific relationships between diet and microbes, microbes and metabolites, microbes and immune functions and microbes and/or their metabolites and some human diseases are being established. Dietary treatments with fibers are the most effective to benefit the metabolome profile, by improving the synthesis of short chain fatty acids and decreasing the level of molecules, such as p-cresyl sulfate, indoxyl sulfate and trimethylamine N-oxide, involved in disease state. Based on the axis diet-microbiota-health, this review aims at describing the most recent knowledge oriented towards a profitable use of diet to provide benefits to human health, both directly and indirectly, through the activity of gut microbiota. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Novel correlations between microbial taxa and amino acid metabolites in mouse cecal contents

USDA-ARS?s Scientific Manuscript database

Gut microbes share a bi-directional relationship with thousands of metabolites in their environment. Many of these microbes and metabolites are associated with human diseases including obesity, cancer, and inflammatory diseases. Further understanding of how microbes affect metabolite concentration i...

Membrane trafficking pathways and their roles in plant-microbe interactions.

PubMed

Inada, Noriko; Ueda, Takashi

2014-04-01

Membrane trafficking functions in the delivery of proteins that are newly synthesized in the endoplasmic reticulum (ER) to their final destinations, such as the plasma membrane (PM) and the vacuole, and in the internalization of extracellular components or PM-associated proteins for recycling or degradative regulation. These trafficking pathways play pivotal roles in the rapid responses to environmental stimuli such as challenges by microorganisms. In this review, we provide an overview of the current knowledge of plant membrane trafficking and its roles in plant-microbe interactions. Although there is little information regarding the mechanism of pathogenic modulation of plant membrane trafficking thus far, recent research has identified many membrane trafficking factors as possible targets of microbial modulation.

Microbial modulation of bacoside A biosynthetic pathway and systemic defense mechanism in Bacopa monnieri under Meloidogyne incognita stress

PubMed Central

Gupta, Rupali; Singh, Akanksha; Srivastava, Madhumita; Singh, Vivek; Gupta, M. M.; Pandey, Rakesh

2017-01-01

Plant-associated beneficial microbes have been explored to fulfill the imperative function for plant health. However, their impact on the host secondary metabolite production and nematode disease management remains elusive. Our present work has shown that chitinolytic microbes viz., Chitiniphilus sp. MTN22 and Streptomyces sp. MTN14 singly as well as in combination modulated the biosynthetic pathway of bacoside A and systemic defense mechanism against Meloidogyne incognita in Bacopa monnieri. Interestingly, expression of bacoside biosynthetic pathway genes (3-Hydroxy-3-methylglutaryl coenzyme A reductase, mevalonate diphosphate decarboxylase, and squalene synthase) were upregulated in plants treated with the microbial combination in the presence as well as in absence of M. incognita stress. These microbes not only augmented bacoside A production (1.5 fold) but also strengthened host resistance via enhancement in chlorophyll a, defense enzymes and phenolic compounds like gallic acid, syringic acid, ferulic acid and cinnamic acid. Furthermore, elevated lignification and callose deposition in the microbial combination treated plants corroborate well with the above findings. Overall, the results provide novel insights into the underlying mechanisms of priming by beneficial microbes and underscore their capacity to trigger bacoside A production in B. monnieri under biotic stress. PMID:28157221

Modulating the gut flora alters amino acid metabolism in neonatal pigs

USDA-ARS?s Scientific Manuscript database

Intestinal microbes consume and produce amino acids (AA). This may impact intestinal threonine (THR) metabolism necessary for adequate gut function. We hypothesized that modulating the gut flora results in an alteration of intestinal THR utilization and hence whole body AA metabolism. Neonatal pigs ...

Inhibiting Microbial Toxins Using Plant-Derived Compounds and Plant Extracts

PubMed Central

Upadhyay, Abhinav; Mooyottu, Shankumar; Yin, Hsinbai; Surendran Nair, Meera; Bhattaram, Varunkumar; Venkitanarayanan, Kumar

2015-01-01

Many pathogenic bacteria and fungi produce potentially lethal toxins that cause cytotoxicity or impaired cellular function either at the site of colonization or other locations in the body through receptor-mediated interactions. Various factors, including biotic and abiotic environments, competing microbes, and chemical cues affect toxin expression in these pathogens. Recent work suggests that several natural compounds can modulate toxin production in pathogenic microbes. However, studies explaining the mechanistic basis for their effect are scanty. This review discusses the potential of various plant-derived compounds for reducing toxin production in foodborne and other microbes. In addition, studies highlighting their anti-toxigenic mechanism(s) are discussed. PMID:28930207

Chemosensation of Bacterial Secondary Metabolites Modulates Neuroendocrine Signaling and Behavior of C. elegans

PubMed Central

Meisel, Joshua D.; Panda, Oishika; Mahanti, Parag; Schroeder, Frank C.; Kim, Dennis H.

2014-01-01

Summary Discrimination among pathogenic and beneficial microbes is essential for host organism immunity and homeostasis. Here, we show that chemosensory detection of two secondary metabolites produced by Pseudomonas aeruginosa modulates a neuroendocrine signaling pathway that promotes avoidance behavior in the simple animal host Caenorhabditis elegans. Secondary metabolites phenazine-1-carboxamide and pyochelin activate a G protein-signaling pathway in the ASJ chemosensory neuron pair that induces expression of the neuromodulator DAF-7/TGF-β. DAF-7, in turn, activates a canonical TGF-β signaling pathway in adjacent interneurons to modulate aerotaxis behavior and promote avoidance of pathogenic P. aeruginosa. Our data provide a chemical, genetic, and neuronal basis for how the behavior and physiology of a simple animal host can be modified by the microbial environment, and suggest that secondary metabolites produced by microbes may provide environmental cues that contribute to pathogen recognition and host survival. PMID:25303524

Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans.

PubMed

Barber, Matthew F; Kronenberg, Zev; Yandell, Mark; Elde, Nels C

2016-05-01

Lactoferrin is a multifunctional mammalian immunity protein that limits microbial growth through sequestration of nutrient iron. Additionally, lactoferrin possesses cationic protein domains that directly bind and inhibit diverse microbes. The implications for these dual functions on lactoferrin evolution and genetic conflicts with microbes remain unclear. Here we show that lactoferrin has been subject to recurrent episodes of positive selection during primate divergence predominately at antimicrobial peptide surfaces consistent with long-term antagonism by bacteria. An abundant lactoferrin polymorphism in human populations and Neanderthals also exhibits signatures of positive selection across primates, linking ancient host-microbe conflicts to modern human genetic variation. Rapidly evolving sites in lactoferrin further correspond to molecular interfaces with opportunistic bacterial pathogens causing meningitis, pneumonia, and sepsis. Because microbes actively target lactoferrin to acquire iron, we propose that the emergence of antimicrobial activity provided a pivotal mechanism of adaptation sparking evolutionary conflicts via acquisition of new protein functions.

Microbes to Biomes at Berkeley Lab

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

None

2015-10-28

Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

Multiplex Identification of Microbes ▿ †

PubMed Central

Hyman, Richard W.; St.Onge, Robert P.; Allen, Edward A.; Miranda, Molly; Aparicio, Ana Maria; Fukushima, Marilyn; Davis, Ronald W.

2010-01-01

We have adapted molecular inversion probe technology to identify microbes in a highly multiplexed procedure. This procedure does not require growth of the microbes. Rather, the technology employs DNA homology twice: once for the molecular probe to hybridize to its homologous DNA and again for the 20-mer oligonucleotide barcode on the molecular probe to hybridize to a commercially available molecular barcode array. As proof of concept, we have designed, tested, and employed 192 molecular probes for 40 microbes. While these particular molecular probes are aimed at our interest in the microbes in the human vagina, this molecular probe method could be employed to identify the microbes in any ecological niche. PMID:20418427

Harnessing the hygroscopic and biofluorescent behaviors of genetically tractable microbial cells to design biohybrid wearables.

PubMed

Wang, Wen; Yao, Lining; Cheng, Chin-Yi; Zhang, Teng; Atsumi, Hiroshi; Wang, Luda; Wang, Guanyun; Anilionyte, Oksana; Steiner, Helene; Ou, Jifei; Zhou, Kang; Wawrousek, Chris; Petrecca, Katherine; Belcher, Angela M; Karnik, Rohit; Zhao, Xuanhe; Wang, Daniel I C; Ishii, Hiroshi

2017-05-01

Cells' biomechanical responses to external stimuli have been intensively studied but rarely implemented into devices that interact with the human body. We demonstrate that the hygroscopic and biofluorescent behaviors of living cells can be engineered to design biohybrid wearables, which give multifunctional responsiveness to human sweat. By depositing genetically tractable microbes on a humidity-inert material to form a heterogeneous multilayered structure, we obtained biohybrid films that can reversibly change shape and biofluorescence intensity within a few seconds in response to environmental humidity gradients. Experimental characterization and mechanical modeling of the film were performed to guide the design of a wearable running suit and a fluorescent shoe prototype with bio-flaps that dynamically modulates ventilation in synergy with the body's need for cooling.

Musing over Microbes in Microgravity: Microbial Physiology Flight Experiment

NASA Technical Reports Server (NTRS)

Schweickart, Randolph; McGinnis, Michael; Bloomberg, Jacob; Lee, Angie (Technical Monitor)

2002-01-01

New York City, the most populated city in the United States, is home to over 8 million humans. This means over 26,000 people per square mile! Imagine, though, what the view would be if you peeked into the world of microscopic organisms. Scientists estimate that a gram of soil may contain up to 1 billion of these microbes, which is as much as the entire human population of China! Scientists also know that the world of microbes is incredibly diverse-possibly 10,000 different species in one gram of soil - more than all the different types of mammals in the world. Microbes fill every niche in the world - from 20 miles below the Earth's surface to 20 miles above, and at temperatures from less than -20 C to hotter than water's boiling point. These organisms are ubiquitous because they can adapt quickly to changing environments, an effective strategy for survival. Although we may not realize it, microbes impact every aspect of our lives. Bacteria and fungi help us break down the food in our bodies, and they help clean the air and water around us. They can also cause the dark, filmy buildup on the shower curtain as well as, more seriously, illness and disease. Since humans and microbes share space on Earth, we can benefit tremendously from a better understanding of the workings and physiology of the microbes. This insight can help prevent any harmful effects on humans, on Earth and in space, as well as reap the benefits they provide. Space flight is a unique environment to study how microbes adapt to changing environmental conditions. To advance ground-based research in the field of microbiology, this STS-107 experiment will investigate how microgravity affects bacteria and fungi. Of particular interest are the growth rates and how they respond to certain antimicrobial substances that will be tested; the same tests will be conducted on Earth at the same times. Comparing the results obtained in flight to those on Earth, we will be able to examine how microgravity induces physiological changes in the microbes.

The microbiome modulates the tumor macroenvironment.

PubMed

Erdman, Susan E; Poutahidis, Theofilos

2014-01-01

Earlier investigations of the tumor microenvironment unveiled systemic networks presenting novel therapeutic opportunities. It has been recently shown that gut microbes modulate whole host immune and neuroendocrine factors impacting the fate of distant preneoplastic lesions toward malignancy or regression. These findings establish a new paradigm of holobiont therapeutic engineering in emerging tumor macroenvironments.

Colonic Fermentation: A Neglected Topic in Human Physiology Education

ERIC Educational Resources Information Center

Valeur, Jorgen; Berstad, Arnold

2010-01-01

Human physiology textbooks tend to limit their discussion of colonic functions to those of absorbing water and electrolytes and storing waste material. However, the colon is a highly active metabolic organ, containing an exceedingly complex society of microbes. By means of fermentation, gastrointestinal microbes break down nutrients that cannot be…

Time for food: The impact of diet on gut microbiota and human health.

PubMed

Zhang, Na; Ju, Zhongjie; Zuo, Tao

There is growing recognition of the role of diet on modulating the composition and metabolic activity of the human gut microbiota, which in turn influence health. Dietary ingredients and food additives have a substantial impact on the gut microbiota and hence affect human health. Updates on current understanding of the gut microbiota in diseases and metabolic disorders are addressed in this review, providing insights into how this can be transferred from bench to bench side as gut microbes are integrated with food. The potency of microbiota-targeted biomarkers as a state-of-art tool for diagnosis of diseases was also discussed, and it would instruct individuals with healthy dietary consumption. Herein, recent advances in understanding the effect of diet on gut microbiota from an ecological perspective, and how these insights might promote health by guiding development of prebiotic and probiotic strategies and functional foods, were explored. Copyright © 2018 Elsevier Inc. All rights reserved.

Indicator microbes correlate with pathogenic bacteria, yeasts and helminthes in sand at a subtropical recreational beach site.

PubMed

Shah, A H; Abdelzaher, A M; Phillips, M; Hernandez, R; Solo-Gabriele, H M; Kish, J; Scorzetti, G; Fell, J W; Diaz, M R; Scott, T M; Lukasik, J; Harwood, V J; McQuaig, S; Sinigalliano, C D; Gidley, M L; Wanless, D; Ager, A; Lui, J; Stewart, J R; Plano, L R W; Fleming, L E

2011-06-01

Research into the relationship between pathogens, faecal indicator microbes and environmental factors in beach sand has been limited, yet vital to the understanding of the microbial relationship between sand and the water column and to the improvement of criteria for better human health protection at beaches. The objectives of this study were to evaluate the presence and distribution of pathogens in various zones of beach sand (subtidal, intertidal and supratidal) and to assess their relationship with environmental parameters and indicator microbes at a non-point source subtropical marine beach. In this exploratory study in subtropical Miami (Florida, USA), beach sand samples were collected and analysed over the course of 6 days for several pathogens, microbial source tracking markers and indicator microbes. An inverse correlation between moisture content and most indicator microbes was found. Significant associations were identified between some indicator microbes and pathogens (such as nematode larvae and yeasts in the genus Candida), which are from classes of microbes that are rarely evaluated in the context of recreational beach use. Results indicate that indicator microbes may predict the presence of some of the pathogens, in particular helminthes, yeasts and the bacterial pathogen Staphylococcus aureus including methicillin-resistant forms. Indicator microbes may thus be useful for monitoring beach sand and water quality at non-point source beaches. The presence of both indicator microbes and pathogens in beach sand provides one possible explanation for human health effects reported at non-point sources beaches. © 2011 The Authors. Journal of Applied Microbiology © 2011 The Society for Applied Microbiology.

The Importance of Microbes in Nutrition and Health of Honey Bee Colonies

USDA-ARS?s Scientific Manuscript database

Microbes play an essential role in the health of nearly every organism. Humans have innumerable microbes in their digestive system to help with the processing of food. Honey bee colonies also have an array of bacteria and fungi that are essential for the storing and processing of food (especially ...

Host-Microbe Interactions in the Neonatal Intestine: Role of Human Milk Oligosaccharides123

PubMed Central

Donovan, Sharon M.; Wang, Mei; Li, Min; Friedberg, Iddo; Schwartz, Scott L.; Chapkin, Robert S.

2012-01-01

The infant intestinal microbiota is shaped by genetics and environment, including the route of delivery and early dietary intake. Data from germ-free rodents and piglets support a critical role for the microbiota in regulating gastrointestinal and immune development. Human milk oligosaccharides (HMO) both directly and indirectly influence intestinal development by regulating cell proliferation, acting as prebiotics for beneficial bacteria and modulating immune development. We have shown that the gut microbiota, the microbial metatranscriptome, and metabolome differ between porcine milk–fed and formula-fed (FF) piglets. Our goal is to define how early nutrition, specifically HMO, shapes host-microbe interactions in breast-fed (BF) and FF human infants. We an established noninvasive method that uses stool samples containing intact sloughed epithelial cells to quantify intestinal gene expression profiles in human infants. We hypothesized that a systems biology approach, combining i) HMO composition of the mother’s milk with the infant’s gut gene expression and fecal bacterial composition, ii) gene expression, and iii short-chain fatty acid profiles would identify important mechanistic pathways affecting intestinal development of BF and FF infants in the first few months of life. HMO composition was analyzed by HLPC Chip/time-of-flight MS and 3 HMO clusters were identified using principle component analysis. Initial findings indicated that both host epithelial cell mRNA expression and the microbial phylogenetic profiles provided strong feature sets that distinctly classified the BF and FF infants. Ongoing analyses are designed to integrate the host transcriptome, bacterial phylogenetic profiles, and functional metagenomic data using multivariate statistical analyses. PMID:22585924

Do plants modulate biomass allocation in response to petroleum pollution?

PubMed Central

Nie, Ming; Yang, Qiang; Jiang, Li-Fen; Fang, Chang-Ming; Chen, Jia-Kuan; Li, Bo

2010-01-01

Biomass allocation is an important plant trait that responds plastically to environmental heterogeneities. However, the effects on this trait of pollutants owing to human activities remain largely unknown. In this study, we investigated the response of biomass allocation of Phragmites australis to petroleum pollution by a 13CO2 pulse-labelling technique. Our data show that plant biomass significantly decreased under petroleum pollution, but the root–shoot ratio for both plant biomass and 13C increased with increasing petroleum concentration, suggesting that plants could increase biomass allocation to roots in petroleum-polluted soil. Furthermore, assimilated 13C was found to be significantly higher in soil, microbial biomass and soil respiration after soils were polluted by petroleum. These results suggested that the carbon released from roots is rapidly turned over by soil microbes under petroleum pollution. This study found that plants can modulate biomass allocation in response to petroleum pollution. PMID:20484231

Microbes to Biomes at Berkeley Lab

ScienceCinema

None

2018-06-21

Microbes are the Earth's most abundant and diverse form of life. Berkeley Lab's Microbes to Biomes initiative -- which will take advantage of research expertise at the Joint Genome Institute, Advanced Light Source, Molecular Foundry, and the new computational science facility -- is designed to explore and reveal the interactions of microbes with one another and with their environment. Microbes power our planet’s biogeochemical cycles, provide nutrients to our plants, purify our water and are integral components in keeping the human body free of disease and may hold the key to the Earth’s future.

Prominent Human Health Impacts from Several Marine Microbes: History, Ecology, and Public Health Implications

PubMed Central

Bienfang, P. K.; DeFelice, S. V.; Laws, E. A.; Brand, L. E.; Bidigare, R. R.; Christensen, S.; Trapido-Rosenthal, H.; Hemscheidt, T. K.; McGillicuddy, D. J.; Anderson, D. M.; Solo-Gabriele, H. M.; Boehm, A. B.; Backer, L. C.

2011-01-01

This paper overviews several examples of important public health impacts by marine microbes and directs readers to the extensive literature germane to these maladies. These examples include three types of dinoflagellates (Gambierdiscus spp., Karenia brevis, and Alexandrium fundyense), BMAA-producing cyanobacteria, and infectious microbes. The dinoflagellates are responsible for ciguatera fish poisoning, neurotoxic shellfish poisoning, and paralytic shellfish poisoning, respectively, that have plagued coastal populations over time. Research interest on the potential for marine cyanobacteria to contribute BMAA into human food supplies has been derived by BMAA's discovery in cycad seeds and subsequent implication as the putative cause of amyotrophic lateral sclerosis/parkinsonism dementia complex among the Chamorro people of Guam. Recent UPLC/MS analyses indicate that recent reports that BMAA is prolifically distributed among marine cyanobacteria at high concentrations may be due to analyte misidentification in the analytical protocols being applied for BMAA. Common infectious microbes (including enterovirus, norovirus, Salmonella, Campylobacter, Shigella, Staphylococcus aureus, Cryptosporidium, and Giardia) cause gastrointestinal and skin-related illness. These microbes can be introduced from external human and animal sources, or they can be indigenous to the marine environment. PMID:20976073

Resource conflict and cooperation between human host and gut microbiota: implications for nutrition and health.

PubMed

Wasielewski, Helen; Alcock, Joe; Aktipis, Athena

2016-05-01

Diet has been known to play an important role in human health since at least the time period of the ancient Greek physician Hippocrates. In the last decade, research has revealed that microorganisms inhabiting the digestive tract, known as the gut microbiota, are critical factors in human health. This paper draws on concepts of cooperation and conflict from ecology and evolutionary biology to make predictions about host-microbiota interactions involving nutrients. To optimally extract energy from some resources (e.g., fiber), hosts require cooperation from microbes. Other nutrients can be utilized by both hosts and microbes (e.g., simple sugars, iron) in their ingested form, which may lead to greater conflict over these resources. This framework predicts that some negative health effects of foods are driven by the direct effects of these foods on human physiology and by indirect effects resulting from microbiome-host competition and conflict (e.g., increased invasiveness and inflammation). Similarly, beneficial effects of some foods on host health may be enhanced by resource sharing and other cooperative behaviors between host and microbes that may downregulate inflammation and virulence. Given that some foods cultivate cooperation between hosts and microbes while others agitate conflict, host-microbe interactions may be novel targets for interventions aimed at improving nutrition and human health. © 2016 The Authors. Annals of the New York Academy of Sciences published by Wiley Periodicals, Inc. on behalf of New York Academy of Sciences.

The microbiome modulates the tumor macroenvironment

PubMed Central

Erdman, Susan E; Poutahidis, Theofilos

2014-01-01

Earlier investigations of the tumor microenvironment unveiled systemic networks presenting novel therapeutic opportunities. It has been recently shown that gut microbes modulate whole host immune and neuroendocrine factors impacting the fate of distant preneoplastic lesions toward malignancy or regression. These findings establish a new paradigm of holobiont therapeutic engineering in emerging tumor macroenvironments. PMID:25050199

Walls talk: Microbial biogeography of homes spanning urbanization

PubMed Central

Ruiz-Calderon, Jean F.; Cavallin, Humberto; Song, Se Jin; Novoselac, Atila; Pericchi, Luis R.; Hernandez, Jean N.; Rios, Rafael; Branch, Oralee H.; Pereira, Henrique; Paulino, Luciana C.; Blaser, Martin J.; Knight, Rob; Dominguez-Bello, Maria G.

2016-01-01

Westernization has propelled changes in urbanization and architecture, altering our exposure to the outdoor environment from that experienced during most of human evolution. These changes might affect the developmental exposure of infants to bacteria, immune development, and human microbiome diversity. Contemporary urban humans spend most of their time indoors, and little is known about the microbes associated with different designs of the built environment and their interaction with the human immune system. This study addresses the associations between architectural design and the microbial biogeography of households across a gradient of urbanization in South America. Urbanization was associated with households’ increased isolation from outdoor environments, with additional indoor space isolation by walls. Microbes from house walls and floors segregate by location, and urban indoor walls contain human bacterial markers of space use. Urbanized spaces uniquely increase the content of human-associated microbes—which could increase transmission of potential pathogens—and decrease exposure to the environmental microbes with which humans have coevolved. PMID:26933683

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome.

PubMed

Maldonado-Gómez, María X; Martínez, Inés; Bottacini, Francesca; O'Callaghan, Amy; Ventura, Marco; van Sinderen, Douwe; Hillmann, Benjamin; Vangay, Pajau; Knights, Dan; Hutkins, Robert W; Walter, Jens

2016-10-12

Live bacteria (such as probiotics) have long been used to modulate gut microbiota and human physiology, but their colonization is mostly transient. Conceptual understanding of the ecological principles as they apply to exogenously introduced microbes in gut ecosystems is lacking. We find that, when orally administered to humans, Bifidobacterium longum AH1206 stably persists in the gut of 30% of individuals for at least 6 months without causing gastrointestinal symptoms or impacting the composition of the resident gut microbiota. AH1206 engraftment was associated with low abundance of resident B. longum and underrepresentation of specific carbohydrate utilization genes in the pre-treatment microbiome. Thus, phylogenetic limiting and resource availability are two factors that control the niche opportunity for AH1206 colonization. These findings suggest that bacterial species and functional genes absent in the gut microbiome of individual humans can be reestablished, providing opportunities for precise and personalized microbiome reconstitution. Copyright © 2016 Elsevier Inc. All rights reserved.

Host-Microbe Interactions in Microgravity: Assessment and Implications

PubMed Central

Foster, Jamie S.; Wheeler, Raymond M.; Pamphile, Regine

2014-01-01

Spaceflight imposes several unique stresses on biological life that together can have a profound impact on the homeostasis between eukaryotes and their associated microbes. One such stressor, microgravity, has been shown to alter host-microbe interactions at the genetic and physiological levels. Recent sequencing of the microbiomes associated with plants and animals have shown that these interactions are essential for maintaining host health through the regulation of several metabolic and immune responses. Disruptions to various environmental parameters or community characteristics may impact the resiliency of the microbiome, thus potentially driving host-microbe associations towards disease. In this review, we discuss our current understanding of host-microbe interactions in microgravity and assess the impact of this unique environmental stress on the normal physiological and genetic responses of both pathogenic and mutualistic associations. As humans move beyond our biosphere and undergo longer duration space flights, it will be essential to more fully understand microbial fitness in microgravity conditions in order to maintain a healthy homeostasis between humans, plants and their respective microbiomes. PMID:25370197

Host-microbe interactions in microgravity: assessment and implications.

PubMed

Foster, Jamie S; Wheeler, Raymond M; Pamphile, Regine

2014-05-26

Spaceflight imposes several unique stresses on biological life that together can have a profound impact on the homeostasis between eukaryotes and their associated microbes. One such stressor, microgravity, has been shown to alter host-microbe interactions at the genetic and physiological levels. Recent sequencing of the microbiomes associated with plants and animals have shown that these interactions are essential for maintaining host health through the regulation of several metabolic and immune responses. Disruptions to various environmental parameters or community characteristics may impact the resiliency of the microbiome, thus potentially driving host-microbe associations towards disease. In this review, we discuss our current understanding of host-microbe interactions in microgravity and assess the impact of this unique environmental stress on the normal physiological and genetic responses of both pathogenic and mutualistic associations. As humans move beyond our biosphere and undergo longer duration space flights, it will be essential to more fully understand microbial fitness in microgravity conditions in order to maintain a healthy homeostasis between humans, plants and their respective microbiomes.

Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies

PubMed Central

Meena, Kamlesh K.; Sorty, Ajay M.; Bitla, Utkarsh M.; Choudhary, Khushboo; Gupta, Priyanka; Pareek, Ashwani; Singh, Dhananjaya P.; Prabha, Ratna; Sahu, Pramod K.; Gupta, Vijai K.; Singh, Harikesh B.; Krishanani, Kishor K.; Minhas, Paramjit S.

2017-01-01

Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant–microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms. PMID:28232845

Abiotic Stress Responses and Microbe-Mediated Mitigation in Plants: The Omics Strategies.

PubMed

Meena, Kamlesh K; Sorty, Ajay M; Bitla, Utkarsh M; Choudhary, Khushboo; Gupta, Priyanka; Pareek, Ashwani; Singh, Dhananjaya P; Prabha, Ratna; Sahu, Pramod K; Gupta, Vijai K; Singh, Harikesh B; Krishanani, Kishor K; Minhas, Paramjit S

2017-01-01

Abiotic stresses are the foremost limiting factors for agricultural productivity. Crop plants need to cope up adverse external pressure created by environmental and edaphic conditions with their intrinsic biological mechanisms, failing which their growth, development, and productivity suffer. Microorganisms, the most natural inhabitants of diverse environments exhibit enormous metabolic capabilities to mitigate abiotic stresses. Since microbial interactions with plants are an integral part of the living ecosystem, they are believed to be the natural partners that modulate local and systemic mechanisms in plants to offer defense under adverse external conditions. Plant-microbe interactions comprise complex mechanisms within the plant cellular system. Biochemical, molecular and physiological studies are paving the way in understanding the complex but integrated cellular processes. Under the continuous pressure of increasing climatic alterations, it now becomes more imperative to define and interpret plant-microbe relationships in terms of protection against abiotic stresses. At the same time, it also becomes essential to generate deeper insights into the stress-mitigating mechanisms in crop plants for their translation in higher productivity. Multi-omics approaches comprising genomics, transcriptomics, proteomics, metabolomics and phenomics integrate studies on the interaction of plants with microbes and their external environment and generate multi-layered information that can answer what is happening in real-time within the cells. Integration, analysis and decipherization of the big-data can lead to a massive outcome that has significant chance for implementation in the fields. This review summarizes abiotic stresses responses in plants in-terms of biochemical and molecular mechanisms followed by the microbe-mediated stress mitigation phenomenon. We describe the role of multi-omics approaches in generating multi-pronged information to provide a better understanding of plant-microbe interactions that modulate cellular mechanisms in plants under extreme external conditions and help to optimize abiotic stresses. Vigilant amalgamation of these high-throughput approaches supports a higher level of knowledge generation about root-level mechanisms involved in the alleviation of abiotic stresses in organisms.

Structural modulation of gut microbiota by chondroitin sulfate and its oligosaccharide.

PubMed

Shang, Qingsen; Shi, Jingjing; Song, Guanrui; Zhang, Meifang; Cai, Chao; Hao, Jiejie; Li, Guoyun; Yu, Guangli

2016-08-01

Chondroitin sulfate (CS) as a dietary supplement and a symptomatic slow acting (SYSA) drug has been used for years. Recently, CS has been demonstrated to be readily degraded and fermented in vitro by specific human gut microbes, hinting that dietary CS may pose a potential effect on gut microbiota composition in vivo. However, until now, little information is available on modulations of gut microbiota by CS. In the present study, modulations of gut microbiota in Kunming mice by CS and its oligosaccharide (CSO) were investigated by high-throughput sequencing. As evidenced by Heatmap and principal component analysis (PCA), the female microbiota were more vulnerable than the male microbiota to CS and CSO treatment. Besides, it is of interest to found that CS and CSO had differing effects on the abundance of Bacteroidales S24-7, Bacteroides, Helicobacter, Odoribacter, Prevotellaceae and Lactobacillus in male mice versus female mice. Collectively, we demonstrated a sex-dependent effect on gut microbiota of CS and CSO. In addition, since gut microbiota exerts a major effect on host physiology, our study highlighted that certain beneficial effects of CS may be associated with modulations of gut microbiota, which merits further investigation. Copyright © 2016 Elsevier B.V. All rights reserved.

Metabolomics of Early Stage Plant Cell–Microbe Interaction Using Stable Isotope Labeling

PubMed Central

Pang, Qiuying; Zhang, Tong; Wang, Yang; Kong, Wenwen; Guan, Qijie; Yan, Xiufeng; Chen, Sixue

2018-01-01

Metabolomics has been used in unraveling metabolites that play essential roles in plant–microbe (including pathogen) interactions. However, the problem of profiling a plant metabolome with potential contaminating metabolites from the coexisting microbes has been largely ignored. To address this problem, we implemented an effective stable isotope labeling approach, where the metabolome of a plant bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000 was labeled with heavy isotopes. The labeled bacterial cells were incubated with Arabidopsis thaliana epidermal peels (EPs) with guard cells, and excessive bacterial cells were subsequently removed from the plant tissues by washing. The plant metabolites were characterized by liquid chromatography mass spectrometry using multiple reactions monitoring, which can differentiate plant and bacterial metabolites. Targeted metabolomic analysis suggested that Pst DC3000 infection may modulate stomatal movement by reprograming plant signaling and primary metabolic pathways. This proof-of-concept study demonstrates the utility of this strategy in differentiation of the plant and microbe metabolomes, and it has broad applications in studying metabolic interactions between microbes and other organisms. PMID:29922325

How Do Small Things Make a Big Difference? Activities to Teach about Human-Microbe Interactions

ERIC Educational Resources Information Center

Jasti, Chandana; Hug, Barbara; Waters, Jillian L.; Whitaker, Rachel J.

2014-01-01

Recent scientific studies are providing increasing evidence for how microbes living in and on us are essential to our good health. However, many students still think of microbes only as germs that harm us. The classroom activities presented here are designed to shift student thinking on this topic. In these guided inquiry activities, students…

Gut Microbiota Profiling: Metabolomics Based Approach to Unravel Compounds Affecting Human Health

PubMed Central

Vernocchi, Pamela; Del Chierico, Federica; Putignani, Lorenza

2016-01-01

The gut microbiota is composed of a huge number of different bacteria, that produce a large amount of compounds playing a key role in microbe selection and in the construction of a metabolic signaling network. The microbial activities are affected by environmental stimuli leading to the generation of a wide number of compounds, that influence the host metabolome and human health. Indeed, metabolite profiles related to the gut microbiota can offer deep insights on the impact of lifestyle and dietary factors on chronic and acute diseases. Metagenomics, metaproteomics and metabolomics are some of the meta-omics approaches to study the modulation of the gut microbiota. Metabolomic research applied to biofluids allows to: define the metabolic profile; identify and quantify classes and compounds of interest; characterize small molecules produced by intestinal microbes; and define the biochemical pathways of metabolites. Mass spectrometry and nuclear magnetic resonance spectroscopy are the principal technologies applied to metabolomics in terms of coverage, sensitivity and quantification. Moreover, the use of biostatistics and mathematical approaches coupled with metabolomics play a key role in the extraction of biologically meaningful information from wide datasets. Metabolomic studies in gut microbiota-related research have increased, focusing on the generation of novel biomarkers, which could lead to the development of mechanistic hypotheses potentially applicable to the development of nutritional and personalized therapies. PMID:27507964

Threats, Challenges, and Promise of Marine Microbes: A NOAA Perspective with Emphasis on Ecological Forecasting

NASA Astrophysics Data System (ADS)

Sandifer, P. A.

2012-12-01

Fully functioning ecosystems, as well as healthy humans, depend on robust and diverse communities of microbes. The diversity of microbes in the marine environment is estimated to be huge, dwarfing diversity of other life forms, and crucial for many ecosystem processes. Despite the ubiquity and extreme importance of microbial life in the sea - from the air-surface interface to the deepest abyss and sediments - we know relatively little about this biotic component that may compose a large proportion of the total biomass on the planet. As the nation's principal steward of marine living resources, NOAA is both responsible for and vitally interested in marine microbes, from a variety of perspectives. These include (1) health threats to humans and other organisms and how these may be affected by climate change and ecosystem alteration; (2) detoxification of organic pollutants such as hydrocarbons (e.g., in the Deep Water Horizon oil catastrophe); (3) production of valuable natural products including potential new pharmaceuticals; (4) roles in biogeochemical cycles (e.g., for carbon, nitrogen, phosphorus, iron, etc.) and how human activities may affect these roles; (5) development and deployment of new methods to detect and quantify certain marine microbes, and incorporation of these into ocean observing systems; (6) development of Earth System models that include much improved understanding of microbial functional diversity and microbially mediated biogeochemical processes; (7) dynamics of bacterial, phyto- and zooplankton blooms, including for harmful algae and bacteria; (8) effects of climate change factors (e.g., temperature, CO2 concentrations, ocean acidification, changes in habitats and species distribution, etc.) on marine microbes; and others. Many of these topics likely will be discussed by others in this session. This presentation will focus primarily on NOAA's activities in addressing health threats emanating from a variety of microbes in the marine environment and the agency's developing efforts to collect routine observational data on selected microbes and establish regular forecasts of such threats and their likely impacts. Such "ecological forecasts" are projected to become a regular part of NOAA's service portfolio and may be expanded beyond disease-causing microbes in the future.

Recombinant Incretin-Secreting Microbe Improves Metabolic Dysfunction in High-Fat Diet Fed Rodents.

PubMed

Ryan, Paul M; Patterson, Elaine; Kent, Robert M; Stack, Helena; O'Connor, Paula M; Murphy, Kiera; Peterson, Veronica L; Mandal, Rupasri; Wishart, David S; Dinan, Timothy G; Cryan, John F; Seeley, Randy J; Stanton, Catherine; Ross, R Paul

2017-10-19

The gut hormone glucagon-like peptide (GLP)-1 and its analogues represent a new generation of anti-diabetic drugs, which have also demonstrated propensity to modulate host lipid metabolism. Despite this, drugs of this nature are currently limited to intramuscular administration routes due to intestinal degradation. The aim of this study was to design a recombinant microbial delivery vector for a GLP-1 analogue and assess the efficacy of the therapeutic in improving host glucose, lipid and cholesterol metabolism in diet induced obese rodents. Diet-induced obese animals received either Lactobacillus paracasei NFBC 338 transformed to express a long-acting analogue of GLP-1 or the isogenic control microbe which solely harbored the pNZ44 plasmid. Short-term GLP-1 microbe intervention in rats reduced serum low-density lipoprotein cholesterol, triglycerides and triglyceride-rich lipoprotein cholesterol substantially. Conversely, extended GLP-1 microbe intervention improved glucose-dependent insulin secretion, glucose metabolism and cholesterol metabolism, compared to the high-fat control group. Interestingly, the microbe significantly attenuated the adiposity associated with the model and altered the serum lipidome, independently of GLP-1 secretion. These data indicate that recombinant incretin-secreting microbes may offer a novel and safe means of managing cholesterol metabolism and diet induced dyslipidaemia, as well as insulin sensitivity in metabolic dysfunction.

TANPOPO: Microbe and micrometeoroid capture experiments on International Space Station.

NASA Astrophysics Data System (ADS)

Yamagishi, Akihiko; Kobayashi, Kensei; Yano, Hajime; Yokobori, Shinichi; Hashimoto, Hirofumi; Kawai, Hideyuki; Yamashita, Masamichi

There is a long history of the microbe-collection experiments at high altitude. Microbes have been collected using balloons, aircraft and meteorological rockets from 1936 to 1976. Spore forming fungi and Bacilli, and Micrococci have been isolated in these experiments. It is not clear how high do microbes go up. If the microbes might have been present even at higher altitudes, the fact would endorse the possibility of interplanetary migration of life. TANPOPO, dandelion, is the name of a grass whose seeds with floss are spread by the wind. We propose the analyses of interplanetary migration of microbes, organic compounds and meteoroids on Japan Experimental Module (JEM) of the International Space Station (ISS). Ultra low-density aerogel will be used to capture micrometeoroid and debris. Particles captured by aerogel will be used for several analyses after the initial inspection of the gel and tracks. Careful analysis of the tracks in the aerogel will provide the size and velocity dependence of debris flux. The particles will be analyzed for mineralogical, organic and microbiological characteristics. Aerogels are ready for production in Japan. Aerogels and trays are space proven. All the analytical techniques are ready. The Tanpopo mission was accepted as a candidate experiments on Exposed Facility of ISS-JEM.

Allometry of animal-microbe interactions and global census of animal-associated microbes.

PubMed

Kieft, Thomas L; Simmons, Karen A

2015-07-07

Animals live in close association with microorganisms, mostly prokaryotes, living in or on them as commensals, mutualists or parasites, and profoundly affecting host fitness. Most animal-microbe studies focus on microbial community structure; for this project, allometry (scaling of animal attributes with animal size) was applied to animal-microbe relationships across a range of species spanning 12 orders of magnitude in animal mass, from nematodes to whales. Microbial abundances per individual animal were gleaned from published literature and also microscopically counted in three species. Abundance of prokaryotes/individual versus animal mass scales as a nearly linear power function (exponent = 1.07, R(2) = 0.94). Combining this power function with allometry of animal abundance indicates that macrofauna have an outsized share of animal-associated microorganisms. The total number of animal-associated prokaryotes in Earth's land animals was calculated to be 1.3-1.4 × 10(25) cells and the total of marine animal-associated microbes was calculated to be 8.6-9.0 × 10(24) cells. Animal-associated microbes thus total 2.1-2.3 × 10(25) of the approximately 10(30) prokaryotes on the Earth. Microbes associated with humans comprise 3.3-3.5% of Earth's animal-associated microbes, and domestic animals harbour 14-20% of all animal-associated microbes, adding a new dimension to the scale of human impact on the biosphere. This novel allometric power function may reflect underlying mechanisms involving the transfer of energy and materials between microorganisms and their animal hosts. Microbial diversity indices of animal gut communities and gut microbial species richness for 60 mammals did not indicate significant scaling relationships with animal body mass; however, further research in this area is warranted. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Non-digestible oligosaccharides directly regulate host kinome to modulate host inflammatory responses without alterations in the gut microbiota.

PubMed

Wu, Richard Y; Määttänen, Pekka; Napper, Scott; Scruten, Erin; Li, Bo; Koike, Yuhki; Johnson-Henry, Kathene C; Pierro, Agostino; Rossi, Laura; Botts, Steven R; Surette, Michael G; Sherman, Philip M

2017-10-10

Prebiotics are non-digestible food ingredients that enhance the growth of certain microbes within the gut microbiota. Prebiotic consumption generates immune-modulatory effects that are traditionally thought to reflect microbial interactions within the gut. However, recent evidence suggests they may also impart direct microbe-independent effects on the host, though the mechanisms of which are currently unclear. Kinome arrays were used to profile the host intestinal signaling responses to prebiotic exposures in the absence of microbes. Identified pathways were functionally validated in Caco-2Bbe1 intestinal cell line and in vivo model of murine endotoxemia. We found that prebiotics directly regulate host mucosal signaling to alter response to bacterial infection. Intestinal epithelial cells (IECs) exposed to prebiotics are hyporesponsive to pathogen-induced mitogen-activated protein kinase (MAPK) and nuclear factor kappa B (NF-κB) activations, and have a kinome profile distinct from non-treated cells pertaining to multiple innate immune signaling pathways. Consistent with this finding, mice orally gavaged with prebiotics showed dampened inflammatory response to lipopolysaccharide (LPS) without alterations in the gut microbiota. These findings provide molecular mechanisms of direct host-prebiotic interactions to support prebiotics as potent modulators of host inflammation.

Commensal bacteria modulate the tumor microenvironment.

PubMed

Poutahidis, Theofilos; Erdman, Susan E

2016-09-28

It has been recently shown that gut microbes modulate whole host immune and hormonal factors impacting the fate of distant preneoplastic lesions toward malignancy or regression. This raises the possibility that the tumor microenvironment interacts with broader systemic microbial-immune networks. These accumulated findings suggest novel therapeutic opportunities for holobiont engineering in emerging tumor microenvironments. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Emerging Role of D-Amino Acid Metabolism in the Innate Defense

PubMed Central

Sasabe, Jumpei; Suzuki, Masataka

2018-01-01

Mammalian innate and adaptive immune systems use the pattern recognition receptors, such as toll-like receptors, to detect conserved bacterial and viral components. Bacteria synthesize diverse D-amino acids while eukaryotes and archaea generally produce two D-amino acids, raising the possibility that many of bacterial D-amino acids are bacteria-specific metabolites. Although D-amino acids have not been identified to bind to any known pattern recognition receptors, D-amino acids are enantioselectively recognized by some other receptors and enzymes including a flavoenzyme D-amino acid oxidase (DAO) in mammals. At host–microbe interfaces in the neutrophils and intestinal mucosa, DAO catalyzes oxidation of bacterial D-amino acids, such as D-alanine, and generates H2O2, which is linked to antimicrobial activity. Intestinal DAO also modifies the composition of microbiota through modulation of growth for some bacteria that are dependent on host nutrition. Furthermore, regulation and recognition of D-amino acids in mammals have additional meanings at various host–microbe interfaces; D-phenylalanine and D-tryptophan regulate chemotaxis of neutrophils through a G-coupled protein receptor, D-serine has a bacteriostatic role in the urinary tract, D-phenylalanine and D-leucine inhibit innate immunity through the sweet taste receptor in the upper airway, and D-tryptophan modulates immune tolerance in the lower airway. This mini-review highlights recent evidence supporting the hypothesis that D-amino acids are utilized as inter-kingdom communication at host–microbe interface to modulate bacterial colonization and host defense. PMID:29867842

Emerging Role of D-Amino Acid Metabolism in the Innate Defense.

PubMed

Sasabe, Jumpei; Suzuki, Masataka

2018-01-01

Mammalian innate and adaptive immune systems use the pattern recognition receptors, such as toll-like receptors, to detect conserved bacterial and viral components. Bacteria synthesize diverse D-amino acids while eukaryotes and archaea generally produce two D-amino acids, raising the possibility that many of bacterial D-amino acids are bacteria-specific metabolites. Although D-amino acids have not been identified to bind to any known pattern recognition receptors, D-amino acids are enantioselectively recognized by some other receptors and enzymes including a flavoenzyme D-amino acid oxidase (DAO) in mammals. At host-microbe interfaces in the neutrophils and intestinal mucosa, DAO catalyzes oxidation of bacterial D-amino acids, such as D-alanine, and generates H 2 O 2 , which is linked to antimicrobial activity. Intestinal DAO also modifies the composition of microbiota through modulation of growth for some bacteria that are dependent on host nutrition. Furthermore, regulation and recognition of D-amino acids in mammals have additional meanings at various host-microbe interfaces; D-phenylalanine and D-tryptophan regulate chemotaxis of neutrophils through a G-coupled protein receptor, D-serine has a bacteriostatic role in the urinary tract, D-phenylalanine and D-leucine inhibit innate immunity through the sweet taste receptor in the upper airway, and D-tryptophan modulates immune tolerance in the lower airway. This mini-review highlights recent evidence supporting the hypothesis that D-amino acids are utilized as inter-kingdom communication at host-microbe interface to modulate bacterial colonization and host defense.

Regulation of DUOX by the Galphaq-phospholipase Cbeta-Ca2+ pathway in Drosophila gut immunity.

PubMed

Ha, Eun-Mi; Lee, Kyung-Ah; Park, Seon Hwa; Kim, Sung-Hee; Nam, Hyuck-Jin; Lee, Hyo-Young; Kang, Dongmin; Lee, Won-Jae

2009-03-01

All metazoan guts are in constant contact with diverse food-borne microorganisms. The signaling mechanisms by which the host regulates gut-microbe interactions, however, are not yet clear. Here, we show that phospholipase C-beta (PLCbeta) signaling modulates dual oxidase (DUOX) activity to produce microbicidal reactive oxygen species (ROS) essential for normal host survival. Gut-microbe contact rapidly activates PLCbeta through Galphaq, which in turn mobilizes intracellular Ca(2+) through inositol 1,4,5-trisphosphate generation for DUOX-dependent ROS production. PLCbeta mutant flies had a short life span due to the uncontrolled propagation of an essential nutritional microbe, Saccharomyces cerevisiae, in the gut. Gut-specific reintroduction of the PLCbeta restored efficient DUOX-dependent microbe-eliminating capacity and normal host survival. These results demonstrate that the Galphaq-PLCbeta-Ca(2+)-DUOX-ROS signaling pathway acts as a bona fide first line of defense that enables gut epithelia to dynamically control yeast during the Drosophila life cycle.

Therapeutic modulation of gut microbiota: current clinical applications and future perspectives.

PubMed

Ianiro, Gianluca; Bibbò, Stefano; Gasbarrini, Antonio; Cammarota, Giovanni

2014-01-01

Human beings and gut microbiota are in a symbiotic relationship, and the hypothesis of a "super organism" composed of the human organism and microbes has been recently proposed. The gut microbiota fulfills important metabolic and immunological tasks, and the impairment of its composition might alter homeostasis and lead to the development of microbiota-related diseases. The most common illnesses associated with alterations of the gut microbiota include inflammatory bowel disease, gastroenteric infections, irritable bowel syndrome and other gastrointestinal functional diseases, colorectal cancer, metabolic syndrome and obesity, liver diseases, allergic diseases, and neurological diseases such as autism. In theory, every disease associated with the impairment of intestinal microflora might benefit from the therapeutic modulation of the gut microbiota. A number of attempts to manipulate the microbiota have not produced identical results for every disease. Although antibiotics and probiotics have been available for a long time, the so-called fecal microbiota transplantation, which is a very old remedy, was only recently re-evaluated as a promising therapeutic approach for microbiota impairment. A comprehensive understanding of the gut microbiota composition, in states of both health and various diseases, is needed for the development of future approaches for microbiota modulation and for developing targeted therapies. In this review, we describe the role of the microbiota in several diseases and the related treatment options that are currently available.

Escherichia coli Nissle 1917 enhances bioavailability of serotonin in gut tissues through modulation of synthesis and clearance

PubMed Central

Nzakizwanayo, Jonathan; Dedi, Cinzia; Standen, Guy; Macfarlane, Wendy M.; Patel, Bhavik A.; Jones, Brian V.

2015-01-01

Accumulating evidence shows indigenous gut microbes can interact with the human host through modulation of serotonin (5-HT) signaling. Here we investigate the impact of the probiotic Escherichia coli Nissle 1917 (EcN) on 5-HT signalling in gut tissues. Ex-vivo mouse ileal tissue sections were treated with either EcN or the human gut commensal MG1655, and effects on levels of 5-HT, precursors, and metabolites, were evaluated using amperometry and high performance liquid chromatography with electrochemical detection (HPLC-EC). Exposure of tissue to EcN cells, but not MG1655 cells, was found to increase levels of extra-cellular 5-HT. These effects were not observed when tissues were treated with cell-free supernatant from bacterial cultures. In contrast, when supernatant recovered from untreated ileal tissue was pre-incubated with EcN, the derivative cell-free supernatant was able to elevate 5-HT overflow when used to treat fresh ileal tissue. Measurement of 5-HT precursors and metabolites indicated EcN also increases intracellular 5-HTP and reduces 5-HIAA. The former pointed to modulation of tryptophan hydroxylase-1 to enhance 5-HT synthesis, while the latter indicates an impact on clearance into enterocytes through SERT. Taken together, these findings show EcN is able to enhance 5-HT bioavailability in ileal tissues through interaction with compounds secreted from host tissues. PMID:26616662

Signaling in host-associated microbial communities

PubMed Central

Fischbach, Michael A.; Segre, Julia A.

2016-01-01

Human-associated microbiota form and stabilize communities based on interspecies interactions. We review how these microbe-microbe and microbe-host interactions are communicated to shape communities over a human’s lifespan, including periods of health and disease. Modeling and dissecting signaling in host-associated communities is crucial to understand their function, and will open the door to therapies that prevent or correct microbial community dysfunction to promote health and treat disease. PMID:26967294

Nanomaterial-microbe cross-talk: physicochemical principles and (patho)biological consequences.

PubMed

Westmeier, D; Hahlbrock, A; Reinhardt, C; Fröhlich-Nowoisky, J; Wessler, S; Vallet, C; Pöschl, U; Knauer, S K; Stauber, R H

2018-05-17

The applications of nanoparticles (NPs) are increasing exponentially in consumer products, biotechnology and biomedicine, and humans, as well as the environment, are increasingly being exposed to NPs. Analogously, various (pathogenic) microorganisms are present at all the major exposure and entry sites for NPs in the human body as well as in environmental habitats. However, the field has just started to explore the complex interplay between NPs and microbes and the (patho)biological consequences. Based on recent insights, herein, we critically reviewed the available knowledge about the interaction of NPs with microbes and the analytical investigations including the latest intravital imaging tools. We have commented on how the NPs' characteristics influence complex formation with microorganisms, presented the underlying physicochemical forces, and provided examples of how this knowledge can be used to rationally control the NP-microbe interaction. We concluded by discussing the role of the biomolecule corona in NP-microbe crosstalk and speculated the impact of NP-microbe complex formation on the (patho)biological outcome and fate of microbial pathogens. The presented insights will not only support the field in engineering NPs with improved anti-microbial activity but also stimulate research on the biomedical and toxicological relevance of nanomaterial-microbiome complex formation for the anthropocene in general.

Prediction of microbe-disease association from the integration of neighbor and graph with collaborative recommendation model.

PubMed

Huang, Yu-An; You, Zhu-Hong; Chen, Xing; Huang, Zhi-An; Zhang, Shanwen; Yan, Gui-Ying

2017-10-16

Accumulating clinical researches have shown that specific microbes with abnormal levels are closely associated with the development of various human diseases. Knowledge of microbe-disease associations can provide valuable insights for complex disease mechanism understanding as well as the prevention, diagnosis and treatment of various diseases. However, little effort has been made to predict microbial candidates for human complex diseases on a large scale. In this work, we developed a new computational model for predicting microbe-disease associations by combining two single recommendation methods. Based on the assumption that functionally similar microbes tend to get involved in the mechanism of similar disease, we adopted neighbor-based collaborative filtering and a graph-based scoring method to compute association possibility of microbe-disease pairs. The promising prediction performance could be attributed to the use of hybrid approach based on two single recommendation methods as well as the introduction of Gaussian kernel-based similarity and symptom-based disease similarity. To evaluate the performance of the proposed model, we implemented leave-one-out and fivefold cross validations on the HMDAD database, which is recently built as the first database collecting experimentally-confirmed microbe-disease associations. As a result, NGRHMDA achieved reliable results with AUCs of 0.9023 ± 0.0031 and 0.9111 in the validation frameworks of fivefold CV and LOOCV. In addition, 78.2% microbe samples and 66.7% disease samples are found to be consistent with the basic assumption of our work that microbes tend to get involved in the similar disease clusters, and vice versa. Compared with other methods, the prediction results yielded by NGRHMDA demonstrate its effective prediction performance for microbe-disease associations. It is anticipated that NGRHMDA can be used as a useful tool to search the most potential microbial candidates for various diseases, and therefore boosts the medical knowledge and drug development. The codes and dataset of our work can be downloaded from https://github.com/yahuang1991/NGRHMDA .

A review of metabolic potential of human gut microbiome in human nutrition.

PubMed

Yadav, Monika; Verma, Manoj Kumar; Chauhan, Nar Singh

2018-03-01

The human gut contains a plethora of microbes, providing a platform for metabolic interaction between the host and microbiota. Metabolites produced by the gut microbiota act as a link between gut microbiota and its host. These metabolites act as messengers having the capacity to alter the gut microbiota. Recent advances in the characterization of the gut microbiota and its symbiotic relationship with the host have provided a platform to decode metabolic interactions. The human gut microbiota, a crucial component for dietary metabolism, is shaped by the genetic, epigenetic and dietary factors. The metabolic potential of gut microbiota explains its significance in host health and diseases. The knowledge of interactions between microbiota and host metabolism, as well as modification of microbial ecology, is really beneficial to have effective therapeutic treatments for many diet-related diseases in near future. This review cumulates the information to map the role of human gut microbiota in dietary component metabolism, the role of gut microbes derived metabolites in human health and host-microbe metabolic interactions in health and diseases.

A new theory of plant-microbe nutrient competition resolves inconsistencies between observations and model predictions.

PubMed

Zhu, Qing; Riley, William J; Tang, Jinyun

2017-04-01

Terrestrial plants assimilate anthropogenic CO 2 through photosynthesis and synthesizing new tissues. However, sustaining these processes requires plants to compete with microbes for soil nutrients, which therefore calls for an appropriate understanding and modeling of nutrient competition mechanisms in Earth System Models (ESMs). Here, we survey existing plant-microbe competition theories and their implementations in ESMs. We found no consensus regarding the representation of nutrient competition and that observational and theoretical support for current implementations are weak. To reconcile this situation, we applied the Equilibrium Chemistry Approximation (ECA) theory to plant-microbe nitrogen competition in a detailed grassland 15 N tracer study and found that competition theories in current ESMs fail to capture observed patterns and the ECA prediction simplifies the complex nature of nutrient competition and quantitatively matches the 15 N observations. Since plant carbon dynamics are strongly modulated by soil nutrient acquisition, we conclude that (1) predicted nutrient limitation effects on terrestrial carbon accumulation by existing ESMs may be biased and (2) our ECA-based approach may improve predictions by mechanistically representing plant-microbe nutrient competition. © 2016 by the Ecological Society of America.

Evolution, human-microbe interactions, and life history plasticity.

PubMed

Rook, Graham; Bäckhed, Fredrik; Levin, Bruce R; McFall-Ngai, Margaret J; McLean, Angela R

2017-07-29

A bacterium was once a component of the ancestor of all eukaryotic cells, and much of the human genome originated in microorganisms. Today, all vertebrates harbour large communities of microorganisms (microbiota), particularly in the gut, and at least 20% of the small molecules in human blood are products of the microbiota. Changing human lifestyles and medical practices are disturbing the content and diversity of the microbiota, while simultaneously reducing our exposures to the so-called old infections and to organisms from the natural environment with which human beings co-evolved. Meanwhile, population growth is increasing the exposure of human beings to novel pathogens, particularly the crowd infections that were not part of our evolutionary history. Thus some microbes have co-evolved with human beings and play crucial roles in our physiology and metabolism, whereas others are entirely intrusive. Human metabolism is therefore a tug-of-war between managing beneficial microbes, excluding detrimental ones, and channelling as much energy as is available into other essential functions (eg, growth, maintenance, reproduction). This tug-of-war shapes the passage of each individual through life history decision nodes (eg, how fast to grow, when to mature, and how long to live). Copyright © 2017 Elsevier Ltd. All rights reserved.

Skin microbiota and allergic symptoms associate with exposure to environmental microbes

PubMed Central

Sinkko, Hanna; Hielm-Björkman, Anna; Tiira, Katriina; Laatikainen, Tiina; Mäkeläinen, Sanna; Kaukonen, Maria; Uusitalo, Liisa; Hanski, Ilkka; Lohi, Hannes; Ruokolainen, Lasse

2018-01-01

A rural environment and farming lifestyle are known to provide protection against allergic diseases. This protective effect is expected to be mediated via exposure to environmental microbes that are needed to support a normal immune tolerance. However, the triangle of interactions between environmental microbes, host microbiota, and immune system remains poorly understood. Here, we have studied these interactions using a canine model (two breeds, n = 169), providing an intermediate approach between complex human studies and artificial mouse model studies. We show that the skin microbiota reflects both the living environment and the lifestyle of a dog. Remarkably, the prevalence of spontaneous allergies is also associated with residential environment and lifestyle, such that allergies are most common among urban dogs living in single-person families without other animal contacts, and least common among rural dogs having opposite lifestyle features. Thus, we show that living environment and lifestyle concurrently associate with skin microbiota and allergies, suggesting that these factors might be causally related. Moreover, microbes commonly found on human skin tend to dominate the urban canine skin microbiota, while environmental microbes are rich in the rural canine skin microbiota. This in turn suggests that skin microbiota is a feasible indicator of exposure to environmental microbes. As short-term exposure to environmental microbes via exercise is not associated with allergies, we conclude that prominent and sustained exposure to environmental microbiotas should be promoted by urban planning and lifestyle changes to support health of urban populations. PMID:29686089

Skin microbiota and allergic symptoms associate with exposure to environmental microbes.

PubMed

Lehtimäki, Jenni; Sinkko, Hanna; Hielm-Björkman, Anna; Salmela, Elina; Tiira, Katriina; Laatikainen, Tiina; Mäkeläinen, Sanna; Kaukonen, Maria; Uusitalo, Liisa; Hanski, Ilkka; Lohi, Hannes; Ruokolainen, Lasse

2018-05-08

A rural environment and farming lifestyle are known to provide protection against allergic diseases. This protective effect is expected to be mediated via exposure to environmental microbes that are needed to support a normal immune tolerance. However, the triangle of interactions between environmental microbes, host microbiota, and immune system remains poorly understood. Here, we have studied these interactions using a canine model (two breeds, n = 169), providing an intermediate approach between complex human studies and artificial mouse model studies. We show that the skin microbiota reflects both the living environment and the lifestyle of a dog. Remarkably, the prevalence of spontaneous allergies is also associated with residential environment and lifestyle, such that allergies are most common among urban dogs living in single-person families without other animal contacts, and least common among rural dogs having opposite lifestyle features. Thus, we show that living environment and lifestyle concurrently associate with skin microbiota and allergies, suggesting that these factors might be causally related. Moreover, microbes commonly found on human skin tend to dominate the urban canine skin microbiota, while environmental microbes are rich in the rural canine skin microbiota. This in turn suggests that skin microbiota is a feasible indicator of exposure to environmental microbes. As short-term exposure to environmental microbes via exercise is not associated with allergies, we conclude that prominent and sustained exposure to environmental microbiotas should be promoted by urban planning and lifestyle changes to support health of urban populations. Copyright © 2018 the Author(s). Published by PNAS.

Screening assays of termite gut microbes that potentially as probiotic for human to digest cellulose as new food source

NASA Astrophysics Data System (ADS)

Abdullah, R.; Ananda, K. R. T.; Wijanarka

2018-05-01

According to UN, earth population will increase approximately 7.3 billion people up to 11.2 billion from 2015 until 2100. On the other side, food needs are not balance with the availability of food on earth. People of the world need solution for a new food source. By cellulose digesting ability, people analyzed can consume cellulose as the new food source to get glucose. The aims of research is obtaining termite gut cellulase bacteria selected which is potential as probiotic to split cellulose. Method used was as follows; isolation of termite gut microbes, microbial cellulase purification by screening method and probiotic test includes microbial pathogenicity test and human stomach acid and salt osmotic concentration resistance test. The result shows, 3 pure isolates of termite gut microbes can break down cellulose in the medium 1% CMC and 0.1% congo red (indicator of cellulose degradation activity) and life at pH 2- 2.5 and osmotic salt condition. Two isolates show the activity of gamma hemolysis (non-pathogenic in terms of pathogenicity on human blood). In conclusion, there are isolated termite gut microbes can be used as probiotic candidate for human to digest cellulose of the new food source for global food scarcity era.

Colonization potential to reconstitute a microbe community in patients detected early after fecal microbe transplant for recurrent C. difficile.

PubMed

Kumar, Ranjit; Maynard, Craig L; Eipers, Peter; Goldsmith, Kelly T; Ptacek, Travis; Grubbs, J Aaron; Dixon, Paula; Howard, Donna; Crossman, David K; Crowley, Michael R; Benjamin, William H; Lefkowitz, Elliot J; Weaver, Casey T; Rodriguez, J Martin; Morrow, Casey D

2016-01-13

Fecal microbiota transplants (FMT) are an effective treatment for patients with gut microbe dysbiosis suffering from recurrent C. difficile infections. To further understand how FMT reconstitutes the patient's gut commensal microbiota, we have analyzed the colonization potential of the donor, recipient and recipient post transplant fecal samples using transplantation in gnotobiotic mice. A total of nine samples from three human donors, recipient's pre and post FMT were transplanted into gnotobiotic mice. Microbiome analysis of three donor fecal samples revealed the presence of a high relative abundance of commensal microbes from the family Bacteriodaceae and Lachnospiraceae that were almost absent in the three recipient pre FMT fecal samples (<0.01%). The microbe composition in gnotobiotic mice transplanted with the donor fecal samples was similar to the human samples. The recipient samples contained Enterobacteriaceae, Lactobacillaceae, Enterococcaceae in relative abundance of 43, 11, 8%, respectively. However, gnotobiotic mice transplanted with the recipient fecal samples had an average relative abundance of unclassified Clostridiales of 55%, approximately 7000 times the abundance in the recipient fecal samples prior to transplant. Microbiome analysis of fecal samples from the three patients early (2-4 weeks) after FMT revealed a microbe composition with the relative abundance of both Bacteriodaceae and Lachnospiraceae that was approximately 7% of that of the donor. In contrast, gnotobioitc mice transplanted with the fecal samples obtained from the three at early times post FMT revealed increases in the relative abundance of Bacteriodaceae and Lachnospiraceae microbe compositions to levels similar to the donor fecal samples. Furthermore, the unclassified Clostridiales in the recipient samples post FMT was reduced to an average of 10%. We have used transplantation into gnotobiotic mice to evaluate the colonization potential of microbiota in FMT patients early after transplant. The commensal microbes present at early times post FMT out competed non-commensal microbes (e.g. such as unclassified Clostridiales) for niche space. The selective advantage of these commensal microbes to occupy niches in the gastrointestinal tract helps to explain the success of FMT to reconstitute the gut microbe community of patients with recurrent C. difficile infections.

Complementary and Alternative Medicine (CAM) and Next-Generation CAM (NG-CAM) Strategies for Therapeutic Gut Microbiota Modulation in Inflammatory Bowel Disease

PubMed Central

Basson, Abigail R; Minh, Lam; Cominelli, Fabio

2018-01-01

SUMMARY The human gastrointestinal tract is resident to a vastly diverse microbial consortium that co-exists through strict rules of invasion, dominance, resilience and succession. While some members possess stronger capabilities for survival than others, each one retains a genome characteristic of their bacterial denomination which subsequently determines survival and ultimately the composition of a human gut microbiome. Collective evidence advocates the concept of gut microbiota modulation via dietary compounds, with or without nutraceutical supplementation. However, consistent reports of strong individuality in responsiveness suggest that initial composition of host microbiota mediates the effect of nutrition modulation. There is also a strong potential for the interaction between mind and microbe to influence responsiveness, although mechanistic understanding of these complex exchanges remains in its infancy at best. Synthetic stool for FMT is a next-generation microbiome-therapy shown effective in treating C.difficile [417] which could provide a feasible alternative to current methods for patients with IBD. Nevertheless, studies investigating optimum timing for FMT administration are essential. Animal and human studies are only starting to highlight the Pandora of interactions that endure between members of gut microbiome, their associated metabolites, dietary compounds, as well as host neurological and immune systems, all of which characteristic to each individual. Advanced research technologies have excelled the scientific evidence in support of CAM and toward generating NG-CAM systems designed for treatment of specific disease states, such as IBD. While the majority of envisioned NG-CAM strategies presently exist in their experimental and discovery phases, many show promise for future clinical application. PMID:29173517

Anaerobic 4-hydroxyproline utilization: Discovery of a new glycyl radical enzyme in the human gut microbiome uncovers a widespread microbial metabolic activity.

PubMed

Huang, Yolanda Y; Martínez-Del Campo, Ana; Balskus, Emily P

2018-02-06

The discovery of enzymes responsible for previously unappreciated microbial metabolic pathways furthers our understanding of host-microbe and microbe-microbe interactions. We recently identified and characterized a new gut microbial glycyl radical enzyme (GRE) responsible for anaerobic metabolism of trans-4-hydroxy-l-proline (Hyp). Hyp dehydratase (HypD) catalyzes the removal of water from Hyp to generate Δ 1 -pyrroline-5-carboxylate (P5C). This enzyme is encoded in the genomes of a diverse set of gut anaerobes and is prevalent and abundant in healthy human stool metagenomes. Here, we discuss the roles HypD may play in different microbial metabolic pathways as well as the potential implications of this activity for colonization resistance and pathogenesis within the human gut. Finally, we present evidence of anaerobic Hyp metabolism in sediments through enrichment culturing of Hyp-degrading bacteria, highlighting the wide distribution of this pathway in anoxic environments beyond the human gut.

Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis.

PubMed

Sung, Jaeyun; Kim, Seunghyeon; Cabatbat, Josephine Jill T; Jang, Sungho; Jin, Yong-Su; Jung, Gyoo Yeol; Chia, Nicholas; Kim, Pan-Jun

2017-06-06

A system-level framework of complex microbe-microbe and host-microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut microbiota, called NJS16. This is an extensive data resource composed of ∼570 microbial species and 3 human cell types metabolically interacting through >4,400 small-molecule transport and macromolecule degradation events. Based on the contents of our network, we develop a mathematical approach to elucidate representative microbial and metabolic features of the gut microbial community in a given population, such as a disease cohort. Applying this strategy to microbiome data from type 2 diabetes patients reveals a context-specific infrastructure of the gut microbial ecosystem, core microbial entities with large metabolic influence, and frequently produced metabolic compounds that might indicate relevant community metabolic processes. Our network presents a foundation towards integrative investigations of community-scale microbial activities within the human gut.

Fecal microbiome in the bovine animal

USDA-ARS?s Scientific Manuscript database

Bacteria in the gastrointestinal tract have often been an afterthought in regard to the mammalian host. In recent year for humans, the gastrointestinal microbes appear to be associated with host immune function, health, and well-being. In addition, microbes can competitively exclude other bacteria...

Exploring: Microbes.

ERIC Educational Resources Information Center

Brand, Judith, Ed.

1997-01-01

This issue of Exploratorium Magazine focuses on microbes. Different types of microorganisms are introduced based on their living environments or whether they are harmful or beneficial. Contents include: (1) "It's a Small World" (Blake Edgar); (2) "The Human Body: A Complex Ecosystem" (Nik Walter); (3) "The Hills That…

Multiscale Analysis of Independent Alzheimer's Cohorts Finds Disruption of Molecular, Genetic, and Clinical Networks by Human Herpesvirus.

PubMed

Readhead, Ben; Haure-Mirande, Jean-Vianney; Funk, Cory C; Richards, Matthew A; Shannon, Paul; Haroutunian, Vahram; Sano, Mary; Liang, Winnie S; Beckmann, Noam D; Price, Nathan D; Reiman, Eric M; Schadt, Eric E; Ehrlich, Michelle E; Gandy, Sam; Dudley, Joel T

2018-06-21

Investigators have long suspected that pathogenic microbes might contribute to the onset and progression of Alzheimer's disease (AD) although definitive evidence has not been presented. Whether such findings represent a causal contribution, or reflect opportunistic passengers of neurodegeneration, is also difficult to resolve. We constructed multiscale networks of the late-onset AD-associated virome, integrating genomic, transcriptomic, proteomic, and histopathological data across four brain regions from human post-mortem tissue. We observed increased human herpesvirus 6A (HHV-6A) and human herpesvirus 7 (HHV-7) from subjects with AD compared with controls. These results were replicated in two additional, independent and geographically dispersed cohorts. We observed regulatory relationships linking viral abundance and modulators of APP metabolism, including induction of APBB2, APPBP2, BIN1, BACE1, CLU, PICALM, and PSEN1 by HHV-6A. This study elucidates networks linking molecular, clinical, and neuropathological features with viral activity and is consistent with viral activity constituting a general feature of AD. Copyright © 2018 Elsevier Inc. All rights reserved.

Microbiota as Therapeutic Targets.

PubMed

Xavier, Ramnik J

Inflammatory bowel disease (IBD) represents a family of diseases including Crohn's disease and ulcerative colitis. IBD has garnered significant attention in recent years due to successes in 2 areas of basic science: complex human genetics and host-microbe interactions. Advances in understanding the genetics of IBD, mainly driven by genome-wide association studies, have identified more than 160 genetic loci that modulate the risk of disease. Notably, several of these genes have pointed to alterations in host-microbe interactions as being critical factors in pathogenesis. Investigations into the microbial communities of the gastrointestinal tract (or the 'gut microbiome') in IBD have yielded important insights into several aspects of interactions between microbiota and the host immune system, including how alterations to microbial community composition and function have important consequences for immune homeostasis. The anatomy of the gastrointestinal tract plays a role in defining not only intestinal function, but also the microbial ecosystem that lives within the gut. Careful investigations into the composition and function of these microbial communities have suggested that patients with IBD have an imbalance in their gut microbiota, termed dysbiosis. These studies, as well as studies using samples from healthy individuals, have begun to uncover mechanisms of crosstalk between particular microbes (and microbial products) and immunomodulatory pathways, alterations which may drive immune diseases such as IBD. Investigations into the role of the microbiome in IBD have provided important clues to potential pathogenic mechanisms. Harnessing this knowledge to develop therapeutics and identify biomarkers is currently a major translational goal, holding great promise for clinically meaningful progress. © 2016 S. Karger AG, Basel.

Failure of the public health testing program for ballast water treatment systems.

PubMed

Cohen, Andrew N; Dobbs, Fred C

2015-02-15

Since 2004, an international testing program has certified 53 shipboard treatment systems as meeting ballast water discharge standards, including limits on certain microbes to prevent the spread of human pathogens. We determined how frequently certification tests failed a minimum requirement for a meaningful evaluation, that the concentration of microbes in the untreated (control) discharge must exceed the regulatory limit for treated discharges. In 95% of cases where the result was accepted as evidence that the treatment system reduced microbes to below the regulatory limit, the discharge met the limit even without treatment. This shows that the certification program for ballast water treatment systems is dysfunctional in protecting human health. In nearly all cases, the treatment systems would have equally well "passed" these tests even if they had never been turned on. Protocols must require minimum concentrations of targeted microbes in test waters, reflecting the upper range of concentrations in waters where ships operate. Copyright © 2014 Elsevier Ltd. All rights reserved.

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota.

PubMed

Milani, Christian; Duranti, Sabrina; Bottacini, Francesca; Casey, Eoghan; Turroni, Francesca; Mahony, Jennifer; Belzer, Clara; Delgado Palacio, Susana; Arboleya Montes, Silvia; Mancabelli, Leonardo; Lugli, Gabriele Andrea; Rodriguez, Juan Miguel; Bode, Lars; de Vos, Willem; Gueimonde, Miguel; Margolles, Abelardo; van Sinderen, Douwe; Ventura, Marco

2017-12-01

The human gut microbiota is engaged in multiple interactions affecting host health during the host's entire life span. Microbes colonize the neonatal gut immediately following birth. The establishment and interactive development of this early gut microbiota are believed to be (at least partially) driven and modulated by specific compounds present in human milk. It has been shown that certain genomes of infant gut commensals, in particular those of bifidobacterial species, are genetically adapted to utilize specific glycans of this human secretory fluid, thus representing a very intriguing example of host-microbe coevolution, where both partners are believed to benefit. In recent years, various metagenomic studies have tried to dissect the composition and functionality of the infant gut microbiome and to explore the distribution across the different ecological niches of the infant gut biogeography of the corresponding microbial consortia, including those corresponding to bacteria and viruses, in healthy and ill subjects. Such analyses have linked certain features of the microbiota/microbiome, such as reduced diversity or aberrant composition, to intestinal illnesses in infants or disease states that are manifested at later stages of life, including asthma, inflammatory bowel disease, and metabolic disorders. Thus, a growing number of studies have reported on how the early human gut microbiota composition/development may affect risk factors related to adult health conditions. This concept has fueled the development of strategies to shape the infant microbiota composition based on various functional food products. In this review, we describe the infant microbiota, the mechanisms that drive its establishment and composition, and how microbial consortia may be molded by natural or artificial interventions. Finally, we discuss the relevance of key microbial players of the infant gut microbiota, in particular bifidobacteria, with respect to their role in health and disease. Copyright © 2017 American Society for Microbiology.

Pathogenomics: an updated European Research Agenda.

PubMed

Demuth, Andreas; Aharonowitz, Yair; Bachmann, Till T; Blum-Oehler, Gabriele; Buchrieser, Carmen; Covacci, Antonello; Dobrindt, Ulrich; Emödy, Levente; van der Ende, Arie; Ewbank, Jonathan; Fernández, Luis Angel; Frosch, Matthias; García-Del Portillo, Francisco; Gilmore, Michael S; Glaser, Philippe; Goebel, Werner; Hasnain, Seyed E; Heesemann, Jürgen; Islam, Khalid; Korhonen, Timo; Maiden, Martin; Meyer, Thomas F; Montecucco, Cesare; Oswald, Eric; Parkhill, Julian; Pucciarelli, M Graciela; Ron, Eliora; Svanborg, Catharina; Uhlin, Bernt Eric; Wai, Sun Nyunt; Wehland, Jürgen; Hacker, Jörg

2008-05-01

The emerging genomic technologies and bioinformatics provide novel opportunities for studying life-threatening human pathogens and to develop new applications for the improvement of human and animal health and the prevention, treatment, and diagnosis of infections. Based on the ecology and population biology of pathogens and related organisms and their connection to epidemiology, more accurate typing technologies and approaches will lead to better means of disease control. The analysis of the genome plasticity and gene pools of pathogenic bacteria including antigenic diversity and antigenic variation results in more effective vaccines and vaccine implementation programs. The study of newly identified and uncultivated microorganisms enables the identification of new threats. The scrutiny of the metabolism of the pathogen in the host allows the identification of new targets for anti-infectives and therapeutic approaches. The development of modulators of host responses and mediators of host damage will be facilitated by the research on interactions of microbes and hosts, including mechanisms of host damage, acute and chronic relationships as well as commensalisms. The study of multiple pathogenic and non-pathogenic microbes interacting in the host will improve the management of multiple infections and will allow probiotic and prebiotic interventions. Needless to iterate, the application of the results of improved prevention and treatment of infections into clinical tests will have a positive impact on the management of human and animal disease. The Pathogenomics Research Agenda draws on discussions with experts of the Network of Excellence "EuroPathoGenomics" at the management board meeting of the project held during 18-21 April 2007, in the Villa Vigoni, Menaggio, Italy. Based on a proposed European Research Agenda in the field of pathogenomics by the ERA-NET PathoGenoMics the meeting's participants updated the established list of topics as the research agenda for the future.

Diversity and population structure of sewage derived microorganisms in wastewater treatment plant influent

PubMed Central

McLellan, S.L.; Huse, S.M.; Mueller-Spitz, S.R.; Andreishcheva, E.N.; Sogin, M.L.

2009-01-01

The release of untreated sewage introduces non-indigenous microbial populations of uncertain composition into surface waters. We used massively parallel 454 sequencing of hypervariable regions in rRNA genes to profile microbial communities from eight untreated sewage influent samples of two wastewater treatment plants (WWTP) in metropolitan Milwaukee. The sewage profiles included a discernable human fecal signature made up of several taxonomic groups including multiple Bifidobacteriaceae, Coriobacteriaceae, Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae genera. The fecal signature made up a small fraction of the taxa present in sewage but the relative abundance of these sequence tags mirrored the population structures of human fecal samples. These genera were much more prevalent in the sewage influent than standard indicators species. High-abundance sequences from taxonomic groups within the Beta- and Gammaproteobacteria dominated the sewage samples but occurred at very low levels in fecal and surface water samples, suggesting that these organisms proliferate within the sewer system. Samples from Jones Island (JI – servicing residential plus a combined sewer system) and South Shore (SS – servicing a residential area) WWTPs had very consistent community profiles, with greater similarity between WWTPs on a given collection day than the same plant collected on different days. Rainfall increased influent flows at SS and JI WWTPs, and this corresponded to greater diversity in the community at both plants. Overall, the sewer system appears to be a defined environment with both infiltration of rainwater and stormwater inputs modulating community composition. Microbial sewage communities represent a combination of inputs from human fecal microbes and enrichment of specific microbes from the environment to form a unique population structure. PMID:19840106

Consumption of Lysozyme-Rich Milk Can Alter Microbial Fecal Populations

PubMed Central

Desai, Prerak T.; Weimer, Bart C.; Dao, Nguyet; Kültz, Dietmar; Murray, James D.

2012-01-01

Human milk contains antimicrobial factors such as lysozyme and lactoferrin that are thought to contribute to the development of an intestinal microbiota beneficial to host health. However, these factors are lacking in the milk of dairy animals. Here we report the establishment of an animal model to allow the dissection of the role of milk components in gut microbiota modulation and subsequent changes in overall and intestinal health. Using milk from transgenic goats expressing human lysozyme at 68%, the level found in human milk and young pigs as feeding subjects, the fecal microbiota was analyzed over time using 16S rRNA gene sequencing and the G2 Phylochip. The two methods yielded similar results, with the G2 Phylochip giving more comprehensive information by detecting more OTUs. Total community populations remained similar within the feeding groups, and community member diversity was changed significantly upon consumption of lysozyme milk. Levels of Firmicutes (Clostridia) declined whereas those of Bacteroidetes increased over time in response to the consumption of lysozyme-rich milk. The proportions of these major phyla were significantly different (P < 0.05) from the proportions seen with control-fed animals after 14 days of feeding. Within phyla, the abundance of bacteria associated with gut health (Bifidobacteriaceae and Lactobacillaceae) increased and the abundance of those associated with disease (Mycobacteriaceae, Streptococcaceae, Campylobacterales) decreased with consumption of lysozyme milk. This study demonstrated that a single component of the diet with bioactivity changed the gut microbiome composition. Additionally, this model enabled the direct examination of the impact of lysozyme on beneficial microbe enrichment versus detrimental microbe reduction in the gut microbiome community. PMID:22752159

Optical diffusion property of cerumen from ear canal and correlation to metal content measured by synchrotron x-ray absorption

NASA Astrophysics Data System (ADS)

Holden, Todd; Dehipawala, Sumudu; Cheung, E.; Golebiewska, U.; Schneider, P.; Tremberger, G., Jr.; Kokkinos, D.; Lieberman, D.; Dehipawala, Sunil; Cheung, T.

2012-03-01

Human (and other mammals) would secrete cerumen (ear wax) to protect the skin of the ear canal against pathogens and insects. The studies of biodiversity of pathogen in human include intestine microbe colony, belly button microbe colony, etc. Metals such as zinc and iron are essentials to bio-molecular pathways and would be related to the underlying pathogen vitality. This project studies the biodiversity of cerumen via its metal content and aims to develop an optical probe for metal content characterization. The optical diffusion mean free path and absorption of human cerumen samples dissolved in solvent have been measured in standard transmission measurements. EXFAS and XANES have been measured at Brookhaven Synchrotron Light Source for the determination of metal contents, presumably embedded within microbes/insects/skin cells. The results show that a calibration procedure can be used to correlate the optical diffusion parameters to the metal content, thus expanding the diagnostic of cerumen in the study of human pathogen biodiversity without the regular use of a synchrotron light source. Although biodiversity measurements would not be seriously affected by dead microbes and absorption based method would do well, the scattering mean free path method would have potential to further study the cell based scattering centers (dead or live) via the information embedded in the speckle pattern in the deep-Fresnel zone.

With a Little Help from My Friends: Microbial Partners in Integrative and Comparative Biology-An Introduction to the Symposium.

PubMed

Kohl, Kevin D; Dearing, M Denise

2017-10-01

The role that host-associated microbes play in animal biology is gaining attention in comparative biology. Numerous research groups study the roles that microbes play in human health and nutrition, or in enhancing the production of agricultural animals. However, inclusion of host-associated microbes into research questions of integrative and comparative biology has lagged behind. We hosted a symposium to bring together top researchers in the field of host-associated microbes who also incorporate aspects of integrative and comparative biology. In this introduction, we highlight recent research demonstrating the profound roles that host-associated microbes play in many aspects of animal biology, such as immune function, endocrinology, and even behavior. It is our hope that integrative and comparative biologists will begin to include aspects of host-associated microbes into their research programs, enhancing both the fields of comparative biology and host-microbe interactions. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Functional characterization of two distinct xyoglucanases from rumenal microbes

USDA-ARS?s Scientific Manuscript database

Xyloglucans are known to function by binding to cellulose microfibrils, crosslinking adjacent fibers forming cellulose-XG networks important for modulation of rigidity and extensibility of the primary cell wall of plants. Enzymatic hydrolysis and modification of xyloglucans has received considerabl...

Incorporating the gut microbiota into models of human and non-human primate ecology and evolution.

PubMed

Amato, Katherine R

2016-01-01

The mammalian gut is home to a diverse community of microbes. Advances in technology over the past two decades have allowed us to examine this community, the gut microbiota, in more detail, revealing a wide range of influences on host nutrition, health, and behavior. These host-gut microbe interactions appear to shape host plasticity and fitness in a variety of contexts, and therefore represent a key factor missing from existing models of human and non-human primate ecology and evolution. However, current studies of the gut microbiota tend to include limited contextual data or are clinical, making it difficult to directly test broad anthropological hypotheses. Here, I review what is known about the animal gut microbiota and provide examples of how gut microbiota research can be integrated into the study of human and non-human primate ecology and evolution with targeted data collection. Specifically, I examine how the gut microbiota may impact primate diet, energetics, disease resistance, and cognition. While gut microbiota research is proliferating rapidly, especially in the context of humans, there remain important gaps in our understanding of host-gut microbe interactions that will require an anthropological perspective to fill. Likewise, gut microbiota research will be an important tool for filling remaining gaps in anthropological research. © 2016 Wiley Periodicals, Inc.

A wide diversity of bacteria from the human gut produces and degrades biogenic amines.

PubMed

Pugin, Benoit; Barcik, Weronika; Westermann, Patrick; Heider, Anja; Wawrzyniak, Marcin; Hellings, Peter; Akdis, Cezmi A; O'Mahony, Liam

2017-01-01

Background : Biogenic amines (BAs) are metabolites produced by the decarboxylation of amino acids with significant physiological functions in eukaryotic and prokaryotic cells. BAs can be produced by bacteria in fermented foods, but little is known concerning the potential for microbes within the human gut microbiota to produce or degrade BAs. Objective : To isolate and identify BA-producing and BA-degrading microbes from the human gastrointestinal tract. Design : Fecal samples from human volunteers were screened on multiple growth media, under multiple growth conditions. Bacterial species were identified using 16S rRNA sequencing and BA production or degradation was assessed using ultra-performance liquid chromatography. Results : In total, 74 BA-producing or BA-degrading strains were isolated from the human gut. These isolates belong to the genera Bifidobacterium , Clostridium , Enterococcus , Lactobacillus , Pediococcus , Streptococcus , Enterobacter , Escherichia , Klebsiella , Morganella and Proteus . While differences in production or degradation of specific BAs were observed at the strain level, our results suggest that these metabolic activities are widely spread across different taxa present within the human gut microbiota. Conclusions : The isolation and identification of microbes from the human gut with BA-producing and BA-degrading metabolic activity is an important first step in developing a better understanding of how these metabolites influence health and disease.

Engineering chemical interactions in microbial communities.

PubMed

Kenny, Douglas J; Balskus, Emily P

2018-03-05

Microbes living within host-associated microbial communities (microbiotas) rely on chemical communication to interact with surrounding organisms. These interactions serve many purposes, from supplying the multicellular host with nutrients to antagonizing invading pathogens, and breakdown of chemical signaling has potentially negative consequences for both the host and microbiota. Efforts to engineer microbes to take part in chemical interactions represent a promising strategy for modulating chemical signaling within these complex communities. In this review, we discuss prominent examples of chemical interactions found within host-associated microbial communities, with an emphasis on the plant-root microbiota and the intestinal microbiota of animals. We then highlight how an understanding of such interactions has guided efforts to engineer microbes to participate in chemical signaling in these habitats. We discuss engineering efforts in the context of chemical interactions that enable host colonization, promote host health, and exclude pathogens. Finally, we describe prominent challenges facing this field and propose new directions for future engineering efforts.

The role of the microbiome in human health and disease: an introduction for clinicians.

PubMed

Young, Vincent B

2017-03-15

Research into the microbiome-the indigenous microbial communities (microbiota) and the host environment that they inhabit-has changed clinicians' ideas about microbes in human health and disease. Perhaps the most radical change is the realization that most of the microbes that inhabit our body supply crucial ecosystem services that benefit the entire host-microbe system. These services include the production of important resources, bioconversion of nutrients, and protection against pathogenic microbes. Thus disease can result from a loss of beneficial functions or the introduction of maladaptive functions by invading microbes. This review will show how an understanding of the dynamics and function of the indigenous microbiota has altered our view of microbes in maintaining homeostasis and causing disease. It will discuss how disruption of the beneficial functions of the microbiota can lead to disease. Methods for studying the microbiota will be introduced as part of a conceptual framework for using these methods to delineate novel roles for microbes in health. Key associations between specific changes in the microbiome and disease will be discussed. This will lead to an explanation of how the intentional manipulation of the microbiota, either by restoring missing functions or eliminating harmful functions, may lead to novel methods to prevent or treat a variety of diseases. With the explosion of studies relating the microbiome to health and disease, this review aims to provide a foundation for clinicians to follow this developing area of biomedical research. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Application of a neutral community model to assess structuring of the human lung microbiome.

PubMed

Venkataraman, Arvind; Bassis, Christine M; Beck, James M; Young, Vincent B; Curtis, Jeffrey L; Huffnagle, Gary B; Schmidt, Thomas M

2015-01-20

DNA from phylogenetically diverse microbes is routinely recovered from healthy human lungs and used to define the lung microbiome. The proportion of this DNA originating from microbes adapted to the lungs, as opposed to microbes dispersing to the lungs from other body sites and the atmosphere, is not known. We use a neutral model of community ecology to distinguish members of the lung microbiome whose presence is consistent with dispersal from other body sites and those that deviate from the model, suggesting a competitive advantage to these microbes in the lungs. We find that the composition of the healthy lung microbiome is consistent with predictions of the neutral model, reflecting the overriding role of dispersal of microbes from the oral cavity in shaping the microbial community in healthy lungs. In contrast, the microbiome of diseased lungs was readily distinguished as being under active selection. We also assessed the viability of microbes from lung samples by cultivation with a variety of media and incubation conditions. Bacteria recovered by cultivation from healthy lungs represented species that comprised 61% of the 16S rRNA-encoding gene sequences derived from bronchoalveolar lavage samples. Neutral distribution of microbes is a distinguishing feature of the microbiome in healthy lungs, wherein constant dispersal of bacteria from the oral cavity overrides differential growth of bacteria. No bacterial species consistently deviated from the model predictions in healthy lungs, although representatives of many of the dispersed species were readily cultivated. In contrast, bacterial populations in diseased lungs were identified as being under active selection. Quantification of the relative importance of selection and neutral processes such as dispersal in shaping the healthy lung microbiome is a first step toward understanding its impacts on host health. Copyright © 2015 Venkataraman et al.

Factors Shaping the Human Exposome in the Built Environment: Opportunities for Engineering Control.

PubMed

Dai, Dongjuan; Prussin, Aaron J; Marr, Linsey C; Vikesland, Peter J; Edwards, Marc A; Pruden, Amy

2017-07-18

The "exposome" is a term describing the summation of one's lifetime exposure to microbes and chemicals. Such exposures are now recognized as major drivers of human health and disease. Because humans spend ∼90% of their time indoors, the built environment exposome merits particular attention. Herein we utilize an engineering perspective to advance understanding of the factors that shape the built environment exposome and its influence on human wellness and disease, while simultaneously informing development of a framework for intentionally controlling the exposome to protect public health. Historically, engineers have been focused on controlling chemical and physical contaminants and on eradicating microbes; however, there is a growing awareness of the role of "beneficial" microbes. Here we consider the potential to selectively control the materials and chemistry of the built environment to positively influence the microbial and chemical components of the indoor exposome. Finally, we discuss research gaps that must be addressed to enable intentional engineering design, including the need to define a "healthy" built environment exposome and how to control it.

Synthetic Biology and the Gut Microbiome.

PubMed

Dou, Jennifer; Bennett, Matthew R

2018-05-01

The gut microbiome plays a crucial role in maintaining human health. Functions performed by gastrointestinal microbes range from regulating metabolism to modulating immune and nervous system development. Scientists have attempted to exploit this importance through the development of engineered probiotics that are capable of producing and delivering small molecule therapeutics within the gut. However, existing synthetic probiotics are simplistic and fail to replicate the complexity and adaptability of native homeostatic mechanisms. In this review, the ways in which the tools and approaches of synthetic biology have been applied to improve the efficacy of therapeutic probiotics, and the ways in which they might be applied in the future is discussed. Simple devices, such as a bistable switches and integrase memory arrays, have been successfully implemented in the mammalian gut, and models for targeted delivery in this environment have also been developed. In the future, it will be necessary to introduce concepts such as logic-gating and biocontainment mechanisms into synthetic probiotics, as well as to expand the collection of relevant biosensors. Ideally, this will bring us closer to a reality in which engineered therapeutic microbes will be able to accurately diagnose and effectively respond to a variety of disease states. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Screening of Probiotic Candidates in Human Oral Bacteria for the Prevention of Dental Disease

PubMed Central

Terai, Tomohiko; Okumura, Takekazu; Imai, Susumu; Nakao, Masumi; Yamaji, Kazuaki; Ito, Masahiko; Nagata, Tsuyoshi; Kaneko, Kimiyuki; Miyazaki, Kouji; Okada, Ayako; Nomura, Yoshiaki; Hanada, Nobuhiro

2015-01-01

The oral cavity in healthy subjects has a well-balanced microbiota that consists of more than 700 species. However, a disturbance of this balance, with an increase of harmful microbes and a decrease of beneficial microbes, causes oral disorders such as periodontal disease or dental caries. Nowadays, probiotics are expected to confer oral health benefits by modulating the oral microbiota. This study screened new probiotic candidates with potential oral health benefits and no harmful effects on the oral cavity. We screened 14 lactobacillus strains and 36 streptococcus strains out of 896 oral isolates derived from healthy subjects. These bacteria did not produce volatile sulfur compounds or water-insoluble glucan, had higher antibacterial activity against periodontal bacteria, and had higher adherence activity to oral epithelial cells or salivary-coated hydroxyapatite in vitro. We then evaluated the risk of primary cariogenicity and infective endocarditis of the selected oral isolates. As a result, Lactobacillus crispatus YIT 12319, Lactobacillus fermentum YIT 12320, Lactobacillus gasseri YIT 12321, and Streptococcus mitis YIT 12322 were selected because they showed no cariogenic potential in an artificial mouth system and a lower risk of experimental infective endocarditis in a rat model. These candidates are expected as new probiotics with potential oral health benefits and no adverse effects on general health. PMID:26053410

Screening of Probiotic Candidates in Human Oral Bacteria for the Prevention of Dental Disease.

PubMed

Terai, Tomohiko; Okumura, Takekazu; Imai, Susumu; Nakao, Masumi; Yamaji, Kazuaki; Ito, Masahiko; Nagata, Tsuyoshi; Kaneko, Kimiyuki; Miyazaki, Kouji; Okada, Ayako; Nomura, Yoshiaki; Hanada, Nobuhiro

2015-01-01

The oral cavity in healthy subjects has a well-balanced microbiota that consists of more than 700 species. However, a disturbance of this balance, with an increase of harmful microbes and a decrease of beneficial microbes, causes oral disorders such as periodontal disease or dental caries. Nowadays, probiotics are expected to confer oral health benefits by modulating the oral microbiota. This study screened new probiotic candidates with potential oral health benefits and no harmful effects on the oral cavity. We screened 14 lactobacillus strains and 36 streptococcus strains out of 896 oral isolates derived from healthy subjects. These bacteria did not produce volatile sulfur compounds or water-insoluble glucan, had higher antibacterial activity against periodontal bacteria, and had higher adherence activity to oral epithelial cells or salivary-coated hydroxyapatite in vitro. We then evaluated the risk of primary cariogenicity and infective endocarditis of the selected oral isolates. As a result, Lactobacillus crispatus YIT 12319, Lactobacillus fermentum YIT 12320, Lactobacillus gasseri YIT 12321, and Streptococcus mitis YIT 12322 were selected because they showed no cariogenic potential in an artificial mouth system and a lower risk of experimental infective endocarditis in a rat model. These candidates are expected as new probiotics with potential oral health benefits and no adverse effects on general health.

Investigation of the Interplanetary Transfer of Microbes in the Tanpopo Mission at the Exposed Facility of the International Space Station.

PubMed

Kawaguchi, Yuko; Yokobori, Shin-Ichi; Hashimoto, Hirofumi; Yano, Hajime; Tabata, Makoto; Kawai, Hideyuki; Yamagishi, Akihiko

2016-05-01

The Tanpopo mission will address fundamental questions on the origin of terrestrial life. The main goal is to test the panspermia hypothesis. Panspermia is a long-standing hypothesis suggesting the interplanetary transport of microbes. Another goal is to test the possible origin of organic compounds carried from space by micrometeorites before the terrestrial origin of life. To investigate the panspermia hypothesis and the possible space origin of organic compounds, we performed space experiments at the Exposed Facility (EF) of the Japanese Experiment Module (JEM) of the International Space Station (ISS). The mission was named Tanpopo, which in Japanese means dandelion. We capture any orbiting microparticles, such as micrometeorites, space debris, and terrestrial particles carrying microbes as bioaerosols, by using blocks of silica aerogel. We also test the survival of microbial species and organic compounds in the space environment for up to 3 years. The goal of this review is to introduce an overview of the Tanpopo mission with particular emphasis on the investigation of the interplanetary transfer of microbes. The Exposed Experiment Handrail Attachment Mechanism with aluminum Capture Panels (CPs) and Exposure Panels (EPs) was exposed on the EF-JEM on May 26, 2015. The first CPs and EPs will be returned to the ground in mid-2016. Possible escape of terrestrial microbes from Earth to space will be evaluated by investigating the upper limit of terrestrial microbes by the capture experiment. Possible mechanisms for transfer of microbes over the stratosphere and an investigation of the effect of the microbial cell-aggregate size on survivability in space will also be discussed. Panspermia-Astrobiology-Low-Earth orbit. Astrobiology 16, 363-376.

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota.

PubMed

Hehemann, Jan-Hendrik; Correc, Gaëlle; Barbeyron, Tristan; Helbert, William; Czjzek, Mirjam; Michel, Gurvan

2010-04-08

Gut microbes supply the human body with energy from dietary polysaccharides through carbohydrate active enzymes, or CAZymes, which are absent in the human genome. These enzymes target polysaccharides from terrestrial plants that dominated diet throughout human evolution. The array of CAZymes in gut microbes is highly diverse, exemplified by the human gut symbiont Bacteroides thetaiotaomicron, which contains 261 glycoside hydrolases and polysaccharide lyases, as well as 208 homologues of susC and susD-genes coding for two outer membrane proteins involved in starch utilization. A fundamental question that, to our knowledge, has yet to be addressed is how this diversity evolved by acquiring new genes from microbes living outside the gut. Here we characterize the first porphyranases from a member of the marine Bacteroidetes, Zobellia galactanivorans, active on the sulphated polysaccharide porphyran from marine red algae of the genus Porphyra. Furthermore, we show that genes coding for these porphyranases, agarases and associated proteins have been transferred to the gut bacterium Bacteroides plebeius isolated from Japanese individuals. Our comparative gut metagenome analyses show that porphyranases and agarases are frequent in the Japanese population and that they are absent in metagenome data from North American individuals. Seaweeds make an important contribution to the daily diet in Japan (14.2 g per person per day), and Porphyra spp. (nori) is the most important nutritional seaweed, traditionally used to prepare sushi. This indicates that seaweeds with associated marine bacteria may have been the route by which these novel CAZymes were acquired in human gut bacteria, and that contact with non-sterile food may be a general factor in CAZyme diversity in human gut microbes.

Friends with social benefits: host-microbe interactions as a driver of brain evolution and development?

PubMed Central

Stilling, Roman M.; Bordenstein, Seth R.; Dinan, Timothy G.; Cryan, John F.

2014-01-01

The tight association of the human body with trillions of colonizing microbes that we observe today is the result of a long evolutionary history. Only very recently have we started to understand how this symbiosis also affects brain function and behavior. In this hypothesis and theory article, we propose how host-microbe associations potentially influenced mammalian brain evolution and development. In particular, we explore the integration of human brain development with evolution, symbiosis, and RNA biology, which together represent a “social triangle” that drives human social behavior and cognition. We argue that, in order to understand how inter-kingdom communication can affect brain adaptation and plasticity, it is inevitable to consider epigenetic mechanisms as important mediators of genome-microbiome interactions on an individual as well as a transgenerational time scale. Finally, we unite these interpretations with the hologenome theory of evolution. Taken together, we propose a tighter integration of neuroscience fields with host-associated microbiology by taking an evolutionary perspective. PMID:25401092

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat

PubMed Central

Hyde, Embriette R.; Navas-Molina, Jose A.; Kueneman, Jordan G.; Ackermann, Gail; Cardona, Cesar; Humphrey, Gregory; Boyer, Don; Weaver, Tom; Mendelson, Joseph R.; McKenzie, Valerie J.; Gilbert, Jack A.

2016-01-01

ABSTRACT Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon (Varanus komodoensis) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon’s environment are similar to the Komodo dragon’s salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals’ environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions. PMID:27822543

The Oral and Skin Microbiomes of Captive Komodo Dragons Are Significantly Shared with Their Habitat.

PubMed

Hyde, Embriette R; Navas-Molina, Jose A; Song, Se Jin; Kueneman, Jordan G; Ackermann, Gail; Cardona, Cesar; Humphrey, Gregory; Boyer, Don; Weaver, Tom; Mendelson, Joseph R; McKenzie, Valerie J; Gilbert, Jack A; Knight, Rob

2016-01-01

Examining the way in which animals, including those in captivity, interact with their environment is extremely important for studying ecological processes and developing sophisticated animal husbandry. Here we use the Komodo dragon ( Varanus komodoensis ) to quantify the degree of sharing of salivary, skin, and fecal microbiota with their environment in captivity. Both species richness and microbial community composition of most surfaces in the Komodo dragon's environment are similar to the Komodo dragon's salivary and skin microbiota but less similar to the stool-associated microbiota. We additionally compared host-environment microbiome sharing between captive Komodo dragons and their enclosures, humans and pets and their homes, and wild amphibians and their environments. We observed similar host-environment microbiome sharing patterns among humans and their pets and Komodo dragons, with high levels of human/pet- and Komodo dragon-associated microbes on home and enclosure surfaces. In contrast, only small amounts of amphibian-associated microbes were detected in the animals' environments. We suggest that the degree of sharing between the Komodo dragon microbiota and its enclosure surfaces has important implications for animal health. These animals evolved in the context of constant exposure to a complex environmental microbiota, which likely shaped their physiological development; in captivity, these animals will not receive significant exposure to microbes not already in their enclosure, with unknown consequences for their health. IMPORTANCE Animals, including humans, have evolved in the context of exposure to a variety of microbial organisms present in the environment. Only recently have humans, and some animals, begun to spend a significant amount of time in enclosed artificial environments, rather than in the more natural spaces in which most of evolution took place. The consequences of this radical change in lifestyle likely extend to the microbes residing in and on our bodies and may have important implications for health and disease. A full characterization of host-microbe sharing in both closed and open environments will provide crucial information that may enable the improvement of health in humans and in captive animals, both of which experience a greater incidence of disease (including chronic illness) than counterparts living under more ecologically natural conditions.

Human Performance and Biosystems (Spring Review)

DTIC Science & Technology

2014-03-01

public release; distribution is unlimited Areas of Emphasis Biofilms/Nanowires – microbe communication, extracellular electron transfer, cyborg ...Artificial Photosynthesis • Algal oil generation • Biofilm, Nanowires, Cyborg Cell • tDCS • Biomarkers 5 Distribution A: Approved for public...release; distribution is unlimited Program Interactions BRI magnetic navigation Microbes/nanowires tDCS/ Cyborg cell Synthetic Biology

Biosphere 2 test module: A ground-based sunlight-driven prototype of a closed ecological life support system

NASA Astrophysics Data System (ADS)

Nelson, Mark; Leigh, Linda; Alling, Abigail; MacCallum, Taber; Allen, John; Alvarez-Romo, Norberto

Constructed in 1986, the Biosphere 2 Test Module has been used since the end of that year for closed ecological systems experiments. It is the largest closed ecological facility ever built, with a sealed variable volume of some 480 cubic meters. It is built with a skin of steel spaceframes with double-laminated glass panels admitting about 65 percent Photosynthetically Active Radiation (PAR). The floor is of welded steel and there is an underground atmospheric connection via an air duct to a variable volume chamber (``lung'') permitting expansion and contraction of the Test Module's air volume caused by changes in temperature and barometric pressure, which causes a slight positive pressure from inside the closed system to the outside thereby insuring that the very small leakage rate is outward. Several series of closed ecological system investigations have been carried out in this facility. One series of experiments investigated the dynamics of higher plants and associated soils with the atmosphere under varying light and temperature conditions. Another series of experiments included one human in the closed system for three, five and twenty-one days. During these experiments the Test Module had subsystems which completely recycled its water and atmosphere; all the human dietary needs were produced within the facility, and all wastes were recycled using a marsh plant/microbe system. Other experiments have examined the capability of individual component systems used, such as the soil bed reactors, to eliminate experimentally introduced trace gases. Analytic systems developed for these experiments include continuous monitors of eleven atmospheric gases in addition to the complete gas chromatography mass spectrometry (GCMS) examinations of potable, waste system and irrigation water quality.

The networks of human gut microbe-metabolite associations are different between health and irritable bowel syndrome.

PubMed

Shankar, Vijay; Homer, Daniel; Rigsbee, Laura; Khamis, Harry J; Michail, Sonia; Raymer, Michael; Reo, Nicholas V; Paliy, Oleg

2015-08-01

The goal of this study was to determine if fecal metabolite and microbiota profiles can serve as biomarkers of human intestinal diseases, and to uncover possible gut microbe-metabolite associations. We employed proton nuclear magnetic resonance to measure fecal metabolites of healthy children and those diagnosed with diarrhea-predominant irritable bowel syndrome (IBS-D). Metabolite levels were associated with fecal microbial abundances. Using several ordination techniques, healthy and irritable bowel syndrome (IBS) samples could be distinguished based on the metabolite profiles of fecal samples, and such partitioning was congruent with the microbiota-based sample separation. Measurements of individual metabolites indicated that the intestinal environment in IBS-D was characterized by increased proteolysis, incomplete anaerobic fermentation and possible change in methane production. By correlating metabolite levels with abundances of microbial genera, a number of statistically significant metabolite-genus associations were detected in stools of healthy children. No such associations were evident for IBS children. This finding complemented the previously observed reduction in the number of microbe-microbe associations in the distal gut of the same cohort of IBS-D children.

[Exploring New Drug Targets through the Identification of Target Molecules of Bioactive Natural Products].

PubMed

Arai, Masayoshi

2016-01-01

With the development of cell biology and microbiology, it has become easy to culture many types of animal cells and microbes, and they are frequently used for phenotypic screening to explore medicinal seeds. On the other hand, it is recognized that cells and pathogenic microbes present in pathologic sites and infected regions of the human body display unique properties different from those under general culture conditions. We isolated several bioactive compounds from marine medicinal resources using constructed bioassay-guided separation focusing on the unique changes in the characteristics of cells and pathogenic microbes (Mycobacterium spp.) in the human body under disease conditions. In addition, we also carried out identification studies of target molecules of the bioactive compounds by methods utilizing the gene expression profile, transformants of cells or microbes, synthetic probe molecules of the isolated compounds, etc., since bioactive compounds isolated from the phenotypic screening system often target new molecules. This review presents our phenotypic screening systems, isolation of bioactive compounds from marine medicinal resources, and target identification of bioactive compounds.

Glucose metabolism: focus on gut microbiota, the endocannabinoid system and beyond.

PubMed

Cani, P D; Geurts, L; Matamoros, S; Plovier, H; Duparc, T

2014-09-01

The gut microbiota is now considered as a key factor in the regulation of numerous metabolic pathways. Growing evidence suggests that cross-talk between gut bacteria and host is achieved through specific metabolites (such as short-chain fatty acids) and molecular patterns of microbial membranes (lipopolysaccharides) that activate host cell receptors (such as toll-like receptors and G-protein-coupled receptors). The endocannabinoid (eCB) system is an important target in the context of obesity, type 2 diabetes (T2D) and inflammation. It has been demonstrated that eCB system activity is involved in the control of glucose and energy metabolism, and can be tuned up or down by specific gut microbes (for example, Akkermansia muciniphila). Numerous studies have also shown that the composition of the gut microbiota differs between obese and/or T2D individuals and those who are lean and non-diabetic. Although some shared taxa are often cited, there is still no clear consensus on the precise microbial composition that triggers metabolic disorders, and causality between specific microbes and the development of such diseases is yet to be proven in humans. Nevertheless, gastric bypass is most likely the most efficient procedure for reducing body weight and treating T2D. Interestingly, several reports have shown that the gut microbiota is profoundly affected by the procedure. It has been suggested that the consistent postoperative increase in certain bacterial groups such as Proteobacteria, Bacteroidetes and Verrucomicrobia (A. muciniphila) may explain its beneficial impact in gnotobiotic mice. Taken together, these data suggest that specific gut microbes modulate important host biological systems that contribute to the control of energy homoeostasis, glucose metabolism and inflammation in obesity and T2D. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes.

PubMed

Saad, Rama; Rizkallah, Mariam R; Aziz, Ramy K

2012-11-30

The influence of resident gut microbes on xenobiotic metabolism has been investigated at different levels throughout the past five decades. However, with the advance in sequencing and pyrotagging technologies, addressing the influence of microbes on xenobiotics had to evolve from assessing direct metabolic effects on toxins and botanicals by conventional culture-based techniques to elucidating the role of community composition on drugs metabolic profiles through DNA sequence-based phylogeny and metagenomics. Following the completion of the Human Genome Project, the rapid, substantial growth of the Human Microbiome Project (HMP) opens new horizons for studying how microbiome compositional and functional variations affect drug action, fate, and toxicity (pharmacomicrobiomics), notably in the human gut. The HMP continues to characterize the microbial communities associated with the human gut, determine whether there is a common gut microbiome profile shared among healthy humans, and investigate the effect of its alterations on health. Here, we offer a glimpse into the known effects of the gut microbiota on xenobiotic metabolism, with emphasis on cases where microbiome variations lead to different therapeutic outcomes. We discuss a few examples representing how the microbiome interacts with human metabolic enzymes in the liver and intestine. In addition, we attempt to envisage a roadmap for the future implications of the HMP on therapeutics and personalized medicine.

Effect of microgravity & space radiation on microbes.

PubMed

Senatore, Giuliana; Mastroleo, Felice; Leys, Natalie; Mauriello, Gianluigi

2018-06-01

One of the new challenges facing humanity is to reach increasingly further distant space targets. It is therefore of upmost importance to understand the behavior of microorganisms that will unavoidably reach the space environment together with the human body and equipment. Indeed, microorganisms could activate their stress defense mechanisms, modifying properties related to human pathogenesis. The host-microbe interactions, in fact, could be substantially affected under spaceflight conditions and the study of microorganisms' growth and activity is necessary for predicting these behaviors and assessing precautionary measures during spaceflight. This review gives an overview of the effects of microgravity and space radiation on microorganisms both in real and simulated conditions.

Gut Microbes and the Brain: Paradigm Shift in Neuroscience

PubMed Central

Knight, Rob; Mazmanian, Sarkis K.; Cryan, John F.; Tillisch, Kirsten

2014-01-01

The discovery of the size and complexity of the human microbiome has resulted in an ongoing reevaluation of many concepts of health and disease, including diseases affecting the CNS. A growing body of preclinical literature has demonstrated bidirectional signaling between the brain and the gut microbiome, involving multiple neurocrine and endocrine signaling mechanisms. While psychological and physical stressors can affect the composition and metabolic activity of the gut microbiota, experimental changes to the gut microbiome can affect emotional behavior and related brain systems. These findings have resulted in speculation that alterations in the gut microbiome may play a pathophysiological role in human brain diseases, including autism spectrum disorder, anxiety, depression, and chronic pain. Ongoing large-scale population-based studies of the gut microbiome and brain imaging studies looking at the effect of gut microbiome modulation on brain responses to emotion-related stimuli are seeking to validate these speculations. This article is a summary of emerging topics covered in a symposium and is not meant to be a comprehensive review of the subject. PMID:25392516

Exopolysaccharides Isolated from Hydrothermal Vent Bacteria Can Modulate the Complement System

PubMed Central

Courtois, Anthony; Berthou, Christian; Guézennec, Jean

2014-01-01

The complement system is involved in the defence against bacterial infection, or in the elimination of tumour cells. However, disturbances in this system contributes to the pathogenesis of various inflammatory diseases. The efficiency of therapeutic anti-tumour antibodies is enhanced when the complement system is stimulated. In contrast, cancer cells are able to inhibit the complement system and thus proliferate. Some marine molecules are currently being developed as new drugs for use in humans. Among them, known exopolyssacharides (EPSs) generally originate from fungi, but few studies have been performed on bacterial EPSs and even fewer on EPSs extracted from deep-sea hydrothermal vent microbes. For use in humans, these high molecular weight EPSs must be depolymerised. Furthermore, the over-sulphation of EPSs can modify their biological activity. The aim of this study was to investigate the immunodulation of the complement system by either native or over-sulphated low molecular weight EPSs isolated from vent bacteria in order to find pro or anti-activators of complement. PMID:24736648

Monitoring marine recreational water quality using multiple microbial indicators in an urban tropical environment

PubMed Central

Shibata, Tomoyuki; Solo-Gabriele, Helena M.; Fleming, Lora E.; Elmir, Samir

2008-01-01

The microbial water quality at two beaches, Hobie Beach and Crandon Beach, in Miami-Dade County, Florida, USA was measured using multiple microbial indicators for the purpose of evaluating correlations between microbes and for identifying possible sources of contamination. The indicator microbes chosen for this study (enterococci, Escherichia coli, fecal coliform, total coliform and C. perfringens) were evaluated through three different sampling efforts. These efforts included daily measurements at four locations during a wet season month and a dry season month, spatially intensive water sampling during low- and high-tide periods, and a sand sampling effort. Results indicated that concentrations did not vary in a consistent fashion between one indicator microbe and another. Daily water quality frequently exceeded guideline levels at Hobie Beach for all indicator microbes except for fecal coliform, which never exceeded the guideline. Except for total coliform, the concentrations of microbes did not change significantly between seasons in spite of the fact that the physical–chemical parameters (rainfall, temperature, pH, and salinity) changed significantly between the two monitoring periods. Spatially intense water sampling showed that the concentrations of microbes were significantly different with distance from the shoreline. The highest concentrations were observed at shoreline points and decreased at offshore points. Furthermore, the highest concentrations of indicator microbe concentrations were observed at high tide, when the wash zone area of the beach was submerged. Beach sands within the wash zone tested positive for all indicator microbes, thereby suggesting that this zone may serve as the source of indicator microbes. Ultimate sources of indicator microbes to this zone may include humans, animals, and possibly the survival and regrowth of indicator microbes due to the unique environmental conditions found within this zone. Overall, the results of this study indicated that the concentrations of indicator microbes do not necessarily correlate with one another. Exceedence of water quality guidelines, and thus the frequency of beach advisories, depends upon which indicator microbe is chosen. PMID:15261551

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome.

PubMed

Warinner, Christina; Speller, Camilla; Collins, Matthew J

2015-01-19

The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.

Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior

USDA-ARS?s Scientific Manuscript database

: It is known that environmental factors can affect the biosynthesis of leaf metabolites. Similarly, specific pairwise plant-microbe interactions modulate specifically the plant’s metabolome by stimulating production of phytoalexins and other defense-related compounds. However, there is no informati...

Gut immunity: Its development and reasons and opportunities for modulation in monogastric production animals

USDA-ARS?s Scientific Manuscript database

The intestine must perform the critical role of nutrient acquisition whilst preventing the passage of undesirable microbes or microbial products from the external environment to sterile body compartments. Various components contribute to antimicrobial defenses in the intestine. The mucus layer(s),...

Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium

PubMed Central

Hill, David R; Huang, Sha; Nagy, Melinda S; Yadagiri, Veda K; Fields, Courtney; Mukherjee, Dishari; Bons, Brooke; Dedhia, Priya H; Chin, Alana M; Tsai, Yu-Hwai; Thodla, Shrikar; Schmidt, Thomas M; Walk, Seth

2017-01-01

The human gastrointestinal tract is immature at birth, yet must adapt to dramatic changes such as oral nutrition and microbial colonization. The confluence of these factors can lead to severe inflammatory disease in premature infants; however, investigating complex environment-host interactions is difficult due to limited access to immature human tissue. Here, we demonstrate that the epithelium of human pluripotent stem-cell-derived human intestinal organoids is globally similar to the immature human epithelium and we utilize HIOs to investigate complex host-microbe interactions in this naive epithelium. Our findings demonstrate that the immature epithelium is intrinsically capable of establishing a stable host-microbe symbiosis. Microbial colonization leads to complex contact and hypoxia driven responses resulting in increased antimicrobial peptide production, maturation of the mucus layer, and improved barrier function. These studies lay the groundwork for an improved mechanistic understanding of how colonization influences development of the immature human intestine. PMID:29110754

Understanding the microbiome: Emerging biomarkers for exploiting the microbiota for personalized medicine against cancer.

PubMed

Rajpoot, Meenakshi; Sharma, Anil K; Sharma, Anil; Gupta, Girish Kumar

2018-02-06

The human body is a home to more than 1 trillion microbes with a diverse variety of commensal microbes that play a crucial role towards the health of the individual. These microbes occupy different habitats such as gut, skin, vagina, oral etc. Not only the types and abundance of microbes are different in different organs, but also these may differ in different individuals. The genome of these microbiota and their ecosystem constitute to form a microbiome. Factors such as diet, environment, host genetics etc. may be the reason behind the wide microbial diversity. A number of studies performed on human microbiome have revealed that microbiota present in healthy and diseased individuals are distinct. Altered microbiome is many a times the reason behind the overexpression of genes which may cause complex diseases including cancer. Manipulation of the human microbiome can be done by microbial supplements such as probiotics or synbiotics, diet or prebiotics and microbial suppression strategies using antibiotics. Recent advances in genome sequencing technologies and metagenomic analysis provide us the broader understanding of these commensal microbes and highlighting the distinctive features of microbiome during healthy and disease states. Molecular pathological epidemiology (MPE) studies have been very helpful in providing insights into the pathological process behind disease evolution and progression by determining the specific etiological factors. New emerging field of research targets the microbiome for therapeutic purposes by which personalized medicines can be made for treating various types of tumors. Screening programmes might be helpful in identifying patients who are at the verge of developing cancer and in delivering appropriate approaches according to individual risk modes so that disease could be prevented. Copyright © 2018 Elsevier Ltd. All rights reserved.

The primate vaginal microbiome: comparative context and implications for human health and disease.

PubMed

Stumpf, Rebecca M; Wilson, Brenda A; Rivera, Angel; Yildirim, Suleyman; Yeoman, Carl J; Polk, John D; White, Bryan A; Leigh, Steven R

2013-12-01

The primate body hosts trillions of microbes. Interactions between primate hosts and these microbes profoundly affect primate physiology, reproduction, health, survival, and ultimately, evolution. It is increasingly clear that primate health cannot be understood fully without knowledge of host-microbial interactions. Our goals here are to review what is known about microbiomes of the female reproductive tract and to explore several factors that influence variation within individuals, as well as within and between primate species. Much of our knowledge of microbial variation derives from studies of humans, and from microbes located in nonreproductive regions (e.g., the gut). We review work suggesting that the vaginal microbiota affects female health, fecundity, and pregnancy outcomes, demonstrating the selective potential for these agents. We explore the factors that correlate with microbial variation within species. Initial colonization by microbes depends on the manner of birth; most microbial variation is structured by estrogen levels that change with age (i.e., at puberty and menopause) and through the menstrual cycle. Microbial communities vary by location within the vagina and can depend on the sampling methods used (e.g., swab, lavage, or pap smear). Interindividual differences also exist, and while this variation is not completely understood, evidence points more to differences in estrogen levels, rather than differences in external physical environment. When comparing across species, reproductive-age humans show distinct microbial communities, generally dominated by Lactobacillus, unlike other primates. We develop evolutionary hypotheses to explain the marked differences in microbial communities. While much remains to be done to test these hypotheses, we argue that the ample variation in primate mating and reproductive behavior offers excellent opportunities to evaluate host-microbe coevolution and adaptation. Copyright © 2013 Wiley Periodicals, Inc.

Breast, milk and microbes: a complex relationship that does not end with lactation.

PubMed

Urbaniak, Camilla; Burton, Jeremy P; Reid, Gregor

2012-07-01

Until relatively recently, the extent of microbiota presence in the human breast was under-appreciated. A high-throughput sequencing study and culture-based studies have demonstrated the extensive presence of microbes in human milk, with their origin believed to be from the skin, oral cavity and via gut translocation. Since formula milk substitutes do not contain these bacteria, what benefits are denied to these infants? The addition of probiotic bacteria to some infant formula is meant to provide some benefits, but these only contain one species and the dose is relatively high compared with breast milk. Many questions of importance to women's health arise from these findings. When, how and what types of microbes colonize the breast at different stages of a woman's life, including postlactation, and what effect do they have on the host in the short and long term? This article discusses some aspects of these questions.

Volatiles of grape inoculated with microorganisms: modulation of grapevine moth oviposition and field attraction

USDA-ARS?s Scientific Manuscript database

Semiochemicals released by plant-microbe associations are used by herbivorous insects to access and evaluate food resources and oviposition sites. Adult insects may utilize microbial-derived nutrients to prolong their lifespan, promote egg development and offer a high nutritional substrate to their ...

Methanol and ethanol modulate responses to danger- and microbe-associated molecular patterns

USDA-ARS?s Scientific Manuscript database

Methanol is a byproduct of cell wall modification, released through the action of pectin methylesterases (PMEs), which demethylesterify cell wall pectins. Plant PMEs play not only a role in developmental processes but also in responses to herbivory and infection by fungal or bacterial pathogens. Mol...

Virulence of Pseudomonas syringae pv. tomato DC3000 is modulated through the Catabolite Repression Control protein Crc

USDA-ARS?s Scientific Manuscript database

Pseudomonas syringae (P.s.) infects diverse plant species and several P.s. pathovars have been used in the study of molecular events that occur during plant-microbe interactions. Although the relationship between bacterial metabolism, nutrient acquisition and virulence has attracted increasing atten...

Gut immune system: a new frontier for nutritional modulation of gut health

USDA-ARS?s Scientific Manuscript database

The gut represents a continuously evolving ecosystem consisting of trillions of commensal bacteria living in symbiosis with the host. The host-microbe interplay plays a crucial role in physiological development and health of the host. There is increasing evidence that shows a dynamic interaction be...

A System Biology Perspective on Environment-Host-Microbe Interactions.

PubMed

Chen, Lianmin; Garmaeva, Sanzhima; Zherankova, Alexandra; Fu, Jingyuan; Wijmenga, Cisca

2018-04-16

A vast, complex and dynamic consortium of microorganisms known as the gut microbiome colonizes the human gut. Over the past few decades we have developed an increased awareness of its important role in human health. In this review we discuss the role of the gut microbiome in complex diseases and the possible causal scenarios behind its interactions with the host genome and environmental factors. We then propose a new analysis framework that combines a systems biology approach, cross-kingdom integration of multiple levels of omics data, and innovative in vitro models to yield an integrated picture of human host-microbe interactions. This new framework will lay the foundation for the development of the next phase in personalized medicine.

Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes

PubMed Central

2012-01-01

The influence of resident gut microbes on xenobiotic metabolism has been investigated at different levels throughout the past five decades. However, with the advance in sequencing and pyrotagging technologies, addressing the influence of microbes on xenobiotics had to evolve from assessing direct metabolic effects on toxins and botanicals by conventional culture-based techniques to elucidating the role of community composition on drugs metabolic profiles through DNA sequence-based phylogeny and metagenomics. Following the completion of the Human Genome Project, the rapid, substantial growth of the Human Microbiome Project (HMP) opens new horizons for studying how microbiome compositional and functional variations affect drug action, fate, and toxicity (pharmacomicrobiomics), notably in the human gut. The HMP continues to characterize the microbial communities associated with the human gut, determine whether there is a common gut microbiome profile shared among healthy humans, and investigate the effect of its alterations on health. Here, we offer a glimpse into the known effects of the gut microbiota on xenobiotic metabolism, with emphasis on cases where microbiome variations lead to different therapeutic outcomes. We discuss a few examples representing how the microbiome interacts with human metabolic enzymes in the liver and intestine. In addition, we attempt to envisage a roadmap for the future implications of the HMP on therapeutics and personalized medicine. PMID:23194438

Understanding the Effects of Host Evolution and Skin Bacteria Composition on Disease Vector Choices

DTIC Science & Technology

2016-04-14

attractiveness of hosts to microbes suggests that if we are to develop a probiotic that deters mosquitoes that its value will depend greatly on the genome of the...influence of a single human gene on the attractiveness of hosts to microbes suggests that if we are to develop a probiotic that deters mosquitoes that

The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae

PubMed Central

Gibbons, John G.; Salichos, Leonidas; Slot, Jason C.; Rinker, David C.; McGary, Kriston L.; King, Jonas G.; Klich, Maren A.; Tabb, David L.; McDonald, W. Hayes; Rokas, Antonis

2012-01-01

Summary The domestication of animals, plants and microbes fundamentally transformed the lifestyle and demography of the human species [1]. Although the genetic and functional underpinnings of animal and plant domestication are well understood, little is known about microbe domestication [2–6]. We systematically examined genome-wide sequence and functional variation between the domesticated fungus Aspergillus oryzae, whose saccharification abilities humans have harnessed for thousands of years to produce sake, soy sauce and miso from starch-rich grains, and its wild relative A. flavus, a potentially toxigenic plant and animal pathogen [7]. We discovered dramatic changes in the sequence variation and abundance profiles of genes and wholesale primary and secondary metabolic pathways between domesticated and wild relative isolates during growth on rice. Through selection by humans, our data suggest that an atoxigenic lineage of A. flavus gradually evolved into a “cell factory” for enzymes and metabolites involved in the saccharification process. These results suggest that whereas animal and plant domestication was largely driven by Neolithic “genetic tinkering” of developmental pathways, microbe domestication was driven by extensive remodeling of metabolism. PMID:22795693

Advances and perspectives in in vitro human gut fermentation modeling.

PubMed

Payne, Amanda N; Zihler, Annina; Chassard, Christophe; Lacroix, Christophe

2012-01-01

The gut microbiota is a highly specialized organ containing host-specific assemblages of microbes whereby metabolic activity directly impacts human health and disease. In vitro gut fermentation models present an unmatched opportunity of performing studies frequently challenged in humans and animals owing to ethical concerns. Multidisciplinary systems biology analyses supported by '-omics' platforms remain widely neglected in the field of in vitro gut fermentation modeling but are key to advancing the significance of these models. Model-driven experimentation using a combination of in vitro gut fermentation and in vitro human cell models represent an advanced approach in identifying complex host-microbe interactions and niches central to gut fermentation processes. The aim of this review is to highlight the advances and challenges exhibited by in vitro human gut fermentation modeling. Copyright © 2011 Elsevier Ltd. All rights reserved.

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

PubMed Central

Warinner, Christina; Speller, Camilla; Collins, Matthew J.

2015-01-01

The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes. PMID:25487328

The interaction of gut microbes with host ABC transporters

PubMed Central

Mercado-Lubo, Regino

2010-01-01

ATP binding cassette (ABC) transporters are increasingly recognized for their ability to modulate the absorption, distribution, metabolism, secretion and toxicity of xenobiotics. In addition to their essential function in drug resistance, there is also emerging evidence documenting the important role ABC transporters play in tissue defense. In this respect, the gastrointestinal tract represents a critical vanguard of defense against oral exposure of drugs while at the same time functions as a physical barrier between the lumenal contents (including bacteria) and the intestinal epithelium. Given emerging evidence suggesting that multidrug resistance protein (MDR) plays an important role in host-bacterial interactions in the gastrointestinal tract, this review will discuss the interplay between MDR of the intestinal epithelial cell barrier and gut microbes in health and disease. In particular, we will explore host-microbe interactions involving three apically restricted ABC transporters of the intestinal epithelium; P-glycoprotein (P-gp), multidrug resistance-associated protein 2 (MRP2) and cystic fibrosis transmembrane regulator (CFTR). PMID:21327038

Wine microbiome: A dynamic world of microbial interactions.

PubMed

Liu, Youzhong; Rousseaux, Sandrine; Tourdot-Maréchal, Raphaëlle; Sadoudi, Mohand; Gougeon, Régis; Schmitt-Kopplin, Philippe; Alexandre, Hervé

2017-03-04

Most fermented products are generated by a mixture of microbes. These microbial consortia perform various biological activities responsible for the nutritional, hygienic, and aromatic qualities of the product. Wine is no exception. Substantial yeast and bacterial biodiversity is observed on grapes, and in both must and wine. The diverse microorganisms present interact throughout the winemaking process. The interactions modulate the hygienic and sensorial properties of the wine. Many studies have been conducted to elucidate the nature of these interactions, with the aim of establishing better control of the two fermentations occurring during wine processing. However, wine is a very complex medium making such studies difficult. In this review, we present the current state of research on microbial interactions in wines. We consider the different kinds of interactions between different microorganisms together with the consequences of these interactions. We underline the major challenges to obtaining a better understanding of how microbes interact. Finally, strategies and methodologies that may help unravel microbe interactions in wine are suggested.

TGF-β in inflammatory bowel disease: a key regulator of immune cells, epithelium, and the intestinal microbiota.

PubMed

Ihara, Sozaburo; Hirata, Yoshihiro; Koike, Kazuhiko

2017-07-01

Inflammatory bowel disease (IBD) is defined as chronic intestinal inflammation, and includes ulcerative colitis and Crohn's disease. Multiple factors are involved in the pathogenesis of IBD, and the condition is characterized by aberrant mucosal immune reactions to intestinal microbes in genetically susceptible hosts. Transforming growth factor-β (TGF-β) is an immune-suppressive cytokine produced by many cell types and activated by integrins. Active TGF-β binds to its receptor and regulates mucosal immune reactions through the TGF-β signaling pathway. Dysregulated TGF-β signaling is observed in the intestines of IBD patients. TGF-β signal impairment in specific cell types, such as T-cells and dendritic cells, results in spontaneous colitis in mouse models. In addition, specific intestinal microbes contribute to immune homeostasis by modulating TGF-β production. In this review, we describe the role of TGF-β in intestinal immunity, focusing on immune cells, epithelium, and intestinal microbes. In addition, we present potential therapeutic strategies for IBD that target TGF-β.

Plant response to biotic stress: Is there a common epigenetic response during plant-pathogenic and symbiotic interactions?

PubMed

Zogli, Prince; Libault, Marc

2017-10-01

Plants constantly interact with pathogenic and symbiotic microorganisms. Recent studies have revealed several regulatory mechanisms controlling these interactions. Among them, the plant defense system is activated not only in response to pathogenic, but also in response to symbiotic microbes. Interestingly, shortly after symbiotic microbial recognition, the plant defense system is suppressed to promote plant infection by symbionts. Research studies have demonstrated the influence of the plant epigenome in modulating both pathogenic and symbiotic plant-microbe interactions, thereby influencing plant survival, adaptation and evolution of the plant response to microbial infections. It is however unclear if plant pathogenic and symbiotic responses share similar epigenomic profiles or if epigenomic changes differentially regulate plant-microbe symbiosis and pathogenesis. In this mini-review, we provide an update of the current knowledge of epigenomic control on plant immune responses and symbiosis, with a special attention being paid to knowledge gap and potential strategies to fill-in the missing links. Copyright © 2017 Elsevier B.V. All rights reserved.

How effectors promote beneficial interactions.

PubMed

Miwa, Hiroki; Okazaki, Shin

2017-08-01

Beneficial microbes such as rhizobia possess effector proteins that are secreted into the host cytoplasm where they modulate host-signaling pathways. Among these effectors, type 3 secreted effectors (T3Es) of rhizobia play roles in promoting nitrogen-fixing nodule symbiosis, suppressing host defenses and directly activating symbiosis-related processes. Rhizobia use the same strategy as pathogenic bacteria to suppress host defenses such as targeting the MAPK cascade. In addition, rhizobial T3E can promote root nodule symbiosis by directly activating Nod factor signaling, which bypasses Nod factor perception. The various strategies employed by beneficial microbes to promote infection and maintain viability in the host are therefore crucial for plant endosymbiosis. Copyright © 2017 Elsevier Ltd. All rights reserved.

The application of the flow cytometry for determination of the action of serotonin on the antigenic composition and amount of DNA of plague microbe cultured at 37°C

NASA Astrophysics Data System (ADS)

Korsukov, Vladimir N.; Schukovskaya, Tatyana N.; Klueva, Svetlana N.; Kravtsov, Alexander L.; Polunina, Tatyana A.; Popov, Youri A.

2003-10-01

The results have been obtained by flow cytometry showed the significant raise of fluorescence intensity of Yersinia pestis EV cells binding FITC-labelled plague polyclonal immunoglobins after 24 h cultivation in Hottinger broth pH 7.2 at 37 °C in the presence of increasing concentration serotonin (5-Hydroxytryptamine). The presence of serotonin (5-HT) in nutrient broth at concentration of 10-5 M, 10-8 M could modulate DNA content in 37 °C growing population of plague microbe. The effect of this action depended of 5-HT concentration.

Human Skin Is the Largest Epithelial Surface for Interaction with Microbes.

PubMed

Gallo, Richard L

2017-06-01

Human skin contains an abundant and diverse population of microbial organisms. Many of these microbes inhabit follicular structures of the skin. Furthermore, numerous studies have shown that the interaction of some members of the skin microbiome with host cells will result in changes in cell function. However, estimates of the potential for the microbiome to influence human health through skin have ignored the inner follicular surface, and therefore vastly underestimated the potential of the skin microbiome to have a systemic effect on the human body. By calculating the surface area of follicular and the interfollicular epithelial surface it is shown that skin provides a vast interface for interactions with the microbiome. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

The roles of the outdoors and occupants in contributing to a potential pan-microbiome of the built environment: a review.

PubMed

Leung, Marcus H Y; Lee, Patrick K H

2016-05-24

Recent high-throughput sequencing technology has led to an expansion of knowledge regarding the microbial communities (microbiome) across various built environments (BEs). The microbiome of the BE is dependent upon building factors and conditions that govern how outdoor microbes enter and persist in the BE. Additionally, occupants are crucial in shaping the microbiome of the BE by releasing human-associated microorganisms and resuspending microbes on floors and surfaces. Therefore, both the outdoors and occupants act as major sources of microorganisms found in the BE. However, most characterizations of the microbiome of the BE have been conducted in the Western world. Notably, outdoor locations and population groups present geographical variations in outdoor and human microbiomes, respectively. Given the influences of the outdoor and human microbiomes on BE microbiology, and the geographical variations in outdoor and human microbiomes, it is likely that the microbiomes of BEs also vary by location. The summation of microbiomes between BEs contribute to a potential BE pan-microbiome, which will both consist of microbes that are ubiquitous in indoor environments around the world, and microbes that appear to be endemic to particular geographical locations. Importantly, the BE pan-microbiome can potentially question the global application of our current views on indoor microbiology. In this review, we first provide an assessment on the roles of building and occupant properties on shaping the microbiome of the BE. This is then followed by a description of geographical variations in the microbiomes of the outdoors and humans, the two main sources of microbes in BEs. We present evidence of differences in microbiomes of BEs around the world, demonstrating the existence of a global pan-microbiome of the BE that is larger than the microbiome of any single indoor environment. Finally, we discuss the significance of understanding the BE pan-microbiome and identifying universal and location-specific relationships between building and occupant characteristics and indoor microbiology. This review highlights the much needed efforts towards determining the pan-microbiome of the BE, thereby identifying general and location-specific links between the microbial communities of the outdoors, human, and BE ecosystems, ultimately improving the health, comfort, and productivity of occupants around the world.

Four-year bacterial monitoring in the International Space Station-Japanese Experiment Module "Kibo" with culture-independent approach.

PubMed

Ichijo, Tomoaki; Yamaguchi, Nobuyasu; Tanigaki, Fumiaki; Shirakawa, Masaki; Nasu, Masao

2016-01-01

Studies on the relationships between humans and microbes in space habitation environments are critical for success in long-duration space missions, to reduce potential hazards to the crew and the spacecraft infrastructure. We performed microbial monitoring in the Japanese Experiment Module "Kibo", a part of the International Space Station, for 4 years after its completion, and analyzed samples with modern molecular microbiological techniques. Sampling was performed in September 2009, February 2011, and October 2012. The surface of the incubator, inside the door of the incubator, an air intake, air diffuser, and handrail were selected as sampling sites. Sampling was performed using the optimized swabbing method. Abundance and phylogenetic affiliation of bacteria on the interior surfaces of Kibo were determined by quantitative PCR and pyrosequencing, respectively. Bacteria in the phyla Proteobacteria (γ-subclass) and Firmicutes were frequently detected on the interior surfaces in Kibo. Families Staphylococcaceae and Enterobacteriaceae were dominant. Most bacteria detected belonged to the human microbiota; thus, we suggest that bacterial cells are transferred to the surfaces in Kibo from the astronauts. Environmental bacteria such as Legionella spp. were also detected. From the data on bacterial abundance and phylogenetic affiliation, Kibo has been microbiologically well maintained; however, the microbial community structure in Kibo may change with prolonged stay of astronauts. Continuous monitoring is required to obtain information on changes in the microbial community structure in Kibo.

Beyond DNA Sequencing in Space: Current and Future Omics Capabilities of the Biomolecule Sequencer Payload

NASA Technical Reports Server (NTRS)

Wallace, Sarah

2017-01-01

Why do we need a DNA sequencer to support the human exploration of space? (A) Operational environmental monitoring; (1) Identification of contaminating microbes, (2) Infectious disease diagnosis, (3) Reduce down mass (sample return for environmental monitoring, crew health, etc.). (B) Research; (1) Human, (2) Animal, (3) Microbes/Cell lines, (4) Plant. (C) Med Ops; (1) Response to countermeasures, (2) Radiation, (3) Real-time analysis can influence medical intervention. (C) Support astrobiology science investigations; (1) Technology superiorly suited to in situ nucleic acid-based life detection, (2) Functional testing for integration into robotics for extraplanetary exploration mission.

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis.

PubMed

Cross, Karissa L; Chirania, Payal; Xiong, Weili; Beall, Clifford J; Elkins, James G; Giannone, Richard J; Griffen, Ann L; Guss, Adam M; Hettich, Robert L; Joshi, Snehal S; Mokrzan, Elaine M; Martin, Roman K; Zhulin, Igor B; Leys, Eugene J; Podar, Mircea

2018-03-13

The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously uncultured Desulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives, D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury were also lost by D. oralis , a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. IMPORTANCE Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing. Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome "dark matter," cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.

Impacts of Human Activity on the Microbial Communities of Devon Island, Canadian High Arctic

NASA Astrophysics Data System (ADS)

Bywaters, K. B.; Burton, A. S.; Wallace, S. L.; Glass, B. J.

2016-09-01

The impacts of human activities on microbial communities in arctic environments are poorly understood. This project compares the distribution of microbes at the HMP Mars analog site prior to and after human settlement.

Tanpopo: Astrobiology Exposure and Micrometeoroid Capture Experiments

NASA Astrophysics Data System (ADS)

Yamagishi, Akihiko; Yano, Hajime; Yamashita, Masamichi; Hashimoto, Hirofumi; Kobayashi, Kensei; Kawai, Hideyuki; Mita, Hajime; Yokobori, Shin-ichi; Tabata, Makoto; Yabuta, Hikaru

2012-07-01

There is a long history of the microbe-collection experiments at high altitude (1). Microbes have been collected using balloons, aircraft and meteorological rockets. Spore forming fungi and Bacilli, and Micrococci have been isolated in these experiments (1). It is not clear how high do microbes go up. If the microbes might have been present even at higher altitudes, the fact would endorse the possibility of interplanetary migration of life. Tanpopo, dandelion, is the name of a grass whose seeds with floss are spread by the wind. We propose the analyses of interplanetary migration of microbes, organic compounds and meteoroids on Japan Experimental Module (JEM) of the International Space Station (ISS) (2). Ultra low-density aerogel will be used to capture micrometeoroid and debris. Particles captured by aerogel will be used for several analyses after the initial inspection of the gel and tracks. Careful analysis of the tracks in the aerogel will provide the size and velocity dependence of debris flux. The particles will be analyzed for mineralogical, organic and microbiological characteristics. Aerogels are ready for production in Japan. Aerogels and trays are space proven. All the analytical techniques are ready. In this presentation, we will present the recent results related to the microbiological analyses. The results suggested that the bleaching speeds and the spectra of fluorescence are different between different origins of the fluorescence: whether it is emitted from microbe or not. It is also shown that PCR analysis of the microbe can be used to determine the species. References 1)Yang, Y., Yokobori, S. and Yamagishi, A.: Assessing panspermia hypothesis by microorganisms collected from the high altitude atmosphere. Biol. Sci. Space, 23 (2009), pp. 151-163. 2) Yamagishi, A., H. Yano, K. Kobayashi, K. Kobayashi, S. Yokobori, M. Tabata, H. Kawai, M. Yamashita, H. Hashimoto, H. Naraoka, & H. Mita (2008) TANPOPO: astrobiology exposure and micrometeoroid capture experiments. International Symposium on Space Technology and Science (ISTS) Web Paper Archives. 2008-k-05.

Tanpopo: Astrobiology exposure and micrometeoroid capture experiments

NASA Astrophysics Data System (ADS)

Yamagishi, Akihiko; Yano, Hajime; Okudaira, Kyoko; Kobayashi, Kensei; Yokobori, Shin-Ichi; Kawai, Hideyuki; Yamashita, Masamichi; Hashimoto, Hirofumi; Yabuta, Hikaru

There is a long history of the microbe-collection experiments at high altitude (1). Microbes have been collected using balloons, aircraft and meteorological rockets. Spore forming fungi and Bacilli, and Micrococci have been isolated in these experiments (1). It is not clear how high do microbes go up. If the microbes might have been present even at higher altitudes, the fact would endorse the possibility of interplanetary migration of life. Tanpopo, dandelion, is the name of a grass whose seeds with floss are spread by the wind. We propose the analyses of interplanetary migration of microbes, organic compounds and meteoroids on Japan Experimental Module (JEM) of the International Space Station (ISS) (2). Ultra low-density aerogel will be used to capture micrometeoroid and debris. Particles captured by aerogel will be used for several analyses after the initial inspection of the gel and tracks. Careful analysis of the tracks in the aerogel will provide the size and velocity dependence of debris flux. The particles will be analyzed for mineralogical, organic and microbiological characteristics. Aerogels are ready for production in Japan. Aerogels and trays are space proven. All the analytical techniques are ready. In this presentation, we will present the recent results related to the microbiological analyses. The results suggested that the bleaching speeds and the spectra of fluorescence are different between different origins of the fluorescence: whether it is emitted from microbe or not. It is also shown that PCR analysis of the microbe can be used to determine the species. References 1)Yang, Y., Yokobori, S. and Yamagishi, A.: Assessing panspermia hypothesis by microorganisms collected from the high altitude atmosphere. Biol. Sci. Space, 23 (2009), pp. 151-163. 2) Yamagishi, A., H. Yano, K. Kobayashi, K. Kobayashi, S. Yokobori, M. Tabata, H. Kawai, M. Yamashita, H. Hashimoto, H. Naraoka, H. Mita (2008) TANPOPO: astrobi-ology exposure and micrometeoroid capture experiments. International Symposium on Space Technology and Science (ISTS) Web Paper Archives. 2008-k-05.

Investigation of detection conditions of captured microbes in space with PCR Microbes capture experiment on ISS proposed in "Tanpopo" mission

NASA Astrophysics Data System (ADS)

Kawaguchi, Yuko; Sugino, Tomohiro; Yang, Yinjie; Yoshimura, Yoshitaka; Tsuji, Takashi; Kobayashi, Kensei; Tabata, Makoto; Hashimoto, Hirofumi; Mita, Hajime; Imai, Eiichi; Kawai, Hideyuki; Okudaira, Kyoko; Hasegawa, Sunao; Yamashita, Masamichi; Yano, Hajime; Yokobori, Shin-Ichi; Yamagishi, Akihiko

Terrestrial life may fly off into outer space by volcanic eruption meteorological impacts, and so on. Microbes have been collected from high altitude up to 70 km since 1936 [1]. We also isolated microbes at high altitude up to 35 km using an airplane and balloons [2, 3]. The two isolates of these microbes are new species, one of which shows higher UV ray tolerance than Deinococcus radiodurans [2, 3]. On the other hand, there is a hypothesis on the origin of terrestrial life called panspermia [4, 5], in which terrestrial life is thought to have come from space (or astronomical bodies other than Earth). This hypothesis suggests that life may migrate between Earth and other planets. If microbes were to exist at the high altitude of low earth orbit (400 km), it would endorse the possibility of interplanetary migration of terrestrial lifeWe proposed, the Tanpopo mission to examine interplanetary migration of microbes and organic compounds on Japan Experimental Module (JEM) of the International Space Station (ISS). We will capture micro-particles including microbes and micro-meteoroids at the altitude of ISS orbit (400 km) with ultra low-density aerogel exposed to space for a given period of time. After retreaving the aerogel, we will investigate captured micro particles and tracks followed by microbiological, organic chemical and mineralogical analyses.Captured particles will be analyzed after the initial curation of the aerogel and tracks. Particles potentially containing microbes will be used for PCR amplification of small subunit (ss) rRNA gene followed by DNA sequencing. Comparision between the determined sequences and known ss rRNA gene sequences of terrestrial organisms will suggest the origin and properties of the organism.The density of microbes at the ISS altitude might be quite low, and microbe cell number on each captured particle may be quite limited. Therefore, it is necessary to establish the effective PCR procedure for quite small amount of DNA template in the presence of other materials such as clay and aerogel.We will report current status of the PCR identification of microbes from test samples. The PCR conditions to amplify ss rRNA gene from quite small number of cells and quite low concentration of genomic DNA with/without clay and aerogel are examined. References. [1] Y. Yang et al. (2009) Biol. Sci. in Space, 23, 151-163[2] Y. Yang et al. (2009) Int. J. Syst. Evol. Microbiol, 59, 1862-1866[3] Y. Yang et al. (2010) Int. J. Syst. Evol. Microbiol, (in press)[4] S. Arrhenius (1908) Worlds in the Making-the Evolution of the Universe. Harper and Brothers Publishers.[5] F. Crick (1981) Life Itself. Simon Schuster.

A Hair & a Fungus: Showing Kids the Size of a Microbe

ERIC Educational Resources Information Center

Richter, Dana L.

2013-01-01

A simple method is presented to show kids the size of a microbe--a fungus hypha--compared to a human hair. Common household items are used to make sterile medium on a stove or hotplate, which is dispensed in the cells of a weekly plastic pill box. Mold fungi can be easily and safely grown on the medium from the classroom environment. A microscope…

Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma.

PubMed

Pérez-Losada, Marcos; Castro-Nallar, Eduardo; Bendall, Matthew L; Freishtat, Robert J; Crandall, Keith A

2015-01-01

High-throughput sequencing (HTS) analysis of microbial communities from the respiratory airways has heavily relied on the 16S rRNA gene. Given the intrinsic limitations of this approach, airway microbiome research has focused on assessing bacterial composition during health and disease, and its variation in relation to clinical and environmental factors, or other microbiomes. Consequently, very little effort has been dedicated to describing the functional characteristics of the airway microbiota and even less to explore the microbe-host interactions. Here we present a simultaneous assessment of microbiome and host functional diversity and host-microbe interactions from the same RNA-seq experiment, while accounting for variation in clinical metadata. Transcriptomic (host) and metatranscriptomic (microbiota) sequences from the nasal epithelium of 8 asthmatics and 6 healthy controls were separated in silico and mapped to available human and NCBI-NR protein reference databases. Human genes differentially expressed in asthmatics and controls were then used to infer upstream regulators involved in immune and inflammatory responses. Concomitantly, microbial genes were mapped to metabolic databases (COG, SEED, and KEGG) to infer microbial functions differentially expressed in asthmatics and controls. Finally, multivariate analysis was applied to find associations between microbiome characteristics and host upstream regulators while accounting for clinical variation. Our study showed significant differences in the metabolism of microbiomes from asthmatic and non-asthmatic children for up to 25% of the functional properties tested. Enrichment analysis of 499 differentially expressed host genes for inflammatory and immune responses revealed 43 upstream regulators differentially activated in asthma. Microbial adhesion (virulence) and Proteobacteria abundance were significantly associated with variation in the expression of the upstream regulator IL1A; suggesting that microbiome characteristics modulate host inflammatory and immune systems during asthma.

Insights into the Roles of Gut Microbes in Obesity

PubMed Central

Sanz, Yolanda; Santacruz, Arlette; De Palma, Giada

2008-01-01

Obesity is a major public health issue as it enhances the risk of suffering several chronic diseases of increasing prevalence. Obesity results from an imbalance between energy intake and expenditure, associated with a chronic low-grade inflammation. Gut microbes are considered to contribute to body weight regulation and related disorders by influencing metabolic and immune host functions. The gut microbiota as a whole improves the host's ability to extract and store energy from the diet leading to body weight gain, while specific commensal microbes seem to exert beneficial effects on bile salt, lipoprotein, and cholesterol metabolism. The gut microbiota and some probiotics also regulate immune functions, protecting the host form infections and chronic inflammation. In contrast, dysbiosis and endotoxaemia may be inflammatory factors responsible for developing insulin resistance and body weight gain. In the light of the link between the gut microbiota, metabolism, and immunity, the use of dietary strategies to modulate microbiota composition is likely to be effective in controlling metabolic disorders. Although so far only a few preclinical and clinical trials have demonstrated the effects of specific gut microbes and prebiotics on biological markers of these disorders, the findings indicate that advances in this field could be of value in the struggle against obesity and its associated-metabolic disorders. PMID:19259329

Twelve testable hypotheses on the geobiology of weathering

Treesearch

S.L. Brantley; J.P. Megonigal; F.N. Scatena; Z. Balogh-Brunstad; R.T. Barnes; M.A. Bruns; P. van Cappelen; K. Dontsova; H.E. Hartnett; A.S. Hartshorn; A. Heimsath; E. Herndon; L. Jin; C.K. Keller; J.R. Leake; W.H. McDowell; F.C. Meinzer; T.J. Mozdzer; S. Petsch; J. Pett-Ridge; K.S. Pretziger; P.A. Raymond; C.S. Riebe; K. Shumaker; A. Sutton-Grier; R. Walter; K. Yoo

2011-01-01

Critical Zone (CZ) research investigates the chemical, physical, and biological processes that modulate the Earth's surface. Here, we advance 12 hypotheses that must be tested to improve our understanding of the CZ: (1) Solar-to-chemical conversion of energy by plants regulates flows of carbon, water, and nutrients through plant-microbe soil networks, thereby...

Root and bacterial secretions regulate the interaction between plants and PGPR leading to distinct plant growth promotion effects

USDA-ARS?s Scientific Manuscript database

Plant growth-promoting rhizobacteria (PGPR) have garnered interest in agriculture due to their ability to influence the growth and production of host plants. ATP-binding cassette (ABC) transporters play important roles in plant-microbe interactions by modulating plant root exudation. The present stu...

[The origin of hydrogen peroxide in oral cavity and its role in oral microecology balance].

PubMed

Keke, Zhang; Xuedong, Zhou; Xin, Xu

2017-04-01

Hydrogen peroxide, an important antimicrobial agent in oral cavity, plays a significant role in the balance of oral microecology. At the early stage of biofilm formation, about 80% of the detected initial colonizers belong to the genus Streptococcus. These oral streptococci use different oxidase to produce hydrogen peroxide. Recent studies showed that the produced hydrogen peroxide plays a critical role in modulating oral microecology. Hydrogen peroxide modulates biofilm development attributed to its growth inhibitory nature. Hydrogen peroxide production is closely associated with extracellular DNA(eDNA) release from microbe and the development of its competent cell which are critical for biofilm development and also serves as source for horizontal gene transfer. Microbe also can reduce the damage to themselves through several detoxification mechanisms. Moreover, hydrogen peroxide is also involved in the regulation of interactions between oral microorganisms and host. Taken together, hydrogen peroxide is an imperative ecological factor that contributes to the microbial equilibrium in the oral cavity. Here we will give a brief review of both the origin and the function in the oral microecology balance of hydrogen peroxide.

The Role of the Polymeric Immunoglobulin Receptor and Secretory Immunoglobulins during Mucosal Infection and Immunity.

PubMed

Turula, Holly; Wobus, Christiane E

2018-05-03

The gastrointestinal tract houses millions of microbes, and thus has evolved several host defense mechanisms to keep them at bay, and prevent their entry into the host. One such mucosal surface defense is the secretion of secretory immunoglobulins (SIg). Secretion of SIg depends on the polymeric immunoglobulin receptor (pIgR), which transports polymeric Ig (IgA or IgM) from the basolateral surface of the epithelium to the apical side. Upon reaching the luminal side, a portion of pIgR, called secretory component (SC) is cleaved off to release Ig, forming SIg. Through antigen-specific and non-specific binding, SIg can modulate microbial communities and pathogenic microbes via several mechanisms: agglutination and exclusion from the epithelial surface, neutralization, or via host immunity and complement activation. Given the crucial role of SIg as a microbial scavenger, some pathogens also evolved ways to modulate and utilize pIgR and SIg to facilitate infection. This review will cover the regulation of the pIgR/SIg cycle, mechanisms of SIg-mediated mucosal protection as well as pathogen utilization of SIg.

Got bacteria? The astounding, yet not-so-surprising, microbiome of human milk.

PubMed

McGuire, Michelle K; McGuire, Mark A

2017-04-01

Contrary to long-held dogma, human milk is not sterile. Instead, it provides infants a rich source of diverse bacteria, particularly microbes belonging to the Staphylococcus, Streptococcus, and Pseudomonas genera. Very little is known about factors that influence variation in the milk microbiome among women and populations, although time postpartum, delivery mode, and maternal factors such as diet and antibiotic use might be important. The origins of the bacteria in milk are thought to include the maternal gastrointestinal tract (via an entero-mammary pathway) and through bacterial exposure of the breast during nursing. Currently, almost nothing is known about whether variation in microbe consumption by the infant via human milk and that of the mammary gland, itself, impacts short-term and/or long-term infant and maternal health although several studies suggest this is likely. We urge the clinical and public health communities to be patient, however, in order to allow human milk and lactation researchers to first understand what constitutes 'normal' in terms of the milk microbiome (as well as factors that impact microbial community structure) prior to jumping the gun to investigate if and how this important source of microbes impacts maternal and infant health. Copyright © 2016. Published by Elsevier Ltd.

“I Am I and My Bacterial Circumstances”: Linking Gut Microbiome, Neurodevelopment, and Depression

PubMed Central

Lima-Ojeda, Juan M.; Rupprecht, Rainer; Baghai, Thomas C.

2017-01-01

Recently, there has been renewed interest in the role played by microbiome in both human health and human disease. A correct equilibrium between the human host and their microorganisms is important for an appropriate physiological function. Extensive research has shown that microbes that inhabit the gastrointestinal tract—or gut microbiota—are involved not only in both nutritive and digestive activities but also in immunological processes. Moreover, the gut microbiome influences both central nervous system and energy homeostasis. An altered gut microbiome has been associated with the pathophysiology of different diseases, including neuropsychiatric disorders. Apparently, both environmental—diet, exposition to antibiotics, and infections—and host-genetic factors have a strong influence on gut microbiome, modulating the risk for neuropsychiatric illness. Also, early life disruption of the microbiome–gut–brain (MGB) axis has been associated with an increased risk of developing depression later in life, suggesting a link between gut microbiome, neurodevelopment, and depression. This review aims to contribute to this growing area of research by exploring the role played by the gut microbiome in neurodevelopment and in the etiology of the depressive syndrome, including nutritional, immunological, and energy homeostasis approaches. PMID:28878696

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

PubMed Central

Magnúsdóttir, Stefanía; Ravcheev, Dmitry; de Crécy-Lagard, Valérie; Thiele, Ines

2015-01-01

The human gut microbiota supplies its host with essential nutrients, including B-vitamins. Using the PubSEED platform, we systematically assessed the genomes of 256 common human gut bacteria for the presence of biosynthesis pathways for eight B-vitamins: biotin, cobalamin, folate, niacin, pantothenate, pyridoxine, riboflavin, and thiamin. On the basis of the presence and absence of genome annotations, we predicted that each of the eight vitamins was produced by 40–65% of the 256 human gut microbes. The distribution of synthesis pathways was diverse; some genomes had all eight biosynthesis pathways, whereas others contained no de novo synthesis pathways. We compared our predictions to experimental data from 16 organisms and found 88% of our predictions to be in agreement with published data. In addition, we identified several pairs of organisms whose vitamin synthesis pathway pattern complemented those of other organisms. This analysis suggests that human gut bacteria actively exchange B-vitamins among each other, thereby enabling the survival of organisms that do not synthesize any of these essential cofactors. This result indicates the co-evolution of the gut microbes in the human gut environment. Our work presents the first comprehensive assessment of the B-vitamin synthesis capabilities of the human gut microbiota. We propose that in addition to diet, the gut microbiota is an important source of B-vitamins, and that changes in the gut microbiota composition can severely affect our dietary B-vitamin requirements. PMID:25941533

Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes.

PubMed

Hehemann, Jan-Hendrik; Kelly, Amelia G; Pudlo, Nicholas A; Martens, Eric C; Boraston, Alisdair B

2012-11-27

Humans host an intestinal population of microbes--collectively referred to as the gut microbiome--which encode the carbohydrate active enzymes, or CAZymes, that are absent from the human genome. These CAZymes help to extract energy from recalcitrant polysaccharides. The question then arises as to if and how the microbiome adapts to new carbohydrate sources when modern humans change eating habits. Recent metagenome analysis of microbiomes from healthy American, Japanese, and Spanish populations identified putative CAZymes obtained by horizontal gene transfer from marine bacteria, which suggested that human gut bacteria evolved to degrade algal carbohydrates-for example, consumed in form of sushi. We approached this hypothesis by studying such a polysaccharide utilization locus (PUL) obtained by horizontal gene transfer by the gut bacterium Bacteroides plebeius. Transcriptomic and growth experiments revealed that the PUL responds to the polysaccharide porphyran from red algae, enabling growth on this carbohydrate but not related substrates like agarose and carrageenan. The X-ray crystallographic and biochemical analysis of two proteins encoded by this PUL, BACPLE_01689 and BACPLE_01693, showed that they are β-porphyranases belonging to glycoside hydrolase families 16 and 86, respectively. The product complex of the GH86 at 1.3 Å resolution highlights the molecular details of porphyran hydrolysis by this new porphyranase. Combined, these data establish experimental support for the argument that CAZymes and associated genes obtained from extrinsic microbes add new catabolic functions to the human gut microbiome.

Staphylococcus aureus Colonization: Modulation of Host Immune Response and Impact on Human Vaccine Design

PubMed Central

Brown, Aisling F.; Leech, John M.; Rogers, Thomas R.; McLoughlin, Rachel M.

2014-01-01

In apparent contrast to its invasive potential Staphylococcus aureus colonizes the anterior nares of 20–80% of the human population. The relationship between host and microbe appears particularly individualized and colonization status seems somehow predetermined. After decolonization, persistent carriers often become re-colonized with their prior S. aureus strain, whereas non-carriers resist experimental colonization. Efforts to identify factors facilitating colonization have thus far largely focused on the microorganism rather than on the human host. The host responds to S. aureus nasal colonization via local expression of anti-microbial peptides, lipids, and cytokines. Interplay with the co-existing microbiota also influences colonization and immune regulation. Transient or persistent S. aureus colonization induces specific systemic immune responses. Humoral responses are the most studied of these and little is known of cellular responses induced by colonization. Intriguingly, colonized patients who develop bacteremia may have a lower S. aureus-attributable mortality than their non-colonized counterparts. This could imply a staphylococcal-specific immune “priming” or immunomodulation occurring as a consequence of colonization and impacting on the outcome of infection. This has yet to be fully explored. An effective vaccine remains elusive. Anti-S. aureus vaccine strategies may need to drive both humoral and cellular immune responses to confer efficient protection. Understanding the influence of colonization on adaptive response is essential to intelligent vaccine design, and may determine the efficacy of vaccine-mediated immunity. Clinical trials should consider colonization status and the resulting impact of this on individual patient responses. We urgently need an increased appreciation of colonization and its modulation of host immunity. PMID:24409186

Environmental microbiology as a mosaic of explored ecosystems and issues.

PubMed

Faure, Denis; Bonin, Patricia; Duran, Robert

2015-09-01

Microbes are phylogenetically (Archaea, Bacteria, Eukarya, and viruses) and functionally diverse. They colonize highly varied environments and rapidly respond to and evolve as a response to local and global environmental changes, including those induced by pollutants resulting from human activities. This review exemplifies the Microbial Ecology EC2CO consortium's efforts to explore the biology, ecology, diversity, and roles of microbes in aquatic and continental ecosystems.

Microbe Detector

NASA Technical Reports Server (NTRS)

1985-01-01

Under NASA contracts, McDonnell Douglas developed a microbial load monitor to detect bacterial contamination. Vitek Systems, Inc., a subsidiary, was created to commercialize the product for analyzing body fluids. With the AutoMicrobic System, infections may be treated more quickly. The process involves injecting the fluid into identification cards and screening the reaction. Antibiotic treatments are also suggested. Time in hospital and human error is reduced. There are also possible industrial and environmental applications.

Gut microbiota and immunopathogenesis of diabetes mellitus type 1 and 2.

PubMed

Wang, Fei; Zhang, Chunfang; Zeng, Qiang

2016-06-01

Diabetes mellitus (DM) is a major increasing global health burden in the aging population. Understanding the etiology of DM is beneficial for its prevention as well as treatment. In light of the metagenome hypothesis, defined as the overall bacterial genome, gut microbes have attracted increasing attention in the pathogenesis of DM. Many studies have found that gut microbes are involved in the immunopathogenesis of DM. Probiotics strengthen the host's intestinal barrier and modulate the immune system, and have therefore been investigated in DM management. Recent epigenetic findings in context of genes associated with inflammation suggest a possible way in which gut microbiota participate in the immunopathogenesis of DM. In this review, we discuss the role of gut microbiota in the immunopathogenesis of DM.

Laser intensity modulated real time monitoring cell growth sensor for bioprocess applications

NASA Astrophysics Data System (ADS)

Kishore, P.; Babu, P. Ravindra; Devi, V. Rama; Maunika, T.; Soujanya, P.; Kishore, P. V. N.; Dinakar, D.

2016-04-01

This article proposes an optical method for monitoring the growth of Escherichia coli in Luria Bertani medium and Saccharomyces cereviciae in YPD. Suitable light is selected which on interaction with the analyte under consideration, gets adsorption / scattered. Required electronic circuitry is designed to drive the laser source and to detect the intensity of light using Photo-detector. All these components are embedded and arranged in a proper way and monitored the growth of the microbs in real time. The sensors results are compared with standard techniques such as colorimeter, Nephelometer and hemocytometer. The experimental results are in good agreement with the existed techniques and well suitable for real time monitoring applications of the growth of the microbs.

Reciprocal Interactions of the Intestinal Microbiota and Immune System

PubMed Central

Maynard, Craig L.; Elson, Charles O.; Hatton, Robin D.; Weaver, Casey T.

2013-01-01

Preface Emergence of the adaptive immune system in vertebrates set the stage for evolution of an advanced symbiotic relationship with the intestinal microbiota. The defining features of specificity and memory that characterize adaptive immunity have afforded vertebrates mechanisms for efficiently tailoring immune responses to diverse types of microbes, whether to promote mutualism or host defense. These same attributes carry risk for immune-mediated diseases that are increasingly linked to the intestinal microbiota. Understanding how the adaptive immune system copes with the remarkable number and diversity of microbes that colonize the digestive tract, and how it integrates with more primitive innate immune mechanisms to maintain immune homeostasis, holds considerable promise for new approaches to modulate immune networks in order to treat and prevent disease. PMID:22972296

The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure?

PubMed Central

Al Khodor, Souhaila; Reichert, Bernd; Shatat, Ibrahim F.

2017-01-01

The surfaces of the human body are heavily populated by a highly diverse microbial ecosystem termed the microbiota. The largest and richest among these highly heterogeneous populations of microbes is the gut microbiota. The collection of microbes and their genes, called the microbiome, has been studied intensely through the past few years using novel metagenomics, metatranscriptomics, and metabolomics approaches. This has enhanced our understanding of how the microbiome affects our metabolic, immunologic, neurologic, and endocrine homeostasis. Hypertension is a leading cause of cardiovascular disease worldwide; it contributes to stroke, heart disease, kidney failure, premature death, and disability. Recently, studies in humans and animals have shown that alterations in microbiota and its metabolites are associated with hypertension and atherosclerosis. In this review, we compile the recent findings and hypotheses describing the interplay between the microbiome and blood pressure, and we highlight some prospects by which utilization of microbiome-related techniques may be incorporated to better understand the pathophysiology and treatment of hypertension. PMID:28674682

Collective decision-making in microbes

PubMed Central

Ross-Gillespie, Adin; Kümmerli, Rolf

2014-01-01

Microbes are intensely social organisms that routinely cooperate and coordinate their activities to express elaborate population level phenotypes. Such coordination requires a process of collective decision-making, in which individuals detect and collate information not only from their physical environment, but also from their social environment, in order to arrive at an appropriately calibrated response. Here, we present a conceptual overview of collective decision-making as it applies to all group-living organisms; we introduce key concepts and principles developed in the context of animal and human group decisions; and we discuss, with appropriate examples, the applicability of each of these concepts in microbial contexts. In particular, we discuss the roles of information pooling, control skew, speed vs. accuracy trade-offs, local feedbacks, quorum thresholds, conflicts of interest, and the reliability of social information. We conclude that collective decision-making in microbes shares many features with collective decision-making in higher taxa, and we call for greater integration between this fledgling field and other allied areas of research, including in the humanities and the physical sciences. PMID:24624121

Food: a new form of personalised (gut microbiome) medicine for chronic diseases?

PubMed

Pallister, Tess; Spector, Tim D

2016-09-01

Filling in the knowledge gaps between what we eat and the diseases we develop may lie in our guts, literally. The human large intestine houses the largest reservoir of microorganisms in or on the human body. With a 100-fold greater gene count than humans, the gut microbiome has huge potential to place a large metabolic burden (or advantage) on its host. The number of diverse gut microbial species is diminished in nearly all modern chronic conditions studied. The 'Western diet', rich in animal protein, fats and artificial additives, and lacking in fibre, beneficial microbes, plant phytochemicals, vitamins and minerals, is thought to drive these conditions by encouraging gut dysbiosis. Evidence from recent dietary intervention studies suggest adopting a plant-based, minimally processed high-fibre diet may rapidly reverse the effects of meat-based diets on the gut microbiome. However, recent work has shown that individual diet responses may be complicated by host genetics and the wide variation in the gut microbiome. Now that we measure genes and microbes more accurately, we are embarking on an exciting era of using both food and microbes as potential therapies. © The Royal Society of Medicine.

Prebiotics as a modulator of gut microbiota in paediatric obesity.

PubMed

Nicolucci, A C; Reimer, R A

2017-08-01

This review highlights our current understanding of the role of gut microbiota in paediatric obesity and the potential role for dietary manipulation of the gut microbiota with prebiotics in managing paediatric obesity. The aetiology of obesity is multifactorial and is now known to include microbial dysbiosis in the gut. Prebiotics are non-digestible carbohydrates which selectively modulate the number and/or composition of gut microbes. The goal of prebiotic consumption is to restore symbiosis and thereby confer health benefits to the host. There is convincing evidence that prebiotics can reduce adiposity and improve metabolic health in preclinical rodent models. Furthermore, there are several clinical trials in adult humans highlighting metabolic and appetite-regulating benefits of prebiotics. In paediatric obesity, however, there are very limited data regarding the potential role of prebiotics as a dietary intervention for obesity management. As the prevalence of paediatric obesity and obesity-associated comorbidities increases globally, interventions that target the progression of obesity from an early age are essential in slowing the obesity epidemic. This review emphasizes the need for further research assessing the role of prebiotics, particularly as an intervention in effectively managing paediatric obesity. © 2016 World Obesity Federation.

Gut epithelial inducible heat-shock proteins and their modulation by diet and the microbiota

PubMed Central

Arnal, Marie-Edith

2016-01-01

The epidemic of metabolic diseases has raised questions about the interplay between the human diet and the gut and its microbiota. The gut has two vital roles: nutrient absorption and intestinal barrier function. Gut barrier defects are involved in many diseases. Excess energy intake disturbs the gut microbiota and favors body entry of microbial compounds that stimulate chronic metabolic inflammation. In this context, the natural defense mechanisms of gut epithelial cells and the potential to boost them nutritionally warrant further study. One such important defense system is the activation of inducible heat-shock proteins (iHSPs) which protect the gut epithelium against oxidative stress and inflammation. Importantly, various microbial components can induce the expression of iHSPs. This review examines gut epithelial iHSPs as the main targets of microbial signals and nutrients and presents data on diseases involving disturbances of gut epithelial iHSPs. In addition, a broad literature analysis of dietary modulation of gut epithelial iHSPs is provided. Future research aims should include the identification of gut microbes that can optimize gut-protective iHSPs and the evaluation of iHSP-mediated health benefits of nutrients and food components. PMID:26883882

Gut microbes and the brain: paradigm shift in neuroscience.

PubMed

Mayer, Emeran A; Knight, Rob; Mazmanian, Sarkis K; Cryan, John F; Tillisch, Kirsten

2014-11-12

The discovery of the size and complexity of the human microbiome has resulted in an ongoing reevaluation of many concepts of health and disease, including diseases affecting the CNS. A growing body of preclinical literature has demonstrated bidirectional signaling between the brain and the gut microbiome, involving multiple neurocrine and endocrine signaling mechanisms. While psychological and physical stressors can affect the composition and metabolic activity of the gut microbiota, experimental changes to the gut microbiome can affect emotional behavior and related brain systems. These findings have resulted in speculation that alterations in the gut microbiome may play a pathophysiological role in human brain diseases, including autism spectrum disorder, anxiety, depression, and chronic pain. Ongoing large-scale population-based studies of the gut microbiome and brain imaging studies looking at the effect of gut microbiome modulation on brain responses to emotion-related stimuli are seeking to validate these speculations. This article is a summary of emerging topics covered in a symposium and is not meant to be a comprehensive review of the subject. Copyright © 2014 the authors 0270-6474/14/3415490-07$15.00/0.

NAD+ and vitamin B3: from metabolism to therapies.

PubMed

Sauve, Anthony A

2008-03-01

The role of NAD(+) metabolism in health and disease is of increased interest as the use of niacin (nicotinic acid) has emerged as a major therapy for treatment of hyperlipidemias and with the recognition that nicotinamide can protect tissues and NAD(+) metabolism in a variety of disease states, including ischemia/reperfusion. In addition, a growing body of evidence supports the view that NAD(+) metabolism regulates important biological effects, including lifespan. NAD(+) exerts potent effects through the poly(ADP-ribose) polymerases, mono-ADP-ribosyltransferases, and the recently characterized sirtuin enzymes. These enzymes catalyze protein modifications, such as ADP-ribosylation and deacetylation, leading to changes in protein function. These enzymes regulate apoptosis, DNA repair, stress resistance, metabolism, and endocrine signaling, suggesting that these enzymes and/or NAD(+) metabolism could be targeted for therapeutic benefit. This review considers current knowledge of NAD(+) metabolism in humans and microbes, including new insights into mechanisms that regulate NAD(+) biosynthetic pathways, current use of nicotinamide and nicotinic acid as pharmacological agents, and opportunities for drug design that are directed at modulation of NAD(+) biosynthesis for treatment of human disorders and infections.

Early-Life Host–Microbiome Interphase: The Key Frontier for Immune Development

PubMed Central

Amenyogbe, Nelly; Kollmann, Tobias R.; Ben-Othman, Rym

2017-01-01

Human existence can be viewed as an “animal in a microbial world.” A healthy interaction of the human host with the microbes in and around us heavily relies on a well-functioning immune system. As development of both the microbiota and the host immune system undergo rapid changes in early life, it is not surprising that even minor alterations during this co-development can have profound consequences. Scrutiny of existing data regarding pre-, peri-, as well as early postnatal modulators of newborn microbiota indeed suggest strong associations with several immune-mediated diseases with onset far beyond the newborn period. We here summarize these data and extract overarching themes. This same effort in turn sets the stage to guide effective countermeasures, such as probiotic administration. The objective of our review is to highlight the interaction of host immune ontogeny with the developing microbiome in early life as a critical window of susceptibility for lifelong disease, as well as to identify the enormous potential to protect and promote lifelong health by specifically targeting this window of opportunity. PMID:28596951

Diet and microbiota in inflammatory bowel disease: The gut in disharmony.

PubMed

Rapozo, Davy C M; Bernardazzi, Claudio; de Souza, Heitor Siffert Pereira

2017-03-28

Bacterial colonization of the gut shapes both the local and the systemic immune response and is implicated in the modulation of immunity in both healthy and disease states. Recently, quantitative and qualitative changes in the composition of the gut microbiota have been detected in Crohn's disease and ulcerative colitis, reinforcing the hypothesis of dysbiosis as a relevant mechanism underlying inflammatory bowel disease (IBD) pathogenesis. Humans and microbes have co-existed and co-evolved for a long time in a mutually beneficial symbiotic association essential for maintaining homeostasis. However, the microbiome is dynamic, changing with age and in response to environmental modifications. Among such environmental factors, food and alimentary habits, progressively altered in modern societies, appear to be critical modulators of the microbiota, contributing to or co-participating in dysbiosis. In addition, food constituents such as micronutrients are important regulators of mucosal immunity, with direct or indirect effects on the gut microbiota. Moreover, food constituents have recently been shown to modulate epigenetic mechanisms, which can result in increased risk for the development and progression of IBD. Therefore, it is likely that a better understanding of the role of different food components in intestinal homeostasis and the resident microbiota will be essential for unravelling the complex molecular basis of the epigenetic, genetic and environment interactions underlying IBD pathogenesis as well as for offering dietary interventions with minimal side effects.

Diet and microbiota in inflammatory bowel disease: The gut in disharmony

PubMed Central

Rapozo, Davy C M; Bernardazzi, Claudio; de Souza, Heitor Siffert Pereira

2017-01-01

Bacterial colonization of the gut shapes both the local and the systemic immune response and is implicated in the modulation of immunity in both healthy and disease states. Recently, quantitative and qualitative changes in the composition of the gut microbiota have been detected in Crohn’s disease and ulcerative colitis, reinforcing the hypothesis of dysbiosis as a relevant mechanism underlying inflammatory bowel disease (IBD) pathogenesis. Humans and microbes have co-existed and co-evolved for a long time in a mutually beneficial symbiotic association essential for maintaining homeostasis. However, the microbiome is dynamic, changing with age and in response to environmental modifications. Among such environmental factors, food and alimentary habits, progressively altered in modern societies, appear to be critical modulators of the microbiota, contributing to or co-participating in dysbiosis. In addition, food constituents such as micronutrients are important regulators of mucosal immunity, with direct or indirect effects on the gut microbiota. Moreover, food constituents have recently been shown to modulate epigenetic mechanisms, which can result in increased risk for the development and progression of IBD. Therefore, it is likely that a better understanding of the role of different food components in intestinal homeostasis and the resident microbiota will be essential for unravelling the complex molecular basis of the epigenetic, genetic and environment interactions underlying IBD pathogenesis as well as for offering dietary interventions with minimal side effects. PMID:28405140

[New nutrient medium for the cultivation and isolation of the plague microbe ChDS-37 as an element of the mobilization reserve of specialized antiepidemic teams of the Russian Inspectorate for the Protection of Consumer Rights and Human Welfare].

PubMed

Mazrukho, A B; Kaminskiĭ, D I; Lomov, Yu M; Telesmanich, N P; Rozhkov, K K; Alutin, I M; Pukhov, Yu M; Prometnoĭ, V I; Fetsaĭlova, O P; Bulakhova, O G; Firsova, I A; Smolikova, L M; Bozhko, N V; Ivanova, V S; Burlakova, O S; Verkina, L M; Trukhachev, A L; Akulova, M V

2011-04-01

A new nutrient medium has been designed to culture and isolate the plague microbe ChDS-37 on the basis of the pancreatic digest of baker's yeast. The results of laboratory tests of the designed medium, by using 10 plague microbe strains and those of approval during the tactical and special training of a specialized antiepidemic team (SAET), suggest that the medium has some advantage over reference media and creates prerequisites for being incorporated into the mobilization reserve of a SAET.

Macrophage–Microbe Interactions: Lessons from the Zebrafish Model

PubMed Central

Yoshida, Nagisa; Frickel, Eva-Maria; Mostowy, Serge

2017-01-01

Macrophages provide front line defense against infections. The study of macrophage–microbe interplay is thus crucial for understanding pathogenesis and infection control. Zebrafish (Danio rerio) larvae provide a unique platform to study macrophage–microbe interactions in vivo, from the level of the single cell to the whole organism. Studies using zebrafish allow non-invasive, real-time visualization of macrophage recruitment and phagocytosis. Furthermore, the chemical and genetic tractability of zebrafish has been central to decipher the complex role of macrophages during infection. Here, we discuss the latest developments using zebrafish models of bacterial and fungal infection. We also review novel aspects of macrophage biology revealed by zebrafish, which can potentiate development of new therapeutic strategies for humans. PMID:29250076

From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota.

PubMed

Bauer, Eugen; Thiele, Ines

2018-01-01

An important hallmark of the human gut microbiota is its species diversity and complexity. Various diseases have been associated with a decreased diversity leading to reduced metabolic functionalities. Common approaches to investigate the human microbiota include high-throughput sequencing with subsequent correlative analyses. However, to understand the ecology of the human gut microbiota and consequently design novel treatments for diseases, it is important to represent the different interactions between microbes with their associated metabolites. Computational systems biology approaches can give further mechanistic insights by constructing data- or knowledge-driven networks that represent microbe interactions. In this minireview, we will discuss current approaches in systems biology to analyze the human gut microbiota, with a particular focus on constraint-based modeling. We will discuss various community modeling techniques with their advantages and differences, as well as their application to predict the metabolic mechanisms of intestinal microbial communities. Finally, we will discuss future perspectives and current challenges of simulating realistic and comprehensive models of the human gut microbiota.

Gut Microbiota and Complications of Liver Disease

PubMed Central

Acharya, Chathur; Bajaj, Jasmohan

2016-01-01

Synopsis The epidemic of chronic liver disease and how to combat its complications has been a challenging aspect for many years. New laboratory techniques have made analysis of the human intestinal microbiome easier and also more detailed. With insight into dysbiosis and how this dysbiosis impacts liver disease, scientists have new targets in the intestine and liver. Dysbiosis is associated with endotoxemia and propagates liver injury in NASH and alcoholic cirrhosis. The composition of the microbiota changes with the development of cirrhosis and decompensation Apart from microbes, the role that bile acids play in this arena are also being discovered and newer treatments like FXR receptor agonists are coming into the picture. Altered gut microbiota plays an important role in cirrhosis and its modulation to prevent disease progression changes, and concomitantly bile acid physiology must be regulated or augmented to help prevent cirrhosis and its complications. PMID:28164848

Cure of tuberculosis using nanotechnology: An overview.

PubMed

Kerry, Rout George; Gouda, Sushanto; Sil, Bikram; Das, Gitishree; Shin, Han-Seung; Ghodake, Gajanan; Patra, Jayanta Kumar

2018-05-01

Mycobacterium tuberculosis is the causative agent of tuberculosis (TB), a major health issue of the present era. The bacterium inhabits the host macrophage and other immune cells where it modulates the lysosome trafficking protein, hinders the formation of phagolysosome, and blocks the TNF receptor-dependent apoptosis of host macrophage/monocytes. Other limitations such as resistance to and low bioavailability and bio-distribution of conventional drugs aid to their high virulence and human mortality. This review highlights the use of nanotechnology-based approaches for drug formulation and delivery which could open new avenues to limit the pathogenicity of tuberculosis. Moreover phytochemicals, such as alkaloids, phenols, saponins, steroids, tannins, and terpenoids, extracted from terrestrial plants and mangroves seem promising against M. tuberculosis through different molecular mechanisms. Further understanding of the genomics and proteomics of this pathogenic microbe could also help overcome various research gaps in the path of developing a suitable therapy against tuberculosis.

Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation

PubMed Central

Agler, Matthew T.; Ruhe, Jonas; Kroll, Samuel; Morhenn, Constanze; Kim, Sang-Tae; Weigel, Detlef; Kemen, Eric M.

2016-01-01

Plant-associated microorganisms have been shown to critically affect host physiology and performance, suggesting that evolution and ecology of plants and animals can only be understood in a holobiont (host and its associated organisms) context. Host-associated microbial community structures are affected by abiotic and host factors, and increased attention is given to the role of the microbiome in interactions such as pathogen inhibition. However, little is known about how these factors act on the microbial community, and especially what role microbe–microbe interaction dynamics play. We have begun to address this knowledge gap for phyllosphere microbiomes of plants by simultaneously studying three major groups of Arabidopsis thaliana symbionts (bacteria, fungi and oomycetes) using a systems biology approach. We evaluated multiple potential factors of microbial community control: we sampled various wild A. thaliana populations at different times, performed field plantings with different host genotypes, and implemented successive host colonization experiments under lab conditions where abiotic factors, host genotype, and pathogen colonization was manipulated. Our results indicate that both abiotic factors and host genotype interact to affect plant colonization by all three groups of microbes. Considering microbe–microbe interactions, however, uncovered a network of interkingdom interactions with significant contributions to community structure. As in other scale-free networks, a small number of taxa, which we call microbial “hubs,” are strongly interconnected and have a severe effect on communities. By documenting these microbe–microbe interactions, we uncover an important mechanism explaining how abiotic factors and host genotypic signatures control microbial communities. In short, they act directly on “hub” microbes, which, via microbe–microbe interactions, transmit the effects to the microbial community. We analyzed two “hub” microbes (the obligate biotrophic oomycete pathogen Albugo and the basidiomycete yeast fungus Dioszegia) more closely. Albugo had strong effects on epiphytic and endophytic bacterial colonization. Specifically, alpha diversity decreased and beta diversity stabilized in the presence of Albugo infection, whereas they otherwise varied between plants. Dioszegia, on the other hand, provided evidence for direct hub interaction with phyllosphere bacteria. The identification of microbial “hubs” and their importance in phyllosphere microbiome structuring has crucial implications for plant–pathogen and microbe–microbe research and opens new entry points for ecosystem management and future targeted biocontrol. The revelation that effects can cascade through communities via “hub” microbes is important to understand community structure perturbations in parallel fields including human microbiomes and bioprocesses. In particular, parallels to human microbiome “keystone” pathogens and microbes open new avenues of interdisciplinary research that promise to better our understanding of functions of host-associated microbiomes. PMID:26788878

Microbial Pre-exposure and Vectorial Competence of Anopheles Mosquitoes

PubMed Central

Dieme, Constentin; Rotureau, Brice; Mitri, Christian

2017-01-01

Anopheles female mosquitoes can transmit Plasmodium, the malaria parasite. During their aquatic life, wild Anopheles mosquito larvae are exposed to a huge diversity of microbes present in their breeding sites. Later, adult females often take successive blood meals that might also carry different micro-organisms, including parasites, bacteria, and viruses. Therefore, prior to Plasmodium ingestion, the mosquito biology could be modulated at different life stages by a suite of microbes present in larval breeding sites, as well as in the adult environment. In this article, we highlight several naturally relevant scenarios of Anopheles microbial pre-exposure that we assume might impact mosquito vectorial competence for the malaria parasite: (i) larval microbial exposures; (ii) protist co-infections; (iii) virus co-infections; and (iv) pathogenic bacteria co-infections. In addition, significant behavioral changes in African Anopheles vectors have been associated with increasing insecticide resistance. We discuss how these ethological modifications may also increase the repertoire of microbes to which mosquitoes could be exposed, and that might also influence their vectorial competence. Studying Plasmodium–Anopheles interactions in natural microbial environments would efficiently contribute to refining the transmission risks. PMID:29376030

Invariant natural killer T cells trigger adaptive lymphocytes to churn up bile.

PubMed

Joyce, Sebastian; Van Kaer, Luc

2008-05-15

How innate immune response causes autoimmunity has remained an enigma. In this issue of Cell Host & Microbe, Mattner et al. demonstrate that invariant natural killer T cells activated by the mucosal commensal Novosphingobium aromaticivorans precipitate chronic T cell-mediated autoimmunity against small bile ducts that mirrors human primary biliary cirrhosis. These findings provide a mechanistic understanding of the role of innate immunity toward a microbe in the development of autoimmunity.

The influence of milk oligosaccharides on microbiota of infants: opportunities for formulas.

PubMed

Chichlowski, Maciej; German, J Bruce; Lebrilla, Carlito B; Mills, David A

2011-01-01

In addition to a nutritive role, human milk also guides the development of a protective intestinal microbiota in the infant. Human milk possesses an overabundance of complex oligosaccharides that are indigestible by the infant yet are consumed by microbial populations in the developing intestine. These oligosaccharides are believed to facilitate enrichment of a healthy infant gastrointestinal microbiota, often associated with bifidobacteria. Advances in glycomics have enabled precise determination of milk glycan structures as well as identification of the specific glycans consumed by various gut microbes. Furthermore, genomic analysis of bifidobacteria from infants has revealed specific genetic loci related to milk oligosaccharide import and processing, suggesting coevolution between the human host, milk glycans, and the microbes they enrich. This review discusses the current understanding of how human milk oligosaccharides interact with the infant microbiota and examines the opportunities for translating this knowledge to improve the functionality of infant formulas.

Evolutionary and ecological forces that shape the bacterial communities of the human gut

PubMed Central

Messer, Jeannette S.; Liechty, Emma R; Vogel, Olivia A.; Chang, Eugene B.

2017-01-01

Since microbes were first described in the mid-1600's, we have come to appreciate that they live all around and within us with both beneficial and detrimental effects on nearly every aspect of our lives. The human gastrointestinal tract is inhabited by a dynamic community of trillions of bacteria that constantly interact with each other and their human host. The acquisition of these bacteria is not stochastic, but determined by circumstance (environment), host rules (genetics, immune state, mucus, etc), and dynamic self-selection among microbes to form stable, resilient communities that are in balance with the host. In this review, we will discuss how these factors lead to formation of the gut bacterial community and influence its interactions with the host. We will also address how gut bacteria contribute to disease and how they could potentially be targeted to prevent and treat a variety of human ailments. PMID:28145439

NIH Human Microbiome Project defines normal bacterial makeup of the body

Cancer.gov

Microbes inhabit just about every part of the human body, living on the skin, in the gut, and up the nose. Sometimes they cause sickness, but most of the time, microorganisms live in harmony with their human hosts, providing vital functions essential for

Ecology of sleeping: the microbial and arthropod associates of chimpanzee beds.

PubMed

Thoemmes, Megan S; Stewart, Fiona A; Hernandez-Aguilar, R Adriana; Bertone, Matthew A; Baltzegar, David A; Borski, Russell J; Cohen, Naomi; Coyle, Kaitlin P; Piel, Alexander K; Dunn, Robert R

2018-05-01

The indoor environment created by the construction of homes and other buildings is often considered to be uniquely different from other environments. It is composed of organisms that are less diverse than those of the outdoors and strongly sourced by, or dependent upon, human bodies. Yet, no one has ever compared the composition of species found in contemporary human homes to that of other structures built by mammals, including those of non-human primates. Here we consider the microbes and arthropods found in chimpanzee beds, relative to the surrounding environment ( n  = 41 and 15 beds, respectively). Based on the study of human homes, we hypothesized that the microbes found in chimpanzee beds would be less diverse than those on nearby branches and leaves and that their beds would be primarily composed of body-associated organisms. However, we found that differences between wet and dry seasons and elevation above sea level explained nearly all of the observed variation in microbial diversity and community structure. While we can identify the presence of a chimpanzee based on the assemblage of bacteria, the dominant signal is that of environmental microbes. We found just four ectoparasitic arthropod specimens, none of which appears to be specialized on chimpanzees or their structures. These results suggest that the life to which chimpanzees are exposed while in their beds is predominately the same as that of the surrounding environment.

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

DOE PAGES

Cross, Karissa L.; Chirania, Payal; Xiong, Weili; ...

2018-03-13

The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously unculturedDesulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives,D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury weremore » also lost byD. oralis, a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing.Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome “dark matter,” cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.« less

Insights into the Evolution of Host Association through the Isolation and Characterization of a Novel Human Periodontal Pathobiont, Desulfobulbus oralis

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

Cross, Karissa L.; Chirania, Payal; Xiong, Weili

The human oral microbiota encompasses representatives of many bacterial lineages that have not yet been cultured. Here we describe the isolation and characterization of previously unculturedDesulfobulbus oralis , the first human-associated representative of its genus. As mammalian-associated microbes rarely have free-living close relatives,D. oralis provides opportunities to study how bacteria adapt and evolve within a host. This sulfate-reducing deltaproteobacterium has adapted to the human oral subgingival niche by curtailing its physiological repertoire, losing some biosynthetic abilities and metabolic independence, and by dramatically reducing environmental sensing and signaling capabilities. The genes that enable free-living Desulfobulbus to synthesize the potent neurotoxin methylmercury weremore » also lost byD. oralis, a notably positive outcome of host association. However, horizontal gene acquisitions from other members of the microbiota provided novel mechanisms of interaction with the human host, including toxins like leukotoxin and hemolysins. Proteomic and transcriptomic analysis revealed that most of those factors are actively expressed, including in the subgingival environment, and some are secreted. Similar to other known oral pathobionts, D. oralis can trigger a proinflammatory response in oral epithelial cells, suggesting a direct role in the development of periodontal disease. Animal-associated microbiota likely assembled as a result of numerous independent colonization events by free-living microbes followed by coevolution with their host and other microbes. Through specific adaptation to various body sites and physiological niches, microbes have a wide range of contributions, from beneficial to disease causing.Desulfobulbus oralis provides insights into genomic and physiological transformations associated with transition from an open environment to a host-dependent lifestyle and the emergence of pathogenicity. Through a multifaceted mechanism triggering a proinflammatory response, D. oralis is a novel periodontal pathobiont. Even though culture-independent approaches can provide insights into the potential role of the human microbiome “dark matter,” cultivation and experimental characterization remain important to studying the roles of individual organisms in health and disease.« less

MICROBES, MONITORING AND HUMAN HEALTH

EPA Science Inventory

There are about 20,000 wastewater treatment plants in the United States. These plants discharge about 50 trillion gallons of wastewater daily into the nation's surface waters. Most wastewater contains human feces, which are a potential source of microbial pathogens. Pathogens ...

Four-year bacterial monitoring in the International Space Station—Japanese Experiment Module “Kibo” with culture-independent approach

PubMed Central

Ichijo, Tomoaki; Yamaguchi, Nobuyasu; Tanigaki, Fumiaki; Shirakawa, Masaki; Nasu, Masao

2016-01-01

Studies on the relationships between humans and microbes in space habitation environments are critical for success in long-duration space missions, to reduce potential hazards to the crew and the spacecraft infrastructure. We performed microbial monitoring in the Japanese Experiment Module “Kibo”, a part of the International Space Station, for 4 years after its completion, and analyzed samples with modern molecular microbiological techniques. Sampling was performed in September 2009, February 2011, and October 2012. The surface of the incubator, inside the door of the incubator, an air intake, air diffuser, and handrail were selected as sampling sites. Sampling was performed using the optimized swabbing method. Abundance and phylogenetic affiliation of bacteria on the interior surfaces of Kibo were determined by quantitative PCR and pyrosequencing, respectively. Bacteria in the phyla Proteobacteria (γ-subclass) and Firmicutes were frequently detected on the interior surfaces in Kibo. Families Staphylococcaceae and Enterobacteriaceae were dominant. Most bacteria detected belonged to the human microbiota; thus, we suggest that bacterial cells are transferred to the surfaces in Kibo from the astronauts. Environmental bacteria such as Legionella spp. were also detected. From the data on bacterial abundance and phylogenetic affiliation, Kibo has been microbiologically well maintained; however, the microbial community structure in Kibo may change with prolonged stay of astronauts. Continuous monitoring is required to obtain information on changes in the microbial community structure in Kibo. PMID:28725725

Use of Gifu Anaerobic Medium for culturing 32 dominant species of human gut microbes and its evaluation based on short-chain fatty acids fermentation profiles.

PubMed

Gotoh, Aina; Nara, Misaki; Sugiyama, Yuta; Sakanaka, Mikiyasu; Yachi, Hiroyuki; Kitakata, Aya; Nakagawa, Akira; Minami, Hiromichi; Okuda, Shujiro; Katoh, Toshihiko; Katayama, Takane; Kurihara, Shin

2017-10-01

Recently, a "human gut microbial gene catalogue," which ranks the dominance of microbe genus/species in human fecal samples, was published. Most of the bacteria ranked in the catalog are currently publicly available; however, the growth media recommended by the distributors vary among species, hampering physiological comparisons among the bacteria. To address this problem, we evaluated Gifu anaerobic medium (GAM) as a standard medium. Forty-four publicly available species of the top 56 species listed in the "human gut microbial gene catalogue" were cultured in GAM, and out of these, 32 (72%) were successfully cultured. Short-chain fatty acids from the bacterial culture supernatants were then quantified, and bacterial metabolic pathways were predicted based on in silico genomic sequence analysis. Our system provides a useful platform for assessing growth properties and analyzing metabolites of dominant human gut bacteria grown in GAM and supplemented with compounds of interest.

Introduction: Microbiome in human reproduction.

PubMed

Franasiak, Jason M; Scott, Richard T

2015-12-01

The human microbiome has been termed the "second human genome" and data that has come about of late certainly makes it appear every bit as complex. The human body contains 10-fold more microbial cells than the human cells and accounts for 1%-3% of our total body mass. As we learn more about this symbiotic relationship, it appears this complex interaction occurs in nearly every part of the body, even those areas at one time considered to be sterile. Indeed, the microbiome in human reproduction has been investigated in terms of both the lower and upper reproductive tract and includes interactions even at the point of gametogenesis. What is all the more fascinating is that we have known about the importance of microbes for over 150 years, even before they existed in name. And now, with the assistance of an exciting technologic revolution which has pushed forward our understanding of the microbiome, we appear to stand on the precipice of a higher level of understanding of microbes, the biofilms they create, and their impact of health and disease in human reproduction. Copyright © 2015. Published by Elsevier Inc.

Food-mediated modulation of immunity in a phytophagous insect: An effect of nutrition rather than parasitic contamination.

PubMed

Vogelweith, Fanny; Moreau, Jérôme; Thiéry, Denis; Moret, Yannick

2015-06-01

Inherent to the cost of immunity, the immune system itself can exhibit tradeoffs between its arms. Phytophagous insects face a wide range of microbial and eukaryotic parasites, each activating different immune pathways that could compromise the activity of the others. Feeding larvae are primarily exposed to microbes, which growth is controlled by antibiotic secondary metabolites produced by the host plant. The resulting variation in abundance of microbes on plants is expected to differentially stimulate the insect antimicrobial immune defenses. Under the above tradeoff hypothesis, stimulation of the insect antimicrobial defenses is expected to compromise immune activity against eukaryote parasites. In the European grape berry moth, Eupoecilia ambiguella, immune effectors directed towards microbes are negatively correlated to those directed towards eukaryotic parasites among host plants. Here, we hypothesize this relationship is caused by a variable control of the microbial community among host plants by their antibiotic metabolites. To test this hypothesis, we first quantified antimicrobial activity in berries of several grape varieties. We then measured immune defenses of E. ambiguella larvae raised on artificial diets in which we mimicked levels of antimicrobial activity of grape berries using tetracycline to control the abundance of growing microbes. Another group of larvae was raised on artificial diets made of berry extracts only to control for the effect of nutrition. We found that controlling microbe abundance with tetracycline in diets did not explain variation in the immune function whereas the presence of berry extracts did. This suggests that variation in immune defenses of E. ambiguella among grape varieties is caused by nutritional difference among host plants rather than microbe abundance. Further study of the effects of berry compounds on larval immune parameters will be needed to explain the observed tradeoff among immune system components. Copyright © 2015 Elsevier Ltd. All rights reserved.

Modulation of host cell biology by plant pathogenic microbes.

PubMed

Le Fevre, Ruth; Evangelisti, Edouard; Rey, Thomas; Schornack, Sebastian

2015-01-01

Plant-pathogen interactions can result in dramatic visual changes in the host, such as galls, phyllody, pseudoflowers, and altered root-system architecture, indicating that the invading microbe has perturbed normal plant growth and development. These effects occur on a cellular level but range up to the organ scale, and they commonly involve attenuation of hormone homeostasis and deployment of effector proteins with varying activities to modify host cell processes. This review focuses on the cellular-reprogramming mechanisms of filamentous and bacterial plant pathogens that exhibit a biotrophic lifestyle for part, if not all, of their lifecycle in association with the host. We also highlight strategies for exploiting our growing knowledge of microbial host reprogramming to study plant processes other than immunity and to explore alternative strategies for durable plant resistance.

Bacterial-modulated host immunity and stem cell activation for gut homeostasis.

PubMed

Lee, Won-Jae

2009-10-01

Although it is widely accepted that dynamic cross-talk between gut epithelia and microorganisms must occur to achieve gut homeostasis, the critical mechanisms by which gut-microbe interactions are regulated remain uncertain. In this issue of Genes & Development, Buchon and colleagues (pp. 2333-2344) revealed that the reaction of the gut to microorganisms is not restricted to activating immune systems, but extends to integrated responses essential for gut tissue homeostasis, including self-renewal and the differentiation of stem cells. Further investigation of the connection between immune response and stem cell regulation at the molecular level in the microbe-laden mucosal epithelia will accelerate our understanding of the regulatory mechanisms of gut homeostasis and of the pathogenesis of diseases such as chronic inflammatory diseases and colorectal cancers.

Diet, microbes, and host genetics: the perfect storm in inflammatory bowel diseases.

PubMed

Leone, Vanessa; Chang, Eugene B; Devkota, Suzanne

2013-03-01

The incidence of inflammatory bowel diseases (IBD), as well as other inflammatory conditions, has dramatically increased over the past half century. While many studies have shown that IBD exhibits a genetic component via genome-wide association studies, genetic drift alone cannot account for this increase, and other factors, such as those found in the environment must play a role, suggesting a "multiple hit" phenomenon that precipitates disease. One major environmental factor, dietary intake, has shifted to a high fat, high carbohydrate Western-type diet in developing nations, nearly in direct correlation with the increasing incidence of IBD. Recent evidence suggests that specific changes in dietary intake have led to a shift in the composite human gut microbiota, resulting in the emergence of pathobionts that can thrive under specific conditions. In the genetically susceptible host, the emerging pathobionts can lead to increasing incidence and severity of IBD and other inflammatory disorders. Since the gut microbiota is plastic and responds to dietary modulations, the use of probiotics, prebiotics, and/or dietary alterations are all intriguing complementary therapeutic approaches to alleviate IBD symptoms. However, the interactions are complex and it is unlikely that a one-size-fits all approach can be utilized across all populations affected by IBD. Exploration into and thoroughly understanding the interactions between host and microbes, primarily in the genetically susceptible host, will help define strategies that can be tailored to an individual as we move towards an era of personalized medicine to treat IBD.

Microfluidics in microbiology: putting a magnifying glass on microbes.

PubMed

Siddiqui, Sanya; Tufenkji, Nathalie; Moraes, Christopher

2016-09-12

Microfluidic technologies enable unique studies in the field of microbiology to facilitate our understanding of microorganisms. Using miniaturized and high-throughput experimental capabilities in microfluidics, devices with controlled microenvironments can be created for microbial studies in research fields such as healthcare and green energy. In this research highlight, we describe recently developed tools for diagnostic assays, high-throughput mutant screening, and the study of human disease development as well as a future outlook on microbes for renewable energy.

Host genetics affect microbial ecosystems via host immunity.

PubMed

El Kafsi, Hela; Gorochov, Guy; Larsen, Martin

2016-10-01

Genetic evolution of multicellular organisms has occurred in response to environmental challenges, including competition for nutrients, climate change, physical and chemical stressors, and pathogens. However, fitness of an organism is dependent not only on defense efficacy, but also on the ability to take advantage of symbiotic organisms. Indeed, microbes not only encompass pathogenicity, but also enable efficient nutrient uptake from diets nondegradable by the host itself. Moreover, microbes play important roles in the development of host immunity. Here we review associations between specific host genes and variance in microbiota composition and compare with interactions between microbes and host immunity. Recent genome-wide association studies reveal that symbiosis between host and microbiota is the exquisite result of genetic coevolution. Moreover, a subset of microbes from human and mouse microbiota have been identified to interact with humoral and cellular immunity. Interestingly, microbes associated with both host genetics and host immunity are taxonomically related. Most involved are Bifidobacterium, Lactobacillus, and Akkermansia, which are dually associated with both host immunity and host genetics. We conclude that future therapeutics targeting microbiota in the context of chronic inflammatory diseases need to consider both immune and genetic host features associated with microbiota homeostasis.

Immunophototherapy for the treatment of AIDS and AIDS-related infections

NASA Astrophysics Data System (ADS)

Schlager, Kenneth J.

1992-06-01

Immunophototherapy (IPT) is an experimental method of medical treatment that seeks to provide for the selective destruction of diseased cells and microbes such as human immunodeficiency virus (HIV)-T4 cells and the rapid elimination of their toxic by-products from the human body. Photosensitive monoclonal or polyclonal antibody fragments, which are specific to the diseased cell or microbe, will be used to treat acquired immunodeficiency syndrome (AIDS) and related infections. These antibody fragments are tagged with photosensitive compounds and metal colloids and then intravenously injected into the patient. The tagged antibodies quickly and selectively bind to the diseased cells or microbes in the blood stream and affected organs. These cells or microbes are then selectively destroyed by irradiation of these complexes with light of the proper wavelength. This light activates the photosensitive material which then creates singlet oxygen that destroys the microbe or cell. Toxic products of lysis are quickly discharged from the body by activation of the reticuloendothelial system. IPT has been demonstrated by Biotronics to be very effective in the in vitro selective destruction of specified cell types. In a proposed AIDS-treatment research program, IPT will be first demonstrated in vitro for a set of infected blood samples using commercially-available antibodies labeled with appropriate photosensitizers. Efficacy will be determined by a p24 antigen immunodiagnostic test that will indicate the % inhibition in comparison to controls and samples treated with the drug AZT. Subcontracted animal efficacy studies will use a SCID-hu mouse model and PCR/DNA-RNA for endpoint analysis. Toxicity studies of animal (rat) models will be based on post-treatment investigations of lymph nodes, spleen, liver and other organs.

Pickle Flavors Relish in Drosophila Immunity.

PubMed

Salminen, Tiina Susanna; Rämet, Mika

2016-09-14

Immune responses must be tightly controlled to avoid host damage. In Drosophila, two NF-κB signaling pathways, Toll and Imd, mediate host immune responses. In this issue of Cell Host & Microbe, Morris et al. (2016) introduce Pickle, a nuclear IκB that inhibits Drosophila immune signaling by modulating the NF-κB Relish. Copyright © 2016 Elsevier Inc. All rights reserved.

Gut microbial adaptation to dietary consumption of fructose, artificial sweeteners and sugar alcohols: implications for host-microbe interactions contributing to obesity.

PubMed

Payne, A N; Chassard, C; Lacroix, C

2012-09-01

The Western diet, comprised of highly refined carbohydrates and fat but reduced complex plant polysaccharides, has been attributed to the prevalence of obesity. A concomitant rise in the consumption of fructose and sugar substitutes such as sugar alcohols, artificial sweeteners, even rare sugars, has mirrored this trend, as both probable contributor and solution to the epidemic. Acknowledgement of the gut microbiota as a factor involved in obesity has sparked much controversy as to the cause and consequence of this relationship. Dietary intakes are a known modulator of gut microbial phylogeny and metabolic activity, frequently exploited to stimulate beneficial bacteria, promoting health benefits. Comparably little research exists on the impact of 'unconscious' dietary modulation on the resident commensal community mediated by increased fructose and sugar substitute consumption. This review highlights mechanisms of potential host and gut microbial fructose and sugar substitute metabolism. Evidence is presented suggesting these sugar compounds, particularly fructose, condition the microbiota, resulting in acquisition of a westernized microbiome with altered metabolic capacity. Disturbances in host-microbe interactions resulting from fructose consumption are also explored. © 2012 The Authors. obesity reviews © 2012 International Association for the Study of Obesity.

Lentinula edodes-derived polysaccharide alters the spatial structure of gut microbiota in mice.

PubMed

Xu, Xiaofei; Zhang, Xuewu

2015-01-01

Lentinula edodes-derived polysaccharides possess many therapeutic characteristics, including anti-tumor and immuno-modulation. The gut microbes play a critical role in modulation of immune function. However, the impact of Lentinula edodes-derived polysaccharides on the gut microbes have not yet been explored. In this study, high-throughput pyrosequencing technique was employed to investigate the effects of a new heteropolysaccharide L2 from Lentinula edodes on microbiota diversity and composition of small intestine, cecum, colon and distal end of colon (feces) in mice. The results demonstrated that along mouse intestine the microbiota exhibit distinctly different space distribution. L2 treatment reduced the diversity and evenness of gut microbiota along the intestine, especially in the cecum and colon. In the fecal microbial communities, the decrease of Bacteroidetes by significantly increasing Proteobacteria were observed, which were characterized by the increased Helicobacteraceae and reduced S24-7 at family level. Some OTUs, corresponding to Bacteroides acidifaciens, Alistipes and Helicobacter suncus, were found to be significantly increased in L2 treated-mice. In particular, 4 phyla Chloroflexi, Gemmatimonadetes, Nitrospirae and Planctomycetes are exclusively present in L2-treated mice. This is helpful for further demonstrating healthy action mechanism of Lentinula edodes-derived polysaccharide L2.

The opposing forces of the intestinal Microbiome and the emerging pathobiome

PubMed Central

Defazio, Jennifer; Fleming, Irma D.; Shakhsheer, Baddr; Zaborina, Olga; Alverdy, John C.

2014-01-01

Objective The purpose of this article is to summarize emerging concepts on the role of the intestinal microbiome in surgical patients. Background Revolutionary research over the past decade has shown that human beings live in close and constant contact with boundless communities of microbes. This new reality has wide-ranging implications for the care of surgical patients. Methods and Results Recent innovations in the study of the human microbiome are reviewed. To demonstrate the applicability of these studies to surgical disease, we discuss in detail what is known about the role of microbes in the pathogenesis of perioperative complications including anastomotic leak, sepsis, and surgical site infections. Conclusions Enhanced awareness of the human microbiome will empower clinicians to adopt novel practices in the prevention and treatment of a wide variety of surgical conditions. PMID:25440116

Linking Antimicrobial Potential of Natural Products Derived from Aquatic Organisms and Microbes Involved in Alzheimer's Disease - A Review.

PubMed

Stojkovic, Dejan; Kostic, Marina; Smiljkovic, Marija; Aleksic, Milena; Vasiljevic, Perica; Nikolic, Milos; Sokovic, Marina

2018-03-08

The following review is oriented towards microbes linked to Alzheimer's disease (AD) and antimicrobial effect of compounds and extracts derived from aquatic organisms against specific bacteria, fungi and viruses which were found previously in patients suffering from AD. Major group of microbes linked to AD include bacteria: Chlamydia pneumoniae, Helicobacter pylori, Porphyromonas gingivalis, Fusobacterium nucleatum, Prevotella intermedia, Actinomyces naeslundii, spirochete group; fungi: Candida sp., Cryptococcus sp., Saccharomyces sp., Malassezia sp., Botrytis sp., and viruses: herpes simplex virus type 1 (HSV-1), Human cytomegalovirus (CMV), hepatitis C virus (HCV). In the light of that fact, this review is the first to link antimicrobial potential of aquatic organisms against these sorts of microbes. This literature review might serve as a starting platform to develop novel supportive therapy for patients suffering from AD and to possibly prevent escalation of the disease in patients already having high risk factors for AD occurrence. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Biotin in microbes, the genes involved in its biosynthesis, its biochemical role and perspectives for biotechnological production.

PubMed

Streit, W R; Entcheva, P

2003-03-01

Biotin (vitamin H) is one of the most fascinating cofactors involved in central pathways in pro- and eukaryotic cell metabolism. Since its original discovery in 1901, research has led to the discovery of the complete biotin biosynthesis pathways in many different microbes and much work has been done on the highly intriguing and complex biochemistry of biotin biosynthesis. While humans and animals require several hundred micrograms of biotin per day, most microbes, plants and fungi appear to be able to synthesize the cofactor themselves. Biotin is added to many food, feed and cosmetic products, creating a world market of 10-30 t/year. However, the majority of the biotin sold is synthesized in a chemical process. Since the chemical synthesis is linked with a high environmental burden, much effort has been put into the development of biotin-overproducing microbes. A summary of biotin biosynthesis and its biological role is presented; and current strategies for the improvement of microbial biotin production using modern biotechnological techniques are discussed.

The possible interplanetary transfer of microbes: assessing the viability of Deinococcus spp. under the ISS Environmental conditions for performing exposure experiments of microbes in the Tanpopo mission.

PubMed

Kawaguchi, Yuko; Yang, Yinjie; Kawashiri, Narutoshi; Shiraishi, Keisuke; Takasu, Masako; Narumi, Issay; Satoh, Katsuya; Hashimoto, Hirofumi; Nakagawa, Kazumichi; Tanigawa, Yoshiaki; Momoki, Yoh-Hei; Tanabe, Maiko; Sugino, Tomohiro; Takahashi, Yuta; Shimizu, Yasuyuki; Yoshida, Satoshi; Kobayashi, Kensei; Yokobori, Shin-Ichi; Yamagishi, Akihiko

2013-10-01

To investigate the possible interplanetary transfer of life, numerous exposure experiments have been carried out on various microbes in space since the 1960s. In the Tanpopo mission, we have proposed to carry out experiments on capture and space exposure of microbes at the Exposure Facility of the Japanese Experimental Module of the International Space Station (ISS). Microbial candidates for the exposure experiments in space include Deinococcus spp.: Deinococcus radiodurans, D. aerius and D. aetherius. In this paper, we have examined the survivability of Deinococcus spp. under the environmental conditions in ISS in orbit (i.e., long exposure to heavy-ion beams, temperature cycles, vacuum and UV irradiation). A One-year dose of heavy-ion beam irradiation did not affect the viability of Deinococcus spp. within the detection limit. Vacuum (10(-1) Pa) also had little effect on the cell viability. Experiments to test the effects of changes in temperature from 80 °C to -80 °C in 90 min (± 80 °C/90 min cycle) or from 60 °C to -60 °C in 90 min (± 60 °C/90 min cycle) on cell viability revealed that the survival rate decreased severely by the ± 80 °C/90 min temperature cycle. Exposure of various thicknesses of deinococcal cell aggregates to UV radiation (172 nm and 254 nm, respectively) revealed that a few hundred micrometer thick aggregate of deinococcal cells would be able to withstand the solar UV radiation on ISS for 1 year. We concluded that aggregated deinococcal cells will survive the yearlong exposure experiments. We propose that microbial cells can aggregate as an ark for the interplanetary transfer of microbes, and we named it 'massapanspermia'.

Transmission of Atherosclerosis Susceptibility with Gut Microbial Transplantation*

PubMed Central

Gregory, Jill C.; Buffa, Jennifer A.; Org, Elin; Wang, Zeneng; Levison, Bruce S.; Zhu, Weifei; Wagner, Matthew A.; Bennett, Brian J.; Li, Lin; DiDonato, Joseph A.; Lusis, Aldons J.; Hazen, Stanley L.

2015-01-01

Recent studies indicate both clinical and mechanistic links between atherosclerotic heart disease and intestinal microbial metabolism of certain dietary nutrients producing trimethylamine N-oxide (TMAO). Here we test the hypothesis that gut microbial transplantation can transmit choline diet-induced TMAO production and atherosclerosis susceptibility. First, a strong association was noted between atherosclerotic plaque and plasma TMAO levels in a mouse diversity panel (n = 22 strains, r = 0.38; p = 0.0001). An atherosclerosis-prone and high TMAO-producing strain, C57BL/6J, and an atherosclerosis-resistant and low TMAO-producing strain, NZW/LacJ, were selected as donors for cecal microbial transplantation into apolipoprotein e null mice in which resident intestinal microbes were first suppressed with antibiotics. Trimethylamine (TMA) and TMAO levels were initially higher in recipients on choline diet that received cecal microbes from C57BL/6J inbred mice; however, durability of choline diet-dependent differences in TMA/TMAO levels was not maintained to the end of the study. Mice receiving C57BL/6J cecal microbes demonstrated choline diet-dependent enhancement in atherosclerotic plaque burden as compared with recipients of NZW/LacJ microbes. Microbial DNA analyses in feces and cecum revealed transplantation of donor microbial community features into recipients with differences in taxa proportions between donor strains that were transmissible to recipients and that tended to show coincident proportions with TMAO levels. Proportions of specific taxa were also identified that correlated with plasma TMAO levels in donors and recipients and with atherosclerotic lesion area in recipients. Atherosclerosis susceptibility may be transmitted via transplantation of gut microbiota. Gut microbes may thus represent a novel therapeutic target for modulating atherosclerosis susceptibility. PMID:25550161

Microbiome/microbiota and allergies.

PubMed

Inoue, Yuzaburo; Shimojo, Naoki

2015-01-01

Allergies are characterized by a hypersensitive immune reaction to originally harmless antigens. In recent decades, the incidence of allergic diseases has markedly increased, especially in developed countries. The increase in the frequency of allergic diseases is thought to be primarily due to environmental changes related to a westernized lifestyle, which affects the commensal microbes in the human body. The human gut is the largest organ colonized by bacteria and contains more than 1000 bacterial species, called the "gut microbiota." The recent development of sequencing technology has enabled researchers to genetically investigate and clarify the diversity of all species of commensal microbes. The collective genomes of commensal microbes are together called the "microbiome." Although the detailed mechanisms remain unclear, it has been proposed that the microbiota/microbiome, especially that in the gut, impacts the systemic immunity and metabolism, thus affecting the development of various immunological diseases, including allergies. In this review, we summarize the recent findings regarding the importance of the microbiome/microbiota in the development of allergic diseases and also the results of interventional studies using probiotics or prebiotics to prevent allergies.

The microbe capture experiment in space: Fluorescence microscopic detection of microbes captured by aerogel

NASA Astrophysics Data System (ADS)

Sugino, Tomohiro; Yokobori, Shin-Ichi; Yang, Yinjie; Kawaguchi, Yuko; Okudaira, Kyoko; Tabata, Makoto; Kawai, Hideyuki; Hasegawa, Sunao; Yamagishi, Akihiko

Microbes have been collected at the altitude up to about 70 km in the sampling experiment done by several groups[1]. We have also collected high altitude microbes, by using an airplane and balloons[2][3][4][5]. We collected new deinococcal strain (Deinococcus aetherius and Deinococ-cus aerius) and several strains of spore-forming bacilli from stratosphere[2][4][5]. However, microbe sampling in space has never been reported. On the other hand, "Panspermia" hy-pothesis, where terrestrial life is originated from outside of Earth, has been proposed[6][7][8][9]. Recent report suggesting existence of the possible microbe fossils in the meteorite of Mars origin opened the serious debate on the possibility of migration of life embedded in meteorites (and cosmic dusts)[10][11]. If we were able to find terrestrial microbes in space, it would suggest that the terrestrial life can travel between astronomical bodies. We proposed a mission "Tanpopo: Astrobiology Exposure and Micrometeoroid Capture Experiments" to examine possible inter-planetary migration of microbes, organic compounds and meteoroids on Japan Experimental Module of the International Space Station (ISS)[12]. Two of six sub themes in this mission are directly related to interplanetary migration of microbes. One is the direct capturing experi-ment of microbes (probably within the particles such as clay) in space by the exposed ultra-low density aerogel. Another is the exposure experiment to examine survivability of the microbes in harsh space environment. They will tell us the possibility of interplanetary migration of microbes (life) from Earth to outside of Earth (or vise versa). In this report, we will report whether aerogel that have been used for the collection of space debris and cosmic dusts can be used for microbe sampling in space. We will discuss how captured particles by aerogel can be detected with DNA-specific fluorescent dye, and how to distinguish microbes from other mate-rials (i.e. aerogel and particles such as clay). The surface of micro-particles captured by aerogel is often vitrified. The non-specific fluorescent light is often observed from vitrified materials. Therefore, we need to distinguish fluorescent light of stained microbes from that of vitrified ma-terials. We are going to use two types of differences (wavelength dependence and attenuation rate of fluorescent) between stained microbes with DNA-specific fluorescent dye and other ma-terials such as clay and aerogel. Fluorescent light of stained microbes shows attenuation faster than that of vitrified materials. Fluorescent light of vitrified materials shows broader range of emission spectra than that of stained microbes. In addition, we simulated the high-speed collision experiment of micro-particles to the aerogel with the two stage light gas gun (ca. 4 km/s). The micro-particles containing pre-stained and dried cells of Deinococcus radiodurans mixed with clay material were used for the collision experiment, and the captured particles were observed with fluorescence microscope. This experiment suggests that the captured microbes can be detected and be distinguished from clay materials. Reference [1] Yang, Y. et al. (2009) Biol. Sci. Space, 23, 151-163. [2] Yang, Y., et al. (2008) Biol. Sci. Space 22:18-25. [3] Yang, Y., et al. (2008) JAXA-RR-08-001: 34-42. [4] Yang, Y., et al. (2009) Internatl. J. Syst. Evol. Bacteriol., 59: 1862-1866. [5] Yang, Y. et al. (2010) Internatl. J. Syst. Evol. Bacteriol. (in press). [6] Arrhenius, S. (1908) Worlds in the Making-the Evolution of the Universe (translation to English by H. Borns) Harper and Brothers Publishers, New York. [7]Crick, F. (1981) Life Itself. Simon Schuster, New York. [8] W.L. Nicholson et al., Microbiol. Mol. Biol. Rev. 64 (2000) 548. [9] G. Horneck et al., Orig. Life Evol. Biosph. 31 (2001) 527. [10] Chyba, C. and C. Sagan (1992) Nature 355: 125-132. [11] Sandford, S. A., et al. (2006) Science 314: 1720-1724. [12] Yamagishi, A., et al. (2008) International Symposium on Space Technology and Science (ISTS) Web Paper Archives. 2008-k-05.

Total Lipopolysaccharide from the Human Gut Microbiome Silences Toll-Like Receptor Signaling.

PubMed

d'Hennezel, Eva; Abubucker, Sahar; Murphy, Leon O; Cullen, Thomas W

2017-01-01

Cohabitation of microbial communities with the host enables the formation of a symbiotic relationship that maintains homeostasis in the gut and beyond. One prevailing model suggests that this relationship relies on the capacity of host cells and tissues to remain tolerant to the strong immune stimulation generated by the microbiota such as the activation of Toll-like receptor 4 (TLR4) pathways by lipopolysaccharide (LPS). Indeed, gut microbial LPS is thought to be one of the most potent activators of innate immune signaling and an important mediator of the microbiome's influence on host physiology. In this study, we performed computational and experimental analyses of healthy human fecal samples to examine the TLR4 signaling capacity of the gut microbiota. These analyses revealed that an immunoinhibitory activity of LPS, conserved across the members of the order Bacteroidales and derived from an underacylated structural feature, silences TLR4 signaling for the entire consortium of organisms inhabiting the human gut. Comparative analysis of metagenomic data from the Human Microbiome Project and healthy-donor samples indicates that immune silencing via LPS is a microbe-intrinsic feature in all healthy adults. These findings challenge the current belief that robust TLR4 signaling is a feature of the microbiome and demonstrate that microbiome-derived LPS has the ability to facilitate host tolerance of gut microbes. These findings have broad implications for how we model host-microbe interactions and for our understanding of microbiome-linked disease. IMPORTANCE While the ability for humans to host a complex microbial ecosystem is an essential property of life, the mechanisms allowing for immune tolerance of such a large microbial load are not completely understood and are currently the focus of intense research. This study shows that an important proinflammatory pathway that is commonly triggered by pathogenic bacteria upon interaction with the host is, in fact, actively repressed by the bacteria of the gut microbiome, supporting the idea that beneficial microbes themselves contribute to the immune tolerance in support of homeostasis. These findings are important for two reasons. First, many currently assume that proinflammatory signaling by lipopolysaccharide is a fundamental feature of the gut flora. This assumption influences greatly how host-microbiome interactions are theoretically modeled but also how they are experimentally studied, by using robust TLR signaling conditions to simulate commensals. Second, elucidation of the mechanisms that support host-microbe tolerance is key to the development of therapeutics for both intestinal and systemic inflammatory disorders.

Literature review of human microbes' interaction with plants

NASA Technical Reports Server (NTRS)

Maguire, B., Jr.

1980-01-01

Human carried microorganisms, which cannot practically be excluded from human supporting agricultural systems of extra terrestrial stations, are considered. These microorganisms damage the plants on which the people depend for oxygen and food. The inclusion of carefully screened or constructed, but more or less normal, phylloplane and rhizosphere microbial communities is studied.

Canine and Human Atopic Dermatitis: Two Faces of the Same Host-Microbe Interaction.

PubMed

Santoro, Domenico; Rodrigues Hoffmann, Aline

2016-06-01

Host-microbe interaction has been suggested to play a critical role in the pathogenesis of atopic dermatitis. The dog has been shown to be the best model to study both pathogenesis and microbiome modifications in atopic dermatitis. Bradley et al. show a significant correlation between microbiome diversity, clinical signs, and skin barrier function in atopic dogs before, during, and after antimicrobial therapy. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Noninvasive photoacoustic identification and imaging of gut microbes.

PubMed

Huang, Xiaoxiao; Shi, Ying; Liu, Yajing; Xu, Hongzhi; Liu, Yu; Xiao, Chuanxing; Ren, Jianlin; Nie, Liming

2017-08-01

Homeostasis of the gut microbiota is indispensable for various physiological functions. Its composition and activity co-develop with the host, and especially associate with human colorectal cancer. However, current composition identification methods are complicated and not timely without spatial distribution information. In this Letter, we explored the photoacoustic imaging (PAI) technique to characterize the composition and quantify the proportions of the gut microbes after optical probe labeling. Our experimental results demonstrated that PAI has the potential to identify different gut bacterial species on the spot.

Methanobrevibacter attenuation via probiotic intervention reduces flatulence in adult human: A non-randomised paired-design clinical trial of efficacy.

PubMed

Seo, Minseok; Heo, Jaeyoung; Yoon, Joon; Kim, Se-Young; Kang, Yoon-Mo; Yu, Jihyun; Cho, Seoae; Kim, Heebal

2017-01-01

The aim of this study was to investigate which of the gut microbes respond to probiotic intervention, as well as study whether they are associated with gastrointestinal symptoms in a healthy adult human. For the experimental purpose, twenty-one healthy adults were recruited and received probiotic mixture, which is composed of five Lactobacilli strains and two Bifidobacteria strains, once a day for 60 days. Defecation survey and Bioelectrical Impedance Analysis were conducted pre- and post-administration to measure phenotypic differences. Stool samples of the subjects were collected twice. The statistical analysis was performed for pair designed metagenome data with 11 phenotypic records of the bioelectrical impedance body composition analyzer and 6 responses of the questionnaires about gastrointestinal symptom. Furthemore, correlation-based network analysis was conducted for exploring complex relationships among microbiome communities. The abundances of Citrobacter, Klebsiella, and Methanobrevibacter were significantly reduced, which are strong candidates to be highly affected by the probiotic administration. In addition, interaction effects were observed between flatulence symptom attenuation and decreasing patterns of the Methanobrevibacter abundance. These results reveal that probiotic intervention modulated the composition of gut microbiota and reduced the abundance of potential pathogens (i.e. Citrobacter and Klebsiella). In addition, methanogens (i.e. Methanobrevibacter) associated with the gastrointestinal symptom in an adult human.

Transplantation of human fetal tissue for neurodegenerative diseases: validation of a new protocol for microbiological analysis and bacterial decontamination.

PubMed

Piroth, Tobias; Pauly, Marie-Christin; Schneider, Christian; Wittmer, Annette; Möllers, Sven; Döbrössy, Máté; Winkler, Christian; Nikkhah, Guido

2014-01-01

Restorative cell therapy concepts in neurodegenerative diseases are aimed at replacing lost neurons. Despite advances in research on pluripotent stem cells, fetal tissue from routine elective abortions is still regarded as the only safe cell source. Progenitor cells isolated from distinct first-trimester fetal CNS regions have already been used in clinical trials and will be used again in a new multicenter trial funded by the European Union (TRANSEURO). Bacterial contamination of human fetal tissue poses a potential risk of causing infections in the brain of the recipient. Thus, effective methods of microbial decontamination and validation of these methods are required prior to approval of a neurorestorative cell therapy trial. We have developed a protocol consisting of subsequent washing steps at different stages of tissue processing. Efficacy of microbial decontamination was assessed on rat embryonic tissue incubated with high concentrations of defined microbe solutions including representative bacterial and fungal species. Experimental microbial contamination was reduced by several log ranks. Subsequently, we have analyzed the spectrum of microbial contamination and the effect of subsequent washing steps on aborted human fetal tissue; 47.7% of the samples taken during human fetal tissue processing were positive for a microbial contamination, but after washing, no sample exhibited bacterial growth. Our data suggest that human fetal tissue for neural repair can carry microbes of various species, highlighting the need for decontamination procedures. The decontamination protocol described in this report has been shown to be effective as no microbes could be detected at the end of the procedure.

Microbial diversity of extreme habitats in human homes.

PubMed

Savage, Amy M; Hills, Justin; Driscoll, Katherine; Fergus, Daniel J; Grunden, Amy M; Dunn, Robert R

2016-01-01

High-throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high-throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH, and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.

Humans as Superorganisms: How Microbes, Viruses, Imprinted Genes, and Other Selfish Entities Shape Our Behavior.

PubMed

Kramer, Peter; Bressan, Paola

2015-07-01

Psychologists and psychiatrists tend to be little aware that (a) microbes in our brains and guts are capable of altering our behavior; (b) viral DNA that was incorporated into our DNA millions of years ago is implicated in mental disorders; (c) many of us carry the cells of another human in our brains; and (d) under the regulation of viruslike elements, the paternally inherited and maternally inherited copies of some genes compete for domination in the offspring, on whom they have opposite physical and behavioral effects. This article provides a broad overview, aimed at a wide readership, of the consequences of our coexistence with these selfish entities. The overarching message is that we are not unitary individuals but superorganisms, built out of both human and nonhuman elements; it is their interaction that determines who we are. © The Author(s) 2015.

Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis

PubMed Central

Sung, Jaeyun; Kim, Seunghyeon; Cabatbat, Josephine Jill T.; Jang, Sungho; Jin, Yong-Su; Jung, Gyoo Yeol; Chia, Nicholas; Kim, Pan-Jun

2017-01-01

A system-level framework of complex microbe–microbe and host–microbe chemical cross-talk would help elucidate the role of our gut microbiota in health and disease. Here we report a literature-curated interspecies network of the human gut microbiota, called NJS16. This is an extensive data resource composed of ∼570 microbial species and 3 human cell types metabolically interacting through >4,400 small-molecule transport and macromolecule degradation events. Based on the contents of our network, we develop a mathematical approach to elucidate representative microbial and metabolic features of the gut microbial community in a given population, such as a disease cohort. Applying this strategy to microbiome data from type 2 diabetes patients reveals a context-specific infrastructure of the gut microbial ecosystem, core microbial entities with large metabolic influence, and frequently produced metabolic compounds that might indicate relevant community metabolic processes. Our network presents a foundation towards integrative investigations of community-scale microbial activities within the human gut. PMID:28585563

New strategy for drug discovery by large-scale association analysis of molecular networks of different species.

PubMed

Zhang, Bo; Fu, Yingxue; Huang, Chao; Zheng, Chunli; Wu, Ziyin; Zhang, Wenjuan; Yang, Xiaoyan; Gong, Fukai; Li, Yuerong; Chen, Xiaoyu; Gao, Shuo; Chen, Xuetong; Li, Yan; Lu, Aiping; Wang, Yonghua

2016-02-25

The development of modern omics technology has not significantly improved the efficiency of drug development. Rather precise and targeted drug discovery remains unsolved. Here a large-scale cross-species molecular network association (CSMNA) approach for targeted drug screening from natural sources is presented. The algorithm integrates molecular network omics data from humans and 267 plants and microbes, establishing the biological relationships between them and extracting evolutionarily convergent chemicals. This technique allows the researcher to assess targeted drugs for specific human diseases based on specific plant or microbe pathways. In a perspective validation, connections between the plant Halliwell-Asada (HA) cycle and the human Nrf2-ARE pathway were verified and the manner by which the HA cycle molecules act on the human Nrf2-ARE pathway as antioxidants was determined. This shows the potential applicability of this approach in drug discovery. The current method integrates disparate evolutionary species into chemico-biologically coherent circuits, suggesting a new cross-species omics analysis strategy for rational drug development.

Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA

PubMed Central

Camunas-Soler, Joan; Kertesz, Michael; De Vlaminck, Iwijn; Koh, Winston; Pan, Wenying; Martin, Lance; Neff, Norma F.; Okamoto, Jennifer; Wong, Ronald J.; Kharbanda, Sandhya; El-Sayed, Yasser; Blumenfeld, Yair; Stevenson, David K.; Shaw, Gary M.; Wolfe, Nathan D.; Quake, Stephen R.

2017-01-01

Blood circulates throughout the human body and contains molecules drawn from virtually every tissue, including the microbes and viruses which colonize the body. Through massive shotgun sequencing of circulating cell-free DNA from the blood, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome. Analyzing cumulative sequence data from 1,351 blood samples collected from 188 patients enabled us to assemble 7,190 contiguous regions (contigs) larger than 1 kbp, of which 3,761 are novel with little or no sequence homology in any existing databases. The vast majority of these novel contigs possess coding sequences, and we have validated their existence both by finding their presence in independent experiments and by performing direct PCR amplification. When their nearest neighbors are located in the tree of life, many of the organisms represent entirely novel taxa, showing that microbial diversity within the human body is substantially broader than previously appreciated. PMID:28830999

Metagenomic insights into the human gut resistome and the forces that shape it.

PubMed

Forslund, Kristoffer; Sunagawa, Shinichi; Coelho, Luis P; Bork, Peer

2014-03-01

We show how metagenomic analysis of the human gut antibiotic resistome, compared across large populations and against environmental or agricultural resistomes, suggests a strong anthropogenic cause behind increasing antibiotic resistance in bacteria. This area has been the subject of intense and polarized debate driven by economic and political concerns; therefore such recently available insights address an important need. We derive and compare antibiotic resistomes of human gut microbes from 832 individuals from ten different countries. We observe and describe significant differences between samples from these countries in the gut resistance potential, in line with expectations from antibiotic usage and exposure in medical and food production contexts. Our results imply roles for both of these sources in increased resistance among pathogens in recent history. In contrast, other available metadata such as age, body mass index, sex, or health status have little effect on the antibiotic resistance potential of human gut microbes. Also watch the Video Abstract. © 2014 WILEY Periodicals, Inc.

Nutrient cycle benchmarks for earth system land model

NASA Astrophysics Data System (ADS)

Zhu, Q.; Riley, W. J.; Tang, J.; Zhao, L.

2017-12-01

Projecting future biosphere-climate feedbacks using Earth system models (ESMs) relies heavily on robust modeling of land surface carbon dynamics. More importantly, soil nutrient (particularly, nitrogen (N) and phosphorus (P)) dynamics strongly modulate carbon dynamics, such as plant sequestration of atmospheric CO2. Prevailing ESM land models all consider nitrogen as a potentially limiting nutrient, and several consider phosphorus. However, including nutrient cycle processes in ESM land models potentially introduces large uncertainties that could be identified and addressed by improved observational constraints. We describe the development of two nutrient cycle benchmarks for ESM land models: (1) nutrient partitioning between plants and soil microbes inferred from 15N and 33P tracers studies and (2) nutrient limitation effects on carbon cycle informed by long-term fertilization experiments. We used these benchmarks to evaluate critical hypotheses regarding nutrient cycling and their representation in ESMs. We found that a mechanistic representation of plant-microbe nutrient competition based on relevant functional traits best reproduced observed plant-microbe nutrient partitioning. We also found that for multiple-nutrient models (i.e., N and P), application of Liebig's law of the minimum is often inaccurate. Rather, the Multiple Nutrient Limitation (MNL) concept better reproduces observed carbon-nutrient interactions.

Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle.

PubMed

Jupe, Julietta; Stam, Remco; Howden, Andrew J M; Morris, Jenny A; Zhang, Runxuan; Hedley, Pete E; Huitema, Edgar

2013-06-25

Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome sequences of both hosts and microbes, little is known about the signal interplay between them during infection. In particular, accurate descriptions of coordinate relationships between host and microbe transcriptional programs are lacking. Here, we explore the molecular interaction between the hemi-biotrophic broad host range pathogen Phytophthora capsici and tomato. Infection assays and use of a composite microarray allowed us to unveil distinct changes in both P. capsici and tomato transcriptomes, associated with biotrophy and the subsequent switch to necrotrophy. These included two distinct transcriptional changes associated with early infection and the biotrophy to necrotrophy transition that may contribute to infection and completion of the P. capsici lifecycle Our results suggest dynamic but highly regulated transcriptional programming in both host and pathogen that underpin P. capsici disease and hemi-biotrophy. Dynamic expression changes of both effector-coding genes and host factors involved in immunity, suggests modulation of host immune signaling by both host and pathogen. With new unprecedented detail on transcriptional reprogramming, we can now explore the coordinate relationships that drive host-microbe interactions and the basic processes that underpin pathogen lifestyles. Deliberate alteration of lifestyle-associated transcriptional changes may allow prevention or perhaps disruption of hemi-biotrophic disease cycles and limit damage caused by epidemics.

Quantifying the Global Nitrous Oxide Emissions Using a Trait-based Biogeochemistry Model

NASA Astrophysics Data System (ADS)

Zhuang, Q.; Yu, T.

2017-12-01

Nitrogen is an essential element for the global biogeochemical cycle. It is a key nutrient for organisms and N compounds including nitrous oxide significantly influence the global climate. The activities of bacteria and archaea are responsible for the nitrification and denitrification in a wide variety of environments, so microbes play an important role in the nitrogen cycle in soils. To date, most existing process-based models treated nitrification and denitrification as chemical reactions driven by soil physical variables including soil temperature and moisture. In general, the effect of microbes on N cycling has not been modeled in sufficient details. Soil organic carbon also affects the N cycle because it supplies energy to microbes. In my study, a trait-based biogeochemistry model quantifying N2O emissions from the terrestrial ecosystems is developed based on an extant process-based model TEM (Terrestrial Ecosystem Model). Specifically, the improvement to TEM includes: 1) Incorporating the N fixation process to account for the inflow of N from the atmosphere to biosphere; 2) Implementing the effects of microbial dynamics on nitrification process; 3) fully considering the effects of carbon cycling on N nitrogen cycling following the principles of stoichiometry of carbon and nitrogen in soils, plants, and microbes. The difference between simulations with and without the consideration of bacterial activity lies between 5% 25% based on climate conditions and vegetation types. The trait based module allows a more detailed estimation of global N2O emissions.

Use of bacterial co-cultures for the efficient production of chemicals.

PubMed

Jones, J Andrew; Wang, Xin

2017-12-02

The microbial production of chemicals has traditionally relied on a single engineered microbe to enable the complete bioconversion of substrate to final product. Recently, a growing fraction of research has transitioned towards employing a modular co-culture engineering strategy using multiple microbes growing together to facilitate a divide-and-conquer approach for chemical biosynthesis. Here, we review key success stories that leverage the unique advantages of co-culture engineering, while also addressing the critical concerns that will limit the wide-spread implementation of this technology. Future studies that address the need to monitor and control the population dynamics of each strain module, while maintaining robust flux routes towards a wide range of desired products will lead the efforts to realize the true potential of co-culture engineering. Copyright © 2017 Elsevier Ltd. All rights reserved.

Atmospheric Sampling of Microorganisms with UAS

NASA Astrophysics Data System (ADS)

Schmale, D. G., III

2017-12-01

Many microorganisms relevant to crops, domestic animals, and humans are transported over long distances through the atmosphere. Some of these atmospheric microbes catalyze the freezing of water at higher temperatures and facilitate the onset of precipitation. A few have crossed continents. New technologies are needed to study the movement of microorganisms in the atmosphere. We have used unmanned aircraft systems (UAS) to study the transport of microorganisms tens to hundreds of meters above the ground. These UAS are equipped with unique devices for collecting microbes in the atmosphere during flight. Autonomous systems enable teams of UAS to perform complex atmospheric sampling tasks, and coordinate flight missions with one another. Data collected with UAS can be used to validate and improve disease forecasting models along highways in the sky, connecting transport scales across farms, states, and continents. Though terrestrial environments are often considered a major contributor to atmospheric microbial aerosols, little is known about aquatic sources of microbial aerosols. Droplets containing microorganisms can aerosolize from the water surface, liberating them into the atmosphere. We are using teams of unmanned surface vehicles (USVs) and UAS to study the aerosolization of microbes from aquatic environments. Controlled flume studies using highspeed video have allowed us to observe unique aerosolization phenomena that can launch microbes out of the water and into the air. Unmanned systems may be used to excite the next generation of biologists and engineers, and raise important ethical considerations about the future of human-robot interactions.

A Mesocosm of Lactobacillus johnsonii, Bifidobacterium longum, and Escherichia coli in the mouse gut.

PubMed

Denou, Emmanuel; Rezzonico, Enea; Panoff, Jean-Michel; Arigoni, Fabrizio; Brüssow, Harald

2009-08-01

The relative contribution of competition and cooperation at the microbe-microbe level is not well understood for the bacteria constituting the gut microbiota. The high number and variability of human gut commensals have hampered the analysis. To get some insight into the question how so many different bacterial species can coexist in the mammalian gut, we studied the interaction between three human gut commensals (Escherichia coli K-12, Lactobacillus johnsonii NCC533, and Bifidobacterium longum NCC2705) in the intestine of gnotobiotic mice. The bacterial titers and their anatomical distribution were studied in the colonized mice. L. johnsonii achieved the highest cell counts in the stomach, while B. longum dominated the colon. The colon was also the intestinal location in which B. longum displayed the highest number of expressed genes, followed by the cecum and the small intestine. Addition of further bacterial strains led to strikingly different results. A Lactobacillus paracasei strain coexisted, while a second B. longum strain was excluded from the system. Notably, this strain lacked an operon involved in the degradation, import, and metabolism of mannosylated glycans. Subsequent introduction of the E. coli Nissle strain resulted in the elimination of L. johnsonii NCC533 and E. coli K-12, while B. longum NCC2705 showed a transient decrease in population size, demonstrating the dynamic nature of microbe-microbe interactions. The study of such simple interacting bacterial systems might help to derive some basic rules governing microbial ecology within the mammalian gut.

Network modules and hubs in plant-root fungal biomes

PubMed Central

Toju, Hirokazu; Yamamoto, Satoshi; Tanabe, Akifumi S.; Hayakawa, Takashi; Ishii, Hiroshi S.

2016-01-01

Terrestrial plants host phylogenetically and functionally diverse groups of below-ground microbes, whose community structure controls plant growth/survival in both natural and agricultural ecosystems. Therefore, understanding the processes by which whole root-associated microbiomes are organized is one of the major challenges in ecology and plant science. We here report that diverse root-associated fungi can form highly compartmentalized networks of coexistence within host roots and that the structure of the fungal symbiont communities can be partitioned into semi-discrete types even within a single host plant population. Illumina sequencing of root-associated fungi in a monodominant south beech forest revealed that the network representing symbiont–symbiont co-occurrence patterns was compartmentalized into clear modules, which consisted of diverse functional groups of mycorrhizal and endophytic fungi. Consequently, terminal roots of the plant were colonized by either of the two largest fungal species sets (represented by Oidiodendron or Cenococcum). Thus, species-rich root microbiomes can have alternative community structures, as recently shown in the relationships between human gut microbiome type (i.e. ‘enterotype’) and host individual health. This study also shows an analytical framework for pinpointing network hubs in symbiont–symbiont networks, leading to the working hypothesis that a small number of microbial species organize the overall root–microbiome dynamics. PMID:26962029

The immunomodulatory properties of probiotic microorganisms beyond their viability (ghost probiotics: proposal of paraprobiotic concept).

PubMed

Taverniti, Valentina; Guglielmetti, Simone

2011-08-01

The probiotic approach represents a potentially effective and mild alternative strategy for the prevention and treatment of either inflammatory or allergic diseases. Several studies have shown that different bacterial strains can exert their probiotic abilities by influencing the host's immune system, thereby modulating immune responses. However, the emerging concern regarding safety problems arising from the extensive use of live microbial cells is enhancing the interest in non-viable microorganisms or microbial cell extracts, as they could eliminate shelf-life problems and reduce the risks of microbial translocation and infection. The purpose of this review is to provide an overview of the scientific literature concerning studies in which dead microbial cells or crude microbial cell fractions have been used as health-promoting agents. Particular attention will be given to the modulation of host immune responses. Possible mechanisms determining the effect on the immune system will also be discussed. Finally, in the light of the FAO/WHO definition of probiotics, indicating that the word 'probiotic' should be restricted to products that contain live microorganisms, and considering the scientific evidence indicating that inactivated microbes can positively affect human health, we propose the new term 'paraprobiotic' to indicate the use of inactivated microbial cells or cell fractions to confer a health benefit to the consumer.

Kefir fermented milk and kefiran promote growth of Bifidobacterium bifidum PRL2010 and modulate its gene expression.

PubMed

Serafini, Fausta; Turroni, Francesca; Ruas-Madiedo, Patricia; Lugli, Gabriele Andrea; Milani, Christian; Duranti, Sabrina; Zamboni, Nicole; Bottacini, Francesca; van Sinderen, Douwe; Margolles, Abelardo; Ventura, Marco

2014-05-16

Bifidobacteria constitute one of the dominant groups of microorganisms colonizing the human gut of infants. Their ability to utilize various host-derived glycans as well as dietary carbohydrates has received considerable scientific attention. However, very little is known about the role of fermented foods, such as kefir, or their constituent glycans, such as kefiran, as substrates for bifidobacterial growth and for the modulation of the expression of bifidobacterial host-effector molecules. Here, we show that Bifidobacterium bifidum PRL2010 exhibits high growth performance among the bifidobacterial strains tested when cultivated on kefir and/or kefiran polymer. Furthermore, a 16S rRNA metagenomic approach revealed that the microbiota of kefir is modified upon the addition of PRL2010 cells to the kefir matrix. Finally, our results show that kefir and kefiran are able to influence the transcriptome of B. bifidum PRL2010 causing increased transcription of genes involved in the metabolism of dietary glycans as well as genes that act as host-microbe effector molecules such as pili. Altogether, these data support the use of kefir as a valuable means for the delivery of effective microbial cells in probiotic therapy. Copyright © 2014 Elsevier B.V. All rights reserved.

Sources and Bioactive Properties of Conjugated Dietary Fatty Acids.

PubMed

Hennessy, Alan A; Ross, Paul R; Fitzgerald, Gerald F; Stanton, Catherine

2016-04-01

The group of conjugated fatty acids known as conjugated linoleic acid (CLA) isomers have been extensively studied with regard to their bioactive potential in treating some of the most prominent human health malignancies. However, CLA isomers are not the only group of potentially bioactive conjugated fatty acids currently undergoing study. In this regard, isomers of conjugated α-linolenic acid, conjugated nonadecadienoic acid and conjugated eicosapentaenoic acid, to name but a few, have undergone experimental assessment. These studies have indicated many of these conjugated fatty acid isomers commonly possess anti-carcinogenic, anti-adipogenic, anti-inflammatory and immune modulating properties, a number of which will be discussed in this review. The mechanisms through which these bioactivities are mediated have not yet been fully elucidated. However, existing evidence indicates that these fatty acids may play a role in modulating the expression of several oncogenes, cell cycle regulators, and genes associated with energy metabolism. Despite such bioactive potential, interest in these conjugated fatty acids has remained low relative to the CLA isomers. This may be partly attributed to the relatively recent emergence of these fatty acids as bioactives, but also due to a lack of awareness regarding sources from which they can be produced. In this review, we will also highlight the common sources of these conjugated fatty acids, including plants, algae, microbes and chemosynthesis.

The Exopolysaccharide Matrix

PubMed Central

Koo, H.; Falsetta, M.L.; Klein, M.I.

2013-01-01

Many infectious diseases in humans are caused or exacerbated by biofilms. Dental caries is a prime example of a biofilm-dependent disease, resulting from interactions of microorganisms, host factors, and diet (sugars), which modulate the dynamic formation of biofilms on tooth surfaces. All biofilms have a microbial-derived extracellular matrix as an essential constituent. The exopolysaccharides formed through interactions between sucrose- (and starch-) and Streptococcus mutans-derived exoenzymes present in the pellicle and on microbial surfaces (including non-mutans) provide binding sites for cariogenic and other organisms. The polymers formed in situ enmesh the microorganisms while forming a matrix facilitating the assembly of three-dimensional (3D) multicellular structures that encompass a series of microenvironments and are firmly attached to teeth. The metabolic activity of microbes embedded in this exopolysaccharide-rich and diffusion-limiting matrix leads to acidification of the milieu and, eventually, acid-dissolution of enamel. Here, we discuss recent advances concerning spatio-temporal development of the exopolysaccharide matrix and its essential role in the pathogenesis of dental caries. We focus on how the matrix serves as a 3D scaffold for biofilm assembly while creating spatial heterogeneities and low-pH microenvironments/niches. Further understanding on how the matrix modulates microbial activity and virulence expression could lead to new approaches to control cariogenic biofilms. PMID:24045647

The exopolysaccharide matrix: a virulence determinant of cariogenic biofilm.

PubMed

Koo, H; Falsetta, M L; Klein, M I

2013-12-01

Many infectious diseases in humans are caused or exacerbated by biofilms. Dental caries is a prime example of a biofilm-dependent disease, resulting from interactions of microorganisms, host factors, and diet (sugars), which modulate the dynamic formation of biofilms on tooth surfaces. All biofilms have a microbial-derived extracellular matrix as an essential constituent. The exopolysaccharides formed through interactions between sucrose- (and starch-) and Streptococcus mutans-derived exoenzymes present in the pellicle and on microbial surfaces (including non-mutans) provide binding sites for cariogenic and other organisms. The polymers formed in situ enmesh the microorganisms while forming a matrix facilitating the assembly of three-dimensional (3D) multicellular structures that encompass a series of microenvironments and are firmly attached to teeth. The metabolic activity of microbes embedded in this exopolysaccharide-rich and diffusion-limiting matrix leads to acidification of the milieu and, eventually, acid-dissolution of enamel. Here, we discuss recent advances concerning spatio-temporal development of the exopolysaccharide matrix and its essential role in the pathogenesis of dental caries. We focus on how the matrix serves as a 3D scaffold for biofilm assembly while creating spatial heterogeneities and low-pH microenvironments/niches. Further understanding on how the matrix modulates microbial activity and virulence expression could lead to new approaches to control cariogenic biofilms.

Companion animals symposium: role of microbes in canine and feline health.

PubMed

Kil, D Y; Swanson, K S

2011-05-01

Whether in an ocean reef, a landfill, or a gastrointestinal tract (GIT), invisible communities of highly active and adaptable microbes prosper. Over time, mammals have developed a symbiosis with microbes that are important inhabitants not only in the GIT, but also in the mouth, skin, and urogenital tract. In the GIT, the number of commensal microbes exceeds the total number of host cells by at least 10 times. The GIT microbes play a critical role in nutritional, developmental, defensive, and physiologic processes in the host. Recent evidence also suggests a role of GIT microbes in metabolic phenotype and disease risk (e.g., obesity, metabolic syndrome) of the host. Proper balance is a key to maintaining GIT health. Balanced microbial colonization is also important for other body regions such as the oral cavity, the region with the greatest prevalence of disease in dogs and cats. A significant obstruction to studying microbial populations has been the lack of tools to identify and quantify microbial communities accurately and efficiently. Most of the current knowledge of microbial populations has been established by traditional cultivation methods that are not only laborious, time-consuming, and often inaccurate, but also greatly limited in scope. However, recent advances in molecular-based techniques have resulted in a dramatic improvement in studying microbial communities. These DNA-based high-throughput technologies have enabled us to more clearly characterize the identity and metabolic activity of microbes living in the host and their association with health and diseases. Despite this recent progress, however, published data pertaining to microbial communities of dogs and cats are still lacking in comparison with data in humans and other animals. More research is required to provide a more detailed description of the canine and feline microbiome and its role in health and disease.

Candida albicans Pathogenesis: Fitting within the Host-Microbe Damage Response Framework

PubMed Central

Kong, Eric F.; Tsui, Christina; Nguyen, M. Hong; Clancy, Cornelius J.; Fidel, Paul L.; Noverr, Mairi

2016-01-01

Historically, the nature and extent of host damage by a microbe were considered highly dependent on virulence attributes of the microbe. However, it has become clear that disease is a complex outcome which can arise because of pathogen-mediated damage, host-mediated damage, or both, with active participation from the host microbiota. This awareness led to the formulation of the damage response framework (DRF), a revolutionary concept that defined microbial virulence as a function of host immunity. The DRF outlines six classifications of host damage outcomes based on the microbe and the strength of the immune response. In this review, we revisit this concept from the perspective of Candida albicans, a microbial pathogen uniquely adapted to its human host. This fungus commonly colonizes various anatomical sites without causing notable damage. However, depending on environmental conditions, a diverse array of diseases may occur, ranging from mucosal to invasive systemic infections resulting in microbe-mediated and/or host-mediated damage. Remarkably, C. albicans infections can fit into all six DRF classifications, depending on the anatomical site and associated host immune response. Here, we highlight some of these diverse and site-specific diseases and how they fit the DRF classifications, and we describe the animal models available to uncover pathogenic mechanisms and related host immune responses. PMID:27430274

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets.

PubMed

Li, Lianwei; Ma, Zhanshan Sam

2016-08-16

The human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health-the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples, we discovered that only 49 communities (less than 1%) satisfied the neutral theory, and concluded that human microbial communities are not neutral in general. The 49 positive cases, although only a tiny minority, do demonstrate the existence of neutral processes. We realize that the traditional doctrine of microbial biogeography "Everything is everywhere, but the environment selects" first proposed by Baas-Becking resolves the apparent contradiction. The first part of Baas-Becking doctrine states that microbes are not dispersal-limited and therefore are neutral prone, and the second part reiterates that the freely dispersed microbes must endure selection by the environment. Therefore, in most cases, it is the host environment that ultimately shapes the community assembly and tip the human microbiome to niche regime.

Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets

PubMed Central

Li, Lianwei; Ma, Zhanshan (Sam)

2016-01-01

The human microbiome project (HMP) has made it possible to test important ecological theories for arguably the most important ecosystem to human health—the human microbiome. Existing limited number of studies have reported conflicting evidence in the case of the neutral theory; the present study aims to comprehensively test the neutral theory with extensive HMP datasets covering all five major body sites inhabited by the human microbiome. Utilizing 7437 datasets of bacterial community samples, we discovered that only 49 communities (less than 1%) satisfied the neutral theory, and concluded that human microbial communities are not neutral in general. The 49 positive cases, although only a tiny minority, do demonstrate the existence of neutral processes. We realize that the traditional doctrine of microbial biogeography “Everything is everywhere, but the environment selects” first proposed by Baas-Becking resolves the apparent contradiction. The first part of Baas-Becking doctrine states that microbes are not dispersal-limited and therefore are neutral prone, and the second part reiterates that the freely dispersed microbes must endure selection by the environment. Therefore, in most cases, it is the host environment that ultimately shapes the community assembly and tip the human microbiome to niche regime. PMID:27527985

Microbial modulation of host immunity with the small molecule phosphorylcholine.

PubMed

Clark, Sarah E; Weiser, Jeffrey N

2013-02-01

All microorganisms dependent on persistence in a host for survival rely on either hiding from or modulating host responses to infection. The small molecule phosphorylcholine, or choline phosphate (ChoP), is used for both of these purposes by a wide array of bacterial and parasitic microbes. While the mechanisms underlying ChoP acquisition and expression are diverse, a unifying theme is the use of ChoP to reduce the immune response to infection, creating an advantage for ChoP-expressing microorganisms. In this minireview, we discuss several benefits of ChoP expression during infection as well as how the immune system fights back against ChoP-expressing pathogens.

Trichomonas vaginalis origins, molecular pathobiology and clinical considerations.

PubMed

Hirt, Robert P; Sherrard, Jackie

2015-02-01

To integrate a selection of the most recent data on Trichomonas vaginalis origins, molecular cell biology and T. vaginalis interactions with the urogenital tract microbiota with trichomoniasis symptoms and clinical management. Transcriptomics and proteomics datasets are accumulating, facilitating the identification and prioritization of key target genes to study T. vaginalis pathobiology. Proteins involved in host sensing and cytoskeletal plasticity during T. vaginalis amoeboid transformation were identified. T. vaginalis was shown to secrete exosomes and a macrophage migration inhibitory factor-like protein that both influence host-parasite interactions. T. vaginalis co-infections with Mycoplasma species and viruses were shown to modulate the inflammatory responses, whereas T. vaginalis interactions with various Lactobacillus species inhibit parasite interactions with human cells. T. vaginalis infections were also shown to be associated with bacterial vaginosis. A broader range of health sequelae is also becoming apparent. Diagnostics for both women and men based on the molecular approaches are being refined, in particular for men. New developments in the molecular and cellular basis of T. vaginalis pathobiology combined with data on the urogenital tract microbiota and immunology have enriched our knowledge on human-microbe interactions that will contribute to increasing our capacity to prevent and treat T. vaginalis and other sexually transmitted infections.

Application of Sequence-based Methods in Human MicrobialEcology

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

Weng, Li; Rubin, Edward M.; Bristow, James

2005-08-29

Ecologists studying microbial life in the environment have recognized the enormous complexity of microbial diversity for many years, and the development of a variety of culture-independent methods, many of them coupled with high-throughput DNA sequencing, has allowed this diversity to be explored in ever greater detail. Despite the widespread application of these new techniques to the characterization of uncultivated microbes and microbial communities in the environment, their application to human health and disease has lagged behind. Because DNA based-techniques for defining uncultured microbes allow not only cataloging of microbial diversity, but also insight into microbial functions, investigators are beginning tomore » apply these tools to the microbial communities that abound on and within us, in what has aptly been called the second Human Genome Project. In this review we discuss the sequence-based methods for microbial analysis that are currently available and their application to identify novel human pathogens, improve diagnosis of known infectious diseases, and to advance understanding of our relationship with microbial communities that normally reside in and on the human body.« less

Anaerobic Probiotics: The Key Microbes for Human Health.

PubMed

El Enshasy, Hesham; Malik, Khairuddin; Malek, Roslinda Abd; Othman, Nor Zalina; Elsayed, Elsayed Ahmed; Wadaan, Mohammad

Human gastrointestinal microbiota (HGIM) incorporate a large number of microbes from different species. Anaerobic bacteria are the dominant organisms in this microbial consortium and play a crucial role in human health. In addition to their functional role as the main source of many essential metabolites for human health, they are considered as biotherapeutic agents in the regulation of different human metabolites. They are also important in the prevention and in the treatment of different physical and mental diseases. Bifidobacteria are the dominant anaerobic bacteria in HGIM and are widely used in the development of probiotic products for infants, children and adults. To develop bifidobacteria-based bioproducts, therefore, it is necessary to develop a large-scale biomass production platform based on a good understanding of the ideal medium and bioprocessing parameters for their growth and viability. In addition, high cell viability should be maintained during downstream processing and storage of probiotic cell powder or the final formulated product. In this work we review the latest information about the biology, therapeutic activities, cultivation and industrial production of bifidobacteria.

Gut Microbiota: Impact of probiotics, prebiotics, synbiotics, pharmabiotics and postbiotics on human health

USDA-ARS?s Scientific Manuscript database

Multidisciplinary approaches enabled a better understanding of the connection between human gut microbes and health. This knowledge is rapidly changing how we think about probiotics and related –biotics (prebiotics, synbiotics, pharmabiotics and postbiotics). Functional –omics approaches are very im...

Using Recombinant Lactococci as an Approach to Dissect the Immunomodulating Capacity of Surface Piliation in Probiotic Lactobacillus rhamnosus GG

PubMed Central

Nummenmaa, Elina; Mäkinen, Veli-Matti; Reunanen, Justus; Satokari, Reetta; de Vos, Willem M.; Palva, Ilkka; Palva, Airi

2013-01-01

Primarily arising from their well understood beneficial health effects, many lactobacilli strains are considered good candidates for use as probiotics in humans and animals. Lactobacillar probiosis can itself be best typified by the Lactobacillus rhamnosus GG strain, which, with its well-documented clinical benefits, has emerged as one of the most widely used probiotics in the food and health-supplement industries. Even so, many facets of its molecular mechanisms and limitations as a beneficial commensal bacterium still remain to be thoroughly explored and dissected. Because L. rhamnosus GG is one of only a few such strains exhibiting surface piliation (called SpaCBA), we sought to examine whether this particular type of cell-surface appendage has a discernible immunomodulating capacity and is able to trigger targeted responses in human immune-related cells. Thus, presented herein for this study, we recombinantly engineered Lactococcus lactis to produce native (and pilin-deleted) SpaCBA pili that were assembled in a structurally authentic form and anchored to the cell surface, and which had retained mucus-binding functionality. By using these recombinant lactococcal constructs, we were able to demonstrate that the SpaCBA pilus can be a contributory factor in the activation of Toll-like receptor 2-dependent signaling in HEK cells as well as in the modulation of pro- and anti-inflammatory cytokine (TNF-α, IL-6, IL-10, and IL-12) production in human monocyte-derived dendritic cells. From these data, we suggest that the recombinant-expressed and surface-anchored SpaCBA pilus, given its projected functioning in the gut environment, might be viewed as a new microbe-associated molecular pattern (MAMP)-like modulator of innate immunity. Accordingly, our study has brought some new insight to the molecular immunogenicity of the SpaCBA pilus, thus opening the way to a better understanding of its possible role in the multifaceted nature of L. rhamnosus GG probiosis within the human gut. PMID:23691212

Vaccine therapy for HIV: a historical review of the treatment of infectious diseases by active specific immunization with microbe-derived antigens.

PubMed

Burke, D S

1993-01-01

A review of the history of 'vaccine therapy' for infectious diseases is presented. The concept originated when Auzias-Turenne introduced 'syphilitic vaccination' or 'syphilization' as a treatment for syphilis in Paris in the mid-1800s; his clinical studies probably influenced Pasteur's successful rabies postexposure vaccine trials. Robert Koch in Berlin in the 1890s observed that inoculation of tuberculin into patients with tuberculosis induced an inflammatory response in affected tissues, and advocated 'tuberculin therapy'. Sir Almroth Wright in London in the early 20th century devised methods to measure changes in serum 'opsonizing' activity in response to therapeutic inoculations with microbe-derived vaccines. Since the advent of antibiotics, active specific immunization with microbe-derived antigens (vaccine therapy) has been largely forgotten as a strategy for treatment of infectious diseases. Advances in antigen production and in molecular immunology now permit new tactics to probe, analyse and selectively alter in vivo human immune responses to infectious microbes. Our recent demonstration that vaccine therapy can boost natural immunity to HIV in infected patients should rekindle interest in this approach.

Bees brought to their knees: microbes affecting honey bee health.

PubMed

Evans, Jay D; Schwarz, Ryan S

2011-12-01

The biology and health of the honey bee Apis mellifera has been of interest to human societies for centuries. Research on honey bee health is surging, in part due to new tools and the arrival of colony-collapse disorder (CCD), an unsolved decline in bees from parts of the United States, Europe, and Asia. Although a clear understanding of what causes CCD has yet to emerge, these efforts have led to new microbial discoveries and avenues to improve our understanding of bees and the challenges they face. Here we review the known honey bee microbes and highlight areas of both active and lagging research. Detailed studies of honey bee-pathogen dynamics will help efforts to keep this important pollinator healthy and will give general insights into both beneficial and harmful microbes confronting insect colonies. Copyright © 2011. Published by Elsevier Ltd.

Noisy neighbourhoods: quorum sensing in fungal–polymicrobial infections

PubMed Central

Dixon, Emily F.

2015-01-01

Summary Quorum sensing was once considered a way in which a species was able to sense its cell density and regulate gene expression accordingly. However, it is now becoming apparent that multiple microbes can sense particular quorum‐sensing molecules, enabling them to sense and respond to other microbes in their neighbourhood. Such interactions are significant within the context of polymicrobial disease, in which the competition or cooperation of microbes can alter disease progression. Fungi comprise a small but important component of the human microbiome and are in constant contact with bacteria and viruses. The discovery of quorum‐sensing pathways in fungi has led to the characterization of a number of interkingdom quorum‐sensing interactions. Here, we review the recent developments in quorum sensing in medically important fungi, and the implications these interactions have on the host's innate immune response. PMID:26243526

Bioactive sterols from marine resources and their potential benefits for human health.

PubMed

Kim, Se-Kwon; Van Ta, Quang

2012-01-01

Bioactive agents from marine resources have shown their valuable health beneficial effects. Therefore, increase knowledge on novel functional ingredients with biological activities from marine animal and microbe has gained much attention. Sterols are recognized as potential in development functional food ingredients and pharmaceutical agents. Marine resources, with a great diversity, can be a very interesting natural resource of sterols. This chapter focuses on biological activities of marine animal and microbe sterols with potential health beneficial applications in functional foods and pharmaceuticals. Copyright © 2012 Elsevier Inc. All rights reserved.

PATHWAYS IN MICROBE-INDUCED OBESITY

PubMed Central

Cox, Laura M.; Blaser, Martin J.

2013-01-01

Diet, host gene composition, and alterations in the intestinal microbiota can contribute to obesity. In microbe-induced obesity, metabolic changes stem from primary perturbation of the microbiota, consequent to modern changes in human biology. Microbiota disruption during early development can result in syndromes of metabolic dysfunction. We focus on the pathways involved in these interactions, particularly related to energy extraction and the role of inflammation in the metabolic phenotypes. Model physiologic systems and perturbations including gastric bypass surgery, pregnancy, and hibernation provide insight into the respective roles of the critical participants. PMID:23747247

Multidrug-resistant pathogens in the food supply.

PubMed

Doyle, Marjorie E

2015-04-01

Antimicrobial resistance, including multidrug resistance (MDR), is an increasing problem globally. MDR bacteria are frequently detected in humans and animals from both more- and less-developed countries and pose a serious concern for human health. Infections caused by MDR microbes may increase morbidity and mortality and require use of expensive drugs and prolonged hospitalization. Humans may be exposed to MDR pathogens through exposure to environments at health-care facilities and farms, livestock and companion animals, human food, and exposure to other individuals carrying MDR microbes. The Centers for Disease Control and Prevention classifies drug-resistant foodborne bacteria, including Campylobacter, Salmonella Typhi, nontyphoidal salmonellae, and Shigella, as serious threats. MDR bacteria have been detected in both meat and fresh produce. Salmonellae carrying genes coding for resistance to multiple antibiotics have caused numerous foodborne MDR outbreaks. While there is some level of resistance to antimicrobials in environmental bacteria, the widespread use of antibiotics in medicine and agriculture has driven the selection of a great variety of microbes with resistance to multiple antimicrobials. MDR bacteria on meat may have originated in veterinary health-care settings or on farms where animals are given antibiotics in feed or to treat infections. Fresh produce may be contaminated by irrigation or wash water containing MDR bacteria. Livestock, fruits, and vegetables may also be contaminated by food handlers, farmers, and animal caretakers who carry MDR bacteria. All potential sources of MDR bacteria should be considered and strategies devised to reduce their presence in foods. Surveillance studies have documented increasing trends in MDR in many pathogens, although there are a few reports of the decline of certain multidrug pathogens. Better coordination of surveillance programs and strategies for controlling use of antimicrobials need to be implemented in both human and animal medicine and agriculture and in countries around the world.

CHEMICAL MARKERS OF HUMAN WASTE CONTAMINATION: ANALYSIS OF UROBILIN AND PHARMACEUTICALS IN SOURCE WATERS

EPA Science Inventory

Giving public water authorities another tool to monitor and measure levels of human waste contamination of waters simply and rapidly would enhance public protection. Most of the methods used today detect such contamination by quantifying microbes occurring in feces in high enough...

Lentinula edodes-Derived Polysaccharide Alters the Spatial Structure of Gut Microbiota in Mice

PubMed Central

Xu, Xiaofei; Zhang, Xuewu

2015-01-01

Lentinula edodes-derived polysaccharides possess many therapeutic characteristics, including anti-tumor and immuno-modulation. The gut microbes play a critical role in modulation of immune function. However, the impact of Lentinula edodes-derived polysaccharides on the gut microbes have not yet been explored. In this study, high-throughput pyrosequencing technique was employed to investigate the effects of a new heteropolysaccharide L2 from Lentinula edodes on microbiota diversity and composition of small intestine, cecum, colon and distal end of colon (feces) in mice. The results demonstrated that along mouse intestine the microbiota exhibit distinctly different space distribution. L2 treatment reduced the diversity and evenness of gut microbiota along the intestine, especially in the cecum and colon. In the fecal microbial communities, the decrease of Bacteroidetes by significantly increasing Proteobacteria were observed, which were characterized by the increased Helicobacteraceae and reduced S24-7 at family level. Some OTUs, corresponding to Bacteroides acidifaciens, Alistipes and Helicobacter suncus, were found to be significantly increased in L2 treated-mice. In particular, 4 phyla Chloroflexi, Gemmatimonadetes, Nitrospirae and Planctomycetes are exclusively present in L2-treated mice. This is helpful for further demonstrating healthy action mechanism of Lentinula edodes-derived polysaccharide L2. PMID:25608087

Barley β-Glucans-Containing Food Enhances Probiotic Performances of Beneficial Bacteria

PubMed Central

Arena, Mattia P.; Caggianiello, Graziano; Fiocco, Daniela; Russo, Pasquale; Torelli, Michele; Spano, Giuseppe; Capozzi, Vittorio

2014-01-01

Currently, the majority of prebiotics in the market are derived from non-digestible oligosaccharides. Very few studies have focused on non-digestible long chain complex polysaccharides in relation to their potential as novel prebiotics. Cereals β-glucans have been investigated for immune-modulating properties and beneficial effects on obesity, cardiovascular diseases, diabetes, and cholesterol levels. Moreover, β-glucans have been reported to be highly fermentable by the intestinal microbiota in the caecum and colon, and can enhance both growth rate and lactic acid production of microbes isolated from the human intestine. In this work, we report the effects of food matrices containing barley β-glucans on growth and probiotic features of four Lactobacillus strains. Such matrices were able to improve the growth rate of the tested bacteria both in unstressed conditions and, importantly, after exposure to in vitro simulation of the digestive tract. Moreover, the effect of β-glucans-containing food on bacterial adhesion to enterocyte-like cells was analyzed and a positive influence on probiotic-enterocyte interaction was observed. PMID:24562330

Gut microbiota and metabolic syndrome.

PubMed

Festi, Davide; Schiumerini, Ramona; Eusebi, Leonardo Henry; Marasco, Giovanni; Taddia, Martina; Colecchia, Antonio

2014-11-21

Gut microbiota exerts a significant role in the pathogenesis of the metabolic syndrome, as confirmed by studies conducted both on humans and animal models. Gut microbial composition and functions are strongly influenced by diet. This complex intestinal "superorganism" seems to affect host metabolic balance modulating energy absorption, gut motility, appetite, glucose and lipid metabolism, as well as hepatic fatty storage. An impairment of the fine balance between gut microbes and host's immune system could culminate in the intestinal translocation of bacterial fragments and the development of "metabolic endotoxemia", leading to systemic inflammation and insulin resistance. Diet induced weight-loss and bariatric surgery promote significant changes of gut microbial composition, that seem to affect the success, or the inefficacy, of treatment strategies. Manipulation of gut microbiota through the administration of prebiotics or probiotics could reduce intestinal low grade inflammation and improve gut barrier integrity, thus, ameliorating metabolic balance and promoting weight loss. However, further evidence is needed to better understand their clinical impact and therapeutic use.

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors.

PubMed

Konermann, Silvana; Lotfy, Peter; Brideau, Nicholas J; Oki, Jennifer; Shokhirev, Maxim N; Hsu, Patrick D

2018-04-19

Class 2 CRISPR-Cas systems endow microbes with diverse mechanisms for adaptive immunity. Here, we analyzed prokaryotic genome and metagenome sequences to identify an uncharacterized family of RNA-guided, RNA-targeting CRISPR systems that we classify as type VI-D. Biochemical characterization and protein engineering of seven distinct orthologs generated a ribonuclease effector derived from Ruminococcus flavefaciens XPD3002 (CasRx) with robust activity in human cells. CasRx-mediated knockdown exhibits high efficiency and specificity relative to RNA interference across diverse endogenous transcripts. As one of the most compact single-effector Cas enzymes, CasRx can also be flexibly packaged into adeno-associated virus. We target virally encoded, catalytically inactive CasRx to cis elements of pre-mRNA to manipulate alternative splicing, alleviating dysregulated tau isoform ratios in a neuronal model of frontotemporal dementia. Our results present CasRx as a programmable RNA-binding module for efficient targeting of cellular RNA, enabling a general platform for transcriptome engineering and future therapeutic development. Copyright © 2018 Elsevier Inc. All rights reserved.

Gut microbiota and metabolic syndrome

PubMed Central

Festi, Davide; Schiumerini, Ramona; Eusebi, Leonardo Henry; Marasco, Giovanni; Taddia, Martina; Colecchia, Antonio

2014-01-01

Gut microbiota exerts a significant role in the pathogenesis of the metabolic syndrome, as confirmed by studies conducted both on humans and animal models. Gut microbial composition and functions are strongly influenced by diet. This complex intestinal “superorganism” seems to affect host metabolic balance modulating energy absorption, gut motility, appetite, glucose and lipid metabolism, as well as hepatic fatty storage. An impairment of the fine balance between gut microbes and host’s immune system could culminate in the intestinal translocation of bacterial fragments and the development of “metabolic endotoxemia”, leading to systemic inflammation and insulin resistance. Diet induced weight-loss and bariatric surgery promote significant changes of gut microbial composition, that seem to affect the success, or the inefficacy, of treatment strategies. Manipulation of gut microbiota through the administration of prebiotics or probiotics could reduce intestinal low grade inflammation and improve gut barrier integrity, thus, ameliorating metabolic balance and promoting weight loss. However, further evidence is needed to better understand their clinical impact and therapeutic use. PMID:25473159

Production of proinflammatory mediators by indoor air bacteria and fungal spores in mouse and human cell lines.

PubMed

Huttunen, Kati; Hyvärinen, Anne; Nevalainen, Aino; Komulainen, Hannu; Hirvonen, Maija-Riitta

2003-01-01

We compared the inflammatory and cytotoxic responses caused by household mold and bacteria in human and mouse cell lines. We studied the fungi Aspergillus versicolor, Penicillium spinulosum, and Stachybotrys chartarum and the bacteria Bacillus cereus, Pseudomonas fluorescens, and Streptomyces californicus for their cytotoxicity and ability to stimulate the production of inflammatory mediators in mouse RAW264.7 and human 28SC macrophage cell lines and in the human A549 lung epithelial cell line in 24-hr exposure to 10(5), 10(6), and 10(7) microbes/mL. We studied time dependency by terminating the exposure to 10(6) microbes/mL after 3, 6, 12, 24, and 48 hr. We analyzed production of the cytokines tumor necrosis factor-alpha and interleukins 6 and 1ss (TNF-alpha, IL-6, IL-1ss, respectively) and measured nitric oxide production using the Griess method, expression of inducible NO-synthase with Western Blot analysis, and cytotoxicity with the MTT-test. All bacteria strongly induced the production of TNF-alpha, IL-6 and, to a lesser extent, the formation of IL-1ss in mouse macrophages. Only the spores of Str. californicus induced the production of NO and IL-6 in both human and mouse cells. In contrast, exposure to fungal strains did not markedly increase the production of NO or any cytokine in the studied cell lines except for Sta. chartarum, which increased IL-6 production somewhat in human lung epithelial cells. These microbes were less cytotoxic to human cells than to mouse cells. On the basis of equivalent numbers of bacteria and spores of fungi added to cell cultures, the overall potency to stimulate the production of proinflammatory mediators decreased in the order Ps. fluorescens > Str. californicus > B. cereus > Sta. chartarum > A. versicolor > P. spinulosum. These data suggest that bacteria in water-damaged buildings should also be considered as causative agents of adverse inflammatory effects.

Production of proinflammatory mediators by indoor air bacteria and fungal spores in mouse and human cell lines.

PubMed Central

Huttunen, Kati; Hyvärinen, Anne; Nevalainen, Aino; Komulainen, Hannu; Hirvonen, Maija-Riitta

2003-01-01

We compared the inflammatory and cytotoxic responses caused by household mold and bacteria in human and mouse cell lines. We studied the fungi Aspergillus versicolor, Penicillium spinulosum, and Stachybotrys chartarum and the bacteria Bacillus cereus, Pseudomonas fluorescens, and Streptomyces californicus for their cytotoxicity and ability to stimulate the production of inflammatory mediators in mouse RAW264.7 and human 28SC macrophage cell lines and in the human A549 lung epithelial cell line in 24-hr exposure to 10(5), 10(6), and 10(7) microbes/mL. We studied time dependency by terminating the exposure to 10(6) microbes/mL after 3, 6, 12, 24, and 48 hr. We analyzed production of the cytokines tumor necrosis factor-alpha and interleukins 6 and 1ss (TNF-alpha, IL-6, IL-1ss, respectively) and measured nitric oxide production using the Griess method, expression of inducible NO-synthase with Western Blot analysis, and cytotoxicity with the MTT-test. All bacteria strongly induced the production of TNF-alpha, IL-6 and, to a lesser extent, the formation of IL-1ss in mouse macrophages. Only the spores of Str. californicus induced the production of NO and IL-6 in both human and mouse cells. In contrast, exposure to fungal strains did not markedly increase the production of NO or any cytokine in the studied cell lines except for Sta. chartarum, which increased IL-6 production somewhat in human lung epithelial cells. These microbes were less cytotoxic to human cells than to mouse cells. On the basis of equivalent numbers of bacteria and spores of fungi added to cell cultures, the overall potency to stimulate the production of proinflammatory mediators decreased in the order Ps. fluorescens > Str. californicus > B. cereus > Sta. chartarum > A. versicolor > P. spinulosum. These data suggest that bacteria in water-damaged buildings should also be considered as causative agents of adverse inflammatory effects. PMID:12515684

The microbes we eat: abundance and taxonomy of microbes consumed in a day's worth of meals for three diet types.

PubMed

Lang, Jenna M; Eisen, Jonathan A; Zivkovic, Angela M

2014-01-01

Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some "probiotic" health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 10(9) CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 10(6) and 1.4 × 10(6) CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked. Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbes, beyond probiotics taken as supplements-i.e., ingested with food-are important contributors to the composition, inter-individual variation, and function of our gut microbiota.

The microbes we eat: abundance and taxonomy of microbes consumed in a day’s worth of meals for three diet types

PubMed Central

Lang, Jenna M.; Eisen, Jonathan A.

2014-01-01

Far more attention has been paid to the microbes in our feces than the microbes in our food. Research efforts dedicated to the microbes that we eat have historically been focused on a fairly narrow range of species, namely those which cause disease and those which are thought to confer some “probiotic” health benefit. Little is known about the effects of ingested microbial communities that are present in typical American diets, and even the basic questions of which microbes, how many of them, and how much they vary from diet to diet and meal to meal, have not been answered. We characterized the microbiota of three different dietary patterns in order to estimate: the average total amount of daily microbes ingested via food and beverages, and their composition in three daily meal plans representing three different dietary patterns. The three dietary patterns analyzed were: (1) the Average American (AMERICAN): focused on convenience foods, (2) USDA recommended (USDA): emphasizing fruits and vegetables, lean meat, dairy, and whole grains, and (3) Vegan (VEGAN): excluding all animal products. Meals were prepared in a home kitchen or purchased at restaurants and blended, followed by microbial analysis including aerobic, anaerobic, yeast and mold plate counts as well as 16S rRNA PCR survey analysis. Based on plate counts, the USDA meal plan had the highest total amount of microbes at 1.3 × 109 CFU per day, followed by the VEGAN meal plan and the AMERICAN meal plan at 6 × 106 and 1.4 × 106 CFU per day respectively. There was no significant difference in diversity among the three dietary patterns. Individual meals clustered based on taxonomic composition independent of dietary pattern. For example, meals that were abundant in Lactic Acid Bacteria were from all three dietary patterns. Some taxonomic groups were correlated with the nutritional content of the meals. Predictive metagenome analysis using PICRUSt indicated differences in some functional KEGG categories across the three dietary patterns and for meals clustered based on whether they were raw or cooked. Further studies are needed to determine the impact of ingested microbes on the intestinal microbiota, the extent of variation across foods, meals and diets, and the extent to which dietary microbes may impact human health. The answers to these questions will reveal whether dietary microbes, beyond probiotics taken as supplements—i.e., ingested with food—are important contributors to the composition, inter-individual variation, and function of our gut microbiota. PMID:25538865

Gut microbial metabolite TMAO enhances platelet hyperreactivity and thrombosis risk

PubMed Central

Zhu, Weifei; Gregory, Jill C.; Org, Elin; Buffa, Jennifer A.; Gupta, Nilaksh; Wang, Zeneng; Li, Lin; Fu, Xiaoming; Wu, Yuping; Mehrabian, Margarete; Sartor, R. Balfour; McIntyre, Thomas M.; Silverstein, Roy L.; Tang, W.H. Wilson; DiDonato, Joseph A.; Brown, J. Mark; Lusis, Aldons J.; Hazen, Stanley L.

2016-01-01

SUMMARY Normal platelet function is critical to blood hemostasis and maintenance of a closed circulatory system. Heightened platelet reactivity, however, is associated with cardiometabolic diseases and enhanced potential for thrombotic events. We now show gut microbes, through generation of trimethylamine N-oxide (TMAO), directly contribute to platelet hyperreactivity and enhanced thrombosis potential. Plasma TMAO levels in subjects (N>4000) independently predicted incident (3 yr) thrombosis (heart attack, stroke) risk. Direct exposure of platelets to TMAO enhanced submaximal stimulus-dependent platelet activation from multiple agonists through augmented Ca2+ release from intracellular stores. Animal model studies employing dietary choline or TMAO, germ-free mice, and microbial transplantation, collectively confirm a role for gut microbiota and TMAO in modulating platelet hyperresponsiveness and thrombosis potential, and identify microbial taxa associated with plasma TMAO and thrombosis potential. Collectively, the present results reveal a previously unrecognized mechanistic link between specific dietary nutrients, gut microbes, platelet function, and thrombosis risk. PMID:26972052

Metagenomic recovery of phage genomes of uncultured freshwater actinobacteria.

PubMed

Ghai, Rohit; Mehrshad, Maliheh; Mizuno, Carolina Megumi; Rodriguez-Valera, Francisco

2017-01-01

Low-GC Actinobacteria are among the most abundant and widespread microbes in freshwaters and have largely resisted all cultivation efforts. Consequently, their phages have remained totally unknown. In this work, we have used deep metagenomic sequencing to assemble eight complete genomes of the first tailed phages that infect freshwater Actinobacteria. Their genomes encode the actinobacterial-specific transcription factor whiB, frequently found in mycobacteriophages and also in phages infecting marine pelagic Actinobacteria. Its presence suggests a common and widespread strategy of modulation of host transcriptional machinery upon infection via this transcriptional switch. We present evidence that some whiB-carrying phages infect the acI lineage of Actinobacteria. At least one of them encodes the ADP-ribosylating component of the widespread bacterial AB toxins family (for example, clostridial toxin). We posit that the presence of this toxin reflects a 'trojan horse' strategy, providing protection at the population level to the abundant host microbes against eukaryotic predators.

Multiscale Simulation of Microbe Structure and Dynamics

PubMed Central

Joshi, Harshad; Singharoy, Abhishek; Sereda, Yuriy V.; Cheluvaraja, Srinath C.; Ortoleva, Peter J.

2012-01-01

A multiscale mathematical and computational approach is developed that captures the hierarchical organization of a microbe. It is found that a natural perspective for understanding a microbe is in terms of a hierarchy of variables at various levels of resolution. This hierarchy starts with the N -atom description and terminates with order parameters characterizing a whole microbe. This conceptual framework is used to guide the analysis of the Liouville equation for the probability density of the positions and momenta of the N atoms constituting the microbe and its environment. Using multiscale mathematical techniques, we derive equations for the co-evolution of the order parameters and the probability density of the N-atom state. This approach yields a rigorous way to transfer information between variables on different space-time scales. It elucidates the interplay between equilibrium and far-from-equilibrium processes underlying microbial behavior. It also provides framework for using coarse-grained nanocharacterization data to guide microbial simulation. It enables a methodical search for free-energy minimizing structures, many of which are typically supported by the set of macromolecules and membranes constituting a given microbe. This suite of capabilities provides a natural framework for arriving at a fundamental understanding of microbial behavior, the analysis of nanocharacterization data, and the computer-aided design of nanostructures for biotechnical and medical purposes. Selected features of the methodology are demonstrated using our multiscale bionanosystem simulator DeductiveMultiscaleSimulator. Systems used to demonstrate the approach are structural transitions in the cowpea chlorotic mosaic virus, RNA of satellite tobacco mosaic virus, virus-like particles related to human papillomavirus, and iron-binding protein lactoferrin. PMID:21802438

Modulation of Gut Microbiota-Brain Axis by Probiotics, Prebiotics, and Diet.

PubMed

Liu, Xiaofei; Cao, Shangqing; Zhang, Xuewu

2015-09-16

There exists a bidirectional communication system between the gastrointestinal tract and the brain. Increasing evidence shows that gut microbiota can play a critical role in this communication; thus, the concept of a gut microbiota and brain axis is emerging. Here, we review recent findings in the relationship between intestinal microbes and brain function, such as anxiety, depression, stress, autism, learning, and memory. We highlight the advances in modulating brain development and behavior by probiotics, prebiotics, and diet through the gut microbiota-brain axis. A variety of mechanisms including immune, neural, and metabolic pathways may be involved in modulation of the gut microbiota-brain axis. We also discuss some future challenges. A deeper understanding of the relationship between the gut bacteria and their hosts is implicated in developing microbial-based therapeutic strategies for brain disorders.

Toward a microbial Neolithic revolution in buildings.

PubMed

Thaler, David S

2016-03-29

The Neolithic revolution--the transition of our species from hunter and gatherer to cultivator--began approximately 14,000 years ago and is essentially complete for macroscopic food. Humans remain largely pre-Neolithic in our relationship with microbes but starting with the gut we continue our hundred-year project of approaching the ability to assess and cultivate benign microbiomes in our bodies. Buildings are analogous to the body and it is time to ask what it means to cultivate benign microbiomes in our built environment. A critical distinction is that we have not found, or invented, niches in buildings where healthful microbial metabolism occurs and/or could be cultivated. Key events affecting the health and healthfulness of buildings such as a hurricane leading to a flood or a burst pipe occur only rarely and unpredictably. The cause may be transient but the effects can be long lasting and, e.g., for moisture damage, cumulative. Non-invasive "building tomography" could find moisture and "sentinel microbes" could record the integral of transient growth. "Seed" microbes are metabolically inert cells able to grow when conditions allow. All microbes and their residue present actinic molecules including immunological epitopes (molecular shapes). The fascinating hygiene and microbial biodiversity hypotheses propose that a healthy immune system requires exposure to a set of microbial epitopes that is rich in diversity. A particular conjecture is that measures of the richness of diversity derived from microbiome next-generation sequencing (NGS) can be mechanistically coupled to--rather than merely correlated with some measures of--human health. These hypotheses and conjectures inspire workers and funders but an alternative is also consequent to the first Neolithic revolution: That the genetic uniformity of contemporary foods may also decrease human exposure to molecular biodiversity in a heath-relevant manner. Understanding the consequences--including the unintended consequences of the first Neolithic revolution--will inform and help us benignly implement the second--the microbial--Neolithic revolution.

Chamber Bioaerosol Study: Outdoor Air and Human Occupants as Sources of Indoor Airborne Microbes

PubMed Central

Adams, Rachel I.; Bhangar, Seema; Pasut, Wilmer; Arens, Edward A.; Taylor, John W.; Lindow, Steven E.; Nazaroff, William W.; Bruns, Thomas D.

2015-01-01

Human occupants are an important source of microbes in indoor environments. In this study, we used DNA sequencing of filter samples to assess the fungal and bacterial composition of air in an environmental chamber under different levels of occupancy, activity, and exposed or covered carpeting. In this office-like, mechanically ventilated environment, results showed a strong influence of outdoor-derived particles, with the indoor microbial composition tracking that of outdoor air for the 2-hour sampling periods. The number of occupants and their activity played a significant but smaller role influencing the composition of indoor bioaerosols. Human-associated taxa were observed but were not particularly abundant, except in the case of one fungus that appeared to be transported into the chamber on the clothing of a study participant. Overall, this study revealed a smaller signature of human body-associated taxa than had been expected based on recent studies of indoor microbiomes, suggesting that occupants may not exert a strong influence on bioaerosol microbial composition in a space that, like many offices, is well ventilated with air that is moderately filtered and moderately occupied. PMID:26024222

Master manipulators: an update on Legionella pneumophila Icm/Dot translocated substrates and their host targets

PubMed Central

Isaac, Dervla T; Isberg, Ralph

2014-01-01

Macrophages are the front line of immune defense against invading microbes. Microbes, however, have evolved numerous and diverse mechanisms to thwart these host immune defenses and thrive intracellularly. Legionella pneumophila, a Gram-negative pathogen of amoebal and mammalian phagocytes, is one such microbe. In humans, it causes a potentially fatal pneumonia referred to as Legionnaires' disease. Armed with the Icm/Dot type IV secretion system, which is required for virulence, and approximately 300 translocated proteins, Legionella is able to enter host cells, direct the biogenesis of its own vacuolar compartment, and establish a replicative niche, where it grows to high levels before lysing the host cell. Efforts to understand the pathogenesis of this bacterium have focused on characterizing the molecular activities of its many effectors. In this article, we highlight recent strides that have been made in understanding how Legionella effectors mediate host-pathogen interactions. PMID:24762308

Pathological and therapeutic interactions between bacteriophages, microbes and the host in inflammatory bowel disease.

PubMed

Babickova, Janka; Gardlik, Roman

2015-10-28

The intestinal microbiome is a dynamic system of interactions between the host and its microbes. Under physiological conditions, a fine balance and mutually beneficial relationship is present. Disruption of this balance is a hallmark of inflammatory bowel disease (IBD). Whether an altered microbiome is the consequence or the cause of IBD is currently not fully understood. The pathogenesis of IBD is believed to be a complex interaction between genetic predisposition, the immune system and environmental factors. In the recent years, metagenomic studies of the human microbiome have provided useful data that are helping to assemble the IBD puzzle. In this review, we summarize and discuss current knowledge on the composition of the intestinal microbiota in IBD, host-microbe interactions and therapeutic possibilities using bacteria in IBD. Moreover, an outlook on the possible contribution of bacteriophages in the pathogenesis and therapy of IBD is provided.

Neutrophil evasion strategies by Streptococcus pneumoniae and Staphylococcus aureus.

PubMed

Lewis, Megan L; Surewaard, Bas G J

2018-03-01

Humans are well equipped to defend themselves against bacteria. The innate immune system employs diverse mechanisms to recognize, control and initiate a response that can destroy millions of different microbes. Microbes that evade the sophisticated innate immune system are able to escape detection and could become pathogens. The pathogens Streptococcus pneumoniae and Staphylococcus aureus are particularly successful due to the development of a wide variety of virulence strategies for bacterial pathogenesis and they invest significant efforts towards mechanisms that allow for neutrophil evasion. Neutrophils are a primary cellular defense and can rapidly kill invading microbes, which is an indispensable function for maintaining host health. This review compares the key features of Streptococcus pneumoniae and Staphylococcus aureus in epidemiology, with a specific focus on virulence mechanisms utilized to evade neutrophils in bacterial pathogenesis. It is important to understand the complex interactions between pathogenic bacteria and neutrophils so that we can disrupt the ability of pathogens to cause disease.

Extending viability of Lactobacillus plantarum and Lactobacillus johnsonii by microencapsulation in alginate microgels.

PubMed

Tiani, Kendra A; Yeung, Timothy W; McClements, D Julian; Sela, David A

2018-03-01

To investigate whether microencapsulation of Lactobacillus in alginate microbeads will lead to increased longevity during refrigerated storage or simulated digestion. Microscopy was used to confirm that Lactobacillus plantarum ATCC BAA-793 and Lactobacillus johnsonii ATCC 33200 were immobilised within the microbeads and laser scattering analysis was used to determine the mean diameter of the microbeads. The number of viable cells were enumerated throughout refrigerated storage and simulated digestion experiments. Microencapsulation was shown to have differing effects on viability depending on the species, but led to extended viability during refrigerated storage and simulated digestion in L. johnsonii and L. plantarum respectively. Fermented functional foods contain microbes beneficial to human health. However, extended shelf storage and the harsh environment of the GI tract significantly reduces the number of viable microbes reaching the consumer. Microencapsulation allows beneficial microbes to reach the gut of the consumer in higher numbers, and thus confer greater health benefits.

Summer Prostate Cancer Research Training Program

DTIC Science & Technology

2017-09-01

Biology, and Human Toxicology Graduate Programs. Michael Henry, PhD; Associate Professor, Department of Physiology & Biophysics (319-335- 7886) http...addition, PSA has also been demonstrated to be antigenic and capable of inducing specific immune responses in both humans and mice. However, up to...for animal immunization. Both BCG and Ad microbes have been demonstrated to be safe and effective for antigen delivery in humans and mice. Since

Dense water plumes modulate richness and productivity of deep sea microbes.

PubMed

Luna, Gian Marco; Chiggiato, Jacopo; Quero, Grazia Marina; Schroeder, Katrin; Bongiorni, Lucia; Kalenitchenko, Dimitri; Galand, Pierre E

2016-12-01

Growing evidence indicates that dense water formation and flow over the continental shelf is a globally relevant oceanographic process, potentially affecting microbial assemblages down to the deep ocean. However, the extent and consequences of this influence have yet to be investigated. Here it is shown that dense water propagation to the deep ocean increases the abundance of prokaryotic plankton, and stimulates carbon production and organic matter degradation rates. Dense waters spilling off the shelf modifies community composition of deep sea microbial assemblages, leading to the increased relevance of taxa likely originating from the sea surface and the seafloor. This phenomenon can be explained by a combination of factors that interplay during the dense waters propagation, such as the transport of surface microbes to the ocean floor (delivering in our site 0.1 megatons of C), the stimulation of microbial metabolism due to increased ventilation and nutrients availability, the sediment re-suspension, and the mixing with ambient waters along the path. Thus, these results highlight a hitherto unidentified role for dense currents flowing over continental shelves in influencing deep sea microbes. In light of climate projections, this process will affect significantly the microbial functioning and biogeochemical cycling of large sectors of the ocean interior. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

Rhizobacterial colonization of roots modulates plant volatile emission and enhances the attraction of a parasitoid wasp to host-infested plants.

PubMed

Pangesti, Nurmi; Weldegergis, Berhane T; Langendorf, Benjamin; van Loon, Joop J A; Dicke, Marcel; Pineda, Ana

2015-08-01

Beneficial root-associated microbes modify the physiological status of their host plants and affect direct and indirect plant defense against insect herbivores. While the effects of these microbes on direct plant defense against insect herbivores are well described, knowledge of the effect of the microbes on indirect plant defense against insect herbivores is still limited. In this study, we evaluate the role of the rhizobacterium Pseudomonas fluorescens WCS417r in indirect plant defense against the generalist leaf-chewing insect Mamestra brassicae through a combination of behavioral, chemical, and gene-transcriptional approaches. We show that rhizobacterial colonization of Arabidopsis thaliana roots results in an increased attraction of the parasitoid Microplitis mediator to caterpillar-infested plants. Volatile analysis revealed that rhizobacterial colonization suppressed the emission of the terpene (E)-α-bergamotene and the aromatics methyl salicylate and lilial in response to caterpillar feeding. Rhizobacterial colonization decreased the caterpillar-induced transcription of the terpene synthase genes TPS03 and TPS04. Rhizobacteria enhanced both the growth and the indirect defense of plants under caterpillar attack. This study shows that rhizobacteria have a high potential to enhance the biocontrol of leaf-chewing herbivores based on enhanced attraction of parasitoids.

Bio-prospectus of cadmium bioadsorption by lactic acid bacteria to mitigate health and environmental impacts.

PubMed

Kumar, Narendra; Kumari, Vandna; Ram, Chand; Thakur, Kiran; Tomar, Sudhir Kumar

2018-02-01

Foodstuffs and water are the key sources of cadmium biomagnifiaction. The available strategies to mitigate this problem are unproductive and expensive for practical large-scale use. Biological decontamination of metals through environmental microbes has been known since long time, whereas lactic acid bacteria (LAB) have not been extensively studied for this purpose. The LAB are known for maintaining homeostasis and suppression of pathogens in humans and animals. They also play a vital role in bioremediation of certain heavy metals. Recently in-vivo research findings strongly complement the in-vitro results in relation to decreased total body cadmium burden in animal model. This review summarizes the currently available information on impact of toxic metal (Cd) on human and animal health as well as cadmium sequestration through microbes placed broadly, whereas preeminent attention grabbed on LAB-cadmium interaction to explore their possible role in bioremediation of cadmium from foods and environment to safeguard human as well as environment health.

Microbiota in Allergy and Asthma and the Emerging Relationship with the Gut Microbiome

PubMed Central

Fujimura, Kei E.; Lynch, Susan V.

2015-01-01

Asthma and atopy, classically associated with hyper-activation of the T helper 2 (Th2) arm of adaptive immunity, are amongst the most common chronic illnesses worldwide. Emerging evidence relates atopy and asthma to the composition and function of the human microbiome, the collection of microbes that reside in and on and interact with the human body. The ability to interrogate microbial ecology of the human host is due in large part to recent technological developments that permit identification of microbes and their products using culture-independent molecular detection techniques. In this review we explore the roles of respiratory, gut and environmental microbiomes in asthma and allergic disease development, manifestation and attenuation. Though still a relatively nascent field of research, evidence to date suggests that the airway and/or gut microbiome may represent fertile targets for prevention or management of allergic asthma and other diseases in which adaptive immune dysfunction is a prominent feature. PMID:25974301

Heterogeneity of Human CD4(+) T Cells Against Microbes.

PubMed

Sallusto, Federica

2016-05-20

CD4(+) T helper (Th) cells play a central role in the adaptive immune response by providing help to B cells and cytotoxic T cells and by releasing different types of cytokines in tissues to mediate protection against a wide range of pathogenic microorganisms. These functions are performed by different types of Th cells endowed with distinct migratory capacities and effector functions. Here we discuss how studies of the human T cell response to microbes have advanced our understanding of Th cell functional heterogeneity, in particular with the discovery of a distinct Th1 subset involved in the response to Mycobacteria and the characterization of two types of Th17 cells specific for extracellular bacteria or fungi. We also review new approaches to dissect at the clonal level the human CD4(+) T cell response induced by pathogens or vaccines that have revealed an unexpected degree of intraclonal diversification and propose a progressive and selective model of CD4(+) T cell differentiation.

Microbiota in allergy and asthma and the emerging relationship with the gut microbiome.

PubMed

Fujimura, Kei E; Lynch, Susan V

2015-05-13

Asthma and atopy, classically associated with hyper-activation of the T helper 2 (Th2) arm of adaptive immunity, are among the most common chronic illnesses worldwide. Emerging evidence relates atopy and asthma to the composition and function of the human microbiome, the collection of microbes that reside in and on and interact with the human body. The ability to interrogate microbial ecology of the human host is due in large part to recent technological developments that permit identification of microbes and their products using culture-independent molecular detection techniques. In this review we explore the roles of respiratory, gut, and environmental microbiomes in asthma and allergic disease development, manifestation, and attenuation. Though still a relatively nascent field of research, evidence to date suggests that the airway and/or gut microbiome may represent fertile targets for prevention or management of allergic asthma and other diseases in which adaptive immune dysfunction is a prominent feature. Copyright © 2015 Elsevier Inc. All rights reserved.

Genomics, the origins of agriculture, and our changing microbe-scape: time to revisit some old tales and tell some new ones.

PubMed

Harper, Kristin N; Armelagos, George J

2013-12-01

Though agriculture is often viewed as one of humanity's crowning achievements, skeletal evidence indicates that dependence on domesticated plants and animals was accompanied by an increase in infectious disease. Scientists have proposed that many important infections emerged in the period following the advent of agriculture, as a result of newly dense populations and novel proximity to domestic animals that served as reservoirs for novel pathogens. Here, we review genomic evidence regarding pathogen origins, analyzing these data using the epidemiological transition framework. Genetic information has forced us to reconsider how and when many important pathogens emerged; it appears that a number of infections thought to result from contact with domesticated animals arose much earlier than agriculture was adopted. We also consider the broader effect of agriculture upon the microbiome, exploring potential consequences for human health. We end by discussing the changes in the human microbe-scape we are likely to see in the future. Copyright © 2013 Wiley Periodicals, Inc.

Generating Germ-Free Drosophila to Study Gut-Microbe Interactions: Protocol to Rear Drosophila Under Axenic Conditions.

PubMed

Kietz, Christa; Pollari, Vilma; Meinander, Annika

2018-06-22

As several diseases have been linked to dysbiosis of the human intestinal microflora, manipulation of the microbiota has emerged as an exciting new strategy for potentially treating and preventing diseases. However, the human microbiota consists of a plethora of different species, and distinguishing the impact of a specific bacterial species on human health is challenging. In tackling this challenge, the fruit fly Drosophila melanogaster, with its far simpler microbial composition, has emerged as a powerful model for unraveling host-microbe interactions. To study the interplay between the resident commensal microbiome and the host, flies can be made germ-free, or axenic. To elucidate the impact of specific bacteria, axenic flies can then be re-introduced to specific microbial species. In this unit, we provide a step-by-step protocol on how to rear Drosophila melanogaster under axenic conditions and confirm the axenity of flies. © 2018 by John Wiley & Sons, Inc. © 2018 John Wiley & Sons, Inc.

Symbiotic Association with Mycoplasma hominis Can Influence Growth Rate, ATP Production, Cytolysis and Inflammatory Response of Trichomonas vaginalis

PubMed Central

Margarita, Valentina; Rappelli, Paola; Dessì, Daniele; Pintus, Gianfranco; Hirt, Robert P.; Fiori, Pier L.

2016-01-01

The symbiosis between the parasitic protist Trichomonas vaginalis and the opportunistic bacterium Mycoplasma hominis is the only one currently described involving two obligate human mucosal symbionts with pathogenic capabilities that can cause independent diseases in the same anatomical site: the lower urogenital tract. Although several aspects of this intriguing microbial partnership have been investigated, many questions on the influence of this symbiosis on the parasite pathobiology still remain unanswered. Here, we examined with in vitro cultures how M. hominis could influence the pathobiology of T. vaginalis by investigating the influence of M. hominis on parasite replication rate, haemolytic activity and ATP production. By comparing isogenic mycoplasma-free T. vaginalis and parasites stably associated with M. hominis we could demonstrate that the latter show a higher replication rate, increased haemolytic activity and are able to produce larger amounts of ATP. In addition, we demonstrated in a T. vaginalis-macrophage co-culture system that M. hominis could modulate an aspect of the innate immuno-response to T. vaginalis infections by influencing the production of nitric oxide (NO) by human macrophages, with the parasite-bacteria symbiosis outcompeting the human cells for the key substrate arginine. These results support a model in which the symbiosis between T. vaginalis and M. hominis influences host-microbes interactions to the benefit of both microbial partners during infections and to the detriment of their host. PMID:27379081

Adsorption of surfactant protein D from human respiratory secretions by carbon nanotubes and polystyrene nanoparticles depends on nanomaterial surface modification and size

PubMed Central

Marchetti, Magda; Shaffer, Milo S. P.; Zambianchi, Martina; Chen, Shu; Superti, Fabiana; Schwander, Stephan; Gow, Andrew; Zhang, Junfeng (Jim); Chung, Kian Fan; Ryan, Mary P.; Porter, Alexandra E.; Tetley, Teresa D.

2015-01-01

The alveolar respiratory unit constitutes one of the main targets of inhaled nanoparticles; the effect of engineered nanomaterials (NMs) on human health is largely unknown. Surfactant protein D (SP-D) is synthesized by alveolar type II epithelial cells and released into respiratory secretions; its main function is in immune defence, notably against inhaled microbes. SP-D also plays an important role in modulating an appropriate inflammatory response in the lung, and reduced SP-D is associated with a number of inflammatory lung diseases. Adsorption of SP-D to inhaled NMs may facilitate their removal via macrophage phagocytosis. This study addresses the hypothesis that the chemistry, size and surface modification of engineered NMs will impact on their interaction with, and adsorption of, SP-D. To this purpose, we have examined the interactions between SP-D in human lung lavage and two NMs, carbon nanotubes and polystyrene nanoparticles, with different surface functionalization. We have demonstrated that particle size, functionalization and concentration affect the adsorption of SP-D from human lung lavage. Functionalization with negatively charged groups enhanced the amount of SP-D binding. While SP-D binding would be expected to enhance macrophage phagocytosis, these results suggest that the degree of binding is markedly affected by the physicochemistry of the NM and that deposition of high levels of some nanoparticles within the alveolar unit might deplete SP-D levels and affect alveolar immune defence mechanisms. PMID:25533095

Antimicrobial Pesticides

MedlinePlus

... requires special tests to ensure efficacy of public health pesticides when the pests are invisible disease-causing microbes, rather than insects or rodents that may be harboring disease organisms. Determining human and ecological risks from exposure to antimicrobial pesticides ...

Kingdom-agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities

PubMed Central

Norman, Jason M.; Handley, Scott A.; Virgin, Herbert W.

2014-01-01

Advanced sequencing techniques have shown that bacteria are not the only complex and important microbes in the human intestine. Non-bacterial organisms, particularly the virome and the mycobiome, are important regulators of intestinal immunity and inflammation. The virome is mucosal and systemic; it can alter the host response to bacteria and interact with host genes and bacteria to contribute to disease pathogenesis. The human mycobiome is also complex and can contribute to intestinal inflammation. We review what has recently been learned about the non-bacterial and non-archaeal microbes in the gastrointestinal tract, discussing their potential effects on health and disease and analytical approaches for their study. Studies of associations between the microbiome and intestinal pathology should incorporate kingdom-agnostic approaches if we are to fully understand intestinal health and disease. PMID:24508599

Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth

PubMed Central

Marcy, Yann; Ouverney, Cleber; Bik, Elisabeth M.; Lösekann, Tina; Ivanova, Natalia; Martin, Hector Garcia; Szeto, Ernest; Platt, Darren; Hugenholtz, Philip; Relman, David A.; Quake, Stephen R.

2007-01-01

We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach enables single-cell genetic analysis of any uncultivated minority member of a microbial community. PMID:17620602

Time of day and eating behaviors are associated with the composition and function of the human gastrointestinal microbiota.

PubMed

Kaczmarek, Jennifer L; Musaad, Salma Ma; Holscher, Hannah D

2017-11-01

Background: Preclinical research has shown that the gastrointestinal microbiota exhibits circadian rhythms and that the timing of food consumption can affect the composition and function of gut microbes. However, there is a dearth of knowledge on these relations in humans. Objective: We aimed to determine whether human gastrointestinal microbes and bacterial metabolites were associated with time of day or behavioral factors, including eating frequency, percentage of energy consumed early in the day, and overnight-fast duration. Design: We analyzed 77 fecal samples collected from 28 healthy men and women. Fecal DNA was extracted and sequenced to determine the relative abundances of bacterial operational taxonomic units (OTUs). Gas chromatography-mass spectroscopy was used to assess short-chain fatty acid concentrations. Eating frequency, percentage of energy consumed before 1400, and overnight-fast duration were determined from dietary records. Data were analyzed by linear mixed models or generalized linear mixed models, which controlled for fiber intake, sex, age, body mass index, and repeated sampling within each participant. Each OTU and metabolite were tested as the outcome in a separate model. Results: Acetate, propionate, and butyrate concentrations decreased throughout the day ( P = 0.006, 0.04, and 0.002, respectively). Thirty-five percent of bacterial OTUs were associated with time. In addition, relations were observed between gut microbes and eating behaviors, including eating frequency, early energy consumption, and overnight-fast duration. Conclusions: These results indicate that the human gastrointestinal microbiota composition and function vary throughout the day, which may be related to the circadian biology of the human body, the microbial community itself, or human eating behaviors. Behavioral factors, including timing of eating and overnight-fast duration, were also predictive of bacterial abundances. Longitudinal intervention studies are needed to determine causality of these biological and behavioral relations. This trial was registered at clinicaltrials.gov as NCT01925560. © 2017 American Society for Nutrition.

Opportunistic pathogens enriched in showerhead biofilms

PubMed Central

Feazel, Leah M.; Baumgartner, Laura K.; Peterson, Kristen L.; Frank, Daniel N.; Harris, J. Kirk; Pace, Norman R.

2009-01-01

The environments we humans encounter daily are sources of exposure to diverse microbial communities, some of potential concern to human health. In this study, we used culture-independent technology to investigate the microbial composition of biofilms inside showerheads as ecological assemblages in the human indoor environment. Showers are an important interface for human interaction with microbes through inhalation of aerosols, and showerhead waters have been implicated in disease. Although opportunistic pathogens commonly are cultured from shower facilities, there is little knowledge of either their prevalence or the nature of other microorganisms that may be delivered during shower usage. To determine the composition of showerhead biofilms and waters, we analyzed rRNA gene sequences from 45 showerhead sites around the United States. We find that variable and complex, but specific, microbial assemblages occur inside showerheads. Particularly striking was the finding that sequences representative of non-tuberculous mycobacteria (NTM) and other opportunistic human pathogens are enriched to high levels in many showerhead biofilms, >100-fold above background water contents. We conclude that showerheads may present a significant potential exposure to aerosolized microbes, including documented opportunistic pathogens. The health risk associated with showerhead microbiota needs investigation in persons with compromised immune or pulmonary systems. PMID:19805310

Skin microbes on frogs prevent morbidity and mortality caused by a lethal skin fungus.

PubMed

Harris, Reid N; Brucker, Robert M; Walke, Jenifer B; Becker, Matthew H; Schwantes, Christian R; Flaherty, Devon C; Lam, Brianna A; Woodhams, Douglas C; Briggs, Cheryl J; Vredenburg, Vance T; Minbiole, Kevin P C

2009-07-01

Emerging infectious diseases threaten human and wildlife populations. Altered ecological interactions between mutualistic microbes and hosts can result in disease, but an understanding of interactions between host, microbes and disease-causing organisms may lead to management strategies to affect disease outcomes. Many amphibian species in relatively pristine habitats are experiencing dramatic population declines and extinctions due to the skin disease chytridiomycosis, which is caused by the chytrid fungus Batrachochytrium dendrobatidis. Using a randomized, replicated experiment, we show that adding an antifungal bacterial species, Janthinobacterium lividum, found on several species of amphibians to the skins of the frog Rana muscosa prevented morbidity and mortality caused by the pathogen. The bacterial species produces the anti-chytrid metabolite violacein, which was found in much higher concentrations on frog skins in the treatments where J. lividum was added. Our results show that cutaneous microbes are a part of amphibians' innate immune system, the microbial community structure on frog skins is a determinant of disease outcome and altering microbial interactions on frog skins can prevent a lethal disease outcome. A bioaugmentation strategy may be an effective management tool to control chytridiomycosis in amphibian survival assurance colonies and in nature.

Microbial strategy for potential lead remediation: a review study.

PubMed

Pan, Xiaohong; Chen, Zhi; Li, Lan; Rao, Wenhua; Xu, Zhangyan; Guan, Xiong

2017-02-01

The extensive exploitation and usage of lead compounds result in severe lead(II) pollution in water and soil environments, even in agricultural land, threatening the health of animals and humans via food chains. The recovery and remediation of lead(II) from water and soil environments have been intensively concerned in recent years. Compared with the traditional physic-chemistry treatment, microbial remediation strategy is a promising alternative to remediate lead(II)-contaminated environments due to its cost-effective and environmentally-friendly properties. Various microorganisms are capable of removing or immobilizing lead(II) from water and soil environments through bioaccumulation, precipitation or accelerated transformation of lead(II) into a very stable mineral, resulting in significant effects on lead(II) mobility and bioavailability. In the present review, we investigated a wide diversity of lead(II) bioremediation induced by different microbes and its multi-mechanisms. Moreover, we also discussed the progress and limitations, summarized the common rules of lead(II)-microbe interaction, and evaluated the environmental significance of microbes in lead biogeochemistry process. In addition, we further deliberated the feasibility and potential application of microbes in developing cost-effective, eco-friendly bioremediation or long-term management strategy for lead(II) contaminated repositories.

Microbe Detector

NASA Technical Reports Server (NTRS)

1977-01-01

The AutoMicrobic System (AMS) represents years of intensive research and development by McDonnell Douglas Corp. that originated with a NASA study aimed at development of a fully automated microbial detection and identification system for spacecraft use. A urine specimen is placed into the system, where it is subjected to different freeze-dried microbe nutrients for the nine most common pathogens. An electro-optical scanner studies each specimen once an hour through a 4-to-13 hour cycle, operating automatically. Changes in cell growths on each culture are monitored by computer. The presence of pathogens is indicated when growth reaches a predetermined level. The system also enumerates the pathogens and specifies the type. Developed initially to handle urine testing, AMS soon is expected to allow analyses of blood, spinal fluid, and other body fluids. An additional capability under development is "susceptibility testing," or the determination of which microbe-killing agents-such as penicillin or other antibiotics-would be most effective in eliminating the pathogens. The whole process of detecting, identifying, and enumerating the pathogens and determining susceptibility is accomplished in less half the time required for the manual procedure. The AMS minimizes human error, reduces technician time , and increases laboratory output.

Metals, minerals and microbes: geomicrobiology and bioremediation.

PubMed

Gadd, Geoffrey Michael

2010-03-01

Microbes play key geoactive roles in the biosphere, particularly in the areas of element biotransformations and biogeochemical cycling, metal and mineral transformations, decomposition, bioweathering, and soil and sediment formation. All kinds of microbes, including prokaryotes and eukaryotes and their symbiotic associations with each other and 'higher organisms', can contribute actively to geological phenomena, and central to many such geomicrobial processes are transformations of metals and minerals. Microbes have a variety of properties that can effect changes in metal speciation, toxicity and mobility, as well as mineral formation or mineral dissolution or deterioration. Such mechanisms are important components of natural biogeochemical cycles for metals as well as associated elements in biomass, soil, rocks and minerals, e.g. sulfur and phosphorus, and metalloids, actinides and metal radionuclides. Apart from being important in natural biosphere processes, metal and mineral transformations can have beneficial or detrimental consequences in a human context. Bioremediation is the application of biological systems to the clean-up of organic and inorganic pollution, with bacteria and fungi being the most important organisms for reclamation, immobilization or detoxification of metallic and radionuclide pollutants. Some biominerals or metallic elements deposited by microbes have catalytic and other properties in nanoparticle, crystalline or colloidal forms, and these are relevant to the development of novel biomaterials for technological and antimicrobial purposes. On the negative side, metal and mineral transformations by microbes may result in spoilage and destruction of natural and synthetic materials, rock and mineral-based building materials (e.g. concrete), acid mine drainage and associated metal pollution, biocorrosion of metals, alloys and related substances, and adverse effects on radionuclide speciation, mobility and containment, all with immense social and economic consequences. The ubiquity and importance of microbes in biosphere processes make geomicrobiology one of the most important concepts within microbiology, and one requiring an interdisciplinary approach to define environmental and applied significance and underpin exploitation in biotechnology.

Uncharted Microbial World: Microbes and Their Activities in the Environment

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

Harwood, Caroline; Buckley, Merry

Microbes are the foundation for all of life. From the air we breathe to the soil we rely on for farming to the water we drink, everything humans need to survive is intimately coupled with the activities of microbes. Major advances have been made in the understanding of disease and the use of microorganisms in the industrial production of drugs, food products and wastewater treatment. However, our understanding of many complicated microbial environments (the gut and teeth), soil fertility, and biogeochemical cycles of the elements is lagging behind due to their enormous complexity. Inadequate technology and limited resources have stymiedmore » many lines of investigation. Today, most environmental microorganisms have yet to be isolated and identified, let alone rigorously studied. The American Academy of Microbiology convened a colloquium in Seattle, Washington, in February 2007, to deliberate the way forward in the study of microorganisms and microbial activities in the environment. Researchers in microbiology, marine science, pathobiology, evolutionary biology, medicine, engineering, and other fields discussed ways to build on and extend recent successes in microbiology. The participants made specific recommendations for targeting future research, improving methodologies and techniques, and enhancing training and collaboration in the field. Microbiology has made a great deal of progress in the past 100 years, and the useful applications for these new discoveries are numerous. Microorganisms and microbial products are now used in industrial capacities ranging from bioremediation of toxic chemicals to probiotic therapies for humans and livestock. On the medical front, studies of microbial communities have revealed, among other things, new ways for controlling human pathogens. The immediate future for research in this field is extremely promising. In order to optimize the effectiveness of community research efforts in the future, scientists should include manageable systems with features like clear physical boundaries, limited microbial diversity, and manipulability with the goal of understanding fundamental principles that may apply to more complex systems. A great deal of microbial genetic and phenotypic diversity remains to be explored, and the commercial and medical potential locked up in these unknowns should compel the field to move forward. Future microbiology research will build on the successes of the past using new techniques and approaches. Uncultivated microbes hold great promise for industry, medicine, and the recycling of precious resources, and research and technology must make inroads in overcoming the barriers that prevent their study. In many cases, we will no longer be able to rely on isolated, pure cultures of microorganisms, but must use communities of microorganisms, which presently are poorly understood. Indeed, community-level studies can benefit from deconstructing microbial communities and analyzing the component members separately, but this is not feasible in every system. The effects of perturbation on microbial communities also require study. Humans rely on the services of microbes in innumerable ways, but we have little or no predictive understanding of how microbial communities respond to disturbance. Research must address current limitations in detecting microscale interactions among microbes by enhancing current technologies and fostering new microscopic tools, biosensors, and gas sensors for appropriate small scales. Genomics, which has enabled great progress in microbiology research of individual species, must be applied to communities of microorganisms. This will require improved methods of DNA extraction and amplification from environmental samples and improved strategies for DNA sequence assembly. In the future, genome sequencing efforts should continue the exploration of evolutionarily diverse microbes, as well as help reveal the mechanisms by which closely related microbes evolve. Technological advances have spurred every great leap in microbial biology, and in order to move forward, new methods for revealing the activities of microorganisms must be continually developed. Today, researchers need access to better techniques for enriching and isolating novel microorganisms, particularly approaches that enable them to mimic the low nutrient conditions to which many environmental microbes are adapted. Other outstanding needs include methods for performing in situ work and bioinformatics tools. Finally, there are several ways that training and education in microbiology are failing to adequately prepare the next generation of scientists for the challenges ahead. Training in some of the long-established disciplines, including enrichment and isolation, physiology, enzymology, and biochemistry, needs to be revitalized.« less

Environmental and social influences on emerging infectious diseases: past, present and future.

PubMed Central

McMichael, A J

2004-01-01

During the processes of human population dispersal around the world over the past 50 000-100 000 years, along with associated cultural evolution and inter-population contact and conflict, there have been several major transitions in the relationships of Homo sapiens with the natural world, animate and inanimate. Each of these transitions has resulted in the emergence of new or unfamiliar infectious diseases.The three great historical transitions since the initial advent of agriculture and livestock herding, from ca. 10 000 years ago, occurred when: (i) early agrarian-based settlements enabled sylvatic enzootic microbes to make contact with Homo sapiens; (ii) early Eurasian civilizations (such as the Greek and Roman empires, China and south Asia) came into military and commercial contact, ca. 3000-2000 years ago, swapping their dominant infections; and (iii) European expansionism, over the past five centuries, caused the transoceanic spread of often lethal infectious diseases. This latter transition is best known in relation to the conquest of the Americas by Spanish conquistadores, when the inadvertent spread of measles, smallpox and influenza devastated the Amerindian populations.Today, we are living through the fourth of these great transitional periods. The contemporary spread and increased lability of various infectious diseases, new and old, reflect the combined and increasingly widespread impacts of demographic, environmental, behavioural, technological and other rapid changes in human ecology. Modern clinical medicine has, via blood transfusion, organ transplantation, and the use of hypodermic syringes, created new opportunities for microbes. These have contributed to the rising iatrogenic problems of hepatitis C, HIV/AIDS and several other viral infections. Meanwhile, the injudicious use of antibiotics has been a rare instance of human action actually increasing 'biodiversity'.Another aspect of this fourth transition is that modern hyper-hygienic living restricts microbial exposure in early life. This, in the 1950s, may have contributed to an epidemic of more serious, disabling, poliomyelitis, affecting older children than those affected in earlier, more endemic decades. As with previous human-microbe transitions, a new equilibrial state may lie ahead. However, it certainly will not entail a world free of infectious diseases. Any mature, sustainable, human ecology must come to terms with both the need for, and the needs of, the microbial species that help to make up the interdependent system of life on Earth. Humans and microbes are not "at war"; rather, both parties are engaged in amoral, self-interested, coevolutionary struggle. We need to understand better, and therefore anticipate, the dynamics of that process. PMID:15306389

Microbial Ecology of Four Coral Atolls in the Northern Line Islands

PubMed Central

Smriga, Steven; Edwards, Robert A.; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A.; Thurber, Rebecca Vega; Willis, Bette L.; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

2008-01-01

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated (∼5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide. PMID:18301735

Microbes in Beach Sands: Integrating Environment, Ecology and Public Health

PubMed Central

Whitman, Richard; Harwood, Valerie J.; Edge, Thomas A.; Nevers, Meredith; Byappanahalli, Muruleedhara; Vijayavel, Kannappan; Brandão, João; Sadowsky, Michael J.; Alm, Elizabeth Wheeler; Crowe, Allan; Ferguson, Donna; Ge, Zhongfu; Halliday, Elizabeth; Kinzelman, Julie; Kleinheinz, Greg; Przybyla-Kelly, Kasia; Staley, Christopher; Staley, Zachery; Solo-Gabriele, Helena M.

2014-01-01

SUMMARY Beach sand is a habitat that supports many microbes, including viruses, bacteria, fungi and protozoa (micropsammon). The apparently inhospitable conditions of beach sand environments belie the thriving communities found there. Physical factors, such as water availability and protection from insolation; biological factors, such as competition, predation, and biofilm formation; and nutrient availability all contribute to the characteristics of the micropsammon. Sand microbial communities include autochthonous species/phylotypes indigenous to the environment. Allochthonous microbes, including fecal indicator bacteria (FIB) and waterborne pathogens, are deposited via waves, runoff, air, or animals. The fate of these microbes ranges from death, to transient persistence and/or replication, to establishment of thriving populations (naturalization) and integration in the autochthonous community. Transport of the micropsammon within the habitat occurs both horizontally across the beach, and vertically from the sand surface and ground water table, as well as at various scales including interstitial flow within sand pores, sediment transport for particle-associated microbes, and the large-scale processes of wave action and terrestrial runoff. The concept of beach sand as a microbial habitat and reservoir of FIB and pathogens has begun to influence our thinking about human health effects associated with sand exposure and recreational water use. A variety of pathogens have been reported from beach sands, and recent epidemiology studies have found some evidence of health risks associated with sand exposure. Persistent or replicating populations of FIB and enteric pathogens have consequences for watershed/beach management strategies and regulatory standards for safe beaches. This review summarizes our understanding of the community structure, ecology, fate, transport, and public health implications of microbes in beach sand. It concludes with recommendations for future work in this vastly under-studied area. PMID:25383070

Microbial ecology of four coral atolls in the Northern Line Islands.

PubMed

Dinsdale, Elizabeth A; Pantos, Olga; Smriga, Steven; Edwards, Robert A; Angly, Florent; Wegley, Linda; Hatay, Mark; Hall, Dana; Brown, Elysa; Haynes, Matthew; Krause, Lutz; Sala, Enric; Sandin, Stuart A; Thurber, Rebecca Vega; Willis, Bette L; Azam, Farooq; Knowlton, Nancy; Rohwer, Forest

2008-02-27

Microbes are key players in both healthy and degraded coral reefs. A combination of metagenomics, microscopy, culturing, and water chemistry were used to characterize microbial communities on four coral atolls in the Northern Line Islands, central Pacific. Kingman, a small uninhabited atoll which lies most northerly in the chain, had microbial and water chemistry characteristic of an open ocean ecosystem. On this atoll the microbial community was equally divided between autotrophs (mostly Prochlorococcus spp.) and heterotrophs. In contrast, Kiritimati, a large and populated ( approximately 5500 people) atoll, which is most southerly in the chain, had microbial and water chemistry characteristic of a near-shore environment. On Kiritimati, there were 10 times more microbial cells and virus-like particles in the water column and these microbes were dominated by heterotrophs, including a large percentage of potential pathogens. Culturable Vibrios were common only on Kiritimati. The benthic community on Kiritimati had the highest prevalence of coral disease and lowest coral cover. The middle atolls, Palmyra and Tabuaeran, had intermediate densities of microbes and viruses and higher percentages of autotrophic microbes than either Kingman or Kiritimati. The differences in microbial communities across atolls could reflect variation in 1) oceaonographic and/or hydrographic conditions or 2) human impacts associated with land-use and fishing. The fact that historically Kingman and Kiritimati did not differ strongly in their fish or benthic communities (both had large numbers of sharks and high coral cover) suggest an anthropogenic component in the differences in the microbial communities. Kingman is one of the world's most pristine coral reefs, and this dataset should serve as a baseline for future studies of coral reef microbes. Obtaining the microbial data set, from atolls is particularly important given the association of microbes in the ongoing degradation of coral reef ecosystems worldwide.

The Gut Commensal Microbiome of Drosophila melanogaster Is Modified by the Endosymbiont Wolbachia

PubMed Central

Fast, Eva M.; Guo, Rong; Vaisman, Natalie; Ortiz, Luis; Bybee, Joanna; Slatko, Barton E.

2017-01-01

ABSTRACT Endosymbiotic Wolbachia bacteria and the gut microbiome have independently been shown to affect several aspects of insect biology, including reproduction, development, life span, stem cell activity, and resistance to human pathogens, in insect vectors. This work shows that Wolbachia bacteria, which reside mainly in the fly germline, affect the microbial species present in the fly gut in a lab-reared strain. Drosophila melanogaster hosts two main genera of commensal bacteria—Acetobacter and Lactobacillus. Wolbachia-infected flies have significantly reduced titers of Acetobacter. Sampling of the microbiome of axenic flies fed with equal proportions of both bacteria shows that the presence of Wolbachia bacteria is a significant determinant of the composition of the microbiome throughout fly development. However, this effect is host genotype dependent. To investigate the mechanism of microbiome modulation, the effect of Wolbachia bacteria on Imd and reactive oxygen species pathways, the main regulators of immune response in the fly gut, was measured. The presence of Wolbachia bacteria does not induce significant changes in the expression of the genes for the effector molecules in either pathway. Furthermore, microbiome modulation is not due to direct interaction between Wolbachia bacteria and gut microbes. Confocal analysis shows that Wolbachia bacteria are absent from the gut lumen. These results indicate that the mechanistic basis of the modulation of composition of the microbiome by Wolbachia bacteria is more complex than a direct bacterial interaction or the effect of Wolbachia bacteria on fly immunity. The findings reported here highlight the importance of considering the composition of the gut microbiome and host genetic background during Wolbachia-induced phenotypic studies and when formulating microbe-based disease vector control strategies. IMPORTANCE Wolbachia bacteria are intracellular bacteria present in the microbiome of a large fraction of insects and parasitic nematodes. They can block mosquitos’ ability to transmit several infectious disease-causing pathogens, including Zika, dengue, chikungunya, and West Nile viruses and malaria parasites. Certain extracellular bacteria present in the gut lumen of these insects can also block pathogen transmission. However, our understanding of interactions between Wolbachia and gut bacteria and how they influence each other is limited. Here we show that the presence of Wolbachia strain wMel changes the composition of gut commensal bacteria in the fruit fly. Our findings implicate interactions between bacterial species as a key factor in determining the overall composition of the microbiome and thus reveal new paradigms to consider in the development of disease control strategies. PMID:28932814

The Gut Commensal Microbiome of Drosophila melanogaster Is Modified by the Endosymbiont Wolbachia.

PubMed

Simhadri, Rama K; Fast, Eva M; Guo, Rong; Schultz, Michaela J; Vaisman, Natalie; Ortiz, Luis; Bybee, Joanna; Slatko, Barton E; Frydman, Horacio M

2017-01-01

Endosymbiotic Wolbachia bacteria and the gut microbiome have independently been shown to affect several aspects of insect biology, including reproduction, development, life span, stem cell activity, and resistance to human pathogens, in insect vectors. This work shows that Wolbachia bacteria, which reside mainly in the fly germline, affect the microbial species present in the fly gut in a lab-reared strain. Drosophila melanogaster hosts two main genera of commensal bacteria- Acetobacter and Lactobacillus . Wolbachia -infected flies have significantly reduced titers of Acetobacter . Sampling of the microbiome of axenic flies fed with equal proportions of both bacteria shows that the presence of Wolbachia bacteria is a significant determinant of the composition of the microbiome throughout fly development. However, this effect is host genotype dependent. To investigate the mechanism of microbiome modulation, the effect of Wolbachia bacteria on Imd and reactive oxygen species pathways, the main regulators of immune response in the fly gut, was measured. The presence of Wolbachia bacteria does not induce significant changes in the expression of the genes for the effector molecules in either pathway. Furthermore, microbiome modulation is not due to direct interaction between Wolbachia bacteria and gut microbes. Confocal analysis shows that Wolbachia bacteria are absent from the gut lumen. These results indicate that the mechanistic basis of the modulation of composition of the microbiome by Wolbachia bacteria is more complex than a direct bacterial interaction or the effect of Wolbachia bacteria on fly immunity. The findings reported here highlight the importance of considering the composition of the gut microbiome and host genetic background during Wolbachia -induced phenotypic studies and when formulating microbe-based disease vector control strategies. IMPORTANCE Wolbachia bacteria are intracellular bacteria present in the microbiome of a large fraction of insects and parasitic nematodes. They can block mosquitos' ability to transmit several infectious disease-causing pathogens, including Zika, dengue, chikungunya, and West Nile viruses and malaria parasites. Certain extracellular bacteria present in the gut lumen of these insects can also block pathogen transmission. However, our understanding of interactions between Wolbachia and gut bacteria and how they influence each other is limited. Here we show that the presence of Wolbachia strain w Mel changes the composition of gut commensal bacteria in the fruit fly. Our findings implicate interactions between bacterial species as a key factor in determining the overall composition of the microbiome and thus reveal new paradigms to consider in the development of disease control strategies.

The changing microbial landscape of Western society: Diet, dwellings and discordance.

PubMed

Broussard, Josiane L; Devkota, Suzanne

2016-09-01

The last 50-100 years has been marked by a sharp rise in so-called "Western-diseases" in those countries that have experienced major industrial advances and shifts towards urbanized living. These diseases include obesity, type 2 diabetes, inflammatory bowel diseases, and food allergies in which chronic dysregulation of metabolic and/or immune processes appear to be involved, and are likely a byproduct of new environmental influences on our ancient genome. What we now appreciate is that this genome consists of both human and co-evolved microbial genes of the trillions of microbes residing in our body. Together, host-microbe interactions may be determined by the changing diets and behaviors of the Western lifestyle, influencing the etiopathogenesis of "new-age" diseases. This review takes an anthropological approach to the potential interplay of the host and its gut microbiome in the post-industrialization rise in chronic inflammatory and metabolic diseases. The discussion highlights both the changes in diet and the physical environment that have co-occurred with these diseases and the latest evidence demonstrating the role of host-microbe interactions in understanding biological responses to the changing environment. Technological advances that have led to changes in agriculture and engineering have altered our eating and living behaviors in ways never before possible in human history. These changes also have altered the bacterial communities within the human body in ways that are seemingly linked with the rise of many intestinal and systemic metabolic and inflammatory diseases. Insights into the mechanisms of this reciprocal exchange between the environment and the human gut microbiome may offer potential to attenuate the chronic health conditions that derail quality of life. This article is part of a special issue on microbiota.

Urban microbiomes and urban ecology: how do microbes in the built environment affect human sustainability in cities?

PubMed

King, Gary M

2014-09-01

Humans increasingly occupy cities. Globally, about 50% of the total human population lives in urban environments, and in spite of some trends for deurbanization, the transition from rural to urban life is expected to accelerate in the future, especially in developing nations and regions. The Republic of Korea, for example, has witnessed a dramatic rise in its urban population, which now accounts for nearly 90% of all residents; the increase from about 29% in 1955 has been attributed to multiple factors, but has clearly been driven by extraordinary growth in the gross domestic product accompanying industrialization. While industrialization and urbanization have unarguably led to major improvements in quality of life indices in Korea and elsewhere, numerous serious problems have also been acknowledged, including concerns about resource availability, water quality, amplification of global warming and new threats to health. Questions about sustainability have therefore led Koreans and others to consider deurbanization as a management policy. Whether this offers any realistic prospects for a sustainable future remains to be seen. In the interim, it has become increasingly clear that built environments are no less complex than natural environments, and that they depend on a variety of internal and external connections involving microbes and the processes for which microbes are responsible. I provide here a definition of the urban microbiome, and through examples indicate its centrality to human function and wellbeing in urban systems. I also identify important knowledge gaps and unanswered questions about urban microbiomes that must be addressed to develop a robust, predictive and general understanding of urban biology and ecology that can be used to inform policy-making for sustainable systems.

Safety Assessment of Probiotics

NASA Astrophysics Data System (ADS)

Lahtinen, Sampo J.; Boyle, Robert J.; Margolles, Abelardo; Frias, Rafael; Gueimonde, Miguel

Viable microbes have been a natural part of human diet throughout the history of mankind. Today, different fermented foods and other foods containing live microbes are consumed around the world, including industrialized countries, where the diet has become increasingly sterile during the last decades. By definition, probiotics are viable microbes with documented beneficial effects on host health. Probiotics have an excellent safety record, both in humans and in animals. Despite the wide and continuously increasing consumption of probiotics, adverse events related to probiotic use are extremely rare. Many popular probiotic strains such as lactobacilli and bifidobacteria can be considered as components of normal healthy intestinal microbiota, and thus are not thought to pose a risk for the host health - in contrast, beneficial effects on health are commonly reported. Nevertheless, the safety of probiotics is an important issue, in particular in the case of new potential probiotics which do not have a long history of safe use, and of probiotics belonging to species for which general assumption of safety cannot be made. Furthermore, safety of probiotics in high-risk populations such as critically ill patients and immunocompromized subjects deserves particular attention, as virtually all reported cases of bacteremia and fungemia associated with probiotic use, involve subjects with underlying diseases, compromised immune system or compromised intestinal integrity.

Potential Use of Antimicrobial Peptides as Vaginal Spermicides/Microbicides

PubMed Central

Tanphaichitr, Nongnuj; Srakaew, Nopparat; Alonzi, Rhea; Kiattiburut, Wongsakorn; Kongmanas, Kessiri; Zhi, Ruina; Li, Weihua; Baker, Mark; Wang, Guanshun; Hickling, Duane

2016-01-01

The concurrent increases in global population and sexually transmitted infection (STI) demand a search for agents with dual spermicidal and microbicidal properties for topical vaginal application. Previous attempts to develop the surfactant spermicide, nonoxynol-9 (N-9), into a vaginal microbicide were unsuccessful largely due to its inefficiency to kill microbes. Furthermore, N-9 causes damage to the vaginal epithelium, thus accelerating microbes to enter the women’s body. For this reason, antimicrobial peptides (AMPs), naturally secreted by all forms of life as part of innate immunity, deserve evaluation for their potential spermicidal effects. To date, twelve spermicidal AMPs have been described including LL-37, magainin 2 and nisin A. Human cathelicidin LL-37 is the most promising spermicidal AMP to be further developed for vaginal use for the following reasons. First, it is a human AMP naturally produced in the vagina after intercourse. Second, LL-37 exerts microbicidal effects to numerous microbes including those that cause STI. Third, its cytotoxicity is selective to sperm and not to the female reproductive tract. Furthermore, the spermicidal effects of LL-37 have been demonstrated in vivo in mice. Therefore, the availability of LL-37 as a vaginal spermicide/microbicide will empower women for self-protection against unwanted pregnancies and STI. PMID:26978373

Progress in directed energy control of vectors for microbes and other cells

NASA Astrophysics Data System (ADS)

Kiel, Johnathan L.; Parker, Jill E.; Holwitt, Eric A.; Vivekananda, Jeeva; Sloan, Mark A.; Stribling, Lucille J. V.

2004-07-01

Biosynthetic semiconductor, diazoluminomelanin (DALM), is a polymer of tyrosine, luminol, and nitrite. DALM has a very large cross section of absorption for light from ultraviolet to radio frequencies. This polymer can be made efficiently in a genetically engineered E.coli, JM109/pIC2ORNR1.1 (ATCC# 69905). We have been pursuing ways to couple electromagnetic radiation to vectors using this polymer. DNA capture elements (DCEs; formerly aptamers) have made this possible. We incorporated DCEs into the plasmid of this E. coli to direct binding to whatever microbe or cell desired and to produce DALM attached to the plasmid DNA. Using two other vectors pSV2neoNR101 or pSV2neoNR8005 (ATCC # 69617 and 69618, respectively), both propagated in the E. coli host HB101, we have also inserted genes necessary for DALM production into animal and human cell lines (mouse monocytic leukemia: ATCC # CRL- 11771, -11772, -1173, mouse mammary adenocarcinoma: ATCC# CRL-12184, -12185; and human carcinoma of the cervix: ATCC # CRL-12510). The DCE/DALM vectors can be used to tag target cells, detectable by broad-spectrum light absorbance, luminescence, or fluorescence. DCE/DALM can further be activated with light, microwave energy, or by oxidative chemistry to kill the targeted microbes or other cells.

Studying Genes

MedlinePlus

... also study the genes of bacteria, viruses and fungi to find ways to prevent or treat infection. Increasingly, these studies are helping them understand how microbes on and in the body affect human health, sometimes in beneficial ways. What types ...

The bee microbiome: impact on bee health and model for evolution and ecology of host-microbe interactions

USDA-ARS?s Scientific Manuscript database

Fanconi anemia (FA) is a rare genetic disorder caused by defects in DNA damage repair. FA patients often develop squamous cell carcinoma (SCC) at sites where high-risk human papillomaviruses (HPVs) are known to cause cancer, including the cervix. However, SCCs found in human FA patients are often HP...

It’s alive: microbes and cells in human milk and their potential benefits to mother and infant.

PubMed

Bode, Lars; McGuire, Mark; Rodriguez, Juan M; Geddes, Donna T; Hassiotou, Foteini; Hartmann, Peter E; McGuire, Michelle K

2014-09-01

Human milk is the optimal source of nutrition for the nursing infant. Classically, the nutrients (water, protein, lipid, carbohydrate, vitamins, and minerals) were studied as the critical components of milk serving the growth needs of the infant for optimum growth. However, human milk contains factors other than the classically defined nutrients for which researchers are investigating potential roles in infant and maternal health, development, and well-being. The symposium addressed some of the exciting factors being studied, including microbes and maternal cells found within milk. Drs. Michelle McGuire and Juan M. Rodríguez addressed the presence of a bacterial community in human milk produced by healthy and mastitic mothers, potential sources of those bacteria, and the impact of milk-derived bacteria on the nursing infant. Drs. Donna Geddes, Peter Hartmann, and Foteini Hassiotou discussed the potential importance of maternal cells. For years, immune cells were known to be present in human milk, but recent evidence suggests that their impact is as much on the infant as on the health of the lactating mammary gland. Finally, the existence of highly plastic stem cells in human milk opens doors for previously unforeseen developmental “training” of the nursing infant.

CHEMICAL MARKERS OF HUMAN WASTE ...

EPA Pesticide Factsheets

Giving public water authorities another tool to monitor and measure levels of human waste contamination of waters simply and rapidly would enhance public protection. Most of the methods used today detect such contamination by quantifying microbes occurring in feces in high enough densities that they can be measured easily. However, most of these microbes, for example E. coli, do not serve as specific markers for any one host species and many can have origins other than feces. As an alternative, chemicals shed in feces and urine might be used to detect human waste contamination of environmental waters. One potential chemical marker of human waste is the compound urobilin. Urobilin is one of the final by-products of hemoglobin breakdown. Urobilin is excreted in both the urine and feces from many mammals, particularly humans. Source waters from 21 sites in New England, Nevada, and Michigan were extracted using hydrophilic-lipophilic balance (HLB) cartridges and then analyzed by high performance liquid chromatography-electrospray-mass spectrometry (HPLC-ES-MS). As a marker of human waste, urobilin was detected in many of the source waters at concentrations ranging from not detectable to 300 ng/L. Besides urobilin, zithromycin, an antibiotic widely prescribed for human-use only in the US, was also detected in many of these waters, with concentrations ranging from not detectable to 77 ng/L. This methodology, using both urobilin and azithromycin (or any other human-use

[Studies on the size distribution of airborne microbes at home in Beijing].

PubMed

Fang, Zhi-Guo; Sun, Ping; Ouyang, Zhi-Yun; Liu, Peng; Sun, Li; Wang, Xiao-Yong

2013-07-01

The effect of airborne microbes on human health not only depends on their compositions (genera and species), but also on their concentrations and sizes. Moreover, there are different mechanisms of airborne microbes of different sizes with different effects on human health. The size distributions and median diameters were investigated in detail with imitated six-stage Andersen sampler in 31 selected family homes with children in Beijing. Results showed that there was similar distribution characteristics of airborne microbes in different home environment, different season, different child's sex, and different apartment's architecture, but different distribution characteristics between airborne bacteria and fungi were observed in family homes in Beijing. In general, although airborne bacteria and fungi were plotted with normal logarithmic distribution, the particle percentage of airborne bacteria increased gradually from stage 1 (> 8.2 microm) to stage 5 (1.0-2.0 microm), and then decreased dramatically in stage 6 (< 1.0 microm), the percentage of airborne fungi increased gradually from stage 1 to stage 4 (2.0-3.5 microm), and then decreased dramatically from stage 4 to stage 6. The size distributions of dominant fungi were different in different fungal genera. Cladosporium, Penicillium and Aspergillus were recorded with normal logarithmic distribution, with the highest percentage detected in stage 4, and Alternaria were observed with skew distribution, with the highest percentage detected in stage 2 (5.0-10.4 microm). Finally, the median diameters of airborne bacteria were larger than those of airborne fungi, and the lowest median diameter of airborne bacteria and fungi was found in winter, while there were no significant variations of airborne bacterial and fungal median diameters in spring, summer and autumn in a year in this study.

The return of infectious disease.

PubMed

Garrett, L

1996-11-01

This article presents the history of efforts to control the spread of infectious disease from the post-antibiotic era to 1995. Since World War II, public health strategy has focused on the eradication of microbes using powerful medical weaponry. The goal was to push humanity through a ¿health transition,¿ leaving the age of infectious disease permanently behind. But recent developments have shown that this grandiose optimism was premature. As people move across international borders, unwanted microbial hitch-hikers tag along, as happened in the case of Ebola. In large cities, sex industries arise and multiple-partner sex becomes more common, prompting rapid increases in sexually transmitted disease. Moreover, the practice of sharing syringes is a ready vehicle for the transmission of microbes while unhygienic health facilities become centers for the dissemination of disease rather than its control. Black market access to antimicrobials has led to overuse or outright misuse of the drugs and the emergence of resistant bacteria and parasites. Consequently, old organisms, aided by mankind's misuse of disinfectants and drugs, may take on new and more lethal forms. Even when allegations of biological warfare are not flying, it is often difficult to obtain accurate information about outbreaks of disease, particularly in countries dependent on foreign investment or tourism or both. Unfortunately, only 6 laboratories in the world meet security and safety standards that would make them suitable sites for research on the world's deadliest microbes. National security warrants bolder steps involving focusing not only on microbes directly dangerous to humans, but also on those that could pose major threats to crops or livestock. Unfortunately, economic crises have led to budget cuts, particularly in health care, at all levels of government in the US.

Presence of Pathogens and Indicator Microbes at a Non-Point Source Subtropical Recreational Marine Beach ▿ †

PubMed Central

Abdelzaher, Amir M.; Wright, Mary E.; Ortega, Cristina; Solo-Gabriele, Helena M.; Miller, Gary; Elmir, Samir; Newman, Xihui; Shih, Peter; Bonilla, J. Alfredo; Bonilla, Tonya D.; Palmer, Carol J.; Scott, Troy; Lukasik, Jerzy; Harwood, Valerie J.; McQuaig, Shannon; Sinigalliano, Chris; Gidley, Maribeth; Plano, Lisa R. W.; Zhu, Xiaofang; Wang, John D.; Fleming, Lora E.

2010-01-01

Swimming in ocean water, including ocean water at beaches not impacted by known point sources of pollution, is an increasing health concern. This study was an initial evaluation of the presence of indicator microbes and pathogens and the association among the indicator microbes, pathogens, and environmental conditions at a subtropical, recreational marine beach in south Florida impacted by non-point sources of pollution. Twelve water and eight sand samples were collected during four sampling events at high or low tide under elevated or reduced solar insolation conditions. The analyses performed included analyses of fecal indicator bacteria (FIB) (fecal coliforms, Escherichia coli, enterococci, and Clostridium perfringens), human-associated microbial source tracking (MST) markers (human polyomaviruses [HPyVs] and Enterococcus faecium esp gene), and pathogens (Vibrio vulnificus, Staphylococcus aureus, enterovirus, norovirus, hepatitis A virus, Cryptosporidium spp., and Giardia spp.). The enterococcus concentrations in water and sand determined by quantitative PCR were greater than the concentrations determined by membrane filtration measurement. The FIB concentrations in water were below the recreational water quality standards for three of the four sampling events, when pathogens and MST markers were also generally undetectable. The FIB levels exceeded regulatory guidelines during one event, and this was accompanied by detection of HPyVs and pathogens, including detection of the autochthonous bacterium V. vulnificus in sand and water, detection of the allochthonous protozoans Giardia spp. in water, and detection of Cryptosporidium spp. in sand samples. The elevated microbial levels were detected at high tide and under low-solar-insolation conditions. Additional sampling should be conducted to further explore the relationships between tidal and solar insolation conditions and between indicator microbes and pathogens in subtropical recreational marine waters impacted by non-point source pollution. PMID:19966020

A microbial biogeochemistry network for soil carbon and nitrogen cycling and methane flux: model structure and application to Asia

NASA Astrophysics Data System (ADS)

Xu, X.; Song, C.; Wang, Y.; Ricciuto, D. M.; Lipson, D.; Shi, X.; Zona, D.; Song, X.; Yuan, F.; Oechel, W. C.; Thornton, P. E.

2017-12-01

A microbial model is introduced for simulating microbial mechanisms controlling soil carbon and nitrogen biogeochemical cycling and methane fluxes. The model is built within the CN (carbon-nitrogen) framework of Community Land Model 4.5, named as CLM-Microbe to emphasize its explicit representation of microbial mechanisms to biogeochemistry. Based on the CLM4.5, three new pools were added: bacteria, fungi, and dissolved organic matter. It has 11 pools and 34 transitional processes, compared with 8 pools and 9 transitional flow in the CLM4.5. The dissolve organic carbon was linked with a new microbial functional group based methane module to explicitly simulate methane production, oxidation, transport and their microbial controls. Comparing with CLM4.5-CN, the CLM-Microbe model has a number of new features, (1) microbial control on carbon and nitrogen flows between soil carbon/nitrogen pools; (2) an implicit representation of microbial community structure as bacteria and fungi; (3) a microbial functional-group based methane module. The model sensitivity analysis suggests the importance of microbial carbon allocation parameters on soil biogeochemistry and microbial controls on methane dynamics. Preliminary simulations validate the model's capability for simulating carbon and nitrogen dynamics and methane at a number of sites across the globe. The regional application to Asia has verified the model in simulating microbial mechanisms in controlling methane dynamics at multiple scales.

Gut microbiota modulates alcohol withdrawal-induced anxiety in mice.

PubMed

Xiao, Hui-Wen; Ge, Chang; Feng, Guo-Xing; Li, Yuan; Luo, Dan; Dong, Jia-Li; Li, Hang; Wang, Haichao; Cui, Ming; Fan, Sai-Jun

2018-05-01

Excessive alcohol consumption remains a major public health problem that affects millions of people worldwide. Accumulative experimental evidence has suggested an important involvement of gut microbiota in the modulation of host's immunological and neurological functions. However, it is previously unknown whether enteric microbiota is implicated in the formation of alcohol withdrawal-induced anxiety. Using a murine model of chronic alcoholism and withdrawal, we examined the impact of alcohol consumption on the possible alterations of gut microbiota as well as alcohol withdrawal-induced anxiety and behavior changes. The 16S rRNA sequencing revealed that alcohol consumption did not alter the abundance of bacteria, but markedly changed the composition of gut microbiota. Moreover, the transplantation of enteric microbes from alcohol-fed mice to normal healthy controls remarkably shaped the composition of gut bacteria, and elicited behavioral signs of alcohol withdrawal-induced anxiety. Using quantitative real-time polymerase chain reaction, we further confirmed that the expression of genes implicated in alcohol addiction, BDNF, CRHR1 and OPRM1, was also altered by transplantation of gut microbes from alcohol-exposed donors. Collectively, our findings suggested a possibility that the alterations of gut microbiota composition might contribute to the development of alcohol withdrawal-induced anxiety, and reveal potentially new etiologies for treating alcohol addiction. Copyright © 2018 The Author(s). Published by Elsevier B.V. All rights reserved.

Ability of the gut microbiota to produce PUFA-derived bacterial metabolites: Proof of concept in germ-free versus conventionalized mice.

PubMed

Druart, Céline; Bindels, Laure B; Schmaltz, Robert; Neyrinck, Audrey M; Cani, Patrice D; Walter, Jens; Ramer-Tait, Amanda E; Delzenne, Nathalie M

2015-08-01

The gut microbiota is able to modulate host physiology through the production of bioactive metabolites. Our recent studies suggest that changes in gut microbiota composition upon prebiotics supplementation alter tissue levels of PUFA-derived metabolites in mice. However, in vivo evidence that gut microbes produces PUFA-derived metabolites is lacking. This study aimed to decipher the contribution of gut microbes versus that of the host in PUFA-derived metabolite production. To achieve this goal, we compared the proportion of PUFA-derived metabolites and the expression of fatty acid desaturases in germ-free (GF) and conventionalized (CONV) mice fed either a low fat or Western diet. Higher concentrations of PUFA-derived metabolites were found in the colonic contents of conventionalized mice (CONV) mice compared to GF mice. The abundance of these metabolites in host tissues was modulated by dietary treatments but not by microbial status. Although microbial status did significantly influence desaturase expression, no correlations between host enzymes and tissue PUFA-derived metabolite levels were observed. Together, these results highlight the ability of the gut microbiota to produce PUFA-derived metabolites from dietary PUFA. However, microbial production of these metabolites in colonic contents is not necessarily associated with modifications of their concentration in host tissues. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

House dust fungal communities' characterization: a double take on the six by sixty by six (6 × 60 × 6) project

NASA Astrophysics Data System (ADS)

Amaro, Raquel; Coelho, Sónia D.; Pastorinho, M. Ramiro; Taborda-Barata, Luís; Vaz-Patto, Maria A.; Monteiro, Marisa; Nepomuceno, Miguel C. S.; Lanzinha, Joăo C. G.; Teixeira, Joăo P.; Pereira, Cristiana C.; Sousa, Ana C. A.

2016-11-01

Fungi are a group of microbes that are found with particular incidence in the indoor environment. Their direct toxicity or capability of generating toxic compounds has been associated with a large number of adverse health effects, such as infectious diseases and allergies. Given that in modern society people spend a large part of their time indoors; fungal communities' characterization of this environmental compartment assumes paramount importance in the comprehension of health effects. House dust is an easy to obtain, time-integrative matrix, being its use in epidemiological studies on human exposure to environmental contaminants highly recommended. Furthermore, dust can carry a great variety of fungal content that undergoes a large number of processes that modulate and further complexify human exposure. Our study aims to identify and quantify the fungal community on house dust samples collected using two different methodologies (an approach not often seen in the literature): active (vacuum cleaner bags) and passive sampling (dust settled in petri dishes). Sampling was performed as part of the ongoing 6 × 60 × 6 Project in which six houses from Covilhă (Portugal), with building dates representative of six decades, were studied for a period of sixty days.

A monograph on the remediation of hazardous phthalates.

PubMed

Benjamin, Sailas; Pradeep, Selvanesan; Josh, Moolakkariyil Sarath; Kumar, Sunil; Masai, Eiji

2015-11-15

Phthalates or phthalic acid esters are a group of xenobiotic and hazardous compounds blended in plastics to enhance their plasticity and versatility. Enormous quantities of phthalates are produced globally for the production of plastic goods, whose disposal and leaching out into the surroundings cause serious concerns to the environment, biota and human health. Though in silico computational, in vitro mechanistic, pre-clinical animal and clinical human studies showed endocrine disruption, hepatotoxic, teratogenic and carcinogenic properties, usage of phthalates continues due to their cuteness, attractive chemical properties, low production cost and lack of suitable alternatives. Studies revealed that microbes isolated from phthalate-contaminated environmental niches efficiently bioremediate various phthalates. Based upon this background, this review addresses the enumeration of major phthalates used in industry, routes of environmental contamination, evidences for health hazards, routes for in situ and ex situ microbial degradation, bacterial pathways involved in the degradation, major enzymes involved in the degradation process, half-lives of phthalates in environments, etc. Briefly, this handy module would enable the readers, environmentalists and policy makers to understand the impact of phthalates on the environment and the biota, coupled with the concerted microbial efforts to alleviate the burden of ever increasing load posed by phthalates. Copyright © 2015 Elsevier B.V. All rights reserved.

Polymicrobial infection and bacterium-mediated epigenetic modification of DNA tumor viruses contribute to pathogenesis.

PubMed

Doolittle, J M; Webster-Cyriaque, J

2014-04-29

ABSTRACT The human body plays host to a wide variety of microbes, commensal and pathogenic. In addition to interacting with their host, different microbes, such as bacteria and viruses, interact with each other, sometimes in ways that exacerbate disease. In particular, gene expression of a number of viruses, including Kaposi's sarcoma-associated herpesvirus (KSHV), Epstein-Barr virus (EBV), and human immunodeficiency virus (HIV), is known to be regulated by epigenetic modifications induced by bacteria. These viruses establish latent infection in their host cells and can be reactivated by bacterial products. Viral reactivation has been suggested to contribute to periodontal disease and AIDS. In addition, bacterium-virus interactions may play a role in cancers, such as Kaposi's sarcoma, gastric cancer, and head and neck cancer. It is important to consider the effects of coexisting bacterial infections when studying viral diseases in vivo.

A microbial survey of the International Space Station (ISS)

PubMed Central

Lang, Jenna M.; Coil, David A.; Neches, Russell Y.; Brown, Wendy E.; Cavalier, Darlene; Severance, Mark; Hampton-Marcell, Jarrad T.; Gilbert, Jack A.

2017-01-01

Background Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the “buildings” in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons. Results Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project. Conclusions While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036–4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain. PMID:29492330

A microbial survey of the International Space Station (ISS).

PubMed

Lang, Jenna M; Coil, David A; Neches, Russell Y; Brown, Wendy E; Cavalier, Darlene; Severance, Mark; Hampton-Marcell, Jarrad T; Gilbert, Jack A; Eisen, Jonathan A

2017-01-01

Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons. Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project. While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036-4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.

Characterization of aerosolized bacteria and fungi from desert dust events in Mali, West Africa

USGS Publications Warehouse

Kellogg, C.A.; Griffin, Dale W.; Garrison, V.H.; Peak, K.K.; Royall, N.; Smith, R.R.; Shinn, E.A.

2004-01-01

Millions of metric tons of African desert dust blow across the Atlantic Ocean each year, blanketing the Caribbean and southeastern United States. Previous work in the Caribbean has shown that atmospheric samples collected during dust events contain living microbes, including plant and opportunistic human pathogens. To better understand the potential downwind public health and ecosystem effects of the dust microbes, it is important to characterize the source population. We describe 19 genera of bacteria and 3 genera of fungi isolated from air samples collected in Mali, a known source region for dust storms, and over which large dust storms travel.

Nutritional modulation of gut microbiota - the impact on metabolic disease pathophysiology.

PubMed

Ojeda, Patricia; Bobe, Alexandria; Dolan, Kyle; Leone, Vanessa; Martinez, Kristina

2016-02-01

The obesity epidemic afflicts over one third of the United States population. With few therapies available to combat obesity, a greater understanding of the systemic causes of this and other metabolic disorders is needed to develop new, effective treatments. The mammalian intestinal microbiota contributes to metabolic processes in the host. This review summarizes the research demonstrating the interplay of diet, intestinal microbiota and host metabolism. We detail the effects of diet-induced modifications in microbial activity and resultant impact on (1) sensory perception of macronutrients and total energy intake; (2) nutrient absorption, transport and storage; (3) liver and biliary function; (4) immune-mediated signaling related to adipose inflammation; and (5) circadian rhythm. We also discuss therapeutic strategies aimed to modify host-microbe interactions, including prebiotics, probiotics and postbiotics, as well as fecal microbiota transplantation. Elucidating the role of gut microbes in shaping metabolic homeostasis or dysregulation provides greater insight into disease development and a promising avenue for improved treatment of metabolic dysfunction. Copyright © 2015 Elsevier Inc. All rights reserved.

Integrating Environmental Genomics and Biogeochemical Models: a Gene-centric Approach

NASA Astrophysics Data System (ADS)

Reed, D. C.; Algar, C. K.; Huber, J. A.; Dick, G.

2013-12-01

Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models that uses genomics data and provides predictions that are readily testable using cutting-edge molecular tools. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modelled to examine key questions about cryptic sulphur cycling and dinitrogen production pathways in OMZs. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

Bacterial-derived uracil as a modulator of mucosal immunity and gut-microbe homeostasis in Drosophila.

PubMed

Lee, Kyung-Ah; Kim, Sung-Hee; Kim, Eun-Kyoung; Ha, Eun-Mi; You, Hyejin; Kim, Boram; Kim, Min-Ji; Kwon, Youngjoo; Ryu, Ji-Hwan; Lee, Won-Jae

2013-05-09

All metazoan guts are subjected to immunologically unique conditions in which an efficient antimicrobial system operates to eliminate pathogens while tolerating symbiotic commensal microbiota. However, the molecular mechanisms controlling this process are only partially understood. Here, we show that bacterial-derived uracil acts as a ligand for dual oxidase (DUOX)-dependent reactive oxygen species generation in Drosophila gut and that the uracil production in bacteria causes inflammation in the gut. The acute and controlled uracil-induced immune response is required for efficient elimination of bacteria, intestinal cell repair, and host survival during infection of nonresident species. Among resident gut microbiota, uracil production is absent in symbionts, allowing harmonious colonization without DUOX activation, whereas uracil release from opportunistic pathobionts provokes chronic inflammation. These results reveal that bacteria with distinct abilities to activate uracil-induced gut inflammation, in terms of intensity and duration, act as critical factors that determine homeostasis or pathogenesis in gut-microbe interactions. Copyright © 2013 Elsevier Inc. All rights reserved.

Antivirulence Activity of the Human Gut Metabolome

PubMed Central

Antunes, L. Caetano M.; McDonald, Julie A. K.; Schroeter, Kathleen; Carlucci, Christian; Ferreira, Rosana B. R.; Wang, Melody; Yurist-Doutsch, Sophie; Hira, Gill; Jacobson, Kevan; Davies, Julian; Allen-Vercoe, Emma

2014-01-01

ABSTRACT The mammalian gut contains a complex assembly of commensal microbes termed microbiota. Although much has been learned about the role of these microbes in health, the mechanisms underlying these functions are ill defined. We have recently shown that the mammalian gut contains thousands of small molecules, most of which are currently unidentified. Therefore, we hypothesized that these molecules function as chemical cues used by hosts and microbes during their interactions in health and disease. Thus, a search was initiated to identify molecules produced by the microbiota that are sensed by pathogens. We found that a secreted molecule produced by clostridia acts as a strong repressor of Salmonella virulence, obliterating expression of the Salmonella pathogenicity island 1 as well as host cell invasion. It has been known for decades that the microbiota protects its hosts from invading pathogens, and these data suggest that chemical sensing may be involved in this phenomenon. Further investigations should reveal the exact biological role of this molecule as well as its therapeutic potential. PMID:25073640

Quantitative Imaging of Gut Microbiota Spatial Organization

PubMed Central

Earle, Kristen A.; Billings, Gabriel; Sigal, Michael; Lichtman, Joshua S.; Hansson, Gunnar C.; Elias, Joshua E.; Amieva, Manuel R.; Huang, Kerwyn Casey; Sonnenburg, Justin L.

2015-01-01

Summary Genomic technologies have significantly advanced our understanding of the composition and diversity of host-associated microbial populations. However, their spatial organization and functional interactions relative to the host have been more challenging to study. Here we present a pipeline for the assessment of intestinal microbiota localization within immunofluorescence images of fixed gut cross-sections that includes a flexible software package, BacSpace, for high-throughput quantification of microbial organization. Applying this pipeline to gnotobiotic and human microbiota-colonized mice, we demonstrate that elimination of microbiota accessible carbohydrates (MACs) from the diet results in thinner mucus in the distal colon, increased proximity of microbes to the epithelium, and heightened expression of the inflammatory marker REG3β. Measurements of microbe-microbe proximity reveal that a MAC-deficient diet alters monophyletic spatial clustering. Furthermore, we quantify the invasion of Helicobacter pylori into the glands of the mouse stomach relative to host mitotic progenitor cells, illustrating the generalizability of this approach. PMID:26439864

Taurocholic acid metabolism by gut microbes and colon cancer

PubMed Central

Ridlon, Jason M.; Wolf, Patricia G.; Gaskins, H. Rex

2016-01-01

ABSTRACT Colorectal cancer (CRC) is one of the most frequent causes of cancer death worldwide and is associated with adoption of a diet high in animal protein and saturated fat. Saturated fat induces increased bile secretion into the intestine. Increased bile secretion selects for populations of gut microbes capable of altering the bile acid pool, generating tumor-promoting secondary bile acids such as deoxycholic acid and lithocholic acid. Epidemiological evidence suggests CRC is associated with increased levels of DCA in serum, bile, and stool. Mechanisms by which secondary bile acids promote CRC are explored. Furthermore, in humans bile acid conjugation can vary by diet. Vegetarian diets favor glycine conjugation while diets high in animal protein favor taurine conjugation. Metabolism of taurine conjugated bile acids by gut microbes generates hydrogen sulfide, a genotoxic compound. Thus, taurocholic acid has the potential to stimulate intestinal bacteria capable of converting taurine and cholic acid to hydrogen sulfide and deoxycholic acid, a genotoxin and tumor-promoter, respectively. PMID:27003186

An internal thioester in a pathogen surface protein mediates covalent host binding

PubMed Central

Walden, Miriam; Edwards, John M; Dziewulska, Aleksandra M; Bergmann, Rene; Saalbach, Gerhard; Kan, Su-Yin; Miller, Ona K; Weckener, Miriam; Jackson, Rosemary J; Shirran, Sally L; Botting, Catherine H; Florence, Gordon J; Rohde, Manfred; Banfield, Mark J; Schwarz-Linek, Ulrich

2015-01-01

To cause disease and persist in a host, pathogenic and commensal microbes must adhere to tissues. Colonization and infection depend on specific molecular interactions at the host-microbe interface that involve microbial surface proteins, or adhesins. To date, adhesins are only known to bind to host receptors non-covalently. Here we show that the streptococcal surface protein SfbI mediates covalent interaction with the host protein fibrinogen using an unusual internal thioester bond as a ‘chemical harpoon’. This cross-linking reaction allows bacterial attachment to fibrin and SfbI binding to human cells in a model of inflammation. Thioester-containing domains are unexpectedly prevalent in Gram-positive bacteria, including many clinically relevant pathogens. Our findings support bacterial-encoded covalent binding as a new molecular principle in host-microbe interactions. This represents an as yet unexploited target to treat bacterial infection and may also offer novel opportunities for engineering beneficial interactions. DOI: http://dx.doi.org/10.7554/eLife.06638.001 PMID:26032562

Paratransgenic Control of Vector Borne Diseases

PubMed Central

Hurwitz, Ivy; Fieck, Annabeth; Read, Amber; Hillesland, Heidi; Klein, Nichole; Kang, Angray; Durvasula, Ravi

2011-01-01

Conventional methodologies to control vector borne diseases with chemical pesticides are often associated with environmental toxicity, adverse effects on human health and the emergence of insect resistance. In the paratransgenic strategy, symbiotic or commensal microbes of host insects are transformed to express gene products that interfere with pathogen transmission. These genetically altered microbes are re-introduced back to the insect where expression of the engineered molecules decreases the host's ability to transmit the pathogen. We have successfully utilized this strategy to reduce carriage rates of Trypanosoma cruzi, the causative agent of Chagas disease, in the triatomine bug, Rhodnius prolixus, and are currently developing this methodology to control the transmission of Leishmania donovani by the sand fly Phlebotomus argentipes. Several effector molecules, including antimicrobial peptides and highly specific single chain antibodies, are currently being explored for their anti-parasite activities in these two systems. In preparation for eventual field use, we are actively engaged in risk assessment studies addressing the issue of horizontal gene transfer from the modified bacteria to environmental microbes. PMID:22110385

The Gut Microbiota in Immune-Mediated Inflammatory Diseases

PubMed Central

Forbes, Jessica D.; Van Domselaar, Gary; Bernstein, Charles N.

2016-01-01

The collection of microbes and their genes that exist within and on the human body, collectively known as the microbiome has emerged as a principal factor in human health and disease. Humans and microbes have established a symbiotic association over time, and perturbations in this association have been linked to several immune-mediated inflammatory diseases (IMID) including inflammatory bowel disease, rheumatoid arthritis, and multiple sclerosis. IMID is a term used to describe a group of chronic, highly disabling diseases that affect different organ systems. Though a cornerstone commonality between IMID is the idiopathic nature of disease, a considerable portion of their pathobiology overlaps including epidemiological co-occurrence, genetic susceptibility loci and environmental risk factors. At present, it is clear that persons with an IMID are at an increased risk for developing comorbidities, including additional IMID. Advancements in sequencing technologies and a parallel explosion of 16S rDNA and metagenomics community profiling studies have allowed for the characterization of microbiomes throughout the human body including the gut, in a myriad of human diseases and in health. The main challenge now is to determine if alterations of gut flora are common between IMID or, if particular changes in the gut community are in fact specific to a single disease. Herein, we review and discuss the relationships between the gut microbiota and IMID. PMID:27462309

A multivariate distance-based analytic framework for microbial interdependence association test in longitudinal study.

PubMed

Zhang, Yilong; Han, Sung Won; Cox, Laura M; Li, Huilin

2017-12-01

Human microbiome is the collection of microbes living in and on the various parts of our body. The microbes living on our body in nature do not live alone. They act as integrated microbial community with massive competing and cooperating and contribute to our human health in a very important way. Most current analyses focus on examining microbial differences at a single time point, which do not adequately capture the dynamic nature of the microbiome data. With the advent of high-throughput sequencing and analytical tools, we are able to probe the interdependent relationship among microbial species through longitudinal study. Here, we propose a multivariate distance-based test to evaluate the association between key phenotypic variables and microbial interdependence utilizing the repeatedly measured microbiome data. Extensive simulations were performed to evaluate the validity and efficiency of the proposed method. We also demonstrate the utility of the proposed test using a well-designed longitudinal murine experiment and a longitudinal human study. The proposed methodology has been implemented in the freely distributed open-source R package and Python code. © 2017 WILEY PERIODICALS, INC.

The mind-body-microbial continuum

PubMed Central

Gonzalez, Antonio; Stombaugh, Jesse; Lozupone, Catherine; Turnbaugh, Peter J.; Gordon, Jeffrey I.; Knight, Rob

2011-01-01

Our understanding of the vast collection of microbes that live on and inside us (microbiota) and their collective genes (microbiome) has been revolutionized by culture-independent “metagenomic” techniques and DNA sequencing technologies. Most of our microbes live in our gut, where they function as a metabolic organ and provide attributes not encoded in our human genome. Metagenomic studies are revealing shared and distinctive features of microbial communities inhabiting different humans. A central question in psychiatry is the relative role of genes and environment in shaping behavior. The human microbiome serves as the interface between our genes and our history of environmental exposures; explorations of our microbiomes thus offer the possibility of providing new insights into our neurodevelopment and our behavioral phenotypes by affecting complex processes such as inter- and intra personal variations in cognition, personality, mood, sleep, and eating behavior, and perhaps even a variety of neuropsychiatric diseases ranging from affective disorders to autism. Better understanding of microbiome-encoded pathways for xenobiotic metabolism also has important implications for improving the efficacy of pharmacologic interventions with neuromodulator agents. PMID:21485746

Transition metals at the host–pathogen interface: How Neisseria exploit human metalloproteins for acquiring iron and zinc

PubMed Central

Neumann, Wilma; Hadley, Rose C.; Nolan, Elizabeth M.

2017-01-01

Transition metals are essential nutrients for all organisms and important players in the host-microbe interaction. During bacterial infection, a tug-of-war between the host and microbe for nutrient metals occurs: the host innate immune system responds to the pathogen by reducing metal availability and the pathogen tries to outmaneuver this response. The outcome of this competition, which involves metal-sequestering host-defense proteins and microbial metal acquisition machinery, is an important variable for whether infection occurs. One strategy bacterial pathogens employ to overcome metal restriction involves hijacking abundant host metalloproteins. The obligate human pathogens Neisseria spp. express TonB-dependent transport systems that capture human metalloproteins, extract the bound metal ions, and deliver these nutrients into the bacterial cell. This Essay highlights structural and mechanistic investigations that provide insights into how Neisseria acquire iron from the Fe(III)-transport protein transferrin, the Fe(III)-chelating host-defense protein lactoferrin, and the oxygen-transport protein hemoglobin, and obtain zinc from the metal-sequestering antimicrobial protein calprotectin. PMID:28487398

Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation.

PubMed

Hegazy, Ahmed N; West, Nathaniel R; Stubbington, Michael J T; Wendt, Emily; Suijker, Kim I M; Datsi, Angeliki; This, Sebastien; Danne, Camille; Campion, Suzanne; Duncan, Sylvia H; Owens, Benjamin M J; Uhlig, Holm H; McMichael, Andrew; Bergthaler, Andreas; Teichmann, Sarah A; Keshav, Satish; Powrie, Fiona

2017-11-01

Interactions between commensal microbes and the immune system are tightly regulated and maintain intestinal homeostasis, but little is known about these interactions in humans. We investigated responses of human CD4 + T cells to the intestinal microbiota. We measured the abundance of T cells in circulation and intestinal tissues that respond to intestinal microbes and determined their clonal diversity. We also assessed their functional phenotypes and effects on intestinal resident cell populations, and studied alterations in microbe-reactive T cells in patients with chronic intestinal inflammation. We collected samples of peripheral blood mononuclear cells and intestinal tissues from healthy individuals (controls, n = 13-30) and patients with inflammatory bowel diseases (n = 119; 59 with ulcerative colitis and 60 with Crohn's disease). We used 2 independent assays (CD154 detection and carboxy-fluorescein succinimidyl ester dilution assays) and 9 intestinal bacterial species (Escherichia coli, Lactobacillus acidophilus, Bifidobacterium animalis subsp lactis, Faecalibacterium prausnitzii, Bacteroides vulgatus, Roseburia intestinalis, Ruminococcus obeum, Salmonella typhimurium, and Clostridium difficile) to quantify, expand, and characterize microbe-reactive CD4 + T cells. We sequenced T-cell receptor Vβ genes in expanded microbe-reactive T-cell lines to determine their clonal diversity. We examined the effects of microbe-reactive CD4 + T cells on intestinal stromal and epithelial cell lines. Cytokines, chemokines, and gene expression patterns were measured by flow cytometry and quantitative polymerase chain reaction. Circulating and gut-resident CD4 + T cells from controls responded to bacteria at frequencies of 40-4000 per million for each bacterial species tested. Microbiota-reactive CD4 + T cells were mainly of a memory phenotype, present in peripheral blood mononuclear cells and intestinal tissue, and had a diverse T-cell receptor Vβ repertoire. These cells were functionally heterogeneous, produced barrier-protective cytokines, and stimulated intestinal stromal and epithelial cells via interleukin 17A, interferon gamma, and tumor necrosis factor. In patients with inflammatory bowel diseases, microbiota-reactive CD4 + T cells were reduced in the blood compared with intestine; T-cell responses that we detected had an increased frequency of interleukin 17A production compared with responses of T cells from blood or intestinal tissues of controls. In an analysis of peripheral blood mononuclear cells and intestinal tissues from patients with inflammatory bowel diseases vs controls, we found that reactivity to intestinal bacteria is a normal property of the human CD4 + T-cell repertoire, and does not necessarily indicate disrupted interactions between immune cells and the commensal microbiota. T-cell responses to commensals might support intestinal homeostasis, by producing barrier-protective cytokines and providing a large pool of T cells that react to pathogens. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Microbial Invasion vs. Tick Immune Regulation.

PubMed

Sonenshine, Daniel E; Macaluso, Kevin R

2017-01-01

Ticks transmit a greater variety of pathogenic agents that cause disease in humans and animals than any other haematophagous arthropod, including Lyme disease, Rocky Mountain spotted fever, human granulocytic anaplasmosis, babesiosis, tick-borne encephalitis, Crimean Congo haemorhagic fever, and many others (Gulia-Nuss et al., 2016). Although diverse explanations have been proposed to explain their remarkable vectorial capacity, among the most important are their blood feeding habit, their long term off-host survival, the diverse array of bioactive molecules that disrupt the host's natural hemostatic mechanisms, facilitate blood flow, pain inhibitors, and minimize inflammation to prevent immune rejection (Hajdušek et al., 2013). Moreover, the tick's unique intracellular digestive processes allow the midgut to provide a relatively permissive microenvironment for survival of invading microbes. Although tick-host-pathogen interactions have evolved over more than 300 million years (Barker and Murrell, 2008), few microbes have been able to overcome the tick's innate immune system, comprising both humoral and cellular processes that reject them. Similar to most eukaryotes, the signaling pathways that regulate the innate immune response, i.e., the Toll, IMD (Immunodeficiency) and JAK-STAT (Janus Kinase/ Signal Transducers and Activators of Transcription) also occur in ticks (Gulia-Nuss et al., 2016). Recognition of pathogen-associated molecular patterns (PAMPs) on the microbial surface triggers one or the other of these pathways. Consequently, ticks are able to mount an impressive array of humoral and cellular responses to microbial challenge, including anti-microbial peptides (AMPs), e.g., defensins, lysozymes, microplusins, etc., that directly kill, entrap or inhibit the invaders. Equally important are cellular processes, primarily phagocytosis, that capture, ingest, or encapsulate invading microbes, regulated by a primordial system of thioester-containing proteins, fibrinogen-related lectins and convertase factors (Hajdušek et al., 2013). Ticks also express reactive oxygen species (ROS) as well as glutathione-S-transferase, superoxide dismutase, heat shock proteins and even protease inhibitors that kill or inhibit microbes. Nevertheless, many tick-borne microorganisms are able to evade the tick's innate immune system and survive within the tick's body. The examples that follow describe some of the many different strategies that have evolved to enable ticks to transmit the agents of human and/or animal disease.

Bifidobacterium breve - HT-29 cell line interaction: modulation of TNF-α induced gene expression.

PubMed

Boesten, R J; Schuren, F H J; Willemsen, L E M; Vriesema, A; Knol, J; De Vos, W M

2011-06-01

To provide insight in the molecular basis for intestinal host-microbe interactions, we determined the genome-wide transcriptional response of human intestinal epithelial cells following exposure to cells of Bifidobacterium breve. To select an appropriate test system reflecting inflammatory conditions, the responsiveness to TNF-α was compared in T84, Caco-2 and HT-29 cells. The highest TNF-α response was observed in HT-29 cells and this cell line was selected for exposure to the B. breve strains M-16V, NR246 and UCC2003. After one hour of bacterial pre-incubation followed by two hours of additional TNF-α stimulation, B. breve M-16V (86%), but to a much lesser extent strains NR246 (50%) or UCC2003 (32%), showed a strain-specific reduction of the HT-29 transcriptional response to the inflammatory treatment. The most important functional groups of genes that were transcriptionally suppressed by the presence of B. breve M-16V, were found to be involved in immune regulation and apoptotic processes. About 54% of the TNF-α induced genes were solely suppressed by the presence of B. breve M-16V. These included apoptosis-related cysteine protease caspase 7 (CASP7), interferon regulatory factor 3 (IRF3), amyloid beta (A4) precursor proteinbinding family A member 1 (APBA1), NADPH oxidase (NOX5), and leukemia inhibitory factor receptor (LIFR). The extracellular IL-8 concentration was determined by an immunological assay but did not change significantly, indicating that B. breve M-16V only partially modulates the TNF-α pathway. In conclusion, this study shows that B. breve strains modulate gene expression in HT-29 cells under inflammatory conditions in a strain-specific way.

Contemporary issues: diseases with a food vector.

PubMed

Archer, D L; Young, F E

1988-10-01

Foodborne disease has become a contemporary issue. Several large, well-publicized outbreaks of foodborne disease have heightened public awareness that harmful microorganisms may be present in food and that chronic as well as acute disease may be caused by foodborne microbes. The field of food microbiology has likewise experienced a resurgence of interest. New tools, such as recombinant deoxyribonucleic acid technology and monoclonal antibody production, used to elucidate microbial virulence factors have facilitated identification of disease-causing microbes once thought to be harmless and demonstrated the complexity of individual virulence mechanisms previously considered to be well understood. Foodborne pathogens are also causing disease via some surprising food vectors, such as chopped, bottled garlic and sauteed onions. In addition to acute gastrointestinal disturbances, certain microorganisms may, through complex interactions with the human immune response, cause chronic diseases that affect several major organ systems. These microbes are serving as models in studies of molecular mimicry and genetic interrelatedness of procaryotes and eucaryotes. Other recently recognized attributes of foodborne microorganisms, such as the heat shock phenomenon and the possible nonculturability of some bacteria, may affect their ability to cause disease in humans. Because foodborne disease is a major cause of morbidity and mortality, the study of these diseases and their causative microorganisms presents a unique challenge to many professionals in the subdisciplines of microbiology, epidemiology, and clinical medicine.

Contemporary issues: diseases with a food vector.

PubMed Central

Archer, D L; Young, F E

1988-01-01

Foodborne disease has become a contemporary issue. Several large, well-publicized outbreaks of foodborne disease have heightened public awareness that harmful microorganisms may be present in food and that chronic as well as acute disease may be caused by foodborne microbes. The field of food microbiology has likewise experienced a resurgence of interest. New tools, such as recombinant deoxyribonucleic acid technology and monoclonal antibody production, used to elucidate microbial virulence factors have facilitated identification of disease-causing microbes once thought to be harmless and demonstrated the complexity of individual virulence mechanisms previously considered to be well understood. Foodborne pathogens are also causing disease via some surprising food vectors, such as chopped, bottled garlic and sauteed onions. In addition to acute gastrointestinal disturbances, certain microorganisms may, through complex interactions with the human immune response, cause chronic diseases that affect several major organ systems. These microbes are serving as models in studies of molecular mimicry and genetic interrelatedness of procaryotes and eucaryotes. Other recently recognized attributes of foodborne microorganisms, such as the heat shock phenomenon and the possible nonculturability of some bacteria, may affect their ability to cause disease in humans. Because foodborne disease is a major cause of morbidity and mortality, the study of these diseases and their causative microorganisms presents a unique challenge to many professionals in the subdisciplines of microbiology, epidemiology, and clinical medicine. PMID:3069199

The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes

PubMed Central

Martens, Eric C.; Kelly, Amelia G.; Tauzin, Alexandra S.; Brumer, Harry

2014-01-01

The critical importance of gastrointestinal microbes to digestion of dietary fiber in humans and other mammals has been appreciated for decades. Symbiotic microorganisms expand mammalian digestive physiology by providing an armament of diverse polysaccharide degrading enzymes, which are largely absent in mammalian genomes. By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on time scales as short as several hours, due to the ability of the gut microbial community to rapidly alter its physiology from meal-to-meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends. Despite a vast amount of sequence-based insight into the metabolic potential of gut microbes, the specific mechanisms by which symbiotic gut microorganisms recognize and attack complex carbohydrates remain largely undefined. Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates. Understanding these relationships at precise mechanistic levels will be essential to obtain a complete understanding of the forces shaping gut microbial ecology and genomic evolution, as well as devising strategies to intentionally manipulate the composition and physiology of the gut microbial community to improve health. PMID:25026064

Comment on ''Effects of long-term high CO2 exposure on two species of coccolithophore'' by Müller et al. (2010)

NASA Astrophysics Data System (ADS)

Collins, S.

2010-07-01

Populations can respond to environmental change over tens or hundreds of generations by shifts in phenotype that can be the result of a sustained physiological response, evolutionary (genetic) change, shifts in community composition, or some combination of these factors. Microbes evolve on human timescales, and evolution may contribute to marine phytoplankton responses to global change over the coming decades. However, it is still unknown whether evolutionary responses are likely to contribute significantly to phenotypic change in marine microbial communities under high pCO2 regimes or other aspects of global change. Recent work by Müller et al. (2010) highlights that long-term responses of marine microbes to global change must be empirically measured and the underlying cause of changes in phenotype explained. Here, I briefly discuss how tools from experimental microbial evolution may be used to detect and measure evolutionary responses in marine phytoplankton grown in high CO2 environments and other environments of interest. I outline why the particular biology of marine microbes makes conventional experimental evolution challenging right now and make a case that marine microbes are good candidates for the development of new model systems in experimental evolution. I suggest that "black box" frameworks that focus on partitioning phenotypic change, such as the Price equation, may be useful in cases where direct measurements of evolutionary responses alone are difficult, and that such approaches could be used to test hypotheses about the underlying causes of phenotypic shifts in marine microbe communities responding to global change.

The devil lies in the details: how variations in polysaccharide fine-structure impact the physiology and evolution of gut microbes.

PubMed

Martens, Eric C; Kelly, Amelia G; Tauzin, Alexandra S; Brumer, Harry

2014-11-25

The critical importance of gastrointestinal microbes to digestion of dietary fiber in humans and other mammals has been appreciated for decades. Symbiotic microorganisms expand mammalian digestive physiology by providing an armament of diverse polysaccharide-degrading enzymes, which are largely absent in mammalian genomes. By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on timescales as short as several hours due to the ability of the gut microbial community to rapidly alter its physiology from meal to meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends. Despite a vast amount of sequence-based insight into the metabolic potential of gut microbes, the specific mechanisms by which symbiotic gut microorganisms recognize and attack complex carbohydrates remain largely undefined. Here, we review the recent literature on this topic and posit that numerous, subtle variations in polysaccharides diversify the spectrum of available nutrient niches, each of which may be best filled by a subset of microorganisms that possess the corresponding proteins to recognize and degrade different carbohydrates. Understanding these relationships at precise mechanistic levels will be essential to obtain a complete understanding of the forces shaping gut microbial ecology and genomic evolution, as well as devising strategies to intentionally manipulate the composition and physiology of the gut microbial community to improve health. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Toxicological Perspective on Disinfection ByProducts

EPA Science Inventory

Disinfection of water is essential for reduction of microbes harmful to human health and chemical disinfection is considered one of the major public health triumphs of the 20th Century. An unintended consequence of disinfection with oxidizing chemicals is formation of disinfectio...

The gut microbiota, obesity and insulin resistance

USDA-ARS?s Scientific Manuscript database

The human gut is densely populated by commensal and symbiotic microbes (the "gut microbiota"), with the majority of the constituent microorganisms being bacteria. Accumulating evidence indicates that the gut microbiota plays a significant role in the development of obesity, obesity-associated inflam...

DETERMINATION OF MICROBIAL COMMUNITY STRUCTURE IN UNTREATED WASTEWATER FROM DIFFERENT GEOGRAPHIC LOCALES

EPA Science Inventory

Microbial sewage communities consist of a combination of human faecal microorganisms and urban infrastructure-derived microbes originating from infiltration of rainwater and stormwater inputs. Together these different sources of microbial diversity form a unique population struc...

Comparative Metagenomics Revealed Commonly Enriched Gene Sets in Human Gut Microbiomes

PubMed Central

Kurokawa, Ken; Itoh, Takehiko; Kuwahara, Tomomi; Oshima, Kenshiro; Toh, Hidehiro; Toyoda, Atsushi; Takami, Hideto; Morita, Hidetoshi; Sharma, Vineet K.; Srivastava, Tulika P.; Taylor, Todd D.; Noguchi, Hideki; Mori, Hiroshi; Ogura, Yoshitoshi; Ehrlich, Dusko S.; Itoh, Kikuji; Takagi, Toshihisa; Sakaki, Yoshiyuki; Hayashi, Tetsuya; Hattori, Masahira

2007-01-01

Numerous microbes inhabit the human intestine, many of which are uncharacterized or uncultivable. They form a complex microbial community that deeply affects human physiology. To identify the genomic features common to all human gut microbiomes as well as those variable among them, we performed a large-scale comparative metagenomic analysis of fecal samples from 13 healthy individuals of various ages, including unweaned infants. We found that, while the gut microbiota from unweaned infants were simple and showed a high inter-individual variation in taxonomic and gene composition, those from adults and weaned children were more complex but showed a high functional uniformity regardless of age or sex. In searching for the genes over-represented in gut microbiomes, we identified 237 gene families commonly enriched in adult-type and 136 families in infant-type microbiomes, with a small overlap. An analysis of their predicted functions revealed various strategies employed by each type of microbiota to adapt to its intestinal environment, suggesting that these gene sets encode the core functions of adult and infant-type gut microbiota. By analysing the orphan genes, 647 new gene families were identified to be exclusively present in human intestinal microbiomes. In addition, we discovered a conjugative transposon family explosively amplified in human gut microbiomes, which strongly suggests that the intestine is a ‘hot spot’ for horizontal gene transfer between microbes. PMID:17916580

Plants + soil/wetland microbes: Food crop systems that also clean air and water

NASA Astrophysics Data System (ADS)

Nelson, Mark; Wolverton, B. C.

2011-02-01

The limitations that will govern bioregenerative life support applications in space, especially volume and weight, make multi-purpose systems advantageous. This paper outlines two systems which utilize plants and associated microbial communities of root or growth medium to both produce food crops and clean air and water. Underlying these approaches are the large numbers and metabolic diversity of microbes associated with roots and found in either soil or other suitable growth media. Biogeochemical cycles have microbial links and the ability of microbes to metabolize virtually all trace gases, whether of technogenic or biogenic origin, has long been established. Wetland plants and the rootzone microbes of wetland soils/media also been extensively researched for their ability to purify wastewaters of a great number of potential water pollutants, from nutrients like N and P, to heavy metals and a range of complex industrial pollutants. There is a growing body of research on the ability of higher plants to purify air and water. Associated benefits of these approaches is that by utilizing natural ecological processes, the cleansing of air and water can be done with little or no energy inputs. Soil and rootzone microorganisms respond to changing pollutant types by an increase of the types of organisms with the capacity to use these compounds. Thus living systems have an adaptive capacity as long as the starting populations are sufficiently diverse. Tightly sealed environments, from office buildings to spacecraft, can have hundreds or even thousands of potential air pollutants, depending on the materials and equipment enclosed. Human waste products carry a plethora of microbes which are readily used in the process of converting its organic load to forms that can be utilized by green plants. Having endogenous means of responding to changing air and water quality conditions represents safety factors as these systems operate without the need for human intervention. We review this research and the ability of systems using these mechanisms to also produce food or other useful crops. Concerns about possible pathogens in soils and wastewater are discussed along with some methods to prevent contact, disease transmission and to pre-screen and decrease risks. The psychological benefits of having systems utilizing green plants are becoming more widely recognized. Some recent applications extending the benefits of plants and microbes to solve new environmental problems are presented. For space applications, we discuss the use of in situ space resources and ways of making these systems compact and light-weight.

Role of Lactobacillus reuteri in Human Health and Diseases

PubMed Central

Mu, Qinghui; Tavella, Vincent J.; Luo, Xin M.

2018-01-01

Lactobacillus reuteri (L. reuteri) is a well-studied probiotic bacterium that can colonize a large number of mammals. In humans, L. reuteri is found in different body sites, including the gastrointestinal tract, urinary tract, skin, and breast milk. The abundance of L. reuteri varies among different individuals. Several beneficial effects of L. reuteri have been noted. First, L. reuteri can produce antimicrobial molecules, such as organic acids, ethanol, and reuterin. Due to its antimicrobial activity, L. reuteri is able to inhibit the colonization of pathogenic microbes and remodel the commensal microbiota composition in the host. Second, L. reuteri can benefit the host immune system. For instance, some L. reuteri strains can reduce the production of pro-inflammatory cytokines while promoting regulatory T cell development and function. Third, bearing the ability to strengthen the intestinal barrier, the colonization of L. reuteri may decrease the microbial translocation from the gut lumen to the tissues. Microbial translocation across the intestinal epithelium has been hypothesized as an initiator of inflammation. Therefore, inflammatory diseases, including those located in the gut as well as in remote tissues, may be ameliorated by increasing the colonization of L. reuteri. Notably, the decrease in the abundance of L. reuteri in humans in the past decades is correlated with an increase in the incidences of inflammatory diseases over the same period of time. Direct supplementation or prebiotic modulation of L. reuteri may be an attractive preventive and/or therapeutic avenue against inflammatory diseases. PMID:29725324

Sugar-coated: exopolysaccharide producing lactic acid bacteria for food and human health applications.

PubMed

Ryan, P M; Ross, R P; Fitzgerald, G F; Caplice, N M; Stanton, C

2015-03-01

The human enteric microbiome represents a veritable organ relied upon by the host for a range of metabolic and homeostatic functions. Through the production of metabolites such as short chain fatty acids (SCFA), folate, vitamins B and K, lactic acid, bacteriocins, peroxides and exopolysaccharides, the bacteria of the gut microbiome provide nutritional components for colonocytes, liver and muscle cells, competitively exclude potential pathogenic organisms and modulate the hosts immune system. Due to the extensive variation in structure, size and composition, microbial exopolysaccharides represent a useful set of versatile natural ingredients for the food industrial sector, both in terms of their rheological properties and in many cases, their associated health benefits. The exopolysaccharide-producing bacteria that fall within the 35 Lactobacillus and five Bifidobacterium species which have achieved qualified presumption of safety (QPS) and generally recognised as safe (GRAS) status are of particular interest, as their inclusion in food products can avoid considerable scrutiny. In addition, additives commonly utilised by the food industry are becoming unattractive to the consumer, due to the demand for a more 'natural' and 'clean labelled' diet. In situ production of exopolysaccharides by food-grade cultures in many cases confers similar rheological and sensory properties in fermented dairy products, as traditional additives, such as hydrocolloids, collagen and alginate. This review will focus on microbial synthesis of exopolysaccharides, the human health benefits of dietary exopolysaccharides and the technofunctional applications of exopolysaccharide-synthesising microbes in the food industry.

The incredible journey of mankind: Helicobacter pylori as the narrator.

PubMed

Desikan, P

2010-01-01

Over the past decade, sequence differences between microbes from various geographical areas have been studied with the intent to interpret population movements of their hosts. An organism that is a reliable storehouse of such data, by virtue of its long association with its human host, is Helicobacter pylori. Functional and comparative analyses of its genome provide fascinating insights into human behaviour in the ancient past.

Structural basis for antagonism of human interleukin 18 by poxvirus interleukin 18-binding protein

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

Krumm, Brian; Meng, Xiangzhi; Li, Yongchao

2009-07-10

Human interleukin-18 (hIL-18) is a cytokine that plays an important role in inflammation and host defense against microbes. Its activity is regulated in vivo by a naturally occurring antagonist, the human IL-18-binding protein (IL-18BP). Functional homologs of human IL-18BP are encoded by all orthopoxviruses, including variola virus, the causative agent of smallpox. They contribute to virulence by suppressing IL-18-mediated immune responses. Here, we describe the 2.0-{angstrom} resolution crystal structure of an orthopoxvirus IL-18BP, ectromelia virus IL-18BP (ectvIL-18BP), in complex with hIL-18. The hIL-18 structure in the complex shows significant conformational change at the binding interface compared with the structure ofmore » ligand-free hIL-18, indicating that the binding is mediated by an induced-fit mechanism. EctvIL-18BP adopts a canonical Ig fold and interacts via one edge of its {beta}-sandwich with 3 cavities on the hIL-18 surface through extensive hydrophobic and hydrogen bonding interactions. Most of the ectvIL-18BP residues that participate in these interactions are conserved in both human and viral homologs, explaining their functional equivalence despite limited sequence homology. EctvIL-18BP blocks a putative receptor-binding site on IL-18, thus preventing IL-18 from engaging its receptor. Our structure provides insights into how IL-18BPs modulate hIL-18 activity. The revealed binding interface provides the basis for rational design of inhibitors against orthopoxvirus IL-18BP (for treating orthopoxvirus infection) or hIL-18 (for treating certain inflammatory and autoimmune diseases).« less

Shifts in priming partly explain impacts of long-term nitrogen input in different chemical forms on soil organic carbon storage.

PubMed

Song, Minghua; Guo, Yu; Yu, Feihai; Zhang, Xianzhou; Cao, Guangmin; Cornelissen, Johannes H C

2018-05-10

Input of labile organic carbon can enhance decomposition of extant soil organic carbon (SOC) through priming. We hypothesized that long-term nitrogen (N) input in different chemical forms alters SOC pools by altering priming effects associated with N-mediated changes in plants and soil microbes. The hypothesis was tested by integrating field experimental data of plants, soil microbes and two incubation experiments with soils that had experienced 10 years of N enrichment with three chemical forms (ammonium, nitrate and both ammonium and nitrate) in an alpine meadow on the Tibetan Plateau. Incubations with glucose- 13 C addition at three rates were used to quantify effects of exogenous organic carbon input on the priming of SOC. Incubations with microbial inocula extracted from soils that had experienced different long-term N treatments were conducted to detect effects of N-mediated changes in soil microbes on priming effects. We found strong evidence and a mechanistic explanation for alteration of SOC pools following 10 years of N enrichment with different chemical forms. We detected significant negative priming effects both in soils collected from ammonium-addition plots and in sterilized soils inoculated with soil microbes extracted from ammonium-addition plots. In contrast, significant positive priming effects were found both in soils collected from nitrate-addition plots and in sterilized soils inoculated with soil microbes extracted from nitrate-addition plots. Meanwhile, the abundance and richness of graminoids were higher and the abundance of soil microbes was lower in ammonium-addition than in nitrate-addition plots. Our findings provide evidence that shifts toward higher graminoid abundance and changes in soil microbial abundance mediated by N chemical forms are key drivers for priming effects and SOC pool changes, thereby linking human interference with the N cycle to climate change. © 2018 John Wiley & Sons Ltd.

The Road to Infection: Host-Microbe Interactions Defining the Pathogenicity of Streptococcus bovis/Streptococcus equinus Complex Members

PubMed Central

Jans, Christoph; Boleij, Annemarie

2018-01-01

The Streptococcus bovis/Streptococcus equinus complex (SBSEC) comprises several species inhabiting the animal and human gastrointestinal tract (GIT). They match the pathobiont description, are potential zoonotic agents and technological organisms in fermented foods. SBSEC members are associated with multiple diseases in humans and animals including ruminal acidosis, infective endocarditis (IE) and colorectal cancer (CRC). Therefore, this review aims to re-evaluate adhesion and colonization abilities of SBSEC members of animal, human and food origin paired with genomic and functional host-microbe interaction data on their road from colonization to infection. SBSEC seem to be a marginal population during GIT symbiosis that can proliferate as opportunistic pathogens. Risk factors for human colonization are considered living in rural areas and animal-feces contact. Niche adaptation plays a pivotal role where Streptococcus gallolyticus subsp. gallolyticus (SGG) retained the ability to proliferate in various environments. Other SBSEC members have undergone genome reduction and niche-specific gene gain to yield important commensal, pathobiont and technological species. Selective colonization of CRC tissue is suggested for SGG, possibly related to increased adhesion to cancerous cell types featuring enhanced collagen IV accessibility. SGG can colonize, proliferate and may shape the tumor microenvironment to their benefit by tumor promotion upon initial neoplasia development. Bacteria cell surface structures including lipotheichoic acids, capsular polysaccharides and pilus loci (pil1, pil2, and pil3) govern adhesion. Only human blood-derived SGG contain complete pilus loci and other disease-associated surface proteins. Rumen or feces-derived SGG and other SBSEC members lack or harbor mutated pili. Pili also contribute to binding to fibrinogen upon invasion and translocation of cells from the GIT into the blood system, subsequent immune evasion, human contact system activation and collagen-I-binding on damaged heart valves. Only SGG carrying complete pilus loci seem to have highest IE potential in humans with significant links between SGG bacteremia/IE and underlying diseases including CRC. Other SBSEC host-microbe combinations might rely on currently unknown mechanisms. Comparative genome data of blood, commensal and food isolates are limited but required to elucidate the role of pili and other virulence factors, understand pathogenicity mechanisms, host specificity and estimate health risks for animals, humans and food alike. PMID:29692760

Biobased polymers for corrosion protection of metals

USDA-ARS?s Scientific Manuscript database

Anticorrosive biobased polymers were developed in our lab. We isolated an exopolysaccharide produced by a microbe that, when coated on metal substrates, exhibited unique corrosion inhibition. Corrosion is a worldwide problem and impacts the economy, jeopardizes human health and safety, and impedes t...

A Microbial Murder Mystery.

ERIC Educational Resources Information Center

Mitchell, Melissa A.; Mitchell, James K.

2002-01-01

Proposes a microbial mystery activity to test students' knowledge of human anatomy and their ability to identify microbes. Provides an opportunity for students to develop logical deductive reasoning. Includes national science education standards related to this activity, activity sheets with whole procedures, and Internet resources. (KHR)

Impact of nasopharyngeal microbiota on the development of respiratory tract diseases.

PubMed

Esposito, S; Principi, N

2018-01-01

Knowledge of whether and how respiratory microbiota composition can prime the immune system and provide colonisation resistance, limiting consecutive pathobiont overgrowth and infections, is essential to improving the prevention and therapy of respiratory disorders. Modulation of dysbiotic ecosystems or reconstitution of missing microbes might be a possible measure to reduce respiratory diseases. The aim of this review is to analyse the role of nasopharyngeal microbiota in the development of respiratory tract disease in paediatric-age subjects. PubMed was used to search for all studies published over the last 15 years using the following key words: "microbiota" or "microbioma" and "nasopharyngeal" or "respiratory" or "nasal" and "children" or "paediatric" or "infant". Analysis of the literature showed that respiratory microbiota can regulate health and disease development in the respiratory tract. Like the gut microbiota, the respiratory microbiota is established at birth, and early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Protective and dangerous bacteria have been identified, and this can be considered the base for developing new approaches to diseases that respond poorly to traditional interventions. Reconstitution of missing microbes can be achieved by the administration of pre- and probiotics. Modulation of respiratory microbiota by favouring colonisation of the upper respiratory tract by beneficial commensals can interfere with the proliferation and activity of resident pathobionts and is a possible new measure to reduce the risk of disease. However, further studies are needed because a deeper understanding of these and related issues can be transferred to clinical practice.

Oral treatment with Lactobacillus rhamnosus attenuates behavioural deficits and immune changes in chronic social stress.

PubMed

Bharwani, Aadil; Mian, M Firoz; Surette, Michael G; Bienenstock, John; Forsythe, Paul

2017-01-11

Stress-related disorders involve systemic alterations, including disruption of the intestinal microbial community. Given the putative connections between the microbiota, immunity, neural function, and behaviour, we investigated the potential for microbe-induced gut-to-brain signalling to modulate the impact of stress on host behaviour and immunoregulation. Male C57BL/6 mice treated orally over 28 days with either Lactobacillus rhamnosus (JB-1) ™ or vehicle were subjected to chronic social defeat and assessed for alterations in behaviour and immune cell phenotype. 16S rRNA sequencing and mass spectrometry were employed to analyse the faecal microbial community and metabolite profile. Treatment with JB-1 decreased stress-induced anxiety-like behaviour and prevented deficits in social interaction with conspecifics. However, JB-1 did not alter development of aggressor avoidance following social defeat. Microbial treatment attenuated stress-related activation of dendritic cells while increasing IL-10+ regulatory T cells. Furthermore, JB-1 modulated the effect of stress on faecal metabolites with neuroactive and immunomodulatory properties. Exposure to social defeat altered faecal microbial community composition and reduced species richness and diversity, none of which was prevented by JB-1. Stress-related microbiota disruptions persisted in vehicle-treated mice for 3 weeks following stressor cessation. These data demonstrate that despite the complexity of the gut microbiota, exposure to a single microbial strain can protect against certain stress-induced behaviours and systemic immune alterations without preventing dysbiosis. This work supports microbe-based interventions for stress-related disorders.

The evolutionary logic of sepsis.

PubMed

Rózsa, Lajos; Apari, Péter; Sulyok, Mihály; Tappe, Dennis; Bodó, Imre; Hardi, Richárd; Müller, Viktor

2017-11-01

The recently proposed Microbiome Mutiny Hypothesis posits that members of the human microbiome obtain information about the host individuals' health status and, when host survival is compromised, switch to an intensive exploitation strategy to maximize residual transmission. In animals and humans, sepsis is an acute systemic reaction to microbes invading the normally sterile body compartments. When induced by formerly mutualistic or neutral microbes, possibly in response to declining host health, sepsis appears to fit the 'microbiome mutiny' scenario except for its apparent failure to enhance transmission of the causative organisms. We propose that the ability of certain species of the microbiome to induce sepsis is not a fortuitous side effect of within-host replication, but rather it might, in some cases, be the result of their adaptive evolution. Whenever host health declines, inducing sepsis can be adaptive for those members of the healthy human microbiome that are capable of colonizing the future cadaver and spread by cadaver-borne transmission. We hypothesize that such microbes might exhibit switches along the 'mutualist - lethal pathogen - decomposer - mutualist again' scenario, implicating a previously unsuspected, surprising level of phenotypic plasticity. This hypothesis predicts that those species of the healthy microbiome that are recurring causative agents of sepsis can participate in the decomposition of cadavers, and can be transmitted as soil-borne or water-borne infections. Furthermore, in individual sepsis cases, the same microbial clones that dominate the systemic infection that precipitates sepsis, should also be present in high concentration during decomposition following death: this prediction is testable by molecular fingerprinting in experimentally induced animal models. Sepsis is a leading cause of human death worldwide. If further research confirms that some cases of sepsis indeed involve the 'mutiny' (facultative phenotypic switching) of normal members of the microbiome, then new strategies could be devised to prevent or treat sepsis by interfering with this process. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Time to abandon the hygiene hypothesis: new perspectives on allergic disease, the human microbiome, infectious disease prevention and the role of targeted hygiene.

PubMed

Bloomfield, Sally F; Rook, Graham Aw; Scott, Elizabeth A; Shanahan, Fergus; Stanwell-Smith, Rosalind; Turner, Paul

2016-07-01

To review the burden of allergic and infectious diseases and the evidence for a link to microbial exposure, the human microbiome and immune system, and to assess whether we could develop lifestyles which reconnect us with exposures which could reduce the risk of allergic disease while also protecting against infectious disease. Using methodology based on the Delphi technique, six experts in infectious and allergic disease were surveyed to allow for elicitation of group judgement and consensus view on issues pertinent to the aim. Key themes emerged where evidence shows that interaction with microbes that inhabit the natural environment and human microbiome plays an essential role in immune regulation. Changes in lifestyle and environmental exposure, rapid urbanisation, altered diet and antibiotic use have had profound effects on the human microbiome, leading to failure of immunotolerance and increased risk of allergic disease. Although evidence supports the concept of immune regulation driven by microbe-host interactions, the term 'hygiene hypothesis' is a misleading misnomer. There is no good evidence that hygiene, as the public understands, is responsible for the clinically relevant changes to microbial exposures. Evidence suggests a combination of strategies, including natural childbirth, breast feeding, increased social exposure through sport, other outdoor activities, less time spent indoors, diet and appropriate antibiotic use, may help restore the microbiome and perhaps reduce risks of allergic disease. Preventive efforts must focus on early life. The term 'hygiene hypothesis' must be abandoned. Promotion of a risk assessment approach (targeted hygiene) provides a framework for maximising protection against pathogen exposure while allowing spread of essential microbes between family members. To build on these findings, we must change public, public health and professional perceptions about the microbiome and about hygiene. We need to restore public understanding of hygiene as a means to prevent infectious disease. © Royal Society for Public Health 2016.

Microbes and Water Quality in Developed Countries

EPA Science Inventory

Safe drinking water has been a concern for mankind through out the world for centuries. In the developed world, governments consider access to safe and clean drinking water to be a basic human right. Government regulations generally address the quality of the source water, adequ...

Microbiomes Have the Power to Help or Hinder Your Health

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

Jansson, Janet

They are everywhere: countless microorganisms that inhabit our world—even in your skin, mouth, gut and other parts of your body. Called microbiomes, these communities play a fundamental role in our ecosystem and our bodies, influencing everything from climate to human health. And scientists at PNNL are studying microbiomes to better understand how they influence our daily lives. Scientist Janet Jansson studies complex microbiomes in soil and the human intestine to understand changes in the composition or function of microbes. In the soil, these microbes are associated with carbon cycling and degrading pollutants, as well as plant health. In the intestine,more » they are responsible for digestion of our food and protection from pathogens. When they go awry, they can be associated with numerous inflammatory bowel diseases, such as Crohn’s. Understanding the factors underlying these microbiome changes will ultimately help researchers develop solutions to problems encountered within our world and our bodies.« less

Microbes and the Next Nitrogen Revolution.

PubMed

Pikaar, Ilje; Matassa, Silvio; Rabaey, Korneel; Bodirsky, Benjamin Leon; Popp, Alexander; Herrero, Mario; Verstraete, Willy

2017-07-05

The Haber Bosch process is among the greatest inventions of the 20th century. It provided agriculture with reactive nitrogen and ultimately mankind with nourishment for a population of 7 billion people. However, the present agricultural practice of growing crops for animal production and human food constitutes a major threat to the sustainability of the planet in terms of reactive nitrogen pollution. In view of the shortage of directly feasible and cost-effective measures to avoid these planetary nitrogen burdens and the necessity to remediate this problem, we foresee the absolute need for and expect a revolution in the use of microbes as a source of protein. Bypassing land-based agriculture through direct use of Haber Bosch produced nitrogen for reactor-based production of microbial protein can be an inspiring concept for the production of high quality animal feed and even straightforward supply of proteinaceous products for human food, without significant nitrogen losses to the environment and without the need for genetic engineering to safeguard feed and food supply for the generations to come.

Effects of heavy metals on soil microbial community

NASA Astrophysics Data System (ADS)

Chu, Dian

2018-02-01

Soil is one of the most important environmental natural resources for human beings living, which is of great significance to the quality of ecological environment and human health. The study of the function of arable soil microbes exposed to heavy metal pollution for a long time has a very important significance for the usage of farmland soil. In this paper, the effects of heavy metals on soil microbial community were reviewed. The main contents were as follows: the effects of soil microbes on soil ecosystems; the effects of heavy metals on soil microbial activity, soil enzyme activities and the composition of soil microbial community. In addition, a brief description of main methods of heavy metal detection for soil pollution is given, and the means of researching soil microbial community composition are introduced as well. Finally, it is concluded that the study of soil microbial community can well reflect the degree of soil heavy metal pollution and the impact of heavy metal pollution on soil ecology.

Prediction and prevention of the next pandemic zoonosis

PubMed Central

Morse, Stephen S; Mazet, Jonna A K; Woolhouse, Mark; Parrish, Colin R; Carroll, Dennis; Karesh, William B; Zambrana-Torrelio, Carlos; Lipkin, W Ian; Daszak, Peter

2013-01-01

Most pandemics—eg, HIV/AIDS, severe acute respiratory syndrome, pandemic influenza—originate in animals, are caused by viruses, and are driven to emerge by ecological, behavioural, or socioeconomic changes. Despite their substantial effects on global public health and growing understanding of the process by which they emerge, no pandemic has been predicted before infecting human beings. We review what is known about the pathogens that emerge, the hosts that they originate in, and the factors that drive their emergence. We discuss challenges to their control and new efforts to predict pandemics, target surveillance to the most crucial interfaces, and identify prevention strategies. New mathematical modelling, diagnostic, communications, and informatics technologies can identify and report hitherto unknown microbes in other species, and thus new risk assessment approaches are needed to identify microbes most likely to cause human disease. We lay out a series of research and surveillance opportunities and goals that could help to overcome these challenges and move the global pandemic strategy from response to pre-emption. PMID:23200504

Symposium on Human Health and Global Climate Change.

DTIC Science & Technology

1996-03-01

Cholera epidemics are typically associated with seacoasts and rivers, for instance, where the cholera organism, Vibrio cholerae , survives by...everywhere. These blooms represent "environmental reservoirs" for microbes, such as Vibrio cholerae , the cause of cholera in humans. Similarly, insect and...nowadays. We find them in New Mexico , in Minnesota, in Virginia, and in New York. Around the world there is a resurgence of cholera , malaria, and yellow

The Gut Microbiome and the Brain

PubMed Central

Galland, Leo

2014-01-01

Abstract The human gut microbiome impacts human brain health in numerous ways: (1) Structural bacterial components such as lipopolysaccharides provide low-grade tonic stimulation of the innate immune system. Excessive stimulation due to bacterial dysbiosis, small intestinal bacterial overgrowth, or increased intestinal permeability may produce systemic and/or central nervous system inflammation. (2) Bacterial proteins may cross-react with human antigens to stimulate dysfunctional responses of the adaptive immune system. (3) Bacterial enzymes may produce neurotoxic metabolites such as D-lactic acid and ammonia. Even beneficial metabolites such as short-chain fatty acids may exert neurotoxicity. (4) Gut microbes can produce hormones and neurotransmitters that are identical to those produced by humans. Bacterial receptors for these hormones influence microbial growth and virulence. (5) Gut bacteria directly stimulate afferent neurons of the enteric nervous system to send signals to the brain via the vagus nerve. Through these varied mechanisms, gut microbes shape the architecture of sleep and stress reactivity of the hypothalamic-pituitary-adrenal axis. They influence memory, mood, and cognition and are clinically and therapeutically relevant to a range of disorders, including alcoholism, chronic fatigue syndrome, fibromyalgia, and restless legs syndrome. Their role in multiple sclerosis and the neurologic manifestations of celiac disease is being studied. Nutritional tools for altering the gut microbiome therapeutically include changes in diet, probiotics, and prebiotics. PMID:25402818

Comparison of Dynamical Behaviors Between Monofunctional and Bifunctional Two-Component Signaling Modules

NASA Astrophysics Data System (ADS)

Yang, Xiyan; Wu, Yahao; Yuan, Zhanjiang

2015-06-01

Two-component signaling modules exist extensively in bacteria and microbes. These modules can be, based on their distinct network structures, divided into two types: the monofunctional system (denoted by MFS) where the sensor kinase (SK) modulates only phosphorylation of the response regulator (RR), and the bifunctional system (denoted by BFS) where the SK catalyzes both phosphorylation and dephosphorylation of the RR. Here, we analyze dynamical behaviors of these two systems based on stability theory, focusing on differences between them. The analysis of the deterministic behavior indicates that there is no difference between the two modules, that is, each system has the unique stable steady state. However, there are significant differences in stochastic behavior between them. Specifically, if the mean phosphorylated SK level is kept the same for the two modules, then the variance and the Fano factor for the phosphorylated RR in the BFS are always no less than those in the MFS, indicating that bifunctionality always enhances fluctuations. The correlation between the phosphorylated SK and the phosphorylated RR in the BFS is always positive mainly due to competition between system components, but this correlation in the MFS may be positive, almost zero, or negative, depending on the ratio between two rate constants. Our overall analysis indicates that differences between dynamical behaviors of monofunctional and bifunctional signaling modules are mainly in the stochastic rather than deterministic aspect.

The Microbiota of the Human Skin.

PubMed

Egert, Markus; Simmering, Rainer

2016-01-01

The aim of this chapter is to sum up important progress in the field of human skin microbiota research that was achieved over the last years.The human skin is one of the largest and most versatile organs of the human body. Owing to its function as a protective interface between the largely sterile interior of the human body and the highly microbially contaminated outer environment, it is densely colonized with a diverse and active microbiota. This skin microbiota is of high importance for human health and well-being. It is implicated in several severe skin diseases and plays a major role in wound infections. Many less severe, but negatively perceived cosmetic skin phenomena are linked with skin microbes, too. In addition, skin microorganisms, in particular on the human hands, are crucial for the field of hygiene research. Notably, apart from being only a potential source of disease and contamination, the skin microbiota also contributes to the protective functions of the human skin in many ways. Finally, the analysis of structure and function of the human skin microbiota is interesting from a basic, evolutionary perspective on human microbe interactions.Key questions in the field of skin microbiota research deal with (a) a deeper understanding of the structure (species inventory) and function (physiology) of the healthy human skin microbiota in space and time, (b) the distinction of resident and transient skin microbiota members, (c) the distinction of beneficial skin microorganisms from microorganisms or communities with an adverse or sickening effect on their hosts, (d) factors shaping the skin microbiota and its functional role in health and disease, (e) strategies to manipulate the skin microbiota for therapeutic reasons.

The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs

PubMed Central

Stewart, Jill R; Gast, Rebecca J; Fujioka, Roger S; Solo-Gabriele, Helena M; Meschke, J Scott; Amaral-Zettler, Linda A; del Castillo, Erika; Polz, Martin F; Collier, Tracy K; Strom, Mark S; Sinigalliano, Christopher D; Moeller, Peter DR; Holland, A Fredrick

2008-01-01

Innovative research relating oceans and human health is advancing our understanding of disease-causing organisms in coastal ecosystems. Novel techniques are elucidating the loading, transport and fate of pathogens in coastal ecosystems, and identifying sources of contamination. This research is facilitating improved risk assessments for seafood consumers and those who use the oceans for recreation. A number of challenges still remain and define future directions of research and public policy. Sample processing and molecular detection techniques need to be advanced to allow rapid and specific identification of microbes of public health concern from complex environmental samples. Water quality standards need to be updated to more accurately reflect health risks and to provide managers with improved tools for decision-making. Greater discrimination of virulent versus harmless microbes is needed to identify environmental reservoirs of pathogens and factors leading to human infections. Investigations must include examination of microbial community dynamics that may be important from a human health perspective. Further research is needed to evaluate the ecology of non-enteric water-transmitted diseases. Sentinels should also be established and monitored, providing early warning of dangers to ecosystem health. Taken together, this effort will provide more reliable information about public health risks associated with beaches and seafood consumption, and how human activities can affect their exposure to disease-causing organisms from the oceans. PMID:19025674

The Link between Microbial Diversity and Nitrogen Cycling in Marine Sediments Is Modulated by Macrofaunal Bioturbation

PubMed Central

Yazdani Foshtomi, Maryam; Braeckman, Ulrike; Derycke, Sofie; Sapp, Melanie; Van Gansbeke, Dirk; Sabbe, Koen; Willems, Anne; Vincx, Magda; Vanaverbeke, Jan

2015-01-01

Objectives The marine benthic nitrogen cycle is affected by both the presence and activity of macrofauna and the diversity of N-cycling microbes. However, integrated research simultaneously investigating macrofauna, microbes and N-cycling is lacking. We investigated spatio-temporal patterns in microbial community composition and diversity, macrofaunal abundance and their sediment reworking activity, and N-cycling in seven subtidal stations in the Southern North Sea. Spatio-Temporal Patterns of the Microbial Communities Our results indicated that bacteria (total and β-AOB) showed more spatio-temporal variation than archaea (total and AOA) as sedimentation of organic matter and the subsequent changes in the environment had a stronger impact on their community composition and diversity indices in our study area. However, spatio-temporal patterns of total bacterial and β-AOB communities were different and related to the availability of ammonium for the autotrophic β-AOB. Highest bacterial richness and diversity were observed in June at the timing of the phytoplankton bloom deposition, while richness of β-AOB as well as AOA peaked in September. Total archaeal community showed no temporal variation in diversity indices. Macrofauna, Microbes and the Benthic N-Cycle Distance based linear models revealed that, independent from the effect of grain size and the quality and quantity of sediment organic matter, nitrification and N-mineralization were affected by respectively the diversity of metabolically active β-AOB and AOA, and the total bacteria, near the sediment-water interface. Separate models demonstrated a significant and independent effect of macrofaunal activities on community composition and richness of total bacteria, and diversity indices of metabolically active AOA. Diversity of β-AOB was significantly affected by macrofaunal abundance. Our results support the link between microbial biodiversity and ecosystem functioning in marine sediments, and provided broad correlative support for the hypothesis that this relationship is modulated by macrofaunal activity. We hypothesized that the latter effect can be explained by their bioturbating and bio-irrigating activities, increasing the spatial complexity of the biogeochemical environment. PMID:26102286

A 100-Year Review: Microbiology and safety of milk handling.

PubMed

Boor, Kathryn J; Wiedmann, Martin; Murphy, Sarah; Alcaine, Sam

2017-12-01

Microbes that may be present in milk can include pathogens, spoilage organisms, organisms that may be conditionally beneficial (e.g., lactic acid bacteria), and those that have not been linked to either beneficial or detrimental effects on product quality or human health. Although milk can contain a full range of organisms classified as microbes (i.e., bacteria, viruses, fungi, and protozoans), with few exceptions (e.g., phages that affect fermentations, fungal spoilage organisms, and, to a lesser extent, the protozoan pathogens Cryptosporidium and Giardia) dairy microbiology to date has focused predominantly on bacteria. Between 1917 and 2017, our understanding of the microbes present in milk and the tools available for studying those microbes have changed dramatically. Improved microbiological tools have enabled enhanced detection of known microbes in milk and dairy products and have facilitated better identification of pathogens and spoilage organisms that were not known or well recognized in the early 20th century. Starting before 1917, gradual introduction and refinement of pasteurization methods throughout the United States and many other parts of the world have improved the safety and quality of milk and dairy products. In parallel to pasteurization, others strategies for reducing microbial contamination throughout the dairy chain (e.g., improved dairy herd health, raw milk tests, clean-in-place technologies) also played an important role in improving microbial milk quality and safety. Despite tremendous advances in reducing microbial food safety hazards and spoilage issues, the dairy industry still faces important challenges, including but not limited to the need for improved science-based strategies for safety of raw milk cheeses, control of postprocessing contamination, and control of sporeforming pathogens and spoilage organisms. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Effect Of Spaceflight On Microbial Gene Expression And Virulence: Preliminary Results From Microbe Payload Flown On-Board STS-115

NASA Technical Reports Server (NTRS)

Wilson, J. W.; HonerzuBentrup, K,; Schurr, M. J.; Buchanan, K.; Morici, L.; Hammond, T.; Allen, P.; Baker, C.; Ott, C. M.; Nelman-Gonzalez M.;

Engineering the cell surface display of cohesins for assembly of cellulosome-inspired enzyme complexes on Lactococcus lactis

PubMed Central

2010-01-01

Background The assembly and spatial organization of enzymes in naturally occurring multi-protein complexes is of paramount importance for the efficient degradation of complex polymers and biosynthesis of valuable products. The degradation of cellulose into fermentable sugars by Clostridium thermocellum is achieved by means of a multi-protein "cellulosome" complex. Assembled via dockerin-cohesin interactions, the cellulosome is associated with the cell surface during cellulose hydrolysis, forming ternary cellulose-enzyme-microbe complexes for enhanced activity and synergy. The assembly of recombinant cell surface displayed cellulosome-inspired complexes in surrogate microbes is highly desirable. The model organism Lactococcus lactis is of particular interest as it has been metabolically engineered to produce a variety of commodity chemicals including lactic acid and bioactive compounds, and can efficiently secrete an array of recombinant proteins and enzymes of varying sizes. Results Fragments of the scaffoldin protein CipA were functionally displayed on the cell surface of Lactococcus lactis. Scaffolds were engineered to contain a single cohesin module, two cohesin modules, one cohesin and a cellulose-binding module, or only a cellulose-binding module. Cell toxicity from over-expression of the proteins was circumvented by use of the nisA inducible promoter, and incorporation of the C-terminal anchor motif of the streptococcal M6 protein resulted in the successful surface-display of the scaffolds. The facilitated detection of successfully secreted scaffolds was achieved by fusion with the export-specific reporter staphylococcal nuclease (NucA). Scaffolds retained their ability to associate in vivo with an engineered hybrid reporter enzyme, E. coli β-glucuronidase fused to the type 1 dockerin motif of the cellulosomal enzyme CelS. Surface-anchored complexes exhibited dual enzyme activities (nuclease and β-glucuronidase), and were displayed with efficiencies approaching 104 complexes/cell. Conclusions We report the successful display of cellulosome-inspired recombinant complexes on the surface of Lactococcus lactis. Significant differences in display efficiency among constructs were observed and attributed to their structural characteristics including protein conformation and solubility, scaffold size, and the inclusion and exclusion of non-cohesin modules. The surface-display of functional scaffold proteins described here represents a key step in the development of recombinant microorganisms capable of carrying out a variety of metabolic processes including the direct conversion of cellulosic substrates into fuels and chemicals. PMID:20840763

Molecular Paths Linking Metabolic Diseases, Gut Microbiota Dysbiosis and Enterobacteria Infections.

PubMed

Serino, Matteo

2018-03-02

Alterations of both ecology and functions of gut microbiota are conspicuous traits of several inflammatory pathologies, notably metabolic diseases such as obesity and type 2 diabetes. Moreover, the proliferation of enterobacteria, subdominant members of the intestinal microbial ecosystem, has been shown to be favored by Western diet, the strongest inducer of both metabolic diseases and gut microbiota dysbiosis. The inner interdependence between the host and the gut microbiota is based on a plethora of molecular mechanisms by which host and intestinal microbes modify each other. Among these mechanisms are as follows: (i) the well-known metabolic impact of short chain fatty acids, produced by microbial fermentation of complex carbohydrates from plants; (ii) a mutual modulation of miRNAs expression, both on the eukaryotic (host) and prokaryotic (gut microbes) side; (iii) the production by enterobacteria of virulence factors such as the genotoxin colibactin, shown to alter the integrity of host genome and induce a senescence-like phenotype in vitro; (iv) the microbial excretion of outer-membrane vesicles, which, in addition to other functions, may act as a carrier for multiple molecules such as toxins to be delivered to target cells. In this review, I describe the major molecular mechanisms by which gut microbes exert their metabolic impact at a multi-organ level (the gut barrier being in the front line) and support the emerging triad of metabolic diseases, gut microbiota dysbiosis and enterobacteria infections. Copyright © 2018 Elsevier Ltd. All rights reserved.

Polymers in the gut compress the colonic mucus hydrogel

PubMed Central

Datta, Sujit S.; Preska Steinberg, Asher

2016-01-01

Colonic mucus is a key biological hydrogel that protects the gut from infection and physical damage and mediates host–microbe interactions and drug delivery. However, little is known about how its structure is influenced by materials it comes into contact with regularly. For example, the gut abounds in polymers such as dietary fibers or administered therapeutics, yet whether such polymers interact with the mucus hydrogel, and if so, how, remains unclear. Although several biological processes have been identified as potential regulators of mucus structure, the polymeric composition of the gut environment has been ignored. Here, we demonstrate that gut polymers do in fact regulate mucus hydrogel structure, and that polymer–mucus interactions can be described using a thermodynamic model based on Flory–Huggins solution theory. We found that both dietary and therapeutic polymers dramatically compressed murine colonic mucus ex vivo and in vivo. This behavior depended strongly on both polymer concentration and molecular weight, in agreement with the predictions of our thermodynamic model. Moreover, exposure to polymer-rich luminal fluid from germ-free mice strongly compressed the mucus hydrogel, whereas exposure to luminal fluid from specific-pathogen-free mice—whose microbiota degrade gut polymers—did not; this suggests that gut microbes modulate mucus structure by degrading polymers. These findings highlight the role of mucus as a responsive biomaterial, and reveal a mechanism of mucus restructuring that must be integrated into the design and interpretation of studies involving therapeutic polymers, dietary fibers, and fiber-degrading gut microbes. PMID:27303035

Anti-biofouling property studies on carboxyl-modified multi-walled carbon nanotubes filled PDMS nanocomposites.

PubMed

Sun, Yuan; Zhang, Zhizhou

2016-09-01

Polydimethylsiloxane (PDMS) with exceptional fouling-release properties is extremely susceptible to the microfouling resulted from the colonization of the pioneer microorganisms in the marine environment. In this study, six carboxyl-modified multi-walled carbon nanotubes (cMWNTs) nanoparticles were incorporated into the PDMS matrix, respectively, in order to produce the cMWNTs-filled PDMS nanocomposites (CPs) with improved antifouling (AF) properties. The AF properties of the six CPs were examined via the field assays conducted in Weihai, China. The effects of the anti-biofouling potential of the CPs (i.e. the P3 surface) on the colonization of the pioneer prokaryotic and eukaryotic microbes were investigated using the single-stranded conformation polymorphism technique via the comparison of the diversity indices. Different CPs have displayed differential and better AF properties as compared to that of the unfilled PDMS (P0). The P3 surface has exhibited exceptional anti-biofouling capacity compared with the other CPs surfaces, which can effectively prevent biofouling for more than 14 weeks in the field. The SSCP analysis revealed that the P3 surface may have significant modulating effect on the pioneer microbial communities. The pioneer eukaryotic microbes seemed more susceptible than the pioneer prokaryotic microbes to be subjected to the major perturbations exerted by the P3 surface. The dramatically reduced eukaryotic-microbial diversity may contribute to the impeding and weakening of the development and growth of the biofilm. The P3 surface has the potential to be used for future maritime applications.

Gene-centric approach to integrating environmental genomics and biogeochemical models.

PubMed

Reed, Daniel C; Algar, Christopher K; Huber, Julie A; Dick, Gregory J

2014-02-04

Rapid advances in molecular microbial ecology have yielded an unprecedented amount of data about the evolutionary relationships and functional traits of microbial communities that regulate global geochemical cycles. Biogeochemical models, however, are trailing in the wake of the environmental genomics revolution, and such models rarely incorporate explicit representations of bacteria and archaea, nor are they compatible with nucleic acid or protein sequence data. Here, we present a functional gene-based framework for describing microbial communities in biogeochemical models by incorporating genomics data to provide predictions that are readily testable. To demonstrate the approach in practice, nitrogen cycling in the Arabian Sea oxygen minimum zone (OMZ) was modeled to examine key questions about cryptic sulfur cycling and dinitrogen production pathways in OMZs. Simulations support previous assertions that denitrification dominates over anammox in the central Arabian Sea, which has important implications for the loss of fixed nitrogen from the oceans. Furthermore, cryptic sulfur cycling was shown to attenuate the secondary nitrite maximum often observed in OMZs owing to changes in the composition of the chemolithoautotrophic community and dominant metabolic pathways. Results underscore the need to explicitly integrate microbes into biogeochemical models rather than just the metabolisms they mediate. By directly linking geochemical dynamics to the genetic composition of microbial communities, the method provides a framework for achieving mechanistic insights into patterns and biogeochemical consequences of marine microbes. Such an approach is critical for informing our understanding of the key role microbes play in modulating Earth's biogeochemistry.

Polymers in the gut compress the colonic mucus hydrogel.

PubMed

Datta, Sujit S; Preska Steinberg, Asher; Ismagilov, Rustem F

2016-06-28

Colonic mucus is a key biological hydrogel that protects the gut from infection and physical damage and mediates host-microbe interactions and drug delivery. However, little is known about how its structure is influenced by materials it comes into contact with regularly. For example, the gut abounds in polymers such as dietary fibers or administered therapeutics, yet whether such polymers interact with the mucus hydrogel, and if so, how, remains unclear. Although several biological processes have been identified as potential regulators of mucus structure, the polymeric composition of the gut environment has been ignored. Here, we demonstrate that gut polymers do in fact regulate mucus hydrogel structure, and that polymer-mucus interactions can be described using a thermodynamic model based on Flory-Huggins solution theory. We found that both dietary and therapeutic polymers dramatically compressed murine colonic mucus ex vivo and in vivo. This behavior depended strongly on both polymer concentration and molecular weight, in agreement with the predictions of our thermodynamic model. Moreover, exposure to polymer-rich luminal fluid from germ-free mice strongly compressed the mucus hydrogel, whereas exposure to luminal fluid from specific-pathogen-free mice-whose microbiota degrade gut polymers-did not; this suggests that gut microbes modulate mucus structure by degrading polymers. These findings highlight the role of mucus as a responsive biomaterial, and reveal a mechanism of mucus restructuring that must be integrated into the design and interpretation of studies involving therapeutic polymers, dietary fibers, and fiber-degrading gut microbes.

Fluorescence imaging of microbe-containing particles shot from a two-stage Light-gas gun into an aerogel.

PubMed

Kawaguchi, Yuko; Sugino, Tomohiro; Tabata, Makoto; Okudaira, Kyoko; Imai, Eichi; Yano, Hajime; Hasegawa, Sunao; Hashimoto, Hirofumi; Yabuta, Hikaru; Kobayashi, Kensei; Kawai, Hideyuki; Mita, Hajime; Yokobori, Shin-ichi; Yamagishi, Akihiko

2014-02-01

We have proposed an experiment (the Tanpopo mission) to capture microbes on the Japan Experimental Module of the International Space Station. An ultra low-density silica aerogel will be exposed to space for more than 1 year. After retrieving the aerogel, particle tracks and particles found in it will be visualized by fluorescence microscopy after staining it with a DNA-specific fluorescence dye. In preparation for this study, we simulated particle trapping in an aerogel so that methods could be developed to visualize the particles and their tracks. During the Tanpopo mission, particles that have an orbital velocity of ~8 km/s are expected to collide with the aerogel. To simulate these collisions, we shot Deinococcus radiodurans-containing Lucentite particles into the aerogel from a two-stage light-gas gun (acceleration 4.2 km/s). The shapes of the captured particles, and their tracks and entrance holes were recorded with a microscope/camera system for further analysis. The size distribution of the captured particles was smaller than the original distribution, suggesting that the particles had fragmented. We were able to distinguish between microbial DNA and inorganic compounds after staining the aerogel with the DNA-specific fluorescence dye SYBR green I as the fluorescence of the stained DNA and the autofluorescence of the inorganic particles decay at different rates. The developed methods are suitable to determine if microbes exist at the International Space Station altitude.

Microbial biodegradation of organic wastes containing surfactants in a continuous-flow reactor.

PubMed

Konopka, A; Zakharova, T; Oliver, L; Turco, R F

1997-04-01

In a continuous flow bioreactor seeded with microbes from municipal activated sludge, complete organic carbon oxidation of simulated graywater (wastewater produced in human residences, excluding toilet wastes) was achieved at dilution rates up to 0.36 h-1 in the presence of 64.1 microM linear alkylbenzenesulfonate (LAS) L-1. At LAS concentrations of 187 microM, the system functioned only at dilution rates up to 0.23 h-1, and the biomass yield was two-fold lower. There were physiological changes in the microbial communities under different operating conditions, as measured by specific contents of ATP and extracellular hydrolases as well as the respiratory potential of the biomass. LAS inhibited the activity of LAS-degrading microbes at >150 microM LAS, and the activity of other microbes at >75 microM LAS. Chemical analysis of graywater indicated that samples consisted primarily of biological polymers (proteins and polysaccharides) and lower concentrations of surfactants. Biological remediation of graywater is possible, although treatment efficiency is influenced by the operating conditions and wastestream composition.

Study of microbes having potentiality for biodegradation of plastics.

PubMed

Ghosh, Swapan Kumar; Pal, Sujoy; Ray, Sumanta

2013-07-01

Plastic is a broad name given to the different types of organic polymers having high molecular weight and is commonly derived from different petrochemicals. Plastics are generally not biodegradable or few are degradable but in a very slow rate. Day by day, the global demand of these polymers is sharply increasing; however, considering their abundance and potentiality in causing different environmental hazards, there is a great concern in the possible methods of degradation of plastics. Recently, there have been some debates at the world stage about the potential degradation procedures of these synthetic polymers and microbial degradation has emerged as one of the potential alternative ways of degradation of plastics. Alternatively, some scientists have also reported many adverse effects of these polymers in human health, and thus, there is an immediate need of a potential screening of some potential microbes to degrade these synthetic polymers. In this review, we have taken an attempt to accumulate all information regarding the chemical nature along with some potential microbes and their enzymatic nature of biodegradation of plastics along with some key factors that affect their biodegradability.

Applying fluorescence microscopy to the investigation of the behavior of foodborne pathogens on produce

NASA Astrophysics Data System (ADS)

Brandl, Maria T.

2009-05-01

In the past decade, the development of new tools to better visualize microbes at the cellular scale has spurred a renaissance in the application of microscopy to the study of bacteria in their natural environment. This renewed interest in microscopy may be largely attributable to the advent of the confocal laser scanning microscope (CLSM) and to the discovery of the green fluorescent protein. This article provides information about the use of fluorescence microscopy combined with fluorescent labels such as GFP, DsRed, and DNA stains, with immunofluorescence, and with digital image analysis, to examine the behavior of bacteria and other microbes on plant surfaces. Some of the advantages and pitfalls of these methods will be described using practical examples derived from studies of the ecology of foodborne pathogens, namely Salmonella enterica and E. coli O157:H7, on fresh fruit and vegetables. Confocal microscopy has been a powerful approach to uncover some of the factors involved in the association of produce with epidemics caused by these human pathogens and their interaction with other microbes in their nonhost environment.

Plants + microbes: Innovative food crop systems that also clean air and water

NASA Astrophysics Data System (ADS)

Nelson, Mark; Wolverton, B. C.

The limitations that will govern bioregenerative life support applications in space, especially volume and weight, make multi-purpose systems advantageous. This paper outlines two systems which utilize plants and associated microbial communities of root or growth medium to both produce food crops and clean air and water. Underlying these approaches are the large numbers and metabolic diversity of microbes associated with roots and found in either soil or other suitable growth media. It is known that most biogeochemical cycles have a microbial link, and the ability of microbes to metabolize virtually all trace gases, whether of technogenic or biogenic origin, have long been established. Wetland plants and soil/media also been extensively researched for their ability to purify wastewaters of all kinds of potential water pollutants, from nutrients like N and P, to heavy metals and a range of complex industrial pollutants. There is a growing body of research on the ability of higher plants to purify air and water. Associated benefits of these approaches is that by utilizing natural ecological processes, the cleansing of air and water can be done with little or no energy inputs. Soil and root microorganisms respond to changing pollutant types by an increase of the types of organisms with the capacity to use these compounds. Thus living systems have an extraordinary adaptive capacity as long as the starting populations are sufficiently diverse. It is known that tightly sealed environments, from office buildings to spacecraft, can have hundreds or even thousands of potential air pollutants, depending on the materials and machines enclosed. Human waste products carry a plethora of microbes can are readily used in the process of converting its organic load to forms that can be utilized by green plants. Having endogenous means of responding to changing air and water quality conditions represents safety factors which operate without the need for human direction. We will review this research and underline the ability of systems using these mechanisms to also produce food or other useful crops. The psychological benefits of having systems utilizing green plants are also becoming more widely recognized. Some recent applications extending the benefits of plants+microbes to solve new environmental problems are presented. For space applications, we discuss methods of making these systems compact and light-weight.

Recognition of microbial glycans by human intelectin-1

DOE PAGES

Wesener, Darryl A.; Wangkanont, Kittikhun; McBride, Ryan; ...

2015-07-06

The glycans displayed on mammalian cells can differ markedly from those on microbes. Such differences could, in principle, be 'read' by carbohydrate-binding proteins, or lectins. In this paper, we used glycan microarrays to show that human intelectin-1 (hIntL-1) does not bind known human glycan epitopes but does interact with multiple glycan epitopes found exclusively on microbes: β-linked D-galactofuranose (β-Galf), D-phosphoglycerol–modified glycans, heptoses, D-glycero-D-talo-oct-2-ulosonic acid (KO) and 3-deoxy-D-manno-oct-2-ulosonic acid (KDO). The 1.6-Å-resolution crystal structure of hIntL-1 complexed with β-Galf revealed that hIntL-1 uses a bound calcium ion to coordinate terminal exocyclic 1,2-diols. N-acetylneuraminic acid (Neu5Ac), a sialic acid widespread in humanmore » glycans, has an exocyclic 1,2-diol but does not bind hIntL-1, probably owing to unfavorable steric and electronic effects. hIntL-1 marks only Streptococcus pneumoniae serotypes that display surface glycans with terminal 1,2-diol groups. Finally, this ligand selectivity suggests that hIntL-1 functions in microbial surveillance.« less

Microbial Impact on Success of Human Exploration Missions

NASA Technical Reports Server (NTRS)

Pierson, Duane L.; Ott, C. Mark; Groves, T. O.; Paloski, W. H. (Technical Monitor)

2000-01-01

The purpose of this study is to identify microbiological risks associated with space exploration and identify potential countermeasures available. Identification of microbial risks associated with space habitation requires knowledge of the sources and expected types of microbial agents. Crew data along with environmental data from water, surfaces, air, and free condensate are utilized in risk examination. Data from terrestrial models are also used. Microbial risks to crew health include bacteria, fungi, protozoa, and viruses. Adverse effects of microbes include: infections, allergic reactions, toxin production, release of volatiles, food spoilage, plant disease, material degradation, and environmental contamination. Risk is difficult to assess because of unknown potential changes in microbes (e.g., mutation) and the human host (e.g., immune changes). Prevention of adverse microbial impacts is preferred over remediation. Preventative measures include engineering measures (e.g., air filtration), crew microbial screening, acceptability standards, and active verification by onboard monitoring. Microbiological agents are important risks to human health and performance during space flight and risks increase with mission duration. Acceptable risk level must be defined. Prevention must be given high priority. Careful screening of crewmembers and payloads is an important element of any risk mitigation plan. Improved quantitation of microbiological risks is a high priority.

Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors.

PubMed

Chan, Alfred A; Bashir, Mina; Rivas, Magali N; Duvall, Karen; Sieling, Peter A; Pieber, Thomas R; Vaishampayan, Parag A; Love, Susan M; Lee, Delphine J

2016-06-21

The microbiome impacts human health and disease. Until recently, human breast tissue and milk were presumed to be sterile. Here, we investigated the presence of microbes in the nipple aspirate fluid (NAF) and their potential association with breast cancer. We compared the NAF microbiome between women with a history of breast cancer (BC) and healthy control women (HC) using 16S rRNA gene amplicon sequencing. The NAF microbiome from BC and HC showed significant differences in community composition. Two Operational Taxonomic Units (OTUs) showed differences in relative abundances between NAF collected from BC and HC. In NAF collected from BC, there was relatively higher incidence of the genus Alistipes. By contrast, an unclassified genus from the Sphingomonadaceae family was relatively more abundant in NAF from HC. These findings reflect the ductal source DNA since there were no differences between areolar skin samples collected from BC and HC. Furthermore, the microbes associated with BC share an enzymatic activity, Beta-Glucuronidase, which may promote breast cancer. This is the first report of bacterial DNA in human breast ductal fluid and the differences between NAF from HC and BC. Further investigation of the ductal microbiome and its potential role in breast cancer are warranted.

Multifunctional biosynthesized silver nanoparticles exhibiting excellent antimicrobial potential against multi-drug resistant microbes along with remarkable anticancerous properties.

PubMed

Jha, Diksha; Thiruveedula, Prasanna Kumar; Pathak, Rajiv; Kumar, Bipul; Gautam, Hemant K; Agnihotri, Shrish; Sharma, Ashwani Kumar; Kumar, Pradeep

2017-11-01

This study demonstrates the therapeutic potential of silver nanoparticles (AgNPs), which were biosynthesized using the extracts of Citrus maxima plant. Characterization through UV-Vis spectrophotometry, Dynamic Light Scattering (DLS), Fourier Transform Infrared spectroscopy (FTIR), X-ray Diffraction (XRD) and Transmission Electron Microscopy (TEM) confirmed the formation of AgNps in nano-size range. These nanoparticles exhibited enhanced antioxidative activity and showed commendable antimicrobial activity against wide range of microbes including multi-drug resistant bacteria that were later confirmed by TEM. These particles exhibited minimal toxicity when cytotoxicity study was performed on normal human lung fibroblast cell line as well as human red blood cells. It was quite noteworthy that these particles showed remarkable cytotoxicity on human fibrosarcoma and mouse melanoma cell line (B16-F10). Additionally, the apoptotic topographies of B16-F10 cells treated with AgNps were confirmed by using acridine orange and ethidium bromide dual dye staining, caspase-3 assay, DNA fragmentation assay followed by cell cycle analysis using fluorescence-activated cell sorting. Taken together, these results advocate promising potential of the biosynthesized AgNps for their use in therapeutic applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Dose-dependent fate of GFP-E. coli in the alimentary canal of adult house flies

USDA-ARS?s Scientific Manuscript database

Adult house flies (Diptera: Muscidae; Musca domestica L.) disseminate bacteria from microbe-rich substrates to areas where humans and domesticated animals reside. Because bacterial abundance fluctuates widely across substrates, flies encounter and ingest varying amounts of bacteria. We investigated ...

MICROBES IN DRINKING WATER: RECENT EPIDEMIOLOGIC RESEARCH TO ASSESS WATERBORNE RISKS

EPA Science Inventory

Microbial caused diarrhea continues to be a major cause of death in many countries. The transmission of these organisms to humans is often mediated by drinking water. These enteric illnesses occur in epidemic form (the occurrence of disease in excess of normal expectancy) an...

MICROBES IN DRINKING WATER: RECENT EPIDEMIOLOGICAL RESEARCH TO ASSESS WATERBORNE RISKS

EPA Science Inventory

The waterborne transmission of enteric pathogens to humans causes illnesses that occur as an epidemic (a temporal excess of cases over some background level of disease), often called an outbreak, or as endemic disease (a background of ongoing disease prevalence that can be consta...

Humans or Animals? Global March of the Resistant Microbe

USDA-ARS?s Scientific Manuscript database

Antimicrobial resistance continues to be a global problem. Pathogens are global regardless of whether they are food borne or not. An example of an early century pathogen is Vibrio cholera and related species. Vibrio were primarily associated with water sources and foodstuffs contaminated with wat...

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City.

PubMed

Bik, Holly M; Maritz, Julia M; Luong, Albert; Shin, Hakdong; Dominguez-Bello, Maria Gloria; Carlton, Jane M

2016-01-01

In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the "urban microbiome" may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads. Microbial swab samples were collected from three boroughs (Manhattan, Queens, and Brooklyn) during June and July 2014, followed by generation of Illumina MiSeq datasets for bacterial (16S rRNA) and eukaryotic (18S rRNA) marker genes. Downstream analysis was carried out in the QIIME pipeline, in conjunction with neighborhood metadata (ethnicity, population, age groups) from the NYC Open Data portal. Neither the 16S nor 18S rRNA datasets showed any clustering patterns related to geography or neighborhood demographics. Bacterial assemblages on ATM keypads were dominated by taxonomic groups known to be associated with human skin communities ( Actinobacteria , Bacteroides , Firmicutes , and Proteobacteria ), although SourceTracker analysis was unable to identify the source habitat for the majority of taxa. Eukaryotic assemblages were dominated by fungal taxa as well as by a low-diversity protist community containing both free-living and potentially pathogenic taxa ( Toxoplasma , Trichomonas ). Our results suggest that ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. DNA obtained from ATM keypads may thus provide a record of both human behavior and environmental sources of microbes. IMPORTANCE Automated teller machine (ATM) keypads represent a specific and unexplored microhabitat for microbial communities. Although the number of built environment and urban microbial ecology studies has expanded greatly in recent years, the majority of research to date has focused on mass transit systems, city soils, and plumbing and ventilation systems in buildings. ATM surfaces, potentially retaining microbial signatures of human inhabitants, including both commensal taxa and pathogens, are interesting from both a biodiversity perspective and a public health perspective. By focusing on ATM keypads in different geographic areas of New York City with distinct population demographics, we aimed to characterize the diversity and distribution of both prokaryotic and eukaryotic microbes, thus making a unique contribution to the growing body of work focused on the "urban microbiome." In New York City, the surface area of urban surfaces in Manhattan far exceeds the geographic area of the island itself. We have only just begun to describe the vast array of microbial taxa that are likely to be present across diverse types of urban habitats.

Exploring Earth's Atmospheric Biology using a Platform-Extensible Sampling Payload

NASA Astrophysics Data System (ADS)

Gentry, D.; Rothschild, L.

2012-12-01

The interactions between Earth's atmosphere and its biosphere, or aerobiology, remain a significant unknown. What few studies have been done conclusively show that Earth's atmosphere has a rich and dynamic microbial presence[Bowers et al., 2010]; that microbes suspended in air survive over long times (1-2 weeks)[Smith et al., 2010] and travel great distances (>5000 km)[Kellogg and Griffin, 2006]; that some airborne bacteria actively nucleate ice crystals, affecting meteorology[Delort et al., 2010]; and that the presence of microbes in the atmosphere has other planetary-scale effects[Delort et al., 2010]. Basic questions, however, such as the number of microbes present, their activity level and state, the different species present and their variance over time and space, remain largely unquantified. Compounding the significant physical and environmental challenges of reliable aerobiological sampling, collection and analysis of biological samples at altitudes above ~10-20 km has traditionally used ad hoc instrumentation and techniques, yielding primarily qualitative analytical results that lack a common basis for comparison[Bowers et al., 2010]. There is a strong need for broad-basis, repeatable, reliably comparable data about aerobiological basics. We describe here a high-altitude environmental and biological sampling project designed specifically to address these issues. The goal is a robust, reliable, re-usable sampling system, with open reproducibility and adaptability for multiple low-cost flight platforms (including ground-tethered systems, high-altitude balloons, and suborbital sounding rockets); by establishing a common modular payload structure for high-altitude sampling with appeal to a broad user base, we hope to encourage widespread collection of comparable aerobiological data. We are on our third prototype iteration, with demonstrated function of two sample capture modules, a support backbone (tracking, data logging, event response, etc.), a simple ground station, and a partially complete environmental sensing module. Successful deployments include ground sampling (Dec. 2011-ongoing, with biological and environmental data correlation) and instrument verification suborbital launches (Apr. 2012). Intensive calibration and characterization of the sampling modules is ongoing. Full three-module balloon flights are scheduled for Sep. 2012. References: Bowers, R. et al. (2010), Spatial variability in airborne bacterial communities across land-use types and their relationship to the bacterial communities of potential source environments, The ISME Journal (2010), 1-12, doi:doi:10.1038/ismej.2010.167. Delort, A. M. et al. (2010), A short overview of the microbial population in clouds: Potential roles in atmospheric chemistry and nucleation processes, Atmospheric Research, 98249-260, doi:10.1016/j.atmosres.2010.07.004. Kellogg, C. A., and Griffin, D. W. (2006), Aerobiology and the global transport of desert dust, Trends in Ecology and Evolution, 21(11), 638-644, doi:10.1016/j.tree.2006.07.004. Smith, D. J. et al. (2010), Stratospheric microbiology at 20 km over the Pacific Ocean, Aerobiologia, 26(1), 35-46, doi:10.1007/s10453-009-9141-7.

Development of hydrogel microtubes for microbe culture in open environment.

PubMed

Ogawa, M; Higashi, K; Miki, N

2015-08-01

This paper describes a microbe culture system in an open environment using hydrogel microtubes. In recent years, oil production microbes, such as Aurantiochytrium, have been found and are studied to produce fuels of new age instead of fossil fuels. Biomass production by microbes is promising, where scale-up, collection of the products and competition against other microbes are the most important challenges. Here, we propose to use hydrogel microtubes to encapsulate, culture, and protect microbes. The tubes can be micro- and mass-fabricated. They allow oxygen and nutrition to go through while they prevent competitive microbes from intruding inside. The microbes and byproducts can be collected together with the tubes. In this paper, we demonstrate the proof-of-concepts experiments: we fabricated hydrogel micro tubes and cultured Coryne glutamicum which produce lactic acid inside the tubes. The microbes were increased inside the tubes and protected even when competitive microbes existed in the culture media. Furthermore, we demonstrated how to collect microbes inside the tubes.

Effects of Material Properties on Bacterial Adhesion and Biofilm Formation.

PubMed

Song, F; Koo, H; Ren, D

2015-08-01

Adhesion of microbes, such as bacteria and fungi, to surfaces and the subsequent formation of biofilms cause multidrug-tolerant infections in humans and fouling of medical devices. To address these challenges, it is important to understand how material properties affect microbe-surface interactions and engineer better nonfouling materials. Here we review the recent progresses in this field and discuss the main challenges and opportunities. In particular, we focus on bacterial biofilms and review the effects of surface energy, charge, topography, and stiffness of substratum material on bacterial adhesion. We summarize how these surface properties influence oral biofilm formation, and we discuss the important findings from nondental systems that have potential applications in dental medicine. © International & American Associations for Dental Research 2015.

A unified initiative to harness Earth’s microbiomes

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

Alivisatos, A Paul; Blaser, M. J.; Brodie, Eoin L.

2015-10-28

Nearly three billion years ago, photosynthetic cyanobacteria transformed Earth’s atmosphere from oxygen-poor to oxygen-rich, enabling the evolution of complex life (1). Microbes shaped our evolutionary origins and their vast impact continues: they are essential constituents of animals and plants and are the most widespread, abundant, and diverse life forms on our planet. Microbial activities enable life but can also imperil it, through unwelcome effects like greenhouse gas production and disease. With a rapidly growing population, centuries of land use, and a changing climate, our planet faces extraordinary challenges. Given their fundamental roles in agriculture, energy production, and the health ofmore » our oceans, forests, and human population, understanding the collective activities of Earth’s microbes has never been more crucial.« less

Polymorphisms in the yeast galactose sensor underlie a natural continuum of nutrient-decision phenotypes.

PubMed

Lee, Kayla B; Wang, Jue; Palme, Julius; Escalante-Chong, Renan; Hua, Bo; Springer, Michael

2017-05-01

In nature, microbes often need to "decide" which of several available nutrients to utilize, a choice that depends on a cell's inherent preference and external nutrient levels. While natural environments can have mixtures of different nutrients, phenotypic variation in microbes' decisions of which nutrient to utilize is poorly studied. Here, we quantified differences in the concentration of glucose and galactose required to induce galactose-responsive (GAL) genes across 36 wild S. cerevisiae strains. Using bulk segregant analysis, we found that a locus containing the galactose sensor GAL3 was associated with differences in GAL signaling in eight different crosses. Using allele replacements, we confirmed that GAL3 is the major driver of GAL induction variation, and that GAL3 allelic variation alone can explain as much as 90% of the variation in GAL induction in a cross. The GAL3 variants we found modulate the diauxic lag, a selectable trait. These results suggest that ecological constraints on the galactose pathway may have led to variation in a single protein, allowing cells to quantitatively tune their response to nutrient changes in the environment.

Methods for and Insights from Phosphoproteome Analysis in Marine Microbes

NASA Astrophysics Data System (ADS)

Held, N. A.; Saito, M. A.; McIlvin, M.

2016-02-01

Phosphorylation, the dynamic addition of a phosphate group to specific amino acids, is a key regulator of protein activity in both prokaryotes and eukaryotes. Protein phosphorylation is known to modulate nutrient acquisition, metabolism, growth and reproduction in model organisms, yet little is known about the role of phosphorylation marine organisms. Recent developments in LC-MS/MS make it possible to identify phosphorylation events in the proteome. We tested various methods in marine bacteria and developed a simple approach to phosphoproteome analysis. We then applied this method to cultured isolates of Prochlorococcus and diatom-associated Alteromonas sp. BB2AT2. We began by comparing the phosphoproteomes of these organisms in exponential and stationary phase growth. We conducted iterative experiments to assess completeness of our analysis, similar to the rarefaction approach used to determine sequence depth in ecology. We also explored semi-quantitative changes in protein phosphorylation when cells were subject to phosphate deplete media and/or phosphatase inhibitors. These early studies demonstrate the promise of phosphoproteomics to advance our understanding of bacterial biochemistry and microbe-environment interactions.

The $100 Genome: Implications for the DoD

DTIC Science & Technology

2010-12-15

Phenotypes Influenced by the Microbiome In a recent study (Vijay-Kumar et al. 2010), gut microbes from obese mice were transferred to thin mice whose gut ...extraordinary genetic diversity of the gut microbiome , it is expected that these organisms (which usually have the first chance to interact with orally...Human Microbiome . In some cases it may be useful to sequence metagenomic samples of the microbiomes that colonize the human gut . oral cavity or other

Epidemiology of Oral and Maxillofacial Infections.

PubMed

Rajendra Santosh, Arvind Babu; Ogle, Orrett E; Williams, Dwight; Woodbine, Edward F

2017-04-01

Dental caries and periodontal disease are the most common dental infections and are constantly increasing worldwide. Distribution, occurrence of dental caries, gingivitis, periodontitis, odontogenic infections, antibiotic resistance, oral mucosal infections, and microbe-related oral cancer are important to understand the public impact and methods of controlling such disease. Distribution of human papilloma virus and human immunodeficiency virus -related oral cancers in the US population is presented. Copyright © 2016 Elsevier Inc. All rights reserved.

A transcription factor hierarchy defines an environmental stress response network.

PubMed

Song, Liang; Huang, Shao-Shan Carol; Wise, Aaron; Castanon, Rosa; Nery, Joseph R; Chen, Huaming; Watanabe, Marina; Thomas, Jerushah; Bar-Joseph, Ziv; Ecker, Joseph R

2016-11-04

Environmental stresses are universally encountered by microbes, plants, and animals. Yet systematic studies of stress-responsive transcription factor (TF) networks in multicellular organisms have been limited. The phytohormone abscisic acid (ABA) influences the expression of thousands of genes, allowing us to characterize complex stress-responsive regulatory networks. Using chromatin immunoprecipitation sequencing, we identified genome-wide targets of 21 ABA-related TFs to construct a comprehensive regulatory network in Arabidopsis thaliana Determinants of dynamic TF binding and a hierarchy among TFs were defined, illuminating the relationship between differential gene expression patterns and ABA pathway feedback regulation. By extrapolating regulatory characteristics of observed canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness and demonstrated their utility to modulate plant resilience to osmotic stress. Copyright © 2016, American Association for the Advancement of Science.

Probiotic modulation of the microbiota-gut-brain axis and behaviour in zebrafish.

PubMed

Borrelli, Luca; Aceto, Serena; Agnisola, Claudio; De Paolo, Sofia; Dipineto, Ludovico; Stilling, Roman M; Dinan, Timothy G; Cryan, John F; Menna, Lucia F; Fioretti, Alessandro

2016-07-15

The gut microbiota plays a crucial role in the bi-directional gut-brain axis, a communication that integrates the gut and central nervous system (CNS) activities. Animal studies reveal that gut bacteria influence behaviour, Brain-Derived Neurotrophic Factor (BDNF) levels and serotonin metabolism. In the present study, we report for the first time an analysis of the microbiota-gut-brain axis in zebrafish (Danio rerio). After 28 days of dietary administration with the probiotic Lactobacillus rhamnosus IMC 501, we found differences in shoaling behaviour, brain expression levels of bdnf and of genes involved in serotonin signalling/metabolism between control and treated zebrafish group. In addition, in microbiota we found a significant increase of Firmicutes and a trending reduction of Proteobacteria. This study demonstrates that selected microbes can be used to modulate endogenous neuroactive molecules in zebrafish.

The biota as ancient and modern modulator of the earth's atmosphere

NASA Technical Reports Server (NTRS)

Margulis, L.; Lovelock, J. E.

1978-01-01

The composition of the terrestrial atmosphere is thought to have been markedly modified by surface microbiota and modulated around quantities of gases optimized for growth of these microbiota. Three diagrams illustrating these suppositions are presented. The first shows a probable order of appearance of major metabolic pathways in microbes that interact with sediment and atmosphere. It is based on evolutionary considerations and is devised independently of the fossil record. The second diagram shows the qualitative emissions and removals of atmospheric gases by anaerobic organisms; it approximates those processes thought to have dominated the terrestrial atmosphere in Archean times. The third diagrams gaseous emissions and removals by the major groups of organisms, including oxygen-releasing and -utilizing forms. Biological gas exchange processes thought to have dominated the atmosphere since the Proterozoic are thus represented.

Linkages among geophysical facies, microbial composition, biogeochemical rates, and seasonal hydrology in the hyporheic zone

NASA Astrophysics Data System (ADS)

Stegen, J.

2016-12-01

The hyporheic zone is a critical ecosystem transition that links terrestrial, aquatic, and subsurface domains. To understand connections among physical, microbial, and biogeochemical components of the hyporheic zone, we obtained freeze cores along the Columbia River in the Hanford 300 Area and performed geologic, molecular, and microbial assays. Mud and sand content were found to be the primary drivers of microbial community attributes (in particular, of nitrite and carbon oxidizers). Microbial community analysis revealed an abundance of nitrifying Archaea (Thaumarchaea) and an absence of nitrifiying Bacteria. Network analysis revealed significant negative correlations between sand content and some statistical modules of microbial taxa, perhaps indicating the importance of pore water residence time on community composition. A similar set of microbial modules was positively correlated with total organic carbon. One such module that also positively correlated with aerobic metabolic rates was dominated by Thaumarchaea and Nitrospira, suggesting that ammonia oxidation was the dominant aerobic process. We also examined temporal changes in hyporheic microbial structure and activity through repeated sampling of attached and pore water microbes across a spatial gradient. We found that microbial communities remained distinct in river, hyporheic, and inland zones across seasonal variation in hydrologic mixing conditions. One reason was temperature-driven increases in microbial species richness in the hyporheic zone. We show that the relative importance of ecological selection and dispersal varied across environments and across geographic zones. Our results also indicated that while selection imposed short-term constraints on microbial community structure, hyporheic sediment communities did not respond to short-term hydrologic variation. Importantly, we demonstrated that the influence of selective pressures varied with phylogenetic affiliation, which may have been responsible for seasonal increases in Thaumarchaea and aerobic activity. Our results elucidate spatiotemporal shifts in composition and activity of hyporheic microbes across sedimentary and seasonal gradients in pore water environments that correlate with the contribution of Thaumarchaea to aerobic processes.

Bees brought to their knees: Microbes affecting honey bee health

USDA-ARS?s Scientific Manuscript database

The biology and health of the honey bee, Apis mellifera, has been of interest to human societies since the advent of beekeeping. Descriptive scientific research on pathogens affecting honey bees have been published for nearly a century, but it wasn’t until the recent outbreak of heavy colony losses...

Detection and molecular characterization of Methicillin Resistant Staphylococcus aureus from table eggs

USDA-ARS?s Scientific Manuscript database

Background: Table eggs are nutritionally important food consumed globally. Despite being protected inside the hard shell and a semi-permeable membrane, the egg contents may be contaminated with microbes and thus become a possible carrier of infectious agents to humans. A number of medically signific...

Detection and molecular characterization of methicillin resistant Staphylococcus aureus from table eggs

USDA-ARS?s Scientific Manuscript database

Table eggs are nutritionally important food consumed globally. Despite being protected inside the hard shell and a semi-permeable membrane, the egg contents may be contaminated with microbes and thus become a possible carrier of infectious agents to humans. A number of medically significant bacteria...

Bile Acid Responses in Methane and Non-Methane Producers to Standard Breakfast Meals

USDA-ARS?s Scientific Manuscript database

Bile acids and their conjugates are important regulators of glucose homeostasis. Previous research has revealed the ratio of cholic acid to deoxycholic acid to affect insulin resistance in humans. Bile acid de-conjugation and intestinal metabolism depend on gut microbes which may be affected by hos...

The human gut microbiome: current knowledge, challenges, and future directions.

PubMed

Dave, Maneesh; Higgins, Peter D; Middha, Sumit; Rioux, Kevin P

2012-10-01

The Human Genome Project was completed a decade ago, leaving a legacy of process, tools, and infrastructure now being turned to the study of the microbes that reside in and on the human body as determinants of health and disease, and has been branded "The Human Microbiome Project." Of the various niches under investigation, the human gut houses the most complex and abundant microbial community and is an arena for important host-microbial interactions that have both local and systemic impact. Initial studies of the human microbiome have been largely descriptive, a testing ground for innovative molecular techniques and new hypotheses. Methods for studying the microbiome have quickly evolved from low-resolution surveys of microbial community structure to high-definition description of composition, function, and ecology. Next-generation sequencing technologies combined with advanced bioinformatics place us at the doorstep of revolutionary insight into the composition, capability, and activity of the human intestinal microbiome. Renewed efforts to cultivate previously "uncultivable" microbes will be important to the overall understanding of gut ecology. There remain numerous methodological challenges to the effective study and understanding of the gut microbiome, largely relating to study design, sample collection, and the number of predictor variables. Strategic collaboration of clinicians, microbiologists, molecular biologists, computational scientists, and bioinformaticians is the ideal paradigm for success in this field. Meaningful interpretation of the gut microbiome requires that host genetic and environmental influences be controlled or accounted for. Understanding the gut microbiome in healthy humans is a foundation for discovering its influence in various important gastrointestinal and nutritional diseases (eg, inflammatory bowel disease, diabetes, and obesity), and for rational translation to human health gains. Copyright © 2012 Mosby, Inc. All rights reserved.

Quantification of Human Polyomaviruses JC Virus and BK Virus by TaqMan Quantitative PCR and Comparison to Other Water Quality Indicators in Water and Fecal Samples▿

PubMed Central

McQuaig, Shannon M.; Scott, Troy M.; Lukasik, Jerzy O.; Paul, John H.; Harwood, Valerie J.

2009-01-01

In the United States, total maximum daily load standards for bodies of water that do not meet bacterial water quality standards are set by each state. The presence of human polyomaviruses (HPyVs) can be used as an indicator of human-associated sewage pollution in these waters. We have developed and optimized a TaqMan quantitative PCR (QPCR) assay based on the conserved T antigen to both quantify and simultaneously detect two HPyVs; JC virus and BK virus. The QPCR assay was able to consistently quantify ≥10 gene copies per reaction and is linear over 5 orders of magnitude. HPyVs were consistently detected in human waste samples (57 of 64) and environmental waters with known human fecal contamination (5 of 5) and were not amplified in DNA extracted from 127 animal waste samples from 14 species. HPyV concentrations in sewage decreased 81.2 and 84.2% over 28 days incubation at 25 and 35°C, respectively. HPyVs results were compared to Escherichia coli, fecal coliform, and enterococci concentrations and the presence of three other human-associated microbes: Bacteroidetes, Methanobrevibacter smithii, and adenovirus. HPyVs were the most frequently detected of these in human and contaminated environmental samples and were more human specific than the Bacteroidetes (HF183) or M. smithii. HPyVs and M. smithii more closely mimicked the persistence of adenovirus in sewage than the other microbes. The use of this rapid and quantitative assay in water quality research could help regulatory agencies to identify sources of water pollution for improved remediation of contaminated waters and ultimately protect humans from exposure to pathogens. PMID:19346361

A direct link between carbohydrate utilization and virulence in the major human pathogen group A Streptococcus.

PubMed

Shelburne, Samuel A; Keith, David; Horstmann, Nicola; Sumby, Paul; Davenport, Michael T; Graviss, Edward A; Brennan, Richard G; Musser, James M

2008-02-05

Although central to pathogenesis, the molecular mechanisms used by microbes to regulate virulence factor production in specific environments during host-pathogen interaction are poorly defined. Several recent ex vivo and in vivo studies have found that the level of group A Streptococcus (GAS) virulence factor gene transcripts is temporally related to altered expression of genes encoding carbohydrate utilization proteins. These findings stimulated us to analyze the role in pathogenesis of catabolite control protein A (CcpA), a GAS ortholog of a key global regulator of carbohydrate metabolism in Bacillus subtilis. Inasmuch as the genomewide effects of CcpA in a human pathogen are unknown, we analyzed the transcriptome of a DeltaccpA isogenic mutant strain grown in nutrient-rich medium. CcpA influences the transcript levels of many carbohydrate utilization genes and several well characterized GAS virulence factors, including the potent cytolysin streptolysin S. Compared with the wild-type parental strain, the DeltaccpA isogenic mutant strain was significantly less virulent in a mouse model of invasive infection. Moreover, the isogenic mutant strain was significantly impaired in ability to colonize the mouse oropharynx. When grown in human saliva, a nutrient-limited environment, CcpA influenced production of several key virulence factors not influenced during growth in nutrient-rich medium. Purified recombinant CcpA bound to the promoter region of the gene encoding streptolysin S. Our discovery that GAS virulence and complex carbohydrate utilization are directly linked through CcpA provides enhanced understanding of a mechanism used by a Gram-positive pathogen to modulate virulence factor production in specific environments.

Phylloremediation of Air Pollutants: Exploiting the Potential of Plant Leaves and Leaf-Associated Microbes

PubMed Central

Wei, Xiangying; Lyu, Shiheng; Yu, Ying; Wang, Zonghua; Liu, Hong; Pan, Dongming; Chen, Jianjun

2017-01-01

Air pollution is air contaminated by anthropogenic or naturally occurring substances in high concentrations for a prolonged time, resulting in adverse effects on human comfort and health as well as on ecosystems. Major air pollutants include particulate matters (PMs), ground-level ozone (O3), sulfur dioxide (SO2), nitrogen dioxides (NO2), and volatile organic compounds (VOCs). During the last three decades, air has become increasingly polluted in countries like China and India due to rapid economic growth accompanied by increased energy consumption. Various policies, regulations, and technologies have been brought together for remediation of air pollution, but the air still remains polluted. In this review, we direct attention to bioremediation of air pollutants by exploiting the potentials of plant leaves and leaf-associated microbes. The aerial surfaces of plants, particularly leaves, are estimated to sum up to 4 × 108 km2 on the earth and are also home for up to 1026 bacterial cells. Plant leaves are able to adsorb or absorb air pollutants, and habituated microbes on leaf surface and in leaves (endophytes) are reported to be able to biodegrade or transform pollutants into less or nontoxic molecules, but their potentials for air remediation has been largely unexplored. With advances in omics technologies, molecular mechanisms underlying plant leaves and leaf associated microbes in reduction of air pollutants will be deeply examined, which will provide theoretical bases for developing leaf-based remediation technologies or phylloremediation for mitigating pollutants in the air. PMID:28804491

Reference independent species level profiling of the largest marine microbial ecosystem.

NASA Astrophysics Data System (ADS)

Mende, D. R.; DeLong, E.; Aylward, F.

2016-02-01

Marine microbes are of immense importance for the flux of matter and energy within the global oceans. Yet, the temporal variability of microbial communities in response to seasonal and environmental changes remains understudied. In addition, there is only a very limited understanding of the effects that changes within microbial communities at a certain depth have on the other microbes within the water column. Further, existing studies have mostly been limited by the lack of good reference databases. Here we present an reference independent analysis of a year long time series at 5 different water depth of the microbial communities at Station ALOHA, a sampling location representative of the largest contiguous ecosystem on earth, the North Pacific Subtropical Gyre (NPSG). Due to the lack the lack of closely related reference genomes most recent meta-genomic studies of marine microbial ecosystems have been limited to a coarse grained view at higher taxonomic levels. In order to gain a fine grained picture of the microbial communities and their dynamics within the NPSG, we extended the mOTU approach that has been successfully applied to the human microbiome to this marine ecosystem using more than 60 deeply sequenced metagenomic samples. This method allows for species level community profiling and diversity estimates, revealing seasonal shifts within the microbial communities. Additionally, we detected a number of microbes that respond to changes of different changing environmental conditions. We further surveyed the depth specificity of microbes at station ALOHA, showing species specific patterns of presence at different depths.

Phylloremediation of Air Pollutants: Exploiting the Potential of Plant Leaves and Leaf-Associated Microbes.

PubMed

Wei, Xiangying; Lyu, Shiheng; Yu, Ying; Wang, Zonghua; Liu, Hong; Pan, Dongming; Chen, Jianjun

2017-01-01

Air pollution is air contaminated by anthropogenic or naturally occurring substances in high concentrations for a prolonged time, resulting in adverse effects on human comfort and health as well as on ecosystems. Major air pollutants include particulate matters (PMs), ground-level ozone (O 3 ), sulfur dioxide (SO 2 ), nitrogen dioxides (NO 2 ), and volatile organic compounds (VOCs). During the last three decades, air has become increasingly polluted in countries like China and India due to rapid economic growth accompanied by increased energy consumption. Various policies, regulations, and technologies have been brought together for remediation of air pollution, but the air still remains polluted. In this review, we direct attention to bioremediation of air pollutants by exploiting the potentials of plant leaves and leaf-associated microbes. The aerial surfaces of plants, particularly leaves, are estimated to sum up to 4 × 10 8 km 2 on the earth and are also home for up to 10 26 bacterial cells. Plant leaves are able to adsorb or absorb air pollutants, and habituated microbes on leaf surface and in leaves (endophytes) are reported to be able to biodegrade or transform pollutants into less or nontoxic molecules, but their potentials for air remediation has been largely unexplored. With advances in omics technologies, molecular mechanisms underlying plant leaves and leaf associated microbes in reduction of air pollutants will be deeply examined, which will provide theoretical bases for developing leaf-based remediation technologies or phylloremediation for mitigating pollutants in the air.

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast

PubMed Central

Libkind, Diego; Hittinger, Chris Todd; Valério, Elisabete; Gonçalves, Carla; Dover, Jim; Johnston, Mark; Gonçalves, Paula; Sampaio, José Paulo

2011-01-01

Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement. PMID:21873232

Analysis of coral mucus as an improved medium for detection of enteric microbes and for determining patterns of sewage contamination in reef environments

USGS Publications Warehouse

Lipp, Erin K.; Griffin, Dale W.

2004-01-01

Traditional fecal indicator bacteria are often subject to a high degree of die-off and dilution in tropical marine waters, particularly in offshore areas such as coral reefs. Furthermore, these microbes are often not associated with human waste, and their presence may not be indicative of health risk. To address the offshore extent of wastewater contamination in the Florida Keys reef tract, we assayed coral surfaces for the presence of human-specific enteric viruses. The overlying water column and surface mucopolysaccharide (mucus) layers from scleractinian corals were sampled from three stations along a nearshore-to-offshore transect beginning at Long Key in the middle Florida Keys, USA. Samples were assayed for standard bacterial water quality indicators (fecal coliform bacteria and enterococci) and for human enteroviruses by direct reverse transcriptase-polymerase chain reaction (RT-PCR). The concentration of the bacterial indicators was greatest at the nearshore station in both the water column and corals, and decreased with distance from shore; no indicator bacteria were detected at the offshore station. Whereas human enteroviruses were not detected in any of the water column samples, they were detected in 50–80% of coral mucus samples at each station. These data provide evidence that human sewage is impacting the reef tract up to ~6.5 km from shore in the middle Florida Keys and that coral mucus is an efficient trap for viral markers associated with anthropogenic pollution.

Probiotics: Interaction with gut microbiome and antiobesity potential.

PubMed

Arora, Tulika; Singh, Satvinder; Sharma, Raj Kumar

2013-04-01

Obesity is a metabolic disorder afflicting people globally. There has been a pivotal advancement in the understanding of the intestinal microbiota composition and its implication in extraintestinal (metabolic) diseases. Therefore, any agent modulating gut microbiota may produce an influential effect in preventing the pathogenesis of disease. Probiotics are live microbes that, when administered in adequate amounts, have been shown to confer health benefits to the host. Over the years, probiotics have been a part of the human diet in the form of different fermented foods consumed around the world. Their influence on different physiologic functions in the host is increasingly being documented. The antiobesity potential of probiotics is also gaining wide attention because of increasing evidence of the role of gut microbiota in energy homeostasis and fat accumulation. Probiotics have also been shown to interact with the resident bacterial members already present in the gut by altering their properties, which may also affect the metabolic pathways involved in the regulation of fat metabolism. The underlying pathways governing the antiobesity effects of probiotics remain unclear. However, it is hoped that the evidence presented and discussed in this review will encourage and thus drive more extensive research in this field. Copyright © 2013 Elsevier Inc. All rights reserved.

EOSINOPHILS: MULTIFACETED BIOLOGIC PROPERTIES AND ROLES IN HEALTH AND DISEASE

PubMed Central

Kita, Hirohito

2011-01-01

Summary Eosinophils are leukocytes resident in mucosal tissues. During Th2-type inflammation, eosinophils are recruited from bone marrow and blood to the sites of immune response. While eosinophils have been considered end-stage cells involved in host protection against parasite infection and immunopathology in hypersensitivity disease, recent studies changed this perspective. Eosinophils are now considered multifunctional leukocytes involved in tissue homeostasis, modulation of adaptive immune responses, and innate immunity to certain microbes. Eosinophils are capable of producing immunoregulatory cytokines and are actively involved in regulation of Th2-type immune responses. However, such new information does not preclude earlier observations showing that eosinophils, in particular human eosinophils, are also effector cells with pro-inflammatory and destructive capabilities. Eosinophils with activation phenotypes are observed in biological specimens from patients with disease, and deposition of eosinophil products is readily seen in the affected tissues from these patients. Therefore, it would be reasonable to consider the eosinophil a multifaceted leukocyte that contributes to various physiological and pathological processes depending on their location and activation status. This review summarizes the emerging concept of the multifaceted immunobiology of eosinophils and discusses the roles of eosinophils in health and disease and the challenges and perspectives in the field. PMID:21682744

Effects of moderate, voluntary ethanol consumption on the rat and human gut microbiome.

PubMed

Kosnicki, Kassi L; Penprase, Jerrold C; Cintora, Patricia; Torres, Pedro J; Harris, Greg L; Brasser, Susan M; Kelley, Scott T

2018-05-11

Many alcohol-induced health complications are directly attributable to the toxicity of alcohol or its metabolites, but another potential health impact of alcohol may be on the microbial communities of the human gut. Clear distinctions between healthy and diseased-state gut microbiota have been observed in subjects with metabolic diseases, and recent studies suggest that chronic alcoholism is linked to gut microbiome dysbiosis. Here, we investigated the effects of moderate levels of alcohol consumption on the gut microbiome in both rats and humans. The gut microbiota of rats voluntarily consuming a 20 percent ethanol solution, on alternate days, were compared with a non-exposed control group to identify differential taxonomic and functional profiles. Gut microbial diversity profiles were determined using culture-independent amplification, next-generation sequencing and bioinformatic analysis of bacterial 16S ribosomal RNA gene sequence libraries. Our results showed that, compared with controls, ethanol-consuming rats experienced a significant decline in the biodiversity of their gut microbiomes, a state generally associated with dysbiosis. We also observed significant shifts in the overall diversity of the gut microbial communities and a dramatic change in the relative abundance of particular microbes, such as the Lactobacilli. We also compared our results to human fecal microbiome data collected as part of the citizen science American Gut Project. In contrast to the rat data, human drinkers had significantly higher gut microbial biodiversity than non-drinkers. However, we also observed that microbes that differed among the human subjects displayed similar trends in the rat model, including bacteria implicated in metabolic disease. © 2018 Society for the Study of Addiction.

Macromolecular networks and intelligence in microorganisms

PubMed Central

Westerhoff, Hans V.; Brooks, Aaron N.; Simeonidis, Evangelos; García-Contreras, Rodolfo; He, Fei; Boogerd, Fred C.; Jackson, Victoria J.; Goncharuk, Valeri; Kolodkin, Alexey

2014-01-01

Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of information and communication technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity – particularly activity of the human brain – with a phenomenon we call “intelligence.” Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as “human” and “brain” out of the defining features of “intelligence,” all forms of life – from microbes to humans – exhibit some or all characteristics consistent with “intelligence.” We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo. PMID:25101076

Teleosts as Model Organisms To Understand Host-Microbe Interactions.

PubMed

Lescak, Emily A; Milligan-Myhre, Kathryn C

2017-08-01

Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis. Copyright © 2017 Lescak and Milligan-Myhre.

Teleosts as Model Organisms To Understand Host-Microbe Interactions

PubMed Central

2017-01-01

ABSTRACT Host-microbe interactions are influenced by complex host genetics and environment. Studies across animal taxa have aided our understanding of how intestinal microbiota influence vertebrate development, disease, and physiology. However, traditional mammalian studies can be limited by the use of isogenic strains, husbandry constraints that result in small sample sizes and limited statistical power, reliance on indirect characterization of gut microbial communities from fecal samples, and concerns of whether observations in artificial conditions are actually reflective of what occurs in the wild. Fish models are able to overcome many of these limitations. The extensive variation in the physiology, ecology, and natural history of fish enriches studies of the evolution and ecology of host-microbe interactions. They share physiological and immunological features common among vertebrates, including humans, and harbor complex gut microbiota, which allows identification of the mechanisms driving microbial community assembly. Their accelerated life cycles and large clutch sizes and the ease of sampling both internal and external microbial communities make them particularly well suited for robust statistical studies of microbial diversity. Gnotobiotic techniques, genetic manipulation of the microbiota and host, and transparent juveniles enable novel insights into mechanisms underlying development of the digestive tract and disease states. Many diseases involve a complex combination of genes which are difficult to manipulate in homogeneous model organisms. By taking advantage of the natural genetic variation found in wild fish populations, as well as of the availability of powerful genetic tools, future studies should be able to identify conserved genes and pathways that contribute to human genetic diseases characterized by dysbiosis. PMID:28439034

Does plant immunity play a critical role during initiation of the legume-rhizobium symbiosis?

PubMed

Tóth, Katalin; Stacey, Gary

2015-01-01

Plants are exposed to many different microbes in their habitats. These microbes may be benign or pathogenic, but in some cases they are beneficial for the host. The rhizosphere provides an especially rich palette for colonization by beneficial (associative and symbiotic) microorganisms, which raises the question as to how roots can distinguish such 'friends' from possible 'foes' (i.e., pathogens). Plants possess an innate immune system that can recognize pathogens, through an arsenal of protein receptors, including receptor-like kinases (RLKs) and receptor-like proteins (RLPs) located at the plasma membrane. In addition, the plant host has intracellular receptors (so called NBS-LRR proteins or R proteins) that directly or indirectly recognize molecules released by microbes into the plant cell. A successful cooperation between legume plants and rhizobia leads to beneficial symbiotic interaction. The key rhizobial, symbiotic signaling molecules [lipo-chitooligosaccharide Nod factors (NF)] are perceived by the host legume plant using lysin motif-domain containing RLKs. Perception of the symbiotic NFs trigger signaling cascades leading to bacterial infection and accommodation of the symbiont in a newly formed root organ, the nodule, resulting in a nitrogen-fixing root nodule symbiosis. The net result of this symbiosis is the intracellular colonization of the plant with thousands of bacteria; a process that seems to occur in spite of the immune ability of plants to prevent pathogen infection. In this review, we discuss the potential of the invading rhizobial symbiont to actively avoid this innate immune response, as well as specific examples of where the plant immune response may modulate rhizobial infection and host range.

CERBERUS and NSP1 of Lotus japonicus are common symbiosis genes that modulate arbuscular mycorrhiza development.

PubMed

Takeda, Naoya; Tsuzuki, Syusaku; Suzaki, Takuya; Parniske, Martin; Kawaguchi, Masayoshi

2013-10-01

Arbuscular mycorrhizal symbiosis (AMS) and root nodule symbiosis (RNS) are mutualistic plant-microbe interactions that confer nutritional benefits to both partners. Leguminous plants possess a common genetic system for intracellular symbiosis with AM fungi and with rhizobia. Here we show that CERBERUS and NSP1, which respectively encode an E3 ubiquitin ligase and a GRAS transcriptional regulator and which have previously only been implicated in RNS, are involved in AM fungal infection in Lotus japonicus. Hyphal elongation along the longitudinal axis of the root was reduced in the cerberus mutant, giving rise to a lower colonization level. Knockout of NSP1 decreased the frequency of plants colonized by AM fungi or rhizobia. CERBERUS and NSP1 showed different patterns of expression in response to infection with symbiotic microbes. A low constitutive level of CERBERUS expression was observed in the root and an increased level of NSP1 expression was detected in arbuscule-containing cells. Induction of AM marker gene was triggered in both cerberus and nsp1 mutants by infection with symbiotic microbes; however, the mutants showed a weaker induction of marker gene expression than the wild type, mirroring their lower level of colonization. The common symbiosis genes are believed to act in an early signaling pathway for recognition of symbionts and for triggering early symbiotic responses. Our quantitative analysis of symbiotic phenotypes revealed developmental defects of the novel common symbiosis mutants in both symbioses, which demonstrates that common symbiosis mechanisms also contribute to a range of functions at later or different stages of symbiont infection.

Water disinfection: microbes versus molecules—an introduction of issues

PubMed Central

Fowle, John R.; Kopfler, Frederick C.

1986-01-01

“Water is, apart from the air one breathes, the only nutrient which is, as a matter of necessity, consumed by every human being from the first day to the last day of his existence, and it is consumed in considerably larger quantities than any other nutritional substance.”(1) PMID:3545806

Agent-Based Models and Optimal Control in Biology: A Discrete Approach

DTIC Science & Technology

2012-01-01

different parts of the human body to cure diseases such as hypertension, cancer, or heart disease. And we need to control microbes for the efficient...antelope herd interacts with an aggregated prey agent such as cheetahs or lions, the size of each may expand or contract accordingly). Of course, such

Comparative analysis of the intestinal bacterial and RNA viral communities from sentinel birds placed on selected broiler chicken farms

USDA-ARS?s Scientific Manuscript database

There is a great deal of interest in characterizing the complex microbial communities in the poultry gut, and in understanding the effects of these dynamic communities on poultry performance, disease status, animal welfare, and microbes with human health significance. Investigations characterizing t...

Comparative analysis of the intestinal bacterial and RNA viral communities from sentinel birds placed on selected broiler chicken farms

USDA-ARS?s Scientific Manuscript database

There is a great deal of interest in characterizing the complex microbial communities in the poultry gut, and in understanding the effects of these dynamic communities on poultry performance, disease status, animal welfare, and microbes with human health significance. Investigations characterizing ...

Argonne News Brief: Here be Dragons! Komodo Dragons Help Understanding of Microbial Health

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

None

Researchers found that captive Komodo Dragons share microbes with their environment, just as humans and pets do within homes. These observations build our understanding of the impact of captivity on health, which could lead to improvements in the care of animals within our homes and other closed environments.

Presence of organic matter and microbial activity in Minebank Run, a restored stream in the Chesapeake Bay watershed

EPA Science Inventory

Abstract: Increasing nitrate levels in streams and ground water are harmful to both the environment and humans. Denitrification, a natural process performed by microbes, removes nitrate from ground water when there is an adequate amount of organic matter present as well as low le...

Micro-managing arthropod invasions: eradication and control of invasive arthropods with microbes

Treesearch

Ann E. Hajek; Patrick C. Tobin

2010-01-01

Non-indigenous arthropods are increasingly being introduced into new areas worldwide and occasionally they cause considerable ecological and economic harm. Many invasive arthropods particularly pose problems to areas of human habitation and native ecosystems. In these cases, the use of environmentally benign materials, such as host-specific entomopathogens, can be more...

Individual- and scattered-tree influences on ultraviolet irradiance

Treesearch

Gordon M. Heisler; Richard H. Gao, Wei Grant

2003-01-01

Many of the potential effects of ultraviolet radiation (UVR--damage to materials, altered herbivory of insects and activity of microbes, modified growth of vegetation, and adverse or beneficial effects on human health?are modified by the presence of trees that influence UVR exposure to various degrees. Though tree effects on total solar irradiance have been...

Role of forage crops and soil microbes in promoting soil health and productivity

USDA-ARS?s Scientific Manuscript database

The United Nations General Assembly has declared 2015 the International Year of Soils (IYS 2015). The IYS 2015 aims to increase awareness and understanding of the importance of soil for food security and essential ecosystem functions. Although often taken for granted, soils are key to human civiliza...

[Sensitivity of meningococci to the antagonistic activity of nasopharyngeal microflora and antibiotics].

PubMed

Bochkov, I A; Larina, L I

1977-12-01

Comparative study of the meningococcus sensitivity of various serological groups with different localization in the human organism to the antagonistic activity of normal microbes of the nasopharynx and the antibiotics it was found that strains isolated from the cerebrospinal fluid of patients suffering from cerebrospinal meningitis, chiefly of serological group A, had the greatest resistance to the antagonists. Taking into consideration the leading epidemiological role of the cultures belonging to the serological group A in the USSR, it can be supposed that meningococcus sensitivity to the nasopharyngeal antagonists was of significance for the manifestation of their pathogenic properties. No association of the antibiotic sensitivity of the same strains with reference to a definite serological group or the site of the microbe localization was revealed.

Evolution of microbiology as seen in the textbooks of Edwin O. Jordan and William H. Park.

PubMed Central

Strick, J.

1999-01-01

Historians of science account the appearance of textbooks as an important step in the formation and consolidation of a new discipline. The texts of Park and Jordan were both very important in this light; however; they also can be used as a gauge of changing concepts within microbiology in the first four decades after its consolidation as a discipline, 1900-1940. This paper tracks these important texts and through them changing attitudes toward several important concepts: bacterial variation, human/bovine tuberculosis, and the existence of a non-symptomatic carrier state in infectious disease. The two texts are also compared regarding their view of microbes as pathogens vs. microbes as important and ubiquitous ecological agents. Images Figure 1 Figure 2 PMID:11049163

Current Trends and Potential Applications of Microbial Interactions for Human Welfare

PubMed Central

Tshikantwa, Tiroyaone Shimane; Ullah, Muhammad Wajid; He, Feng; Yang, Guang

2018-01-01

For a long time, it was considered that interactions between microbes are only inhibitory in nature. However, latest developments in research have demonstrated that within our environment, several classes of microbes exist which produce different products upon interaction and thus embrace a wider scope of useful and potentially valuable aspects beyond simple antibiosis. Therefore, the current review explores different types of microbial interactions and describes the role of various physical, chemical, biological, and genetic factors regulating such interactions. It further explains the mechanism of action of biofilm formation and role of secondary metabolites regulating bacteria-fungi interaction. Special emphasis and focus is placed on microbial interactions which are important in medicine, food industry, agriculture, and environment. In short, this review reveals the recent contributions of microbial interaction for the benefit of mankind.

Multilocus sequence typing of bifidobacterial strains from infant's faeces and human milk: are bifidobacteria being sustainably shared during breastfeeding?

PubMed

Makino, H; Martin, R; Ishikawa, E; Gawad, A; Kubota, H; Sakai, T; Oishi, K; Tanaka, R; Ben-Amor, K; Knol, J; Kushiro, A

2015-01-01

Bifidobacteria are considered to be one of the most important beneficial intestinal bacteria for infants, contributing to the priming of the mucosal immune system. These microbes can also be detected in mother's milk, suggesting a potential role of human milk in the colonisation of infant's gut. However, little is known about the timing of bacteria appearance in human milk, and whether human milk is the first source of inoculation. Here, we investigated whether specific strains are shared sustainably between maternal milk and infant's gut. Faecal samples and human milk were collected from 102 healthy mother-infant pairs (infant's faeces: meconium, 7, 30 days of age; mother's milk: once before delivery, colostrum, 7, 30 days after delivery). Bifidobacterial strains were isolated from these samples, and were discriminated by means of multilocus sequencing typing. No bifidobacteria were detected from human milk collected before delivery, or colostrum. Strains were isolated only from human milk samples obtained 7 days after birth or later. On the other hand, bifidobacterial strains were obtained from infant's faeces throughout the study period, sometimes as early as the first day of life (meconium). We have found that bifidobacterial species belonging to Bifidobacterium bifidum, Bifidobacterium breve, and Bifidobacterium longum subsp. longum could be identified as monophyletic between infant's faeces and their mother's milk. These strains were confirmed to be sustainably shared between maternal milk and infant's gut. Moreover, monophyletic strains were isolated at the same time point or earlier from infant's faeces than from human milk, and none were isolated earlier from human milk than from infant's faeces. Although it remains unclear whether human milk is the first source of microbes for infants, our results confirm that human milk is a reservoir of bifidobacteria, and specific strains are shared between infant's intestine and human milk during breastfeeding.

The Microcosm Mediates the Persistence of Shiga Toxin-Producing Escherichia coli in Freshwater Ecosystems

PubMed Central

Mauro, Steven A.; Opalko, Hannah; Lindsay, Kyle; Colon, Michael P.

2013-01-01

Water is a major route for infection of humans by exotoxin-producing bacteria, including Shiga toxin-producing Escherichia coli (STEC). While STEC has the potential to be present in nearly every type of water source, its distribution is sporadic, and an understanding of factors that govern its emergence and persistence within water is lacking. In this study, we examined the influence of microbe content on STEC persistence in freshwater. We found that depletion of microbes in the water leads to a considerable increase in the persistence of STEC, an effect that can be mitigated by adding grazing protists to the water. STEC strains appear to be more resistant to the impact of grazing protists than E. coli strains that lack the Shiga toxin (stx) gene. Our results demonstrate that the microcosm can dramatically influence the persistence of STEC in aquatic ecosystems and that the overall impact by microbes on STEC strains is fundamentally different from that of non-STEC strains of bacteria. Overall, these results provide insight into why STEC and possibly other exotoxin-producing bacterial pathogens display such variability in abundance, distribution, and persistence in aquatic ecosystems. PMID:23747699

Taxonomy, Epidemiology, and Clinical Relevance of the Genus Arcobacter

PubMed Central

Collado, Luis; Figueras, Maria José

2011-01-01

Summary: The genus Arcobacter, defined almost 20 years ago from members of the genus Campylobacter, has become increasingly important because its members are being considered emergent enteropathogens and/or potential zoonotic agents. Over recent years information that is relevant for microbiologists, especially those working in the medical and veterinary fields and in the food safety sector, has accumulated. Recently, the genus has been enlarged with several new species. The complete genomes of Arcobacter butzleri and Arcobacter nitrofigilis are available, with the former revealing diverse pathways characteristic of free-living microbes and virulence genes homologous to those of Campylobacter. The first multilocus sequence typing analysis showed a great diversity of sequence types, with no association with specific hosts or geographical regions. Advances in detection and identification techniques, mostly based on molecular methods, have been made. These microbes have been associated with water outbreaks and with indicators of fecal pollution, with food products and water as the suspected routes of transmission. This review updates this knowledge and provides the most recent data on the taxonomy, species diversity, methods of detection, and identification of these microbes as well as on their virulence potential and implication in human and animal diseases. PMID:21233511

Microbes in the coral holobiont: partners through evolution, development, and ecological interactions

PubMed Central

Thompson, Janelle R.; Rivera, Hanny E.; Closek, Collin J.; Medina, Mónica

2015-01-01

In the last two decades, genetic and genomic studies have revealed the astonishing diversity and ubiquity of microorganisms. Emergence and expansion of the human microbiome project has reshaped our thinking about how microbes control host health—not only as pathogens, but also as symbionts. In coral reef environments, scientists have begun to examine the role that microorganisms play in coral life history. Herein, we review the current literature on coral-microbe interactions within the context of their role in evolution, development, and ecology. We ask the following questions, first posed by McFall-Ngai et al. (2013) in their review of animal evolution, with specific attention to how coral-microbial interactions may be affected under future environmental conditions: (1) How do corals and their microbiome affect each other's genomes? (2) How does coral development depend on microbial partners? (3) How is homeostasis maintained between corals and their microbial symbionts? (4) How can ecological approaches deepen our understanding of the multiple levels of coral-microbial interactions? Elucidating the role that microorganisms play in the structure and function of the holobiont is essential for understanding how corals maintain homeostasis and acclimate to changing environmental conditions. PMID:25621279

Talking microbes: When gut bacteria interact with diet and host organs

PubMed Central

Everard, Amandine

2016-01-01

Obesity and diabetes have reached epidemic proportions. Evidence suggests that besides dietary habits and physical activity, other environmental factors, such as gut microbes, are recognized as additional partners implicated in the control of energy homeostasis. Studies on the human gut microbiota have shown that the general population can be stratified on the sole basis of three dominant bacteria (i.e., the concept of enterotypes), while some others have suggested categorizing the population according to their microbiome gene richness. Both aspects have been strengthened by recent studies investigating the impact of nutrients (e.g., dietary fibers, fat feeding) and dietary habits (i.e., vegans versus omnivores) of different populations. Using preclinical models, quite a few novel mechanisms have been proposed in these gut microbiota–host interactions, including the role of novel bacteria, the regulation of antimicrobial peptide production, the maintenance of the gut barrier function and intestinal innate immunity. In this review, we discuss several of the aforementioned aspects. Nonetheless, determining the overall mechanisms by which microbes dialogue with host cells will require further investigations before anticipating the development of next‐generation nutritional interventions using prebiotics, probiotics, synbiotics, or even specific nutrients for promoting health benefits. PMID:26178924

Meet the Microbes through the Microbe World Activities with Microbe the Magnificent and Mighty Microbe.

ERIC Educational Resources Information Center

Frame, Kathy, Ed.; Ryan, Karen, Ed.

The activities presented in this book are the product of the Community Outreach Initiative of the Microbial Literacy Collaborative (MLC). This activity book presents a balanced view of microbes, their benefits, and the diseases they cause. Each activity starts with an interesting introductory statement and includes goals, activity time, time to…

Gut Microbiota and the Paradox of Cancer Immunotherapy

PubMed Central

Poutahidis, Theofilos; Kleinewietfeld, Markus; Erdman, Susan E.

2014-01-01

It is recently shown that beneficial environmental microbes stimulate integrated immune and neuroendocrine factors throughout the body, consequently modulating regulatory T-lymphocyte phenotypes, maintaining systemic immune balance, and determining the fate of preneoplastic lesions toward regression while sustaining whole body good health. Stimulated by a gut microbiota-centric systemic homeostasis hypothesis, we set out to explore the influence of the gut microbiome to explain the paradoxical roles of regulatory T-lymphocytes in cancer development and growth. This paradigm shift places cancer prevention and treatment into a new broader context of holobiont engineering to cultivate a tumor-suppressive macroenvironment. PMID:24778636

Gut microbiota and the paradox of cancer immunotherapy.

PubMed

Poutahidis, Theofilos; Kleinewietfeld, Markus; Erdman, Susan E

2014-01-01

It is recently shown that beneficial environmental microbes stimulate integrated immune and neuroendocrine factors throughout the body, consequently modulating regulatory T-lymphocyte phenotypes, maintaining systemic immune balance, and determining the fate of preneoplastic lesions toward regression while sustaining whole body good health. Stimulated by a gut microbiota-centric systemic homeostasis hypothesis, we set out to explore the influence of the gut microbiome to explain the paradoxical roles of regulatory T-lymphocytes in cancer development and growth. This paradigm shift places cancer prevention and treatment into a new broader context of holobiont engineering to cultivate a tumor-suppressive macroenvironment.

Adaptive evolution has targeted the C-terminal domain of the RXLR effectors of plant pathogenic oomycetes.

PubMed

Win, Joe; Kamoun, Sophien

2008-04-01

Plant pathogenic microbes deliver effector proteins inside host cells to modulate plant defense circuitry and enable parasitic colonization. As genome sequences from plant pathogens become available, genome-wide evolutionary analyses will shed light on how pathogen effector genes evolved and adapted to the cellular environment of their host plants. In the August 2007 issue of Plant Cell, we described adaptive evolution (positive selection) in the cytoplasmic RXLR effectors of three recently sequenced oomycete plant pathogens. Here, we summarize our findings and describe additional data that further validate our approach.

The diversity of anti-microbial secondary metabolites produced by fungal endophytes: an interdisciplinary perspective.

PubMed

Mousa, Walaa Kamel; Raizada, Manish N

2013-01-01

Endophytes are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing on anti-microbial compounds, synthesized by fungal endophytes including terpenoids, alkaloids, phenylpropanoids, aliphatic compounds, polyketides, and peptides from the interdisciplinary perspectives of biochemistry, genetics, fungal biology, host plant biology, human and plant pathology. Several trends were apparent. First, host plants are often investigated for endophytes when there is prior indigenous knowledge concerning human medicinal uses (e.g., Chinese herbs). However, within their native ecosystems, and where investigated, endophytes were shown to produce compounds that target pathogens of the host plant. In a few examples, both fungal endophytes and their hosts were reported to produce the same compounds. Terpenoids and polyketides are the most purified anti-microbial secondary metabolites from endophytes, while flavonoids and lignans are rare. Examples are provided where fungal genes encoding anti-microbial compounds are clustered on chromosomes. As different genera of fungi can produce the same metabolite, genetic clustering may facilitate sharing of anti-microbial secondary metabolites between fungi. We discuss gaps in the literature and how more interdisciplinary research may lead to new opportunities to develop bio-based commercial products to combat global crop and human pathogens.

Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors

PubMed Central

Chan, Alfred A.; Bashir, Mina; Rivas, Magali N.; Duvall, Karen; Sieling, Peter A.; Pieber, Thomas R.; Vaishampayan, Parag A.; Love, Susan M.; Lee, Delphine J.

2016-01-01

The microbiome impacts human health and disease. Until recently, human breast tissue and milk were presumed to be sterile. Here, we investigated the presence of microbes in the nipple aspirate fluid (NAF) and their potential association with breast cancer. We compared the NAF microbiome between women with a history of breast cancer (BC) and healthy control women (HC) using 16S rRNA gene amplicon sequencing. The NAF microbiome from BC and HC showed significant differences in community composition. Two Operational Taxonomic Units (OTUs) showed differences in relative abundances between NAF collected from BC and HC. In NAF collected from BC, there was relatively higher incidence of the genus Alistipes. By contrast, an unclassified genus from the Sphingomonadaceae family was relatively more abundant in NAF from HC. These findings reflect the ductal source DNA since there were no differences between areolar skin samples collected from BC and HC. Furthermore, the microbes associated with BC share an enzymatic activity, Beta-Glucuronidase, which may promote breast cancer. This is the first report of bacterial DNA in human breast ductal fluid and the differences between NAF from HC and BC. Further investigation of the ductal microbiome and its potential role in breast cancer are warranted. PMID:27324944

The Diversity of Anti-Microbial Secondary Metabolites Produced by Fungal Endophytes: An Interdisciplinary Perspective

PubMed Central

Mousa, Walaa Kamel; Raizada, Manish N.

2013-01-01

Endophytes are microbes that inhabit host plants without causing disease and are reported to be reservoirs of metabolites that combat microbes and other pathogens. Here we review diverse classes of secondary metabolites, focusing on anti-microbial compounds, synthesized by fungal endophytes including terpenoids, alkaloids, phenylpropanoids, aliphatic compounds, polyketides, and peptides from the interdisciplinary perspectives of biochemistry, genetics, fungal biology, host plant biology, human and plant pathology. Several trends were apparent. First, host plants are often investigated for endophytes when there is prior indigenous knowledge concerning human medicinal uses (e.g., Chinese herbs). However, within their native ecosystems, and where investigated, endophytes were shown to produce compounds that target pathogens of the host plant. In a few examples, both fungal endophytes and their hosts were reported to produce the same compounds. Terpenoids and polyketides are the most purified anti-microbial secondary metabolites from endophytes, while flavonoids and lignans are rare. Examples are provided where fungal genes encoding anti-microbial compounds are clustered on chromosomes. As different genera of fungi can produce the same metabolite, genetic clustering may facilitate sharing of anti-microbial secondary metabolites between fungi. We discuss gaps in the literature and how more interdisciplinary research may lead to new opportunities to develop bio-based commercial products to combat global crop and human pathogens. PMID:23543048

ILSI Southeast Asia Region conference proceedings: The gut, its microbes and health: relevance for Asia.

PubMed

Lee, Yuan Kun; Conway, Patricia; Pettersson, Sven; Nair, G Balakrish; Surono, Ingrid; Egayanti, Yusra; Amarra, Maria Sofia

2017-01-01

The human being is a complex entity, involving interaction between microbes and the human host. Evidence shows that the nutritional value of food is influenced in part by the structure and operations of an individual's gut microbial community, and food in turn shapes the individual's microbiome. A conference was held to promote understanding of the intestinal microbiome and its implications for health and disease, particularly among Asian populations. Papers describing 1) the intestinal ecosystem in Asian populations, 2) changes in intestinal microbiota through life and its effects, 3) the Asian gut microbiota in disease conditions, 4) indigenous probiotics to maintain a healthy gut microbiota, 5) probiotic regulation in an Asian country, and 6) the results of a panel discussion are included in this report. The gut microbial inhabitants of Asian people differ from those of Europe and North America. Geographic location, diet, and ethnic background influence intestinal microbial composition. Urbanization and economic development have brought changes in traditional Asian diets, which in turn affected the gut microbiome, contributing to a shift in the region's health burden from infectious diseases to non-communicable chronic diseases. Novel probiotic strains of Indonesian origin demonstrated significant enhancement of humoral immune response in human studies. Knowledge gaps and implications for research to further understand the Asian gut microbiome were discussed.

From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways

PubMed Central

Rogers, G B; Keating, D J; Young, R L; Wong, M-L; Licinio, J; Wesselingh, S

2016-01-01

The human body hosts an enormous abundance and diversity of microbes, which perform a range of essential and beneficial functions. Our appreciation of the importance of these microbial communities to many aspects of human physiology has grown dramatically in recent years. We know, for example, that animals raised in a germ-free environment exhibit substantially altered immune and metabolic function, while the disruption of commensal microbiota in humans is associated with the development of a growing number of diseases. Evidence is now emerging that, through interactions with the gut–brain axis, the bidirectional communication system between the central nervous system and the gastrointestinal tract, the gut microbiome can also influence neural development, cognition and behaviour, with recent evidence that changes in behaviour alter gut microbiota composition, while modifications of the microbiome can induce depressive-like behaviours. Although an association between enteropathy and certain psychiatric conditions has long been recognized, it now appears that gut microbes represent direct mediators of psychopathology. Here, we examine roles of gut microbiome in shaping brain development and neurological function, and the mechanisms by which it can contribute to mental illness. Further, we discuss how the insight provided by this new and exciting field of research can inform care and provide a basis for the design of novel, microbiota-targeted, therapies. PMID:27090305

Microbiota promote secretory cell determination in the intestinal epithelium by modulating host Notch signaling.

PubMed

Troll, Joshua V; Hamilton, M Kristina; Abel, Melissa L; Ganz, Julia; Bates, Jennifer M; Stephens, W Zac; Melancon, Ellie; van der Vaart, Michiel; Meijer, Annemarie H; Distel, Martin; Eisen, Judith S; Guillemin, Karen

2018-02-23

Resident microbes promote many aspects of host development, although the mechanisms by which microbiota influence host tissues remain unclear. We showed previously that the microbiota is required for allocation of appropriate numbers of secretory cells in the zebrafish intestinal epithelium. Because Notch signaling is crucial for secretory fate determination, we conducted epistasis experiments to establish whether the microbiota modulates host Notch signaling. We also investigated whether innate immune signaling transduces microbiota cues via the Myd88 adaptor protein. We provide the first evidence that microbiota-induced, Myd88-dependent signaling inhibits host Notch signaling in the intestinal epithelium, thereby promoting secretory cell fate determination. These results connect microbiota activity via innate immune signaling to the Notch pathway, which also plays crucial roles in intestinal homeostasis throughout life and when impaired can result in chronic inflammation and cancer. © 2018. Published by The Company of Biologists Ltd.

Modulation of host cell function by Legionella pneumophila type IV effectors.

PubMed

Hubber, Andree; Roy, Craig R

2010-01-01

Macrophages and protozoa ingest bacteria by phagocytosis and destroy these microbes using a conserved pathway that mediates fusion of the phagosome with lysosomes. To survive within phagocytic host cells, bacterial pathogens have evolved a variety of strategies to avoid fusion with lysosomes. A virulence strategy used by the intracellular pathogen Legionella pneumophila is to manipulate host cellular processes using bacterial proteins that are delivered into the cytosolic compartment of the host cell by a specialized secretion system called Dot/Icm. The proteins delivered by the Dot/Icm system target host factors that play evolutionarily conserved roles in controlling membrane transport in eukaryotic cells, which enables L. pneumophila to create an endoplasmic reticulum-like vacuole that supports intracellular replication in both protozoan and mammalian host cells. This review focuses on intracellular trafficking of L. pneumophila and describes how bacterial proteins contribute to modulation of host processes required for survival within host cells.

Human pathogens on plants: designing a multidisciplinary strategy for research.

PubMed

Fletcher, Jacqueline; Leach, Jan E; Eversole, Kellye; Tauxe, Robert

2013-04-01

Recent efforts to address concerns about microbial contamination of food plants and resulting foodborne illness have prompted new collaboration and interactions between the scientific communities of plant pathology and food safety. This article provides perspectives from scientists of both disciplines and presents selected research results and concepts that highlight existing and possible future synergisms for audiences of both disciplines. Plant pathology is a complex discipline that encompasses studies of the dissemination, colonization, and infection of plants by microbes such as bacteria, viruses, fungi, and oomycetes. Plant pathologists study plant diseases as well as host plant defense responses and disease management strategies with the goal of minimizing disease occurrences and impacts. Repeated outbreaks of human illness attributed to the contamination of fresh produce, nuts and seeds, and other plant-derived foods by human enteric pathogens such as Shiga toxin-producing Escherichia coli and Salmonella spp. have led some plant pathologists to broaden the application of their science in the past two decades, to address problems of human pathogens on plants (HPOPs). Food microbiology, which began with the study of microbes that spoil foods and those that are critical to produce food, now also focuses study on how foods become contaminated with pathogens and how this can be controlled or prevented. Thus, at the same time, public health researchers and food microbiologists have become more concerned about plant-microbe interactions before and after harvest. New collaborations are forming between members of the plant pathology and food safety communities, leading to enhanced research capacity and greater understanding of the issues for which research is needed. The two communities use somewhat different vocabularies and conceptual models. For example, traditional plant pathology concepts such as the disease triangle and the disease cycle can help to define cross-over issues that pertain also to HPOP research, and can suggest logical strategies for minimizing the risk of microbial contamination. Continued interactions and communication among these two disciplinary communities is essential and can be achieved by the creation of an interdisciplinary research coordination network. We hope that this article, an introduction to the multidisciplinary HPOP arena, will be useful to researchers in many related fields.

Human Pathogens on Plants: Designing a Multidisciplinary Strategy for Research.

PubMed

Fletcher, Jacqueline; Leach, Jan E; Eversole, Kellye; Tauxe, Robert

2014-10-15

Recent efforts to address concerns about microbial contamination of food plants and resulting foodborne illness have prompted new collaboration and interactions between the scientific communities of plant pathology and food safety. This article provides perspectives from scientists of both disciplines and presents selected research results and concepts that highlight existing and possible future synergisms for audiences of both disciplines. Plant pathology is a complex discipline that encompasses studies of the dissemination, colonization, and infection of plants by microbes such as bacteria, viruses, fungi, and oomycetes. Plant pathologists study plant diseases as well as host plant defense responses and disease management strategies with the goal of minimizing disease occurrences and impacts. Repeated outbreaks of human illness attributed to the contamination of fresh produce, nuts and seeds, and other plant-derived foods by human enteric pathogens such as Shiga toxin-producing Escherichia coli and Salmonella spp. have led some plant pathologists to broaden the application of their science in the past two decades, to address problems of human pathogens on plants (HPOPs). Food microbiology, which began with the study of microbes that spoil foods and those that are critical to produce food, now also focuses study on how foods become contaminated with pathogens and how this can be controlled or prevented. Thus, at the same time, public health researchers and food microbiologists have become more concerned about plant-microbe interactions before and after harvest. New collaborations are forming between members of the plant pathology and food safety communities, leading to enhanced research capacity and greater understanding of the issues for which research is needed. The two communities use somewhat different vocabularies and conceptual models. For example, traditional plant pathology concepts such as the disease triangle and the disease cycle can help to define cross-over issues that pertain also to HPOP research, and can suggest logical strategies for minimizing the risk of microbial contamination. Continued interactions and communication among these two disciplinary communities is essential and can be achieved by the creation of an interdisciplinary research coordination network. We hope that this article, an introduction to the multidisciplinary HPOP arena, will be useful to researchers in many related fields.

Microbes, Immunity, and Behavior: Psychoneuroimmunology Meets the Microbiome

PubMed Central

Dinan, Timothy G; Cryan, John F

2017-01-01

There is now a large volume of evidence to support the view that the immune system is a key communication pathway between the gut and brain, which plays an important role in stress-related psychopathologies and thus provides a potentially fruitful target for psychotropic intervention. The gut microbiota is a complex ecosystem with a diverse range of organisms and a sophisticated genomic structure. Bacteria within the gut are estimated to weigh in excess of 1 kg in the adult human and the microbes within not only produce antimicrobial peptides, short chain fatty acids, and vitamins, but also most of the common neurotransmitters found in the human brain. That the microbial content of the gut plays a key role in immune development is now beyond doubt. Early disruption of the host-microbe interplay can have lifelong consequences, not just in terms of intestinal function but in distal organs including the brain. It is clear that the immune system and nervous system are in continuous communication in order to maintain a state of homeostasis. Significant gaps in knowledge remain about the effect of the gut microbiota in coordinating the immune-nervous systems dialogue. However, studies using germ-free animals, infective models, prebiotics, probiotics, and antibiotics have increased our understanding of the interplay. Early life stress can have a lifelong impact on the microbial content of the intestine and permanently alter immune functioning. That early life stress can also impact adult psychopathology has long been appreciated in psychiatry. The challenge now is to fully decipher the molecular mechanisms that link the gut microbiota, immune, and central nervous systems in a network of communication that impacts behavior patterns and psychopathology, to eventually translate these findings to the human situation both in health and disease. Even at this juncture, there is evidence to pinpoint key sites of communication where gut microbial interventions either with drugs or diet or perhaps fecal microbiota transplantation may positively impact mental health. PMID:27319972

Microbial Community Patterns Associated with Automated Teller Machine Keypads in New York City

PubMed Central

Maritz, Julia M.; Luong, Albert

2016-01-01

ABSTRACT In densely populated urban environments, the distribution of microbes and the drivers of microbial community assemblages are not well understood. In sprawling metropolitan habitats, the “urban microbiome” may represent a mix of human-associated and environmental taxa. Here we carried out a baseline study of automated teller machine (ATM) keypads in New York City (NYC). Our goal was to describe the biodiversity and biogeography of both prokaryotic and eukaryotic microbes in an urban setting while assessing the potential source of microbial assemblages on ATM keypads. Microbial swab samples were collected from three boroughs (Manhattan, Queens, and Brooklyn) during June and July 2014, followed by generation of Illumina MiSeq datasets for bacterial (16S rRNA) and eukaryotic (18S rRNA) marker genes. Downstream analysis was carried out in the QIIME pipeline, in conjunction with neighborhood metadata (ethnicity, population, age groups) from the NYC Open Data portal. Neither the 16S nor 18S rRNA datasets showed any clustering patterns related to geography or neighborhood demographics. Bacterial assemblages on ATM keypads were dominated by taxonomic groups known to be associated with human skin communities (Actinobacteria, Bacteroides, Firmicutes, and Proteobacteria), although SourceTracker analysis was unable to identify the source habitat for the majority of taxa. Eukaryotic assemblages were dominated by fungal taxa as well as by a low-diversity protist community containing both free-living and potentially pathogenic taxa (Toxoplasma, Trichomonas). Our results suggest that ATM keypads amalgamate microbial assemblages from different sources, including the human microbiome, eukaryotic food species, and potentially novel extremophilic taxa adapted to air or surfaces in the built environment. DNA obtained from ATM keypads may thus provide a record of both human behavior and environmental sources of microbes. IMPORTANCE Automated teller machine (ATM) keypads represent a specific and unexplored microhabitat for microbial communities. Although the number of built environment and urban microbial ecology studies has expanded greatly in recent years, the majority of research to date has focused on mass transit systems, city soils, and plumbing and ventilation systems in buildings. ATM surfaces, potentially retaining microbial signatures of human inhabitants, including both commensal taxa and pathogens, are interesting from both a biodiversity perspective and a public health perspective. By focusing on ATM keypads in different geographic areas of New York City with distinct population demographics, we aimed to characterize the diversity and distribution of both prokaryotic and eukaryotic microbes, thus making a unique contribution to the growing body of work focused on the “urban microbiome.” In New York City, the surface area of urban surfaces in Manhattan far exceeds the geographic area of the island itself. We have only just begun to describe the vast array of microbial taxa that are likely to be present across diverse types of urban habitats. PMID:27904880

Self-disseminating vaccines for emerging infectious diseases.

PubMed

Murphy, Aisling A; Redwood, Alec J; Jarvis, Michael A

2016-01-01

Modern human activity fueled by economic development is profoundly altering our relationship with microorganisms. This altered interaction with microbes is believed to be the major driving force behind the increased rate of emerging infectious diseases from animals. The spate of recent infectious disease outbreaks, including Ebola virus disease and Middle East respiratory syndrome, emphasize the need for development of new innovative tools to manage these emerging diseases. Disseminating vaccines are one such novel approach to potentially interrupt animal to human (zoonotic) transmission of these pathogens.

Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice.

PubMed

Sharpton, Thomas; Lyalina, Svetlana; Luong, Julie; Pham, Joey; Deal, Emily M; Armour, Courtney; Gaulke, Christopher; Sanjabi, Shomyseh; Pollard, Katherine S

2017-01-01

The gut microbiome is linked to inflammatory bowel disease (IBD) severity and altered in late-stage disease. However, it is unclear how gut microbial communities change over the course of IBD development, especially in regard to function. To investigate microbiome-mediated disease mechanisms and discover early biomarkers of IBD, we conducted a longitudinal metagenomic investigation in an established mouse model of IBD, where damped transforming growth factor β (TGF-β) signaling in T cells leads to peripheral immune activation, weight loss, and severe colitis. IBD development is associated with abnormal gut microbiome temporal dynamics, including damped acquisition of functional diversity and significant differences in abundance trajectories for KEGG modules such as glycosaminoglycan degradation, cellular chemotaxis, and type III and IV secretion systems. Most differences between sick and control mice emerge when mice begin to lose weight and heightened T cell activation is detected in peripheral blood. However, levels of lipooligosaccharide transporter abundance diverge prior to immune activation, indicating that it could be a predisease indicator or microbiome-mediated disease mechanism. Taxonomic structure of the gut microbiome also significantly changes in association with IBD development, and the abundances of particular taxa, including several species of Bacteroides , correlate with immune activation. These discoveries were enabled by our use of generalized linear mixed-effects models to test for differences in longitudinal profiles between healthy and diseased mice while accounting for the distributions of taxon and gene counts in metagenomic data. These findings demonstrate that longitudinal metagenomics is useful for discovering the potential mechanisms through which the gut microbiome becomes altered in IBD. IMPORTANCE IBD patients harbor distinct microbial communities with functional capabilities different from those seen with healthy people. But is this cause or effect? Answering this question requires data on changes in gut microbial communities leading to disease onset. By performing weekly metagenomic sequencing and mixed-effects modeling on an established mouse model of IBD, we identified several functional pathways encoded by the gut microbiome that covary with host immune status. These pathways are novel early biomarkers that may either enable microbes to live inside an inflamed gut or contribute to immune activation in IBD mice. Future work will validate the potential roles of these microbial pathways in host-microbe interactions and human disease. This study was novel in its longitudinal design and focus on microbial pathways, which provided new mechanistic insights into the role of gut microbes in IBD development.

Development of Inflammatory Bowel Disease Is Linked to a Longitudinal Restructuring of the Gut Metagenome in Mice

PubMed Central

Sharpton, Thomas; Lyalina, Svetlana; Luong, Julie; Pham, Joey; Deal, Emily M.; Armour, Courtney; Gaulke, Christopher; Sanjabi, Shomyseh

2017-01-01

ABSTRACT The gut microbiome is linked to inflammatory bowel disease (IBD) severity and altered in late-stage disease. However, it is unclear how gut microbial communities change over the course of IBD development, especially in regard to function. To investigate microbiome-mediated disease mechanisms and discover early biomarkers of IBD, we conducted a longitudinal metagenomic investigation in an established mouse model of IBD, where damped transforming growth factor β (TGF-β) signaling in T cells leads to peripheral immune activation, weight loss, and severe colitis. IBD development is associated with abnormal gut microbiome temporal dynamics, including damped acquisition of functional diversity and significant differences in abundance trajectories for KEGG modules such as glycosaminoglycan degradation, cellular chemotaxis, and type III and IV secretion systems. Most differences between sick and control mice emerge when mice begin to lose weight and heightened T cell activation is detected in peripheral blood. However, levels of lipooligosaccharide transporter abundance diverge prior to immune activation, indicating that it could be a predisease indicator or microbiome-mediated disease mechanism. Taxonomic structure of the gut microbiome also significantly changes in association with IBD development, and the abundances of particular taxa, including several species of Bacteroides, correlate with immune activation. These discoveries were enabled by our use of generalized linear mixed-effects models to test for differences in longitudinal profiles between healthy and diseased mice while accounting for the distributions of taxon and gene counts in metagenomic data. These findings demonstrate that longitudinal metagenomics is useful for discovering the potential mechanisms through which the gut microbiome becomes altered in IBD. IMPORTANCE IBD patients harbor distinct microbial communities with functional capabilities different from those seen with healthy people. But is this cause or effect? Answering this question requires data on changes in gut microbial communities leading to disease onset. By performing weekly metagenomic sequencing and mixed-effects modeling on an established mouse model of IBD, we identified several functional pathways encoded by the gut microbiome that covary with host immune status. These pathways are novel early biomarkers that may either enable microbes to live inside an inflamed gut or contribute to immune activation in IBD mice. Future work will validate the potential roles of these microbial pathways in host-microbe interactions and human disease. This study was novel in its longitudinal design and focus on microbial pathways, which provided new mechanistic insights into the role of gut microbes in IBD development. PMID:28904997

Detection of right-to-left shunts: comparison between the International Consensus and Spencer Logarithmic Scale criteria.

PubMed

Lao, Annabelle Y; Sharma, Vijay K; Tsivgoulis, Georgios; Frey, James L; Malkoff, Marc D; Navarro, Jose C; Alexandrov, Andrei V

2008-10-01

International Consensus Criteria (ICC) consider right-to-left shunt (RLS) present when Transcranial Doppler (TCD) detects even one microbubble (microB). Spencer Logarithmic Scale (SLS) offers more grades of RLS with detection of >30 microB corresponding to a large shunt. We compared the yield of ICC and SLS in detection and quantification of a large RLS. We prospectively evaluated paradoxical embolism in consecutive patients with ischemic strokes or transient ischemic attack (TIA) using injections of 9 cc saline agitated with 1 cc of air. Results were classified according to ICC [negative (no microB), grade I (1-20 microB), grade II (>20 microB or "shower" appearance of microB), and grade III ("curtain" appearance of microB)] and SLS criteria [negative (no microB), grade I (1-10 microB), grade II (11-30 microB), grade III (31100 microB), grade IV (101300 microB), grade V (>300 microB)]. The RLS size was defined as large (>4 mm) using diameter measurement of the septal defects on transesophageal echocardiography (TEE). TCD comparison to TEE showed 24 true positive, 48 true negative, 4 false positive, and 2 false negative cases (sensitivity 92.3%, specificity 92.3%, positive predictive value (PPV) 85.7%, negative predictive value (NPV) 96%, and accuracy 92.3%) for any RLS presence. Both ICC and SLS were 100% sensitive for detection of large RLS. ICC and SLS criteria yielded a false positive rate of 24.4% and 7.7%, respectively when compared to TEE. Although both grading scales provide agreement as to any shunt presence, using the Spencer Scale grade III or higher can decrease by one-half the number of false positive TCD diagnoses to predict large RLS on TEE.

Genomics approach to the environmental community of microorganisms

NASA Astrophysics Data System (ADS)

Kawarabayasi, Y.; Maruyama, A.

2004-12-01

It was indicated by microscopic observation or comparison of 16S rDNA sequence that many extremophiles were surviving in many hydrothermal environments. But it is generally said that over 99% of total microbes are now uncultivable. Thus, we planned to identify uncultivable microbes through direct sequencing of environmental DNA. At first, shotgun plasmid libraries were directly constructed with the DNA molecules prepared from mixed microbes collected from low-temperature hydrothermal water at RM24 in the Southern East Pacific Rise (S-EPR). It was shown that the sequences of some number of clones indicated the similar feature to the intron in eukaryote or tandem repetitive sequence identified in some human familiar diseases. The results indicated that many microorganisms with eukaryotic feature were dominant in low temperature water of S-EPR. Secondly, shotgun plasmid libraries were constructed from the environmental DNA prepared from Beppu hot springs. The ORFs were easily identified all clones determined entire sequence. Thus it can be said that hot springs is good resources for searching novel genes. At last, the mixed microbes isolated from Suiyo seamount were used for construction of shotgun library. The clones in this library contained the ORFs. From some clones in hot spring and Suiyo sample, aminoacyl-tRNA synthatase, which is generally present in all organisms, was isolated by similarity. The phylogenetic analysis of aminoacyl-tRNA synthetase identified indicated that novel and unidentified microorganisms should be present in hot spring or Suiyo seamount. The novel genes identified from Suiyo seamount were also utilized for expression in E. coli. Some gene products were successfully obtained from the E. coli cells as soluble proteins. Some protein indicated the thermostability up to 70_E#8249;C, meaning that the original host cell of this gene should be stable up to the same temperature. Our work indicates that environmental genomics, including the direct cloning, sequencing of environmental DNA and expression of gene identified, is powerful approach to collect novel uncultivable microbes or novel active genes.