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Sample records for albus ruminococcus flavefaciens

  1. Effect of soluble carbohydrates on digestion of cellulose by pure cultures of rumen bacteria. [Ruminococcus flavefaciens, R. albus, Bacteroides succinogenes

    SciTech Connect

    Hiltner, P.; Dehority, B.A.

    1983-09-01

    The rate of cellulose digestion in the presence of either glucose or cellobiose was studied for the three predominant species of cellulolytic rumen bacteria: Ruminococcus albus, Ruminococcus flavefaciens, and Bacteroides succinogenes. When a soluble carbohydrate was added to cellulose broth, the lag phase of cellulose digestion was shortened. Presumably, this was due to greater numbers of bacteria, because increasing the size of the inoculum had a similar effect. Cellulose digestion occurred simultaneously with utilization of the soluble carbohydrate. The rate of cellulose digestion slowed markedly for B. succinogenes and R. flavefaciens and slowed less for R. albus after the cellobiose or glucose had been utilized, and was accompanied by a decrease in pH. Both the rate and the extent of cellulose digestion were partially inhibited when the initial pH of the medium was 6.3 or below. R. albus appeared to be less affected by a low-pH medium than were B. succinogenes and R. flavefaciens. When a soluble carbohydrate was added to the fermentation during the maximum-rate phase of cellulose digestion, the rate of cellulose digestion was not affected until after the soluble carbohydrate had been depleted and the pH had decreased markedly. Prolonged exposure of the bacteria to a low pH had little if any effect on their subsequent ability to digest cellulose. Cellulase activity of intact bacterial cells appeared to be constitutive in nature for these three species of rumen bacteria. 30 references.

  2. Muralytic Activities of Ruminococcus albus 8

    PubMed Central

    Greve, L. Carl; Labavitch, John M.; Stack, Robert J.; Hungate, Robert E.

    1984-01-01

    Ruminococcus albus 8 was cultured with isolated alfalfa cell walls as the carbon source. The culture broth was assayed for muralytic enzyme activities. The effect, with respect to the production of such muralytic enzymes, of growing the microorganism on different carbon sources was also investigated. Also, the rates of solubilization and utilization by R. albus of individual alfalfa cell wall sugars during a 96-h growth period were examined. PMID:16346542

  3. Cellulosomal Scaffoldin-Like Proteins from Ruminococcus flavefaciens

    PubMed Central

    Ding, Shi-You; Rincon, Marco T.; Lamed, Raphael; Martin, Jennifer C.; McCrae, Sheila I.; Aurilia, Vincenzo; Shoham, Yuval; Bayer, Edward A.; Flint, Harry J.

    2001-01-01

    Two tandem cellulosome-associated genes were identified in the cellulolytic rumen bacterium, Ruminococcus flavefaciens. The deduced gene products represent multimodular scaffoldin-related proteins (termed ScaA and ScaB), both of which include several copies of explicit cellulosome signature sequences. The scaB gene was completely sequenced, and its upstream neighbor scaA was partially sequenced. The sequenced portion of scaA contains repeating cohesin modules and a C-terminal dockerin domain. ScaB contains seven relatively divergent cohesin modules, two extremely long T-rich linkers, and a C-terminal domain of unknown function. Collectively, the cohesins of ScaA and ScaB are phylogenetically distinct from the previously described type I and type II cohesins, and we propose that they define a new group, which we designated here type III cohesins. Selected modules from both genes were overexpressed in Escherichia coli, and the recombinant proteins were used as probes in affinity-blotting experiments. The results strongly indicate that ScaA serves as a cellulosomal scaffoldin-like protein for several R. flavefaciens enzymes. The data are supported by the direct interaction of a recombinant ScaA cohesin with an expressed dockerin-containing enzyme construct from the same bacterium. The evidence also demonstrates that the ScaA dockerin binds to a specialized cohesin(s) on ScaB, suggesting that ScaB may act as an anchoring protein, linked either directly or indirectly to the bacterial cell surface. This study is the first direct demonstration in a cellulolytic rumen bacterium of a cellulosome system, mediated by distinctive cohesin-dockerin interactions. PMID:11222592

  4. Functional phylotyping approach for assessing intraspecific diversity of Ruminococcus albus within the rumen microbiome.

    PubMed

    Rozman Grinberg, Inna; Yin, Guohua; Borovok, Ilya; Berg Miller, Margret E; Yeoman, Carl J; Dassa, Bareket; Yu, Zhongtang; Mizrahi, Itzhak; Flint, Harry J; Bayer, Edward A; White, Bryan A; Lamed, Raphael

    2015-01-01

    Ruminococcus albus, a cellulolytic bacterium, is a critical member of the rumen community. Ruminococcus albus lacks a classical cellulosome complex, but it possesses a unique family 37 carbohydrate-binding module (CBM37), which is integrated into a variety of carbohydrate-active enzymes. We developed a potential molecular tool for functional phylotyping of the R. albus population in the rumen, based on a variable region in the cel48A gene. cel48A encodes a single copy of the CBM37-associated family 48 glycoside hydrolase in all known strains of this bacterium. A segment of the cel48A gene was amplified from rumen metagenomic samples of four bovines, and its abundance and diversity were evaluated. Analysis of the obtained sequences revealed the co-existence of multiple functional phylotypes of cel48A in all four animals. These included sequences identical or similar to those of R. albus isolates (reference strains), as well as several novel sequences. The dominant cel48A type varied among animals. This method can be used for detection of intraspecific diversity of R. albus in metagenomic samples. Together with scaC, a previously reported gene marker for R. flavefaciens, we present a set of two species-specific markers for phylotyping of Ruminococci in the herbivore rumen. PMID:25673657

  5. Complete Genome of the Cellulolytic Ruminal Bacterium Ruminococcus albus 7

    SciTech Connect

    Suen, Garret; Stevenson, David M; Bruce, David; Chertkov, Olga; Copeland, A; Cheng, Jan-Fang; Detter, J. Chris; Goodwin, Lynne A.; Han, Cliff; Hauser, Loren John; Ivanova, N; Kyrpides, Nikos C; Land, Miriam L; Lapidus, Alla L.; Lucas, Susan; Ovchinnikova, Galina; Pitluck, Sam; Tapia, Roxanne; Woyke, Tanja; Boyum, Julie; Mead, David; Weimer, Paul J

    2011-01-01

    Ruminococcus albus 7 is a highly cellulolytic ruminal bacterium that is a member of the phylum Firmicutes. Here, we describe the complete genome of this microbe. This genome will be useful for rumen microbiology and cellulosome biology and in biofuel production, as one of its major fermentation products is ethanol.

  6. Purification and properties of NADP-dependent glutamate dehydrogenase from Ruminococcus flavefaciens FD-1.

    PubMed Central

    Duncan, P A; White, B A; Mackie, R I

    1992-01-01

    Glutamate dehydrogenase (GDH) (L-glutamate:NADP+ oxidoreductase, deaminating, EC 1.4.1.4) from the cellulolytic ruminal bacterium Ruminococcus flavefaciens has been purified and characterized. The native enzyme and subunit are 280 and 48 kDa, respectively, suggesting that the native enzyme is a hexamer. The enzyme requires 0.5 M KCl for optimal activity and has a pH optimum of 6.9 to 7.0. The Kms for ammonia, alpha-ketoglutarate, and glutamate are 19, 0.41, and 62 mM, respectively. The sigmoidal NADPH saturation curve revealed positive cooperativity for the binding of this coenzyme. The first residue in the N-terminal amino acid sequence from R. flavefaciens GDH was alanine, suggesting that the protein may be modified posttranslationally. Comparison of the N-terminal sequence with those of Escherichia coli, Salmonella typhimurium, and Clostridium symbiosum revealed only 39% amino acid homologies. The GDH from R. flavefaciens was unique in that its specific activity was highest during ammonia-limited growth but was not affected by ammonia shock treatment (20 mM). Images PMID:1335719

  7. Cellulase from Ruminococcus albus and mixed rumen microorganisms.

    PubMed

    Leatherwood, J M

    1965-09-01

    Cellulase in the cultural filtrates of Ruminococcus albus and cellulase extracted from mixed rumen microorganisms were investigated with acid-swollen cellulose and carboxymethylcellulose as substrates. Maximal activity occurred at approximately pH 5.8 and 47 C. Apparent Michaelis constants (K(m)) varied between 0.53 and 0.02% carboxymethylcellulose, depending on the level of activity and the method of assay. R. albus cellulase has a lower K(m) value than the enzyme extracted from mixed rumen microorganisms. Antisera from rabbits immunized with a cellulase preparation from R. albus inhibited the cellulolytic activity of both systems. Based on the relative degree of inhibition, approximately 20% of the cellulase of the mixed rumen microorganisms was immunologically similar to R. albus cellulase. Ratios of activity in different assay techniques showed the two sources of activity to be similar in the mechanisms of degradation. However, glucose is the main product of cellulose degradation by mixed rumen microorganisms, and cellobiose is the product of degradation by R. albus.

  8. Complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition

    PubMed Central

    Venditto, Immacolata; Luis, Ana S.; Rydahl, Maja; Schückel, Julia; Fernandes, Vânia O.; Vidal-Melgosa, Silvia; Bule, Pedro; Goyal, Arun; Pires, Virginia M. R.; Dourado, Catarina G.; Ferreira, Luís M. A.; Coutinho, Pedro M.; Henrissat, Bernard; Knox, J. Paul; Baslé, Arnaud; Najmudin, Shabir; Gilbert, Harry J.; Willats, William G. T.; Fontes, Carlos M. G. A.

    2016-01-01

    The breakdown of plant cell wall (PCW) glycans is an important biological and industrial process. Noncatalytic carbohydrate binding modules (CBMs) fulfill a critical targeting function in PCW depolymerization. Defining the portfolio of CBMs, the CBMome, of a PCW degrading system is central to understanding the mechanisms by which microbes depolymerize their target substrates. Ruminococcus flavefaciens, a major PCW degrading bacterium, assembles its catalytic apparatus into a large multienzyme complex, the cellulosome. Significantly, bioinformatic analyses of the R. flavefaciens cellulosome failed to identify a CBM predicted to bind to crystalline cellulose, a key feature of the CBMome of other PCW degrading systems. Here, high throughput screening of 177 protein modules of unknown function was used to determine the complete CBMome of R. flavefaciens. The data identified six previously unidentified CBM families that targeted β-glucans, β-mannans, and the pectic polysaccharide homogalacturonan. The crystal structures of four CBMs, in conjunction with site-directed mutagenesis, provide insight into the mechanism of ligand recognition. In the CBMs that recognize β-glucans and β-mannans, differences in the conformation of conserved aromatic residues had a significant impact on the topology of the ligand binding cleft and thus ligand specificity. A cluster of basic residues in CBM77 confers calcium-independent recognition of homogalacturonan, indicating that the carboxylates of galacturonic acid are key specificity determinants. This report shows that the extended repertoire of proteins in the cellulosome of R. flavefaciens contributes to an extended CBMome that supports efficient PCW degradation in the absence of CBMs that specifically target crystalline cellulose. PMID:27298375

  9. Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer.

    PubMed

    Præsteng, Kirsti E; Pope, Phillip B; Cann, Isaac K O; Mackie, Roderick I; Mathiesen, Svein D; Folkow, Lars P; Eijsink, Vincent G H; Sundset, Monica A

    2013-11-01

    Highly cellulolytic bacterial species such as Ruminococcus flavefaciens are regarded essential for the microbial breakdown of cellulose in the rumen. We have investigated the effect of ruminal dosing of R. flavefaciens strain 8/94-32 during realimentation of starved reindeer (males, n = 3). Microbiome function measured as in situ digestion of cellulose and food pellets (percent DMD; dry matter disappearance) decreased after probiotic dosing. Microbial community analyses (>100,000 16S rDNA gene sequences for 27 samples) demonstrated that ruminal dosing influenced the microbiome structure; reflected by increased phylogenetic distances from background samples (unweighted UniFrac analysis) and reduced species diversity and evenness. Despite the inability to detect strain 8/94-32 post-dosing, the relative abundance of its affiliate family Ruminococcaceae remained consistent throughout the trial, whilst a dominant peak in the genus Prevotella and decline in uncharacterized Bacteroidetes (uBacNR) were observed in treatment samples. No clear relationships were observed between the relative abundance of Ruminococcaceae, Prevotella and uBacNR with cellulose DMD; however, Prevotella (negative) and uBacNR (positive) exhibited relationships with pellet DMD. These unexpected effects of ruminal dosing of a cellulolytic bacterium on digestibility are relevant for other studies on rumen manipulation. PMID:23959114

  10. Probiotic dosing of Ruminococcus flavefaciens affects rumen microbiome structure and function in reindeer.

    PubMed

    Præsteng, Kirsti E; Pope, Phillip B; Cann, Isaac K O; Mackie, Roderick I; Mathiesen, Svein D; Folkow, Lars P; Eijsink, Vincent G H; Sundset, Monica A

    2013-11-01

    Highly cellulolytic bacterial species such as Ruminococcus flavefaciens are regarded essential for the microbial breakdown of cellulose in the rumen. We have investigated the effect of ruminal dosing of R. flavefaciens strain 8/94-32 during realimentation of starved reindeer (males, n = 3). Microbiome function measured as in situ digestion of cellulose and food pellets (percent DMD; dry matter disappearance) decreased after probiotic dosing. Microbial community analyses (>100,000 16S rDNA gene sequences for 27 samples) demonstrated that ruminal dosing influenced the microbiome structure; reflected by increased phylogenetic distances from background samples (unweighted UniFrac analysis) and reduced species diversity and evenness. Despite the inability to detect strain 8/94-32 post-dosing, the relative abundance of its affiliate family Ruminococcaceae remained consistent throughout the trial, whilst a dominant peak in the genus Prevotella and decline in uncharacterized Bacteroidetes (uBacNR) were observed in treatment samples. No clear relationships were observed between the relative abundance of Ruminococcaceae, Prevotella and uBacNR with cellulose DMD; however, Prevotella (negative) and uBacNR (positive) exhibited relationships with pellet DMD. These unexpected effects of ruminal dosing of a cellulolytic bacterium on digestibility are relevant for other studies on rumen manipulation.

  11. Fermentation of Insoluble Cellulose by Continuous Cultures of Ruminococcus albus

    PubMed Central

    Pavlostathis, Spyros G.; Miller, Terry L.; Wolin, Meyer J.

    1988-01-01

    The hydrolysis and fermentation of insoluble cellulose (Avicel) by continuous cultures of Ruminococcus albus 7 was studied. An anaerobic continuous culture apparatus was designed which permitted gas collection, continuous feeding, and wasting at different retention times. The operation of the apparatus was controlled by a personal computer. Cellulose destruction ranged from ca. 30 to 70% for hydraulic retention times of 0.5 to 2.0 days. Carbon recovery in products was 92 to 97%, and the oxidation-reduction ratios ranged from 0.91 to 1.15. The total product yield (biomass not included) per gram of cellulose (expressed as glucose) was 0.83 g g−1, and the ethanol yield was 0.41 g g−1. The product yield was constant, indicating that product formation was growth linked. PMID:16347769

  12. Phenylacetic acid stimulation of cellulose digestion by Ruminococcus albus 8

    SciTech Connect

    Stack, R.J.; Hungate, R.E.; Opsahl, W.P.

    1983-09-01

    The rate of cellulose digestion by Ruminococcus albus 8 grown on a defined medium could be increased by adding a minimum of 6.6% (vol/vol) rumen fluid. Strain 8 was grown on half this concentration, and the culture medium before and after growth was analyzed by gas chromatography-mass spectrometry to determine which components of the rumen fluid were used. Phenylacetic acid was identified as the component needed to make the defined medium nutritionally equivalent to one supplemented with rumen fluid. (/sup 14/C)phenylacetic acid fed to cultures of strain 8 was primarily incorporated into protein. Hydrolysis of protein samples and separation of the resulting amino acids showed that only phenylalanine was labeled. The results indicate that cellulose digestion by strain 8 was probably limited by phenylalanine biosynthesis in our previously reported medium. The data obtained on the utilization of other rumen fluid components, as well as on the production of metabolites, illustrate the potential usefulness of this method in formulating defined media to simulate those in nature. 14 references.

  13. Preliminary X-ray characterization of a novel type of anchoring cohesin from the cellulosome of Ruminococcus flavefaciens

    SciTech Connect

    Alber, Orly; Noach, Ilit; Lamed, Raphael; Shimon, Linda J. W.; Bayer, Edward A.; Frolow, Felix

    2008-02-01

    The cloning, expression, purification, crystallization and preliminary X-ray characterization of a novel class of cohesin module (type III) from the R. flavefaciens ScaE anchoring scaffoldin are described. Ruminococcus flavefaciens is an anaerobic bacterium that resides in the gastrointestinal tract of ruminants. It produces a highly organized multi-enzyme cellulosome complex that plays a key role in the degradation of plant cell walls. ScaE is one of the critical structural components of its cellulosome that serves to anchor the complex to the cell wall. The seleno-l-methionine-labelled derivative of the ScaE cohesin module has been cloned, expressed, purified and crystallized. The crystals belong to space group C2, with unit-cell parameters a = 155.6, b = 69.3, c = 93.0 Å, β = 123.4°, and contain four molecules in the asymmetric unit. Diffraction data were phased to 1.95 Å using the anomalous signal from the Se atoms.

  14. Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bacteria in the genus Ruminococcus are important and ubiquitous members of mammalian guts. In particular, ruminococci are key contributors to the rumen ecosystem because they are capable of digesting a wide range of plant cell wall polysaccharides. In bovines, Ruminococcus albus 7 is a primary cellu...

  15. Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides

    PubMed Central

    Devendran, Saravanan; Abdel-Hamid, Ahmed M.; Evans, Anton F.; Iakiviak, Michael; Kwon, In Hyuk; Mackie, Roderick I.; Cann, Isaac

    2016-01-01

    Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose. PMID:27748409

  16. Multiple cellobiohydrolases and cellobiose phosphorylases cooperate in the ruminal bacterium Ruminococcus albus 8 to degrade cellooligosaccharides

    NASA Astrophysics Data System (ADS)

    Devendran, Saravanan; Abdel-Hamid, Ahmed M.; Evans, Anton F.; Iakiviak, Michael; Kwon, In Hyuk; Mackie, Roderick I.; Cann, Isaac

    2016-10-01

    Digestion of plant cell wall polysaccharides is important in energy capture in the gastrointestinal tract of many herbivorous and omnivorous mammals, including humans and ruminants. The members of the genus Ruminococcus are found in both the ruminant and human gastrointestinal tract, where they show versatility in degrading both hemicellulose and cellulose. The available genome sequence of Ruminococcus albus 8, a common inhabitant of the cow rumen, alludes to a bacterium well-endowed with genes that target degradation of various plant cell wall components. The mechanisms by which R. albus 8 employs to degrade these recalcitrant materials are, however, not clearly understood. In this report, we demonstrate that R. albus 8 elaborates multiple cellobiohydrolases with multi-modular architectures that overall enhance the catalytic activity and versatility of the enzymes. Furthermore, our analyses show that two cellobiose phosphorylases encoded by R. albus 8 can function synergistically with a cognate cellobiohydrolase and endoglucanase to completely release, from a cellulosic substrate, glucose which can then be fermented by the bacterium for production of energy and cellular building blocks. We further use transcriptomic analysis to confirm the over-expression of the biochemically characterized enzymes during growth of the bacterium on cellulosic substrates compared to cellobiose.

  17. Cellulosomics, a Gene-Centric Approach to Investigating the Intraspecific Diversity and Adaptation of Ruminococcus flavefaciens within the Rumen

    PubMed Central

    Brulc, Jennifer M.; Yeoman, Carl J.; Wilson, Melissa K.; Berg Miller, Margret E.; Jeraldo, Patricio; Jindou, Sadanari; Goldenfeld, Nigel; Flint, Harry J.; Lamed, Raphael; Borovok, Ilya; Vodovnik, Maša; Nelson, Karen E.; Bayer, Edward A.; White, Bryan A.

    2011-01-01

    Background The bovine rumen maintains a diverse microbial community that serves to break down indigestible plant substrates. However, those bacteria specifically adapted to degrade cellulose, the major structural component of plant biomass, represent a fraction of the rumen microbiome. Previously, we proposed scaC as a candidate for phylotyping Ruminococcus flavefaciens, one of three major cellulolytic bacterial species isolated from the rumen. In the present report we examine the dynamics and diversity of scaC-types both within and between cattle temporally, following a dietary switch from corn-silage to grass-legume hay. These results were placed in the context of the overall bacterial population dynamics measured using the 16S rRNA. Principal Findings As many as 117 scaC-types were estimated, although just nineteen were detected in each of three rumens tested, and these collectively accounted for the majority of all types present. Variation in scaC populations was observed between cattle, between planktonic and fiber-associated fractions and temporally over the six-week survey, and appeared related to scaC phylogeny. However, by the sixth week no significant separation of scaC populations was seen between animals, suggesting enrichment of a constrained set of scaC-types. Comparing the amino-acid translation of each scaC-type revealed sequence variation within part of the predicted dockerin module but strong conservation in the N-terminus, where the cohesin module is located. Conclusions The R. flavefaciens species comprises a multiplicity of scaC-types in-vivo. Enrichment of particular scaC-types temporally, following a dietary switch, and between fractions along with the phylogenetic congruence suggests that functional differences exist between types. Observed differences in dockerin modules suggest at least part of the functional heterogeneity may be conferred by scaC. The polymorphic nature of scaC enables the relative distribution of R. flavefaciens strains

  18. Anaerobic bioconversion of cellulose by Ruminococcus albus, Methanobrevibacter smithii, and Methanosarcina barkeri.

    PubMed

    Miller, T L; Currenti, E; Wolin, M J

    2000-10-01

    A system is described that combines the fermentation of cellulose to acetate, CH4, and CO2 by Ruminococcus albus and Methanobrevibacter smithii with the fermentation of acetate to CH4 and CO2 by Methanosarcina barkeri to convert cellulose to CH4 and CO2. A cellulose-containing medium was pumped into a co-culture of the cellulolytic R. albus and the H2-using methanogen, Mb. smithii. The effluent was fed into a holding reservoir, adjusted to pH 4.5, and then pumped into a culture of Ms. barkeri maintained at constant volume by pumping out culture contents. Fermentation of 1% cellulose to CH4 and CO2 was accomplished during 132 days of operation with retention times (RTs) of the Ms. barkeri culture of 7.5-3.8 days. Rates of acetate utilization were 9.5-17.3 mmol l(-1) day(-1) and increased with decreasing RT. The Ks for acetate utilization was 6-8 mM. The two-stage system can be used as a model system for studying biological and physical parameters that influence the bioconversion process. Our results suggest that manipulating the different phases of cellulose fermentation separately can effectively balance the pH and ionic requirements of the acid-producing phase with the acid-using phase of the overall fermentation. PMID:11092623

  19. Kinetics of Insoluble Cellulose Fermentation by Continuous Cultures of Ruminococcus albus

    PubMed Central

    Pavlostathis, Spyros G.; Miller, Terry L.; Wolin, Meyer J.

    1988-01-01

    Data from analyses of continuous culture fermentation of insoluble cellulose by Ruminococcus albus 7 were used to derive constants for the rate of cellulose hydrolysis and fermentation, growth yield, and maintenance. Cellulose concentration was 1% in the nutrient reservoir, and hydraulic retention times of 0.5, 1.0, 1.5, 1.75, and 2.0 days were used. Concentrations of reducing sugars in the cultures were negligible (less than 1%) compared with the amount of hydrolyzed cellulose, indicating that cellulose hydrolysis was the rate-limiting step of the fermentation. The rate of utilization of cellulose depended on the steady-state concentration of cellulose and was first order with a rate constant (k) of 1.18 day−1. The true microbial growth yield (Y) was 0.11 g g−1, the maintenance coefficient (m) was 0.10 g g−1 h−1, and the maximum YATP was 7.7 g of biomass (dry weight) mol of ATP−1. PMID:16347770

  20. Studies of the Extracellular Glycocalyx of the Anaerobic Cellulolytic Bacterium Ruminococcus albus 7▿

    PubMed Central

    Weimer, Paul J.; Price, Neil P. J.; Kroukamp, Otini; Joubert, Lydia-Marie; Wolfaardt, Gideon M.; Van Zyl, Willem H.

    2006-01-01

    Anaerobic cellulolytic bacteria are thought to adhere to cellulose via several mechanisms, including production of a glycocalyx containing extracellular polymeric substances (EPS). As the compositions and structures of these glycocalyces have not been elucidated, variable-pressure scanning electron microscopy (VP-SEM) and chemical analysis were used to characterize the glycocalyx of the ruminal bacterium Ruminococcus albus strain 7. VP-SEM revealed that growth of this strain was accompanied by the formation of thin cellular extensions that allowed the bacterium to adhere to cellulose, followed by formation of a ramifying network that interconnected individual cells to one another and to the unraveling cellulose microfibrils. Extraction of 48-h-old whole-culture pellets (bacterial cells plus glycocalyx [G] plus residual cellulose [C]) with 0.1 N NaOH released carbohydrate and protein in a ratio of 1:5. Boiling of the cellulose fermentation residue in a neutral detergent solution removed almost all of the adherent cells and protein while retaining a residual network of adhering noncellular material. Trifluoroacetic acid hydrolysis of this residue (G plus C) released primarily glucose, along with substantial amounts of xylose and mannose, but only traces of galactose, the most abundant sugar in most characterized bacterial exopolysaccharides. Linkage analysis and characterization by nuclear magnetic resonance suggested that most of the glucosyl units were not present as partially degraded cellulose. Calculations suggested that the energy demand for synthesis of the nonprotein fraction of EPS by this organism represents only a small fraction (<4%) of the anabolic ATP expenditure of the bacterium. PMID:17028224

  1. Functional and modular analyses of diverse endoglucanases from Ruminococcus albus 8, a specialist plant cell wall degrading bacterium

    PubMed Central

    Iakiviak, Michael; Devendran, Saravanan; Skorupski, Anna; Moon, Young Hwan; Mackie, Roderick I.; Cann, Isaac

    2016-01-01

    Ruminococcus albus 8 is a specialist plant cell wall degrading ruminal bacterium capable of utilizing hemicellulose and cellulose. Cellulose degradation requires a suite of enzymes including endoglucanases, exoglucanases, and β-glucosidases. The enzymes employed by R. albus 8 in degrading cellulose are yet to be completely elucidated. Through bioinformatic analysis of a draft genome sequence of R. albus 8, seventeen putatively cellulolytic genes were identified. The genes were heterologously expressed in E. coli, and purified to near homogeneity. On biochemical analysis with cellulosic substrates, seven of the gene products (Ra0185, Ra0259, Ra0325, Ra0903, Ra1831, Ra2461, and Ra2535) were identified as endoglucanases, releasing predominantly cellobiose and cellotriose. Each of the R. albus 8 endoglucanases, except for Ra0259 and Ra0325, bound to the model crystalline cellulose Avicel, confirming functional carbohydrate binding modules (CBMs). The polypeptides for Ra1831 and Ra2535 were found to contain distantly related homologs of CBM65. Mutational analysis of residues within the CBM65 of Ra1831 identified key residues required for binding. Phylogenetic analysis of the endoglucanases revealed three distinct subfamilies of glycoside hydrolase family 5 (GH5). Our results demonstrate that this fibrolytic bacterium uses diverse GH5 catalytic domains appended with different CBMs, including novel forms of CBM65, to degrade cellulose. PMID:27439730

  2. Purification and crystallographic studies of a putative carbohydrate-binding module from the Ruminococcus flavefaciens FD-1 endoglucanase Cel5A.

    PubMed

    Pires, Ana José; Ribeiro, Teresa; Thompson, Andrew; Venditto, Immacolata; Fernandes, Vânia O; Bule, Pedro; Santos, Helena; Alves, Victor D; Pires, Virginia; Ferreira, Luis M A; Fontes, Carlos M G A; Najmudin, Shabir

    2015-08-01

    Ruminant herbivores meet their carbon and energy requirements from a symbiotic relationship with cellulosome-producing anaerobic bacteria that efficiently degrade plant cell-wall polysaccharides. The assembly of carbohydrate-active enzymes (CAZymes) into cellulosomes enhances protein stability and enzyme synergistic interactions. Cellulosomes comprise diverse CAZymes displaying a modular architecture in which a catalytic domain is connected, via linker sequences, to one or more noncatalytic carbohydrate-binding modules (CBMs). CBMs direct the appended catalytic modules to their target substrates, thus facilitating catalysis. The genome of the ruminal cellulolytic bacterium Ruminococcus flavefaciens strain FD-1 contains over 200 modular proteins containing the cellulosomal signature dockerin module. One of these is an endoglucanase Cel5A comprising two family 5 glycoside hydrolase catalytic modules (GH5) flanking an unclassified CBM (termed CBM-Rf2) and a C-terminal dockerin. This novel CBM-Rf2 has been purified and crystallized, and data from cacodylate-derivative crystals were processed to 1.02 and 1.29 Å resolution. The crystals belonged to the orthorhombic space group P212121. The CBM-Rf2 structure was solved by a single-wavelength anomalous dispersion experiment at the As edge.

  3. Functional Analyses of Multiple Lichenin-Degrading Enzymes from the Rumen Bacterium Ruminococcus albus 8▿†

    PubMed Central

    Iakiviak, Michael; Mackie, Roderick I.; Cann, Isaac K. O.

    2011-01-01

    Ruminococcus albus 8 is a fibrolytic ruminal bacterium capable of utilization of various plant cell wall polysaccharides. A bioinformatic analysis of a partial genome sequence of R. albus revealed several putative enzymes likely to hydrolyze glucans, including lichenin, a mixed-linkage polysaccharide of glucose linked together in β-1,3 and β-1,4 glycosidic bonds. In the present study, we demonstrate the capacity of four glycoside hydrolases (GHs), derived from R. albus, to hydrolyze lichenin. Two of the genes encoded GH family 5 enzymes (Ra0453 and Ra2830), one gene encoded a GH family 16 enzyme (Ra0505), and the last gene encoded a GH family 3 enzyme (Ra1595). Each gene was expressed in Escherichia coli, and the recombinant protein was purified to near homogeneity. Upon screening on a wide range of substrates, Ra0453, Ra2830, and Ra0505 displayed different hydrolytic properties, as they released unique product profiles. The Ra1595 protein, predicted to function as a β-glucosidase, preferred cleavage of a nonreducing end glucose when linked by a β-1,3 glycosidic bond to the next glucose residue. The major product of Ra0505 hydrolysis of lichenin was predicted to be a glucotriose that was degraded only by Ra0453 to glucose and cellobiose. Most importantly, the four enzymes functioned synergistically to hydrolyze lichenin to glucose, cellobiose, and cellotriose. This lichenin-degrading enzyme mix should be of utility as an additive to feeds administered to monogastric animals, especially those high in fiber. PMID:21890664

  4. Biochemical Analyses of Multiple Endoxylanases from the Rumen Bacterium Ruminococcus albus 8 and Their Synergistic Activities with Accessory Hemicellulose-Degrading Enzymes ▿ †

    PubMed Central

    Moon, Young Hwan; Iakiviak, Michael; Bauer, Stefan; Mackie, Roderick I.; Cann, Isaac K. O.

    2011-01-01

    Ruminococcus albus 8 is a ruminal bacterium capable of metabolizing hemicellulose and cellulose, the major components of the plant cell wall. The enzymes that allow this bacterium to capture energy from the two polysaccharides, therefore, have potential application in plant cell wall depolymerization, a process critical to biofuel production. For this purpose, a partial genome sequence of R. albus 8 was generated. The genomic data depicted a bacterium endowed with multiple forms of plant cell wall-degrading enzymes. The endoxylanases of R. albus 8 exhibited diverse modular architectures, including incorporation of a catalytic module, a carbohydrate binding module, and a carbohydrate esterase module in a single polypeptide. The accessory enzymes of xylan degradation were a β-xylosidase, an α-l-arabinofuranosidase, and an α-glucuronidase. We hypothesized that due to the chemical complexity of the hemicellulose encountered in the rumen, the bacterium uses multiple endoxylanases, with subtle differences in substrate specificities, to attack the substrate, while the accessory enzymes hydrolyze the products to simple sugars for metabolism. To test this hypothesis, the genes encoding the predicted endoxylanases were expressed, and the proteins were biochemically characterized either alone or in combination with accessory enzymes. The different endoxylanase families exhibited different patterns of product release, with the family 11 endoxylanases releasing more products in synergy with the accessory enzymes from the more complex substrates. Aside from the insights into hemicellulose degradation by R. albus 8, this report should enhance our knowledge on designing effective enzyme cocktails for release of fermentable sugars in the biofuel industry. PMID:21666020

  5. Hydrogen Formation and Its Regulation in Ruminococcus albus: Involvement of an Electron-Bifurcating [FeFe]-Hydrogenase, of a Non-Electron-Bifurcating [FeFe]-Hydrogenase, and of a Putative Hydrogen-Sensing [FeFe]-Hydrogenase

    PubMed Central

    Zheng, Yanning; Kahnt, Jörg; Kwon, In Hyuk; Mackie, Roderick I.

    2014-01-01

    Ruminococcus albus 7 has played a key role in the development of the concept of interspecies hydrogen transfer. The rumen bacterium ferments glucose to 1.3 acetate, 0.7 ethanol, 2 CO2, and 2.6 H2 when growing in batch culture and to 2 acetate, 2 CO2, and 4 H2 when growing in continuous culture in syntrophic association with H2-consuming microorganisms that keep the H2 partial pressure low. The organism uses NAD+ and ferredoxin for glucose oxidation to acetyl coenzyme A (acetyl-CoA) and CO2, NADH for the reduction of acetyl-CoA to ethanol, and NADH and reduced ferredoxin for the reduction of protons to H2. Of all the enzymes involved, only the enzyme catalyzing the formation of H2 from NADH remained unknown. Here, we report that R. albus 7 grown in batch culture on glucose contained, besides a ferredoxin-dependent [FeFe]-hydrogenase (HydA2), a ferredoxin- and NAD-dependent electron-bifurcating [FeFe]-hydrogenase (HydABC) that couples the endergonic formation of H2 from NADH to the exergonic formation of H2 from reduced ferredoxin. Interestingly, hydA2 is adjacent to the hydS gene, which is predicted to encode an [FeFe]-hydrogenase with a C-terminal PAS domain. We showed that hydS and hydA2 are part of a larger transcriptional unit also harboring putative genes for a bifunctional acetaldehyde/ethanol dehydrogenase (Aad), serine/threonine protein kinase, serine/threonine protein phosphatase, and a redox-sensing transcriptional repressor. Since HydA2 and Aad are required only when R. albus grows at high H2 partial pressures, HydS could be a H2-sensing [FeFe]-hydrogenase involved in the regulation of their biosynthesis. PMID:25157086

  6. Novel Organization and Divergent Dockerin Specificities in the Cellulosome System of Ruminococcus flavefaciens†

    PubMed Central

    Rincon, Marco T.; Ding, Shi-You; McCrae, Sheila I.; Martin, Jennifer C.; Aurilia, Vincenzo; Lamed, Raphael; Shoham, Yuval; Bayer, Edward A.; Flint, Harry J.

    2003-01-01

    The DNA sequence coding for putative cellulosomal scaffolding protein ScaA from the rumen cellulolytic anaerobe Ruminococcus flavefaciens 17 was completed. The mature protein exhibits a calculated molecular mass of 90,198 Da and comprises three cohesin domains, a C-terminal dockerin, and a unique N-terminal X domain of unknown function. A novel feature of ScaA is the absence of an identifiable cellulose-binding module. Nevertheless, native ScaA was detected among proteins that attach to cellulose and appeared as a glycosylated band migrating at around 130 kDa. The ScaA dockerin was previously shown to interact with the cohesin-containing putative surface-anchoring protein ScaB. Here, six of the seven cohesins from ScaB were overexpressed as histidine-tagged products in E. coli; despite their considerable sequence differences, each ScaB cohesin specifically recognized the native 130-kDa ScaA protein. The binding specificities of dockerins found in R. flavefaciens plant cell wall-degrading enzymes were examined next. The dockerin sequences of the enzymes EndA, EndB, XynB, and XynD are all closely related but differ from those of XynE and CesA. A recombinant ScaA cohesin bound selectively to dockerin-containing fragments of EndB, but not to those of XynE or CesA. Furthermore, dockerin-containing EndB and XynB, but not XynE or CesA, constructs bound specifically to native ScaA. XynE- and CesA-derived probes did however bind a number of alternative R. flavefaciens bands, including an ∼110-kDa supernatant protein expressed selectively in cultures grown on xylan. Our findings indicate that in addition to the ScaA dockerin-ScaB cohesin interaction, at least two distinct dockerin-binding specificities are involved in the novel organization of plant cell wall-degrading enzymes in this species and suggest that different scaffoldins and perhaps multiple enzyme complexes may exist in R. flavefaciens. PMID:12533446

  7. THE CESA (CE3B) CARBOXY-TERMINAL DOMAIN OF RUMINOCOCCUS FLAVEFACIENS 17 HAS GLUCURONOYL ESTERASE ACTIVITY

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Several types of covalent linkages between lignin and xylan in plant cell walls have been shown. One of such linkages could be an ester bond between hydroxyl groups of lignin moieties and the carboxyl group of the 4-O-methyl-D-glucuronic acid (MeGlcA) side groups of glucuronoxylan. Enzymes capable...

  8. Unique Organization of Extracellular Amylases into Amylosomes in the Resistant Starch-Utilizing Human Colonic Firmicutes Bacterium Ruminococcus bromii

    PubMed Central

    Ze, Xiaolei; Ben David, Yonit; Laverde-Gomez, Jenny A.; Dassa, Bareket; Sheridan, Paul O.; Duncan, Sylvia H.; Louis, Petra; Henrissat, Bernard; Juge, Nathalie; Koropatkin, Nicole M.; Bayer, Edward A.

    2015-01-01

    ABSTRACT Ruminococcus bromii is a dominant member of the human gut microbiota that plays a key role in releasing energy from dietary starches that escape digestion by host enzymes via its exceptional activity against particulate “resistant” starches. Genomic analysis of R. bromii shows that it is highly specialized, with 15 of its 21 glycoside hydrolases belonging to one family (GH13). We found that amylase activity in R. bromii is expressed constitutively, with the activity seen during growth with fructose as an energy source being similar to that seen with starch as an energy source. Six GH13 amylases that carry signal peptides were detected by proteomic analysis in R. bromii cultures. Four of these enzymes are among 26 R. bromii proteins predicted to carry dockerin modules, with one, Amy4, also carrying a cohesin module. Since cohesin-dockerin interactions are known to mediate the formation of protein complexes in cellulolytic ruminococci, the binding interactions of four cohesins and 11 dockerins from R. bromii were investigated after overexpressing them as recombinant fusion proteins. Dockerins possessed by the enzymes Amy4 and Amy9 are predicted to bind a cohesin present in protein scaffoldin 2 (Sca2), which resembles the ScaE cell wall-anchoring protein of a cellulolytic relative, R. flavefaciens. Further complexes are predicted between the dockerin-carrying amylases Amy4, Amy9, Amy10, and Amy12 and two other cohesin-carrying proteins, while Amy4 has the ability to autoaggregate, as its dockerin can recognize its own cohesin. This organization of starch-degrading enzymes is unprecedented and provides the first example of cohesin-dockerin interactions being involved in an amylolytic system, which we refer to as an “amylosome.” PMID:26419877

  9. Direct ethanol production from cellulosic materials by Zymobacter palmae carrying Cellulomonas endoglucanase and Ruminococcus β-glucosidase genes.

    PubMed

    Kojima, Motoki; Okamoto, Kenji; Yanase, Hideshi

    2013-06-01

    In order to reduce the cost of bioethanol production from lignocellulosic biomass, we conferred the ability to ferment cellulosic materials directly on Zymobacter palmae by co-expressing foreign endoglucanase and β-glucosidase genes. Z. palmae is a novel ethanol-fermenting bacterium capable of utilizing a broad range of sugar substrates, but not cellulose. Therefore, the six genes encoding the cellulolytic enzymes (CenA, CenB, CenD, CbhA, CbhB, and Cex) from Cellulomonas fimi were introduced and expressed in Z. palmae. Of these cellulolytic enzyme genes cloned, CenA degraded carboxymethylcellulose and phosphoric acid-swollen cellulose (PASC) efficiently. The extracellular CenA catalyzed the hydrolysis of barley β-glucan and PASC to liberate soluble cello-oligosaccharides, indicating that CenA is the most suitable enzyme for cellulose degradation among those cellulolytic enzymes expressed in Z. palmae. Furthermore, the cenA gene and β-glucosidase gene (bgl) from Ruminococcus albus were co-expressed in Z. palmae. Of the total endoglucanase and β-glucosidase activities, 57.1 and 18.1 % were localized in the culture medium of the strain. The genetically engineered strain completely saccharified and fermented 20 g/l barley β-glucan to ethanol within 84 h, producing 79.5 % of the theoretical yield. Thus, the production and secretion of CenA and BGL enabled Z. palmae to efficiently ferment a water-soluble cellulosic polysaccharide to ethanol.

  10. Characterization of hybrid proteins consisting of the catalytic domains of Clostridium and Ruminococcus endoglucanases, fused to Pseudomonas non-catalytic cellulose-binding domains.

    PubMed Central

    Poole, D M; Durrant, A J; Hazlewood, G P; Gilbert, H J

    1991-01-01

    The N-terminal 160 or 267 residues of xylanase A from Pseudomonas fluorescens subsp. cellulosa, containing a non-catalytic cellulose-binding domain (CBD), were fused to the N-terminus of the catalytic domain of endoglucanase E (EGE') from Clostridium thermocellum. A further hybrid enzyme was constructed consisting of the 347 N-terminal residues of xylanase C (XYLC) from P. fluorescens subsp. cellulosa, which also constitutes a CBD, fused to the N-terminus of endoglucanase A (EGA) from Ruminococcus albus. The three hybrid enzymes bound to insoluble cellulose, and could be eluted such that cellulose-binding capacity and catalytic activity were retained. The catalytic properties of the fusion enzymes were similar to EGE' and EGA respectively. Residues 37-347 and 34-347 of XYLC were fused to the C-terminus of EGE' and the 10 amino acids encoded by the multiple cloning sequence of pMTL22p respectively. The two hybrid proteins did not bind cellulose, although residues 39-139 of XYLC were shown previously to constitute a functional CBD. The putative role of the P. fluorescens subsp. cellulosa CBD in cellulase action is discussed. Images Fig. 2. Fig. 3. Fig. 4. PMID:1953672

  11. Ecology of invasive Melilotus albus on Alaskan glacial river floodplains

    USGS Publications Warehouse

    Conn, Jeff S.; Werdin-Pfisterer, Nancy R.; Beattie, Katherine L.; Densmore, Roseann V.

    2011-01-01

    Melilotus albus (white sweetclover) has invaded Alaskan glacial river floodplains. We measured cover and density of plant species and environmental variables along transects perpendicular to the Nenana, Matanuska, and Stikine Rivers to study interactions between M. albus and other plant species and to characterize the environment where it establishes. Melilotus albus was a pioneer species on recently disturbed sites and did not persist into closed canopy forests. The relationships between M. albus cover and density and other species were site-specific.Melilotus albus was negatively correlated with native species Elaeagnus commutata at the Nenana River, but not at the Matanuska River. Melilotus albus was positively correlated with the exotic species Crepis tectorumand Taraxacum officinale at the Matanuska River and T. officinale on the upper Stikine River. However, the high density of M. albus at a lower Stikine River site was negatively correlated with T. officinale and several native species including Lathyrus japonicus var. maritimus and Salix alaxensis. Glacial river floodplains in Alaska are highly disturbed and are corridors for exotic plant species movement. Melilotus albus at moderate to low densities may facilitate establishment of exotic species, but at high densities can reduce the cover and density of both exotic and native species.

  12. Ultramafic soils from New Caledonia structure Pisolithus albus in ecotype.

    PubMed

    Jourand, Philippe; Ducousso, Marc; Loulergue-Majorel, Clarisse; Hannibal, Laure; Santoni, Sylvain; Prin, Yves; Lebrun, Michel

    2010-05-01

    Isolates of ectomycorrhizal Pisolithus albus were sampled from both ultramafic and volcano-sedimentary soils in New Caledonia, a tropical hotspot of biodiversity, to investigate the relationships between genetic diversity and edaphic constraint through tolerance to nickel (Ni). Carpophore description, spore morphology and phylogenetic analysis based on internal transcribed spacer (ITS) rDNA sequences confirmed that all isolates belong to P. albus and are closely related to other Australasian specimens. Using molecular tools, ITS-restriction fragment length polymorphism and amplified fragment length polymorphism markers, we showed the existence of two distinct genetic clusters within P. albus: ultramafic and volcano-sedimentary. Mycelia response to Ni toxicity supports such a population structure. Pisolithus albus from ultramafic soils included isolates with a high diversity of in vitro Ni tolerance, with both Ni-tolerant isolates (average Ni EC(50) at 575 microM) and Ni-sensitive isolates (average Ni EC(50) at 37 microM). In contrast, all isolates from volcano-sedimentary soils were found to be Ni sensitive (average Ni EC(50) at 32 microM). We highlight that (1) P. albus population from ultramafic soils of New Caledonia are genetically structured in ecotype, and that (2) Ni tolerance among ultramafic isolates suggests an adaptive physiological response to Ni toxicity.

  13. Studies on some characteristics of hydrogen production by cell-free extracts of rumen anaerobic bacteria.

    PubMed

    Joyner, A E; Winter, W T; Godbout, D M

    1977-03-01

    Hydrogen production was studied in the following rumen anaerobes: Bacteroides clostridiiformis, Butyrivibrio fibrisolvens, Enbacterium limosum, Fusobacterium necrophorum, Megasphaera elsdenii, Ruminococcus albus, and Ruminococcus flavefaciens. Clostridium pasteurianum and Escherichia coli were included for comparative purposes. Hydrogen production from dithionite, dithionite-reduced methyl viologen, pyruvate, and formate was determined. All species tested produced hydrogen from dithionite-reduce methyl viologen, but only C. pasteurianum, B. clostridiiformis, E. limosum, and M. elsdenii produced hydrogen from dithionite. All species except E. coli produced hydrogen from pyruvate, but activity was low or absent in extracts of E. limosum, F. necrophorum, R. albus, and R. flavefaciens unless methyl viologen was added. Hydrogen was produced from formate only by E. coli, B. clostridiiformis, E. limosum, F. necrophorum, and R. flavefaciens. Extracts were subjected to ultracentrifugation in an effort to determine the solubility of hydrogenase. The hydrogenase of all species except E. coli appeared to be soluble, although variable amounts of hydrogenase activity were detected in the pellet. Treatment of extracts of the rumen microbial species with DEAE-cellulose resulted in loss ofhydrogen production from pyruvate. Activity was restored by the addition of methyl viologen. It is concluded that hydrogen production in these rumen microorganisms is similar to that in the saccharolytic clostridia.

  14. Mycobiota of Lupinus albus seed from a public germplasm collection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seedborne mycobiota of Lupinus albus was assessed using blotter paper and agar media with Rose Bengal or semi-selective for Pythium or Fusarium. Samples of 200 seeds were taken from each of 16 inventories, comprising 14 accessions originating from Germany, France, Ukraine, Syria, Hungary or Spain, a...

  15. Organic Weed Control in White Lupin (Lupinus albus L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Legumes such as white lupin (Lupinus albus L.) provide a valuable nitrogen source in organic agriculture. With organic farming becoming an increasing sector of US agriculture and white lupin interest increasing in the southeastern USA because winter hardy cultivars are available, non-chemical weed c...

  16. Isolation and whole genome sequencing of a Ruminococcus-like bacterium, associated with irritable bowel syndrome.

    PubMed

    Hynönen, Ulla; Rasinkangas, Pia; Satokari, Reetta; Paulin, Lars; de Vos, Willem M; Pietilä, Taija E; Kant, Ravi; Palva, Airi

    2016-06-01

    In our previous studies on the intestinal microbiota in irritable bowel syndrome (IBS), we identified a bacterial phylotype with higher abundance in patients suffering from diarrhea than in healthy controls. In the present work, we have isolated in pure culture strain RT94, belonging to this phylotype, determined its whole genome sequence and performed an extensive genomic analysis and phenotypical testing. This revealed strain RT94 to be a strict anaerobe apparently belonging to a novel species with only 94% similarity in the 16S rRNA gene sequence to the closest relatives Ruminococcus torques and Ruminococcus lactaris. The G + C content of strain RT94 is 45.2 mol% and the major long-chain cellular fatty acids are C16:0, C18:0 and C14:0. The isolate is metabolically versatile but not a mucus or cellulose utilizer. It produces acetate, ethanol, succinate, lactate and formate, but very little butyrate, as end products of glucose metabolism. The mechanisms underlying the association of strain RT94 with diarrhea-type IBS are discussed. PMID:26946362

  17. Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis and proposals to emend the description of Streptomyces albus and describe Streptomyces pathocidini sp. nov

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In phylogenetic analyses of the genus Streptomyces using 16S rRNA gene sequences, Streptomyces albus subsp. albus NRRL B-1811T forms a cluster with 5 other species having identical or nearly identical 16S rRNA gene sequences. Moreover, the morphological and physiological characteristics of these oth...

  18. Strain-Level Diversity of Secondary Metabolism in Streptomyces albus

    PubMed Central

    Seipke, Ryan F.

    2015-01-01

    Streptomyces spp. are robust producers of medicinally-, industrially- and agriculturally-important small molecules. Increased resistance to antibacterial agents and the lack of new antibiotics in the pipeline have led to a renaissance in natural product discovery. This endeavor has benefited from inexpensive high quality DNA sequencing technology, which has generated more than 140 genome sequences for taxonomic type strains and environmental Streptomyces spp. isolates. Many of the sequenced streptomycetes belong to the same species. For instance, Streptomyces albus has been isolated from diverse environmental niches and seven strains have been sequenced, consequently this species has been sequenced more than any other streptomycete, allowing valuable analyses of strain-level diversity in secondary metabolism. Bioinformatics analyses identified a total of 48 unique biosynthetic gene clusters harboured by Streptomyces albus strains. Eighteen of these gene clusters specify the core secondary metabolome of the species. Fourteen of the gene clusters are contained by one or more strain and are considered auxiliary, while 16 of the gene clusters encode the production of putative strain-specific secondary metabolites. Analysis of Streptomyces albus strains suggests that each strain of a Streptomyces species likely harbours at least one strain-specific biosynthetic gene cluster. Importantly, this implies that deep sequencing of a species will not exhaust gene cluster diversity and will continue to yield novelty. PMID:25635820

  19. 40 CFR 180.1319 - Banda de Lupinus albus doce (BLAD); exemption from the requirement of a tolerance.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... catabolism of a seed storage protein (β-conglutin) of sweet lupines (Lupinus albus), in or on all food... RESIDUES IN FOOD Exemptions From Tolerances § 180.1319 Banda de Lupinus albus doce (BLAD); exemption...

  20. Control of common bunt of wheat under field conditions with the biofumigant fungus Muscodor albus.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Field experiments were conducted to evaluate the biological control potential of the fungus Muscodor albus, when applied as a seed treatment or an in furrow soil treatment, for control of common bunt (CB) of wheat caused by Tilletia caries. For seed treatments, dry rye grain culture of M. albus wa...

  1. Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In phylogenetic analyses of the genus Streptomyces using 16S rRNA gene sequences, Streptomyces albus subsp. albus NRRL B-1811T formed a cluster with 5 other species having identical or nearly identical 16S rRNA gene sequences. Moreover, the morphological and physiological characteristics of these ot...

  2. Restriction of a bacteriophage of Streptomyces albus G involving endonuclease SalI.

    PubMed

    Chater, K F; Wilde, L C

    1976-11-01

    The bacteriophage Pa16, isolated from soil on Streptomyces albus G, was restricted when transferred from an alternative host back to S. albus G. Extracted unmodified Pa16 deoxyribonucleic acid was cleaved at a single site by a cell-free extract of S. albus G. Fractions cleaving Pal6 deoxyribonucleic acid contained the endonuclease SalI first described by J. Arrand, P. Myers, and R. J. Roberts (unpublished data). A mutant of S. albus G was isolated which was defective in both restriction and modification of Pal6. This mutant lacked SalI activity. It is concluded that SalI is the agent of restriction of Pal6 by S. albus G.

  3. Restriction of a bacteriophage of Streptomyces albus G involving endonuclease SalI.

    PubMed Central

    Chater, K F; Wilde, L C

    1976-01-01

    The bacteriophage Pa16, isolated from soil on Streptomyces albus G, was restricted when transferred from an alternative host back to S. albus G. Extracted unmodified Pa16 deoxyribonucleic acid was cleaved at a single site by a cell-free extract of S. albus G. Fractions cleaving Pal6 deoxyribonucleic acid contained the endonuclease SalI first described by J. Arrand, P. Myers, and R. J. Roberts (unpublished data). A mutant of S. albus G was isolated which was defective in both restriction and modification of Pal6. This mutant lacked SalI activity. It is concluded that SalI is the agent of restriction of Pal6 by S. albus G. Images PMID:977549

  4. The Missouri River Scaphirhynchus albus (pallid sturgeon) effects analysis

    USGS Publications Warehouse

    Jacobson, Robert B.

    2016-08-05

    The Missouri River Pallid Sturgeon Effects Analysis (EA) was designed to assess how Missouri River management has affected—and may affect—the endangered Scaphirhynchus albus (pallid sturgeon) population. The EA emerged from the recognition that the direction and focus of the Missouri River Recovery Program would benefit from an updated, thorough evaluation of what is known, what is not known, and what needs to be known for effective actions. This fact sheet documents the steps in the EA process and the four core reports, culminating in the 2016 integrative report.

  5. The mucin-degradation strategy of Ruminococcus gnavus: The importance of intramolecular trans-sialidases

    PubMed Central

    Crost, Emmanuelle H.; Tailford, Louise E.; Monestier, Marie; Swarbreck, David; Henrissat, Bernard; Crossman, Lisa C.; Juge, Nathalie

    2016-01-01

    ABSTRACT We previously identified and characterized an intramolecular trans-sialidase (IT-sialidase) in the gut symbiont Ruminococcus gnavus ATCC 29149, which is associated to the ability of the strain to grow on mucins. In this work we have obtained and analyzed the draft genome sequence of another R. gnavus mucin-degrader, ATCC 35913, isolated from a healthy individual. Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans. R. gnavus ATCC 35913 also encodes a predicted IT-sialidase and harbors a Nan cluster dedicated to sialic acid utilization. We showed that the Nan cluster was upregulated when the strains were grown in presence of mucin. In addition we demonstrated that both R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source. Taken together these data further support the hypothesis that IT-sialidase expressing gut microbes, provide commensal bacteria such as R. gnavus with a nutritional competitive advantage, by accessing and transforming a source of nutrient to their own benefit. PMID:27223845

  6. Utilisation of Mucin Glycans by the Human Gut Symbiont Ruminococcus gnavus Is Strain-Dependent

    PubMed Central

    Crost, Emmanuelle H.; Tailford, Louise E.; Le Gall, Gwenaelle; Fons, Michel; Henrissat, Bernard; Juge, Nathalie

    2013-01-01

    Commensal bacteria often have an especially rich source of glycan-degrading enzymes which allow them to utilize undigested carbohydrates from the food or the host. The species Ruminococcus gnavus is present in the digestive tract of ≥90% of humans and has been implicated in gut-related diseases such as inflammatory bowel diseases (IBD). Here we analysed the ability of two R. gnavus human strains, E1 and ATCC 29149, to utilize host glycans. We showed that although both strains could assimilate mucin monosaccharides, only R. gnavus ATCC 29149 was able to grow on mucin as a sole carbon source. Comparative genomic analysis of the two R. gnavus strains highlighted potential clusters and glycoside hydrolases (GHs) responsible for the breakdown and utilization of mucin-derived glycans. Transcriptomic and functional activity assays confirmed the importance of specific GH33 sialidase, and GH29 and GH95 fucosidases in the mucin utilisation pathway. Notably, we uncovered a novel pathway by which R. gnavus ATCC 29149 utilises sialic acid from sialylated substrates. Our results also demonstrated the ability of R. gnavus ATCC 29149 to produce propanol and propionate as the end products of metabolism when grown on mucin and fucosylated glycans. These new findings provide molecular insights into the strain-specificity of R. gnavus adaptation to the gut environment advancing our understanding of the role of gut commensals in health and disease. PMID:24204617

  7. Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus

    PubMed Central

    Sagheddu, Valeria; Patrone, Vania; Miragoli, Francesco; Puglisi, Edoardo; Morelli, Lorenzo

    2016-01-01

    Lachnospiraceae is a bacterial family usually isolated from human and mammalian intestinal microbiota. However, its presence and role in the infant microbiota is not fully elucidated. This may be due to the strictly anaerobic behavior of its members that hampers the possibility of culture-dependent enumeration. Here, we report on the presence of this bacterial group, using biomolecular techniques, in stool samples from 25 babies aged between 1 and 24 months. Denaturing gradient gel electrophoresis (DGGE) was used as a first detection step, and data were confirmed by quantitative PCR (qPCR). The DGGE showed the presence of Lachnospiraceae in infant fecal specimens and indicated the prevalence of Ruminococcus gnavus (R. gnavus). The qPCR confirmed the presence of the Clostridium XVIa group, Blautia genus, and R. gnavus, which are the main members of this family. We detected R. gnavus in 22 of 25 (88%) samples with a qPCR probe assay. Despite the difficulties associated with their detection and enumeration, Lachnospiraceae, and in particular R. gnavus, should be included in future studies on the infant microbiota composition. PMID:27313996

  8. Cardiovascular anatomy and cardiac function in the air-breathing swamp eel (Monopterus albus).

    PubMed

    Iversen, Nina K; Lauridsen, Henrik; Do, Thi Thanh Huong; Nguyen, Van Cong; Gesser, Hans; Buchanan, Rasmus; Bayley, Mark; Pedersen, Michael; Wang, Tobias

    2013-01-01

    Monopterus albus, a swamp eel inhabiting the freshwaters of South East Asia, relies on an extensive vascularisation of the buccal cavity, pharynx and anterior oesophagus for gas exchange, while the gills are much reduced. In the present study we describe the macro-circulation in the cephalic region and the vascularisation of the buccal cavity of M. albus using vascular fillings and micro-computed tomography (μCT). We also show that M. albus has the capacity to use the buccal cavity for aquatic gas exchange, being able to maintain normal arterial blood gas composition, blood pressure, heart rate and cardiac output throughout 10h of forced submergence. M. albus therefore can be characterised as a facultative air-breather. Because M. albus aestivates for many months in moist mud during the dry season we characterised in vivo cardiovascular function during exposure to anoxia as well as the effects of anoxia on in vitro contractility of strip preparations from atria and ventricle. Both studies revealed a low anoxia tolerance, rendering it unlikely that M. albus can survive prolonged exposure to anoxia.

  9. Responses of Noccaea caerulescens and Lupinus albus in trace elements-contaminated soils.

    PubMed

    Martínez-Alcalá, Isabel; Hernández, Luis E; Esteban, Elvira; Walker, David J; Bernal, M Pilar

    2013-05-01

    Plants exposed to trace elements can suffer from oxidative stress, which is characterised by the accumulation of reactive oxygen species, alteration in the cellular antioxidant defence system and ultimately lipid peroxidation. We assessed the most-appropriate stress indexes to describe the response of two plant species, with different strategies for coping with trace elements (TEs), to particular contaminants. Noccaea caerulescens, a hyperaccumulator, and Lupinus albus, an excluder, were grown in three soils of differing pH: an acidic soil, a neutral soil (both contaminated mainly by Cu, Zn and As) and a control soil. Then, plant stress indicators were measured. As expected, N. caerulescens accumulated higher levels of Zn and Cd in shoots than L. albus, this effect being stronger in the acid soil, reflecting greater TE solubility in this soil. However, the shoot concentrations of Mn were higher in L. albus than in N. caerulescens, while the As concentration was similar in the two species. In L. albus, the phenolic content and lipid peroxidation were related with the Cu concentration, whereas the Zn and Cd concentrations in N. caerulescens were more closely related to glutathione content and lipid peroxidation. Interestingly, phytochelatins were only found in L. albus grown in polluted soils. Hence, the two species differed with respect to the TEs which provoked stress and the biochemical indicators of the stress, there being a close relationship between the accumulation of TEs and their associated stress indicators in the different plant organs.

  10. Growth conditions determine different melatonin levels in Lupinus albus L.

    PubMed

    Arnao, Marino B; Hernández-Ruiz, Josefa

    2013-09-01

    Melatonin, an indoleamine, which has recently been assigned several roles in plant physiology as a growth promoter, as rooting agent, and as antioxidant in senescence delay and cytoprotection, seems to have a relevant function in plant stress situations. The presence of melatonin increases the resistance of lupin plant tissues (Lupinus albus L.) against natural or artificially induced adverse situations. In this work, we studied the response of lupin plants in controlled stress situations (drought-, anaerobic-, pH-, and cold stress and using ZnSO4 , NaCl, and H2 O2 as chemical stressors) and measured the changes in endogenous melatonin levels in lupin plants. Also, the effect of abscisic acid, ethylene, and natural environmental conditions were evaluated. In general, nearly all stressful factors caused an increase in melatonin in the investigated organs. The chemical stress provoked by ZnSO4 or NaCl caused the most pronounced changes in the endogenous level of melatonin, followed by cold and drought stressors. In some cases, the level of melatonin increased 12-fold with respect to the levels in control plants, indicating that melatonin biosynthesis is upregulated in common stress situations, in which it may serve as a signal molecule and/or as a direct antistress agent due to its well-known antioxidative properties.

  11. The Marr and Albus Theories of the Cerebellum: Two Eary Models of Associative Memory

    NASA Technical Reports Server (NTRS)

    Albus, James S.

    1989-01-01

    The Marr and Albus theories of the cerebellum are compared and contrasted. They are shown to be similar in their analysis of the function of the mossy fibers, granule cells, Golgi cells, and Purkinje cells. They both predict motor learning in the parallel fiber synapses on the Purkinje dendrites mediated by concurrent climbing fiber input. This prediction has been confirmed by experimental evidence. In contrast, Marr predicts these synapses would be facilitated by learning, while Albus predicts they would be weakened. Experimental evidence confirms synaptic weakening.

  12. Complete mitochondrial genome of the white char Salvelinus albus (Salmoniformes, Salmonidae).

    PubMed

    Balakirev, Evgeniy S; Parensky, Valery A; Kovalev, Mikhail Yu; Ayala, Francisco J

    2016-09-01

    The complete mitochondrial genome was sequenced in two individuals of white char Salvelinus albus. The genome sequences are 16 653 bp in size, and the gene arrangement, composition, and size are very similar to the salmonid fish genomes published previously. The low level of sequence divergence detected between the genome of S. albus and the GenBank complete mitochondrial genomes of the Northern Dolly Varden char S. malma (KJ746618) and the Arctic char S. alpinus (AF154851) may likely be due to recent divergence of the species and/or historical hybridization and interspecific replacement of mtDNA.

  13. Properties of D-Xylose Isomerase from Streptomyces albus

    PubMed Central

    Sanchez, Sergio; Smiley, Karl L.

    1975-01-01

    A partially purified D-xylose isomerase has been isolated from cells of Streptomyces albus NRRL 5778 and some of its properties have been determined. D-Glucose, D-xylose, D-ribose, L-arabinose, and L-rhamnose served as substrates for the enzyme with respective Km values of 86, 93, 350, 153, and 312 mM and Vmax values measuring 1.23, 2.9, 2.63, 0.153, and 0.048 μmol/min per mg of protein. The hexose D-allose was also isomerized. The enzyme was strongly activated by 1.0 mM Mg2+ but only partially activated by 1.0 mM Co2+. The respective Km values for Mg2+ and Co2+ were 0.3 and 0.003 mM. Mg2+ and Co2+ appear to have separate binding sites on the isomerase. These cations also protect the enzyme from thermal denaturation and from D-sorbitol inhibition. The optimum temperature for ketose formation was 70 to 80 C at pH values ranging from 7 to 9. D-Sorbitol acts as a competitive inhibitor with a Ki of 5.5 mM against D-glucose, D-xylose, and D-ribose. Induction experiments, Mg2+ activation, and D-sorbitol D-sorbitol inhibition indicated that a single enzyme (D-xylose isomerase) was responsible for the isomerization of the pentoses, methyl pentose, and glucose. PMID:239628

  14. Paenibacillus lupini sp. nov., isolated from nodules of Lupinus albus.

    PubMed

    Carro, Lorena; Flores-Félix, José David; Ramírez-Bahena, Martha-Helena; García-Fraile, Paula; Martínez-Hidalgo, Pilar; Igual, José M; Tejedor, Carmen; Peix, Alvaro; Velázquez, Encarna

    2014-09-01

    A bacterial strain designated RLAHU15(T) was isolated from root nodules of Lupinus albus in Spain. Phylogenetic analyses based on 16S rRNA gene sequences placed the isolate in the genus Paenibacillus, with its closest relatives being Paenibacillus catalpae D75(T), Paenibacillus glycanilyticus DS-1(T), Paenibacillus endophyticus PECAE04(T) and Paenibacillus xinjiangensis B538(T) with 98.8 %, 98.9 %, 97.4 % and 97.4 % similarity, respectively. DNA-DNA hybridization studies showed values lower than 45 % between the strain RLAHU15(T) and any of these species. The isolate was a Gram-stain positive, motile and sporulating rod. Catalase activity was weak and oxidase activity was positive. Casein and starch were hydrolysed but gelatin was not. Growth was supported by many carbohydrates and organic acids as carbon sources. MK-7 was the only menaquinone detected and anteiso-C15 : 0 and iso-C16 : 0 were the major fatty acids. The major polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, three unidentified phospholipids and an unidentified lipid. meso-Diaminopimelic acid was detected in the peptidoglycan. The DNA G+C content was 54.4 mol%. Phylogenetic, chemotaxonomic and phenotypic analyses showed that strain RLAHU15(T) represents a novel species of the genus Paenibacillus, for which the name Paenibacillus lupini sp. nov. is proposed. The type strain is RLAHU15(T) ( = LMG 27296(T) = CECT 8235(T)).

  15. Overexpression of D-psicose 3-epimerase from Ruminococcus sp. in Escherichia coli and its potential application in D-psicose production.

    PubMed

    Zhu, Yueming; Men, Yan; Bai, Wei; Li, Xiaobo; Zhang, Lili; Sun, Yuanxia; Ma, Yanhe

    2012-10-01

    The D-psicose 3-epimerase (DPE) gene from Ruminococcus sp. was cloned and overexpressed in Escherichia coli. The recombinant protein was purified and characterized. It was optimally active at pH 7.5-8.0 and 60 °C. Activity was not dependent on the presence of metal ions; however, it became more thermostable with added Mn(2+). The K (m) of the enzyme for D-psicose (48 mM) was lower than that for D-tagatose (230 mM), suggesting that D-psicose is the optimum substrate. More importantly, the thermostability of the novel DPE from Ruminococcus is the strongest among all of the D-psicose and D-tagatose 3-epimerases and may be suitable for the industrial production of D-psicose from fructose.

  16. Effects of non-native Melilotus albus on pollination and reproduction in two boreal shrubs.

    PubMed

    Spellman, Katie V; Schneller, Laura C; Mulder, Christa P H; Carlson, Matthew L

    2015-10-01

    The establishment of abundantly flowered, highly rewarding non-native plant species is expected to have strong consequences for native plants through altered pollination services, particularly in boreal forest where the flowering season is short and the pollinator pool is small. In 18 boreal forest sites, we added flowering Melilotus albus to some sites and left some sites as controls in 2 different years to test if the invasive plant influences the pollination and reproductive success of two co-flowering ericaceous species: Vaccinium vitis-idaea and Rhododendron groenlandicum. We found that M. albus increased the pollinator diversity and tended to increase visitation rates to the focal native plant species compared to control sites. Melilotus albus facilitated greater seed production per berry in V. vitis-idaea when we added 120 plants compared to when we added 40 plants or in control sites. In R. groenlandicum, increasing numbers of M. albus inflorescences lowered conspecific pollen loads and percentage of flowers pollinated; however, no differences in fruit set were detected. The number of M. albus inflorescences had greater importance in explaining R. groenlandicum pollination compared to other environmental variables such as weather and number of native flowers, and had greater importance in lower quality black spruce sites than in mixed deciduous and white spruce sites for explaining the percentage of V. vitis-idaea flowers pollinated. Our data suggest that the identity of new pollinators attracted to the invaded sites, degree of shared pollinators between invasive and native species, and variation in resource limitation among sites are likely determining factors in the reproductive responses of boreal native plants in the presence of an invasive.

  17. Muscodor albus MOW12 an Endophyte of Piper nigrum L. (Piperaceae) Collected from North East India Produces Volatile Antimicrobials.

    PubMed

    Banerjee, Debdulal; Pandey, Akhil; Jana, Maloy; Strobel, Gary

    2014-03-01

    Muscodor albus MOW12, an endophytic fungus isolated from Piper nigrum in Mawlong, Meghalaya, India, resembles some cultural and hyphal characteristics of previous isolates of Muscodor sp. In addition, it possesses about 99 % similarity in its ITS rDNA with other M. albus isolates and thus is nicely centered within the genetic tree to other Muscodor spp. This xylariaceae fungus effectively inhibits and kills certain plant pathogenic fungi by virtue of a mixture of volatile compounds that it produces. The majority of these compounds were identified by gas chromatography/mass spectrometry as small molecular weight esters, alcohols, and acids. The main ester components of this isolate of M. albus in its volatile mixture are acetic acid, ethyl ester; propanoic acid, 2-methyl-, methyl ester and acetic acid, 2-methylpropyl ester. This appears to be the first report of any M. albus strain from India.

  18. Antimicrobial activity of Brazilian propolis extracts against rumen bacteria in vitro.

    PubMed

    de Aguiar, Sílvia Cristina; Zeoula, Lúcia Maria; Franco, Selma Lucy; Peres, Lucimar Pontara; Arcuri, Pedro Braga; Forano, Evelyne

    2013-10-01

    The antimicrobial activity of three Brazilian propolis extracts was evaluated on bacterial strains representing major rumen functional groups. The extracts were prepared using different concentrations of propolis and alcohol, resulting in different phenolic compositions. The propolis extracts inhibited the growth of Fibrobacter succinogenes S85, Ruminococcus flavefaciens FD-1, Ruminococcus albus 7, Butyrivibrio fibrisolvens D1, Prevotella albensis M384, Peptostreptococcus sp. D1, Clostridium aminophilum F and Streptococcus bovis Pearl11, while R. albus 20, Prevotella bryantii B₁4 and Ruminobacter amylophilus H18 were resistant to all the extracts. The inhibited strains showed also different sensitivity to propolis; the hyper-ammonia-producing bacteria (C. aminophilum F and Peptostreptococcus sp. D1) being the most sensitive. Inhibition of hyper-ammonia-producing bacteria by propolis would be beneficial to the animal. The extract containing the lowest amount of phenolic compounds (LLOS C3) showed the lowest antimicrobial activity against all the bacteria. The major phenolic compounds identified in the propolis extracts (naringenin, chrysin, caffeic acid, p-coumaric acid and Artepillin C) were also evaluated on four sensitive strains. Only naringenin showed inhibitory effect against all strains, suggesting that naringenin is one of the components participating to the antibacterial activity of propolis.

  19. First evidence of bioflocculant from Shinella albus with flocculation activity on harvesting of Chlorella vulgaris biomass.

    PubMed

    Li, Yi; Xu, Yanting; Liu, Lei; Jiang, Xiaobing; Zhang, Kun; Zheng, Tianling; Wang, Hailei

    2016-10-01

    Bioflocculant from Shinella albus xn-1 could be used to harvest energy-producing microalga Chlorella vulgaris biomass for the first time. In this study, we investigated the flocculation activity and mode of strain xn-1, the characteristics of bioflocculant, the effect of flocculation conditions and optimized the flocculation efficiency. The results indicated that strain xn-1 exhibited flocculation activity through secreting bioflocculant; the bioflocculant with high thermal stability, pH stability and low molecular weight was proved to be not protein and polysaccharide, and flocculation active component was confirmed to contain triple bond and cumulated double bonds; algal pH, temperature and metal ions showed great impacts on the flocculation efficiency of bioflocculant; the maximum flocculation activity of bioflocculant reached 85.65% after the response surface optimization. According to the results, the bioflocculant from S. albus xn-1 could be a good potential in applications for high-efficiency harvesting of microalgae.

  20. Root tip-dependent, active riboflavin secretion by Hyoscyamus albus hairy roots under iron deficiency.

    PubMed

    Higa, Ataru; Miyamoto, Erika; ur Rahman, Laiq; Kitamura, Yoshie

    2008-04-01

    Hyoscyamus albus hairy roots with/without an exogenous gene (11 clones) were established by inoculation of Agrobacterium rhizogenes. All clones cultured under iron-deficient condition secreted riboflavin from the root tips into the culture medium and the productivity depended on the number and size of root tips among the clones. A decline of pH was observed before riboflavin production and root development. By studying effects of proton-pump inhibitors, medium acidification with external organic acid, and riboflavin addition upon pH change and riboflavin productivity, we indicate that riboflavin efflux is not directly connected to active pH reduction, and more significantly active riboflavin secretion occurs as a response to an internal requirement in H. albus hairy roots under iron deficiency. PMID:18367404

  1. First evidence of bioflocculant from Shinella albus with flocculation activity on harvesting of Chlorella vulgaris biomass.

    PubMed

    Li, Yi; Xu, Yanting; Liu, Lei; Jiang, Xiaobing; Zhang, Kun; Zheng, Tianling; Wang, Hailei

    2016-10-01

    Bioflocculant from Shinella albus xn-1 could be used to harvest energy-producing microalga Chlorella vulgaris biomass for the first time. In this study, we investigated the flocculation activity and mode of strain xn-1, the characteristics of bioflocculant, the effect of flocculation conditions and optimized the flocculation efficiency. The results indicated that strain xn-1 exhibited flocculation activity through secreting bioflocculant; the bioflocculant with high thermal stability, pH stability and low molecular weight was proved to be not protein and polysaccharide, and flocculation active component was confirmed to contain triple bond and cumulated double bonds; algal pH, temperature and metal ions showed great impacts on the flocculation efficiency of bioflocculant; the maximum flocculation activity of bioflocculant reached 85.65% after the response surface optimization. According to the results, the bioflocculant from S. albus xn-1 could be a good potential in applications for high-efficiency harvesting of microalgae. PMID:27423548

  2. Longitudinal study of circulating immune complexes in a patient with Staphylococcus albus-induced shunt nephritis.

    PubMed

    Harkiss, G D; Brown, D L; Evans, D B

    1979-08-01

    The direct measurement and partial characterization of circulating immune complexes has been performed in a longitudinal study of a patient with Staphylococcus albus-induced shunt nephritis. The high levels of immune complexes were associated with cryoglobulinaemia and hypocomplementaemia. The activation of complement was found to be via the classical pathway, but the functioning of the alternative pathway may have been impaired in vivo due to very low levels of C3. The host response to the infection was also characterized by the production of a marked macroglobulinaemia, high titres of rheumatoid factor and a typical acute phase increase in the C-reactive protein level. Immune complex levels were persistently elevated many months after the removal of the focus of the infection. A possible explanation for this surprising finding may lie in the nature of the antigens in the immune complexes. It was found that the immune complexes contained both antibodies to and antigens from Staphlococcus albus. In particular, glycerol teichoic acid and staphylococcal nuclease were identified as components of the immune complexes present during the acute phase. Glycerol teichoic acid was also identified in the immune complexes found later although other Staphylococcus albus antigens as yet unidentified were also present and persisted in the circulation for several months.

  3. Complete mitogenome of the edible sea urchin Loxechinus albus: genetic structure and comparative genomics within Echinozoa.

    PubMed

    Cea, Graciela; Gaitán-Espitia, Juan Diego; Cárdenas, Leyla

    2015-06-01

    The edible Chilean red sea urchin, Loxechinus albus, is the only species of its genus and endemic to the Southeastern Pacific. In this study, we reconstructed the mitochondrial genome of L. albus by combining Sanger and pyrosequencing technologies. The mtDNA genome had a length of 15,737 bp and encoded the same 13 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes as other animal mtDNAs. The size of this mitogenome was similar to those of other Echinodermata species. Structural comparisons showed a highly conserved structure, composition, and gene order within Echinoidea and Holothuroidea, and nearly identical gene organization to that found in Asteroidea and Crinoidea, with the majority of differences explained by the inversions of some tRNA genes. Phylogenetic reconstruction supported the monophyly of Echinozoa and recovered the monophyletic relationship of Holothuroidea and Echinoidea. Within Holothuroidea, Bayesian and maximum likelihood analyses recovered a sister-group relationship between Dendrochirotacea and Aspidochirotida. Similarly within Echinoidea, these analyses revealed that L. albus was closely related to Paracentrotus lividus, both being part of a sister group to Strongylocentrotidae and Echinometridae. In addition, two major clades were found within Strongylocentrotidae. One of these clades comprised all of the representative species Strongylocentrotus and Hemicentrotus, whereas the other included species of Mesocentrotus and Pseudocentrotus.

  4. Influence of forage phenolics on ruminal fibrolytic bacteria and in vitro fiber degradation.

    PubMed

    Varel, V H; Jung, H J

    1986-08-01

    In vitro cultures of ruminal microorganisms were used to determine the effect of cinnamic acid and vanillin on the digestibility of cellulose and xylan. Cinnamic acid and vanillin depressed in vitro dry matter disappearance of cellulose 14 and 49%, respectively, when rumen fluid was the inoculum. The number of viable Bacteroides succinogenes cells, the predominant cellulolytic organism, was threefold higher for fermentations which contained vanillin than for control fermentations. When xylan replaced cellulose as the substrate, a 14% decrease in the digestibility of xylan was observed with vanillin added; however, the number of viable xylanolytic bacteria cultured from the batch fermentation was 10-fold greater than that of control fermentations. The doubling time of B. succinogenes was increased from 2.32 to 2.58 h when vanillin was added to cellobiose medium, and absorbance was one-half that of controls after 18 h. The growth rate of Ruminococcus albus and Ruminococcus flavefaciens was inhibited more by p-coumaric acid than by vanillin, although no reduction of final absorbance was observed in their growth cycles. Vanillin, and to a lesser extent cinnamic acid, appeared to prevent the attachment of B. succinogenes cells to cellulose particles, but did not affect dissociation of cells from the particles. B. succinogenes, R. albus, R. flavefaciens, and Butyrivibrio fibrisolvens all modified the parent monomers cinnamic acid, p-coumaric acid, ferulic acid, and vanillin, with B. fibrisolvens causing the most extensive modification. These results suggest that phenolic monomers can inhibit digestibility of cellulose and xylan, possibly by influencing attachment of the fibrolytic microorganisms to fiber particles. The reduced bacterial attachment to structural carbohydrates in the presence of vanillin may generate more free-floating fibrolytic organisms, thus giving a deceptively higher viable count.

  5. [Genetic divergence of mitochondrial DNA in white char Salvelinus albus and northern Dolly Varden char Salvelinus malma malma].

    PubMed

    Oleĭnik, A G; Skurikhina, L A; Brykov, Vl A

    2010-03-01

    Comparative analysis of mitochondrial DNA variation was performed in white char Salvelinus albus and in its putative ancestor species, northern Dolly Varden char Salvelinus malma malma. Highly statistically significant differentiation of S. albus and S. m. malma in the areas of sympatric (Kamchatka River basin) and allopatric (Kronotskoe Lake and Kronotskaya River) residence was demonstrated. The mtDNA divergence between S. albus and S. m. malma did not exceed the range ofintraspecific variation in the populations of northern Dolly Varden char. At the same time, clusterization pattern of the Salvelinus chars provides hypothesis on the common origin of two allopatric populations of white char. Genealogical analysis of haplotypes indicates that S. albus and S. m. malma currently demonstrate incomplete radiation of mitochondrial lineages. The low nucleotide divergence estimates between S. albus and S. m. malma reflect the short time period since the beginning of the radiation of ancestral lineages. These estimates are determined by ancestral polymorphism and haplotype exchange between the diverged phylogenetic groups as a result of introgressive hybridization.

  6. [Genetic Connectivity Between Sympatric Populations of Closely Related Char Species, Dolly Varden Salvelinus malma and White Char Salvelinus albus].

    PubMed

    Salmenkova, E A

    2016-01-01

    The closely related chars Salvelinus malma and Salvelinus albus, which sympatrically inhabit the Kamchatka River basin and Kronotsky Lake (Kamchatka), attract the attention of the researchers because of their debated origin and taxonomic status. Previous studies of sympatric populations of these chars revealed small but statistically significant genetic differences between these species at a number of molecular markers, suggesting the presence of the genetic exchange and hybridization. In this study, based on genotypic characterization of nine microsatellite loci, a considerable level of historical and contemporary genetic migration between sympatric populations of these chars was demonstrated. At the individual level a high degree of hybridization was observed, mainly among the Dolly Varden individuals from the studied populations. The obtained evidence on the genetic connectivity between sympatric S. malma and S. albus do not support the separate species status of S. albus.

  7. Exudation of organic acids by Lupinus albus and Lupinus angustifolius as affected by phosphorus supply

    NASA Astrophysics Data System (ADS)

    Hentschel, Werner; Wiche, Oliver

    2016-04-01

    In phytomining and phytoremediation research mixed cultures of bioenergy crops with legumes hold promise to enhance availability of trace metals and metalloids in the soil plant system. This is due to the ability of certain legumes to mobilize trace elements during acquisition of nutrients making these elements available for co-cultured species. The legumes achieve this element mobilization by exudating carboxylates and enzymes as well as by lowering the pH value in the rhizosphere. The aim of our research was to determine characteristics and differences in the exudation of Lupinus albus and Lupinus angustifolius regarding to quantitative as to qualitative aspects. Especially the affection by phosphorus (P) supply was a point of interest. Thus we conducted laboratory batch experiments, wherein the plants were grown over four weeks under controlled light, moisture and nutritional conditions on sand as substrate. Half of the plants were supplied with 12 mg P per kg substrate, the other half were cultivated under a total lack of P. After cultivation the plants were transferred from the cultivation substrate into a 0,05 mmolṡL‑1 CaCl2 solution. After two hours the plants were removed, moist and dry mass off shoots and roots were measured together with the root length (Tennants' method). Concentrations of exudated carboxylates in the CaCl2 solution were determined via IC (column: Metrosept OrganicAcids, eluent 0.5 molṡL‑1 H2SO4 + 15% acetone, pH=3; 0.5 mLṡmin‑1). As a result four different organic acids were identified (citric acid, fumaric acid, tartaric acid, malic acid) in concentration ranges of 0.15 mgṡL‑1 (fumaric acid) to 9.21 mgṡL‑1 (citric acid). Lupinus angustifolius showed a higher exudation rate (in nmol per cm root length per hour) than Lupinus albus in the presence of phosphorus (e.g. regarding citric acid: 1.99 vs 0.64 nmolṡ(gṡh)‑1). However, as the root complexity and length of L. albus were far higher than of L. angustifolius

  8. Exudation of organic acids by Lupinus albus and Lupinus angustifolius as affected by phosphorus supply

    NASA Astrophysics Data System (ADS)

    Hentschel, Werner; Wiche, Oliver

    2016-04-01

    In phytomining and phytoremediation research mixed cultures of bioenergy crops with legumes hold promise to enhance availability of trace metals and metalloids in the soil plant system. This is due to the ability of certain legumes to mobilize trace elements during acquisition of nutrients making these elements available for co-cultured species. The legumes achieve this element mobilization by exudating carboxylates and enzymes as well as by lowering the pH value in the rhizosphere. The aim of our research was to determine characteristics and differences in the exudation of Lupinus albus and Lupinus angustifolius regarding to quantitative as to qualitative aspects. Especially the affection by phosphorus (P) supply was a point of interest. Thus we conducted laboratory batch experiments, wherein the plants were grown over four weeks under controlled light, moisture and nutritional conditions on sand as substrate. Half of the plants were supplied with 12 mg P per kg substrate, the other half were cultivated under a total lack of P. After cultivation the plants were transferred from the cultivation substrate into a 0,05 mmolṡL-1 CaCl2 solution. After two hours the plants were removed, moist and dry mass off shoots and roots were measured together with the root length (Tennants' method). Concentrations of exudated carboxylates in the CaCl2 solution were determined via IC (column: Metrosept OrganicAcids, eluent 0.5 molṡL-1 H2SO4 + 15% acetone, pH=3; 0.5 mLṡmin-1). As a result four different organic acids were identified (citric acid, fumaric acid, tartaric acid, malic acid) in concentration ranges of 0.15 mgṡL-1 (fumaric acid) to 9.21 mgṡL-1 (citric acid). Lupinus angustifolius showed a higher exudation rate (in nmol per cm root length per hour) than Lupinus albus in the presence of phosphorus (e.g. regarding citric acid: 1.99 vs 0.64 nmolṡ(gṡh)-1). However, as the root complexity and length of L. albus were far higher than of L. angustifolius, the total

  9. High blood oxygen affinity in the air-breathing swamp eel Monopterus albus.

    PubMed

    Damsgaard, Christian; Findorf, Inge; Helbo, Signe; Kocagoz, Yigit; Buchanan, Rasmus; Huong, Do Thi Thanh; Weber, Roy E; Fago, Angela; Bayley, Mark; Wang, Tobias

    2014-12-01

    The Asian swamp eel (Monopterus albus, Zuiew 1793) is a facultative air-breathing fish with reduced gills. Previous studies have shown that gas exchange seems to occur across the epithelium of the buccopharyngeal cavity, the esophagus and the integument, resulting in substantial diffusion limitations that must be compensated by adaptations in others steps of the O₂ transport system to secure adequate O₂ delivery to the respiring tissues. We therefore investigated O₂ binding properties of whole blood, stripped hemoglobin (Hb), two major isoHb components and the myoglobin (Mb) from M. albus. Whole blood was sampled using indwelling catheters for blood gas analysis and determination of O₂ equilibrium curves. Hb was purified to assess the effects of endogenous allosteric effectors, and Mb was isolated from heart and skeletal muscle to determine its O₂ binding properties. The blood of M. albus has a high O₂ carrying capacity [hematocrit (Hct) of 42.4±4.5%] and binds O₂ with an unusually high affinity (P₅₀=2.8±0.4mmHg at 27°C and pH7.7), correlating with insensitivity of the Hb to the anionic allosteric effectors that normally decrease Hb-O₂ affinity. In addition, Mb is present at high concentrations in both heart and muscle (5.16±0.99 and 1.08±0.19mg ∙ g wet tissue⁻¹, respectively). We suggest that the high Hct and high blood O₂ affinity serve to overcome the low diffusion capacity in the relatively inefficient respiratory surfaces, while high Hct and Mb concentration aid in increasing the O₂ flux from the blood to the muscles.

  10. Enhanced salinomycin production by adjusting the supply of polyketide extender units in Streptomyces albus.

    PubMed

    Lu, Chenyang; Zhang, Xiaojie; Jiang, Ming; Bai, Linquan

    2016-05-01

    The anticoccidial salinomycin is a polyketide produced by Streptomyces albus and requires malonyl-CoAs, methylmalonyl-CoAs, and ethylmalonyl-CoAs for the backbone assembly. Genome sequencing of S. albus DSM 41398 revealed a high percentage of genes involved in lipid metabolism, supporting the high salinomycin yield in oil-rich media. Seven PKS/PKS-NRPS gene clusters in the genome were found to be actively transcribed and had been individually deleted, which resulted in significantly improved salinomycin production. However, a combined deletion of PKS-NRPS-2 and PKS-6 showed no further improvement. Whereas the concentrations of malonyl-CoA and methylmalonyl-CoA were increased, the concentration of ethylmalonyl-CoA remained low in the mutants. An endogenous crotonyl-CoA reductase gene (ccr) was overexpressed in the ΔPKS-NRPS-2/ΔPKS-6 mutant, resulting in improved production. Combination of cluster deletions and over-expression of ccr gene led to an overall titer improvement of salinomycin from 0.60 to 6.60g/L. This engineering strategy can be implemented for various natural polyketides production.

  11. Purification and partial characterization of glutathione transferase from the teleost Monopterus albus.

    PubMed

    Huang, Qing; Liang, Li; Wei, Tao; Zhang, Daming; Zeng, Qing-Yin

    2008-01-01

    Glutathione transferases (GSTs) catalyze the transfer of glutathione to a variety of xenobiotic and toxic endogenous compounds. GSTs are phase II biotransformation enzymes and are proposed as biomarkers of environmental pollution. In this study, a cytosolic glutathione transferase (maGST) was purified from liver of the freshwater fish Monopterus albus by affinity chromatography. The maGST appeared to be a homodimer composed of two subunits each with a molecular weight of 26 kDa. This maGST showed high activity towards the substrates 1-chloro-2,4-dinitrobenzene (CDNB) and 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole (NBD-Cl). Kinetic analysis with CDNB as substrate revealed a K(m) of 0.28 mM and V(max) of 15.68 micromol/min per mg of protein. It had maximum activity in the pH range 7.0-7.5, a broad optimum T(m) range of 30 degrees C-55 degrees C, and a high thermal stability with 77% of its initial activity at 45 degrees C. This high thermal stability of maGST could be related to the physiological adaptation of M. albus to high temperatures in tropical and subtropical environments.

  12. Haloglycomyces albus gen. nov., sp. nov., a halophilic, filamentous actinomycete of the family Glycomycetaceae.

    PubMed

    Guan, Tong-Wei; Tang, Shu-Kun; Wu, Jin-Yuan; Zhi, Xiao-Yang; Xu, Li-Hua; Zhang, Li-Li; Li, Wen-Jun

    2009-06-01

    A novel halophilic actinobacterium, designated YIM 92370(T), was isolated from a hypersaline habitat in Xinjiang Province, north-west China. The strain was aerobic, Gram-positive-staining and halophilic, with an optimum NaCl concentration for growth of 8-12 % (w/v). The whole-cell sugar pattern consisted of ribose, xylose and glucose. The predominant menaquinone was MK-9(H(4)) and the major fatty acids were iso-C(16 : 0), iso-C(17 : 0) and anteiso-C(17 : 0). The phospholipid pattern consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannosides, two unknown phosphoglycolipids and one unknown phospholipid. The G+C content of the genomic DNA was 60.8 mol%. Phylogenetic analysis showed that strain YIM 92370(T) can be distinguished from representatives of Glycomyces and Stackebrandtia, the two existing genera in the family Glycomycetaceae, by low 16S rRNA gene sequence similarities (<93.7 %). Strain YIM 92370(T) therefore represents a novel genus and species of the family Glycomycetaceae, for which the name Haloglycomyces albus gen. nov., sp. nov. is proposed. The type strain of Haloglycomyces albus is YIM 92370(T) (=DSM 45210(T) =KCTC 19481(T)). PMID:19502305

  13. Molecular characterization and expression profile of the estrogen receptor α gene during different reproductive phases in Monopterus albus

    PubMed Central

    Ding, Weidong; Cao, Liping; Cao, Zheming; Bing, Xuwen; Zhao, Fazhen

    2016-01-01

    To understand the molecular mechanism of estrogen and to evaluate the role of the estrogen receptor in mediating estrogen action, the full-length cDNA of estrogen receptor α (ERα) was cloned from Monopterus albus, and its expression pattern and distribution were investigated. The ERα cDNA of M. albus includes an open reading frame of 1863 bp, a 140-bp 5’-untranslated region and a 797-bp 3’-untranslated region. Amino acid sequence homology analysis showed that the Monopterus albus ERα has a moderate degree of similarity with Sebastes schlegelii, Zoarces viviparus and Haplochromis burtoni (81.1%, 80.7% and 80.4%, respectively). Quantitative PCR results showed that the highest level of ERα expression was in the liver; the next highest level of expression was observed in the gonads, where it was expressed at high levels particularly in the ovary in developmental stages IV and V and in the testis in developmental stage II/III. Immunohistochemistry analysis showed that ERα was present as slender particles distributed mainly in the membranes of spermatocytes and oocytes in the testis and ovary, whereas no positive signal was observed in the cytoplasm of sperm cells. This report describes the first molecular characterization of full-length ERα and its tissue-specific distribution in M. albus. PMID:27295422

  14. Mycofumigation by the Volatile Organic Compound-Producing Fungus Muscodor albus Induces Bacterial Cell Death through DNA Damage

    PubMed Central

    Alpha, Cambria J.; Campos, Manuel; Jacobs-Wagner, Christine

    2014-01-01

    Muscodor albus belongs to a genus of endophytic fungi that inhibit and kill other fungi, bacteria, and insects through production of a complex mixture of volatile organic compounds (VOCs). This process of mycofumigation has found commercial application for control of human and plant pathogens, but the mechanism of the VOC toxicity is unknown. Here, the mode of action of these volatiles was investigated through a series of genetic screens and biochemical assays. A single-gene knockout screen revealed high sensitivity for Escherichia coli lacking enzymes in the pathways of DNA repair, DNA metabolic process, and response to stress when exposed to the VOCs of M. albus. Furthermore, the sensitivity of knockouts involved in the repair of specific DNA alkyl adducts suggests that the VOCs may induce alkylation. Evidence of DNA damage suggests that these adducts lead to breaks during DNA replication or transcription if not properly repaired. Additional cytotoxicity profiling indicated that during VOC exposure, E. coli became filamentous and demonstrated an increase in cellular membrane fluidity. The volatile nature of the toxic compounds produced by M. albus and their broad range of inhibition make this fungus an attractive biological agent. Understanding the antimicrobial effects and the VOC mode of action will inform the utility and safety of potential mycofumigation applications for M. albus. PMID:25452287

  15. Mycofumigation by the volatile organic compound-producing Fungus Muscodor albus induces bacterial cell death through DNA damage.

    PubMed

    Alpha, Cambria J; Campos, Manuel; Jacobs-Wagner, Christine; Strobel, Scott A

    2015-02-01

    Muscodor albus belongs to a genus of endophytic fungi that inhibit and kill other fungi, bacteria, and insects through production of a complex mixture of volatile organic compounds (VOCs). This process of mycofumigation has found commercial application for control of human and plant pathogens, but the mechanism of the VOC toxicity is unknown. Here, the mode of action of these volatiles was investigated through a series of genetic screens and biochemical assays. A single-gene knockout screen revealed high sensitivity for Escherichia coli lacking enzymes in the pathways of DNA repair, DNA metabolic process, and response to stress when exposed to the VOCs of M. albus. Furthermore, the sensitivity of knockouts involved in the repair of specific DNA alkyl adducts suggests that the VOCs may induce alkylation. Evidence of DNA damage suggests that these adducts lead to breaks during DNA replication or transcription if not properly repaired. Additional cytotoxicity profiling indicated that during VOC exposure, E. coli became filamentous and demonstrated an increase in cellular membrane fluidity. The volatile nature of the toxic compounds produced by M. albus and their broad range of inhibition make this fungus an attractive biological agent. Understanding the antimicrobial effects and the VOC mode of action will inform the utility and safety of potential mycofumigation applications for M. albus.

  16. Overwintering strategy of wild free-ranging and enclosure-housed Japanese raccoon dogs ( Nyctereutes procyonoides albus)

    NASA Astrophysics Data System (ADS)

    Kitao, Naoya; Fukui, Daisuke; Hashimoto, Masaaki; Osborne, Peter G.

    2009-03-01

    The raccoon dog, Nyctereutes procyonoides, is a canid with a passive overwintering strategy in northern Europe. However, the behaviour and physiology of the Japanese subspecies, N. p. albus, which has fewer chromosomes than the other subspecies, remain unknown. We measured body temperature, body composition and blood biochemistry of wild free-ranging and fasted enclosure-housed N. p. albus during boreal winter in Hokkaido, Japan. Body temperature of N. p. albus decreased from 38°C in autumn to 35.9-36.7°C while maintaining a circadian rhythm in late February ( n = 3). A transient 18-36% decrease in resting heart rate occurred when body temperature was low ( n = 2). Despite a 33-45% decrease in body weight due to winter fasting, circulating glucose, total protein and triglyceride levels were maintained ( n = 4). Serum urea nitrogen dropped by 43-45% from autumn to spring, suggesting protein conservation during fasting. The overwintering survival strategy of N. p. albus in central Hokkaido is based upon large changes in seasonal activity patterns, winter denning and communal housing without the large decrease in body temperature that is characteristic of subarctic animals exhibiting hibernation or torpor.

  17. Complete Genome Sequence of Streptomyces albus SM254, a Potent Antagonist of Bat White-Nose Syndrome Pathogen Pseudogymnoascus destructans

    PubMed Central

    Badalamenti, Jonathan P.; Erickson, Joshua D.

    2016-01-01

    We sequenced and annotated the complete 7,170,504-bp genome of a novel secondary metabolite-producing Streptomyces strain, Streptomyces albus SM254, isolated from copper-rich subsurface fluids at ~220-m depth within the Soudan Iron Mine (Soudan, MN, USA). PMID:27081146

  18. Complete Genome Sequence of Streptomyces albus SM254, a Potent Antagonist of Bat White-Nose Syndrome Pathogen Pseudogymnoascus destructans.

    PubMed

    Badalamenti, Jonathan P; Erickson, Joshua D; Salomon, Christine E

    2016-01-01

    We sequenced and annotated the complete 7,170,504-bp genome of a novel secondary metabolite-producingStreptomycesstrain,Streptomyces albusSM254, isolated from copper-rich subsurface fluids at ~220-m depth within the Soudan Iron Mine (Soudan, MN, USA). PMID:27081146

  19. Quantification of Uncultured Ruminococcus obeum-Like Bacteria in Human Fecal Samples by Fluorescent In Situ Hybridization and Flow Cytometry Using 16S rRNA-Targeted Probes

    PubMed Central

    Zoetendal, Erwin G.; Ben-Amor, Kaouther; Harmsen, Hermie J. M.; Schut, Frits; Akkermans, Antoon D. L.; de Vos, Willem M.

    2002-01-01

    A 16S rRNA-targeted probe was designed and validated in order to quantify the number of uncultured Ruminococcus obeum-like bacteria by fluorescent in situ hybridization (FISH). These bacteria have frequently been found in 16S ribosomal DNA clone libraries prepared from bacterial communities in the human intestine. Thirty-two reference strains from the human intestine, including a phylogenetically related strain and strains of some other Ruminococcus species, were used as negative controls and did not hybridize with the new probe. Microscopic and flow cytometric analyses revealed that a group of morphologically similar bacteria in feces did hybridize with this probe. Moreover, it was found that all hybridizing cells also hybridized with a probe specific for the Clostridium coccoides-Eubacterium rectale group, a group that includes the uncultured R. obeum-like bacteria. Quantification of the uncultured R. obeum-like bacteria and the C. coccoides-E. rectale group by flow cytometry and microscopy revealed that these groups comprised approximately 2.5 and 16% of the total community in fecal samples, respectively. The uncultured R. obeum-like bacteria comprise about 16% of the C. coccoides-E. rectale group. These results indicate that the uncultured R. obeum-like bacteria are numerically important in human feces. Statistical analysis revealed no significant difference between the microscopic and flow cytometric counts and the different feces sampling times, while a significant host-specific effect on the counts was observed. Our data demonstrate that the combination of FISH and flow cytometry is a useful approach for studying the ecology of uncultured bacteria in the human gastrointestinal tract. PMID:12200269

  20. SRY-related genes in the genome of the rice field eel (Monopterus albus)

    PubMed Central

    Zhou, Rongjia; Cheng, Hanhua; Zhang, Quiyang; Guo, Yiqing; Cooper, Richard K; Tiersch, Terrence R

    2002-01-01

    The mammalian sex determining gene, SRY, is the founding member of the new growing family of Sox (SRY-like HMG-box gene) genes. Sox genes encode transcription factors with diverse roles in development, and a few of them are involved in sex determination and differentiation. We report here the existence of Sox genes in the rice field eel, Monopterus albus, and DNA sequence information of the HMG box region of five Sox genes. The Sox1, Sox4 and Sox14 genes do not have introns in the HMG box region. The Sox9 gene and Sox17 gene, which each have an intron in the conserved region, show strong identity at the amino acid level with the corresponding genes of mammals and chickens. Similar structure and identity of the Sox9 and Sox17 genes among mammals, chickens and fish suggest that these genes have evolutionarily conserved roles, potentially including sex determination and differentiation. PMID:11929629

  1. Population structure and linkage disequilibrium in Lupinus albus L. germplasm and its implication for association mapping.

    PubMed

    Iqbal, Muhammad Javed; Mamidi, Sujan; Ahsan, Rubina; Kianian, Shahryar F; Coyne, Clarice J; Hamama, Anwar A; Narina, Satya S; Bhardwaj, Harbans L

    2012-08-01

    White lupin (Lupinus albus L.) has been around since 300 B.C. and is recognized for its ability to grow on poor soils and application as green manure in addition to seed harvest. The seed has very high levels of protein (33-47 %) and oil (6-13 %). It also has many secondary metabolites that are potentially of nutraceutical value to animals and humans. Despite such a great potential, lupins role in modern agriculture began only in the twentieth century. Although a large collection of Lupinus germplasm accessions is available worldwide, rarely have they been genetically characterized. Additionally, scarce genomic resources in terms of recombinant populations and genome information have been generated for L. albus. With the advancement in association mapping methods, the natural populations have the potential to replace the recombinant populations in gene mapping and marker-trait associations. Therefore, we studied the genetic similarity, population structure and marker-trait association in a USDA germplasm collection for their current and future application in this crop improvement. A total of 122 PI (Plant Inventory) lines were screened with 18 AFLP primer pairs that generated 2,277 fragments. A subset of 892 polymorphic markers with MAF >0.05 (minor allele frequency) were used for association mapping. The cluster analysis failed to group accessions on the basis of their passport information, and a weak structure and low linkage disequilibrium (LD) were observed indicating the usefulness of the collection for association mapping. Moreover, we were also able to identify two markers (a p value of 1.53 × 10(-4) and 2.3 × 10(-4)) that explained 22.69 and 20.5 % of seed weight variation determined using R (LR) (2) . The implications of lack of geographic clustering, population structure, low LD and the ability of AFLP to map seed weight trait using association mapping and the usefulness of the PI collections in breeding programs are discussed.

  2. Isolation and identification of a lethal rhabdovirus from farmed rice field eels Monopterus albus.

    PubMed

    Ou, Tong; Zhu, Ruo-Lin; Chen, Zhong-Yuan; Zhang, Qi-Ya

    2013-11-01

    We provide the first description of a virus responsible for a systemic hemorrhagic disease causing high mortality in farmed rice field eels Monopterus albus in China. Typical signs exhibited by the diseased fish were extensive hemorrhages in the skin and viscera and some neurological signs, such as loss of equilibrium and disorganized swimming. Histopathological examination revealed various degrees of necrosis within the spleen and liver. Virus isolation was attempted from visceral tissues of diseased fish by inoculation on 6 fish cell lines. Typical cytopathic effects (CPE) were produced in bluegill fry (BF2) cells, so this cell line was chosen for further isolation and propagation of the virus. Electron microscopy observation showed that the negative stained viral particles had the characteristic bullet shape of rhabdoviruses and an estimated size of 60 × 120 nm. We therefore tentatively refer to this virus as Monopterus albus rhabdovirus (MoARV). Molecular characterization of MoARV, including sequence analysis of the nucleoprotein (N), phosphoprotein (P), and glycoprotein (G) genes, revealed 94.5 to 97.3% amino acid similarity to that of Siniperca chuatsi rhabdovirus. Phylogenetic analysis based on the amino acid sequences of N and G proteins indicated that MoARV should be a member of the genus Vesiculovirus. Koch's postulates were fulfilled by infecting healthy rice field eels with MoARV, which produced an acute infection. RT-PCR analysis demonstrated that MoARV RNA could be detected in both naturally and experimentally infected fish. The data suggest that MoARV was the causative pathogen of the disease.

  3. Aquibacillus halophilus gen. nov., sp. nov., a moderately halophilic bacterium from a hypersaline lake, and reclassification of Virgibacillus koreensis as Aquibacillus koreensis comb. nov. and Virgibacillus albus as Aquibacillus albus comb. nov.

    PubMed

    Amoozegar, Mohammad Ali; Bagheri, Maryam; Didari, Maryam; Mehrshad, Maliheh; Schumann, Peter; Spröer, Cathrin; Sánchez-Porro, Cristina; Ventosa, Antonio

    2014-11-01

    A novel Gram-stain-positive, moderately halophilic bacterium, designated strain B6B(T), was isolated from the water of an Iranian hypersaline lake, Aran-Bidgol, and characterized taxonomically using a polyphasic approach. Cells of strain B6B(T) were rod-shaped, motile and produced ellipsoidal endospores in terminal positions in non-swollen sporangia. Strain B6B(T) was a strictly aerobic bacterium and catalase- and oxidase-positive. The strain was able to grow at NaCl concentrations of 0.5-20.0% (w/v), with optimum growth occurring at 10.0% (w/v) NaCl. The optimum temperature and pH for growth were 35 °C and pH 7.0. On the basis of 16S rRNA gene sequence analysis, strain B6B(T) was shown to belong to the phylum Firmicutes and its closest phylogenetic similarities were with the species Virgibacillus koreensis BH30097(T) (97.5%), Virgibacillus albus YIM 93624(T) (97.4%), Sediminibacillus halophilus EN8d(T) (96.8%), Sediminibacillus albus NHBX5(T) (96.6%), Virgibacillus carmonensis LMG 20964(T) (96.3%) and Paraliobacillus quinghaiensis YIM-C158(T) (96.0%), respectively. Phylogenetic analysis revealed that strain B6B(T), along with V. koreensis BH30097(T) and V. albus YIM 93624(T), clustered in a separate clade in the family Bacillaceae. The DNA G+C content of the novel isolate was 35.8 mol%. DNA-DNA hybridization experiments revealed low levels of relatedness between strain B6B(T)and V. koreensis BH30097(T) (13%) and V. albus YIM 93624(T) (33%). The major cellular fatty acid of strain B6B(T) was anteiso-C15 : 0 (75.1%) and its polar lipid pattern consisted of phosphatidylglycerol, diphosphatidylglycerol, an unknown phospholipid and an unknown glycolipid. The isoprenoid quinones were MK-7 (90%) and MK-6 (3%). The peptidoglycan contained meso-diaminopimelic acid as the diagnostic diamino acid. All of these features support the placement of isolate B6B(T) within the phylum Firmicutes. It is closely related to V. koreensis and V. albus, but with features that clearly

  4. Nutrient digestibility and ruminal fermentation characteristic in swamp buffaloes fed on chemically treated rice straw and urea.

    PubMed

    Nguyen, Vinh Thi; Wanapat, Metha; Khejornsart, Pichad; Kongmun, Phongthorn

    2012-03-01

    The experiment was conducted to determine effects of urea-lime-treated rice straw and urea levels in concentrate on rumen fermentation, apparent nutrient digestibility, and cellulolytic bacteria population of 4-year-old, rumen-fistulated swamp buffaloes. All animals were randomly assigned according to a 2 × 2 factorial arrangement in a 4 × 4 Latin square design to receive four dietary treatments: factor A, two sources of roughage (rice straw and 2%urea + 2%lime-treated rice straw); factor B, two levels of urea in concentrate mixture (0% and 4%). Roughages were given ad libitum together with 0.3% BW of concentrate. It was found that voluntary feed intake, the digestibility of DM, OM, CP, NDF, acetate, and propionate concentration were significantly increased (P < 0.05) by treated rice straw, while NH(3)-N, BUN, and propionic acid concentration were increased by both factors of treated rice straw and 4% urea in concentrate. The real-time PCR quantification of Fibrobacter succinogenes and Ruminococcus albus population, and anaerobic fungi were greater (P < 0.05), but the population of Ruminococcus flavefaciens, protozoa, and methanogenic bacteria were reduced (P > 0.05) as influenced by treated rice straw and urea level. In conclusion, the combined use of urea-lime-treated rice straw and fed with concentrate (4% urea) could improve rumen ecology, rumen fermentation efficiency, and nutrient digestibility in swamp buffaloes. PMID:21805305

  5. Microbial population in the rumen of swamp buffalo (Bubalus bubalis) as influenced by coconut oil and mangosteen peel supplementation.

    PubMed

    Pilajun, R; Wanapat, M

    2013-06-01

    Four, rumen fistulated swamp buffalo bulls were used to study microbial populations in the rumen when supplemented with coconut oil and mangosteen peel. Animals were randomly assigned to a 4 × 4 Latin square design. Four treatments were un-supplemented (Control), supplementation with coconut oil at 50 g/kg (CO5), supplementation with mangosteen peel at 30 g/kg (MP3) and supplementation with CO5 and MP3 (COM), of total DM intake. Animals received concentrate at 10 g/kg of BW, and rice straw was given ad libitum. Abundance of total bacteria was increased by CO5 supplementation, whereas populations of protozoa and Fibrobacter succinogenes were reduced by CO5 and COM supplementation. Dietary supplementation did not affect methanogen, Ruminococcus flavefaciens or Ruminococcus albus abundances. Dietary treatments changed denaturing gradient gel electrophoresis (DGGE) band patterns of methanogens and protozoa when compared with the control group, especially when supplemented with MP3. Supplementation of COM resulted in the greatest difference in pattern of DGGE bands for total bacteria compared with the control. Coconut oil and mangosteen peel supplementation resulted in changing of rumen microbial abundances and communities; however, combination of them could be more benefit to improve rumen fermentation of swamp buffalo fed on rice straw.

  6. Influence of the composition of the cellulolytic flora on the development of hydrogenotrophic microorganisms, hydrogen utilization, and methane production in the rumens of gnotobiotically reared lambs.

    PubMed

    Chaucheyras-Durand, Frédérique; Masséglia, Sébastien; Fonty, Gérard; Forano, Evelyne

    2010-12-01

    We investigated the influence of the composition of the fibrolytic microbial community on the development and activities of hydrogen-utilizing microorganisms in the rumens of gnotobiotically reared lambs. Two groups of lambs were reared. The first group was inoculated with Fibrobacter succinogenes, a non-H(2)-producing species, as the main cellulolytic organism, and the second group was inoculated with Ruminococcus albus, Ruminococcus flavefaciens, and anaerobic fungi that produce hydrogen. The development of hydrogenotrophic bacterial communities, i.e., acetogens, fumarate and sulfate reducers, was monitored in the absence of methanogens and after inoculation of methanogens. Hydrogen production and utilization and methane production were measured in rumen content samples incubated in vitro in the presence of exogenous hydrogen (supplemented with fumarate or not supplemented with fumarate) or in the presence of ground alfalfa hay as a degradable substrate. Our results show that methane production was clearly reduced when the dominant fibrolytic species was a non-H(2)-producing species, such as Fibrobacter succinogenes, without significantly impairing fiber degradation and fermentations in the rumen. The addition of fumarate to the rumen contents stimulated H(2) utilization only by the ruminal microbiota inoculated with F. succinogenes, suggesting that these communities could play an important role in fumarate reduction in vivo.

  7. Lovastatin-Enriched Rice Straw Enhances Biomass Quality and Suppresses Ruminal Methanogenesis

    PubMed Central

    Faseleh Jahromi, Mohammad; Liang, Juan Boo; Mohamad, Rosfarizan; Goh, Yong Meng; Shokryazdan, Parisa; Ho, Yin Wan

    2013-01-01

    The primary objective of this study was to test the hypothesis that solid state fermentation (SSF) of agro-biomass (using rice straw as model); besides, breaking down its lignocellulose content to improve its nutritive values also produces lovastatin which could be used to suppress methanogenesis in the rumen ecosystem. Fermented rice straw (FRS) containing lovastatin after fermentation with Aspergillus terreus was used as substrate for growth study of rumen microorganisms using in vitro gas production method. In the first experiment, the extract from the FRS (FRSE) which contained lovastatin was evaluated for its efficacy for reduction in methane (CH4) production, microbial population, and activity in the rumen fluid. FRSE reduced total gas and CH4 productions (P < 0.01). It also reduced (P < 0.01) total methanogens population and increased the cellulolytic bacteria including Ruminococcus albus, Fibrobacter succinogenes (P < 0.01), and Ruminococcus flavefaciens (P < 0.05). Similarly, FRS reduced total gas and CH4 productions, methanogens population, but increased in vitro dry mater digestibility compared to the non-fermented rice straw. Lovastatin in the FRSE and the FRS significantly increased the expression of HMG-CoA reductase gene that produces HMG-CoA reductase, a key enzyme for cell membrane production in methanogenic Archaea. PMID:23484116

  8. Enzymatic profiling of cellulosomal enzymes from the human gut bacterium, Ruminococcus champanellensis, reveals a fine-tuned system for cohesin-dockerin recognition.

    PubMed

    Moraïs, Sarah; Ben David, Yonit; Bensoussan, Lizi; Duncan, Sylvia H; Koropatkin, Nicole M; Martens, Eric C; Flint, Harry J; Bayer, Edward A

    2016-02-01

    Ruminococcus champanellensis is considered a keystone species in the human gut that degrades microcrystalline cellulose efficiently and contains the genetic elements necessary for cellulosome production. The basic elements of its cellulosome architecture, mainly cohesin and dockerin modules from scaffoldins and enzyme-borne dockerins, have been characterized recently. In this study, we cloned, expressed and characterized all of the glycoside hydrolases that contain a dockerin module. Among the 25 enzymes, 10 cellulases, 4 xylanases, 3 mannanases, 2 xyloglucanases, 2 arabinofuranosidases, 2 arabinanases and one β-glucanase were assessed for their comparative enzymatic activity on their respective substrates. The dockerin specificities of the enzymes were examined by ELISA, and 80 positives out of 525 possible interactions were detected. Our analysis reveals a fine-tuned system for cohesin-dockerin specificity and the importance of diversity among the cohesin-dockerin sequences. Our results imply that cohesin-dockerin pairs are not necessarily assembled at random among the same specificity types, as generally believed for other cellulosome-producing bacteria, but reveal a more organized cellulosome architecture. Moreover, our results highlight the importance of the cellulosome paradigm for cellulose and hemicellulose degradation by R. champanellensis in the human gut.

  9. Iron plaque formed under aerobic conditions efficiently immobilizes arsenic in Lupinus albus L roots.

    PubMed

    Fresno, Teresa; Peñalosa, Jesús M; Santner, Jakob; Puschenreiter, Markus; Prohaska, Thomas; Moreno-Jiménez, Eduardo

    2016-09-01

    Arsenic is a non-threshold carcinogenic metalloid. Thus, human exposure should be minimised, e.g. by chemically stabilizing As in soil. Since iron is a potential As immobiliser, it was investigated whether root iron plaque, formed under aerobic conditions, affects As uptake, metabolism and distribution in Lupinus albus plants. White lupin plants were cultivated in a continuously aerated hydroponic culture containing Fe/EDDHA or FeSO4 and exposed to arsenate (5 or 20 μM). Only FeSO4 induced surficial iron plaque in roots. LA-ICP-MS analysis accomplished on root sections corroborated the association of As to this surficial Fe. Additionally, As(V) was the predominant species in FeSO4-treated roots, suggesting less efficient As uptake in the presence of iron plaque. Fe/EDDHA-exposed roots neither showed such surficial FeAs co-localisation nor As(V) accumulation; in contrast As(III) was the predominant species in root tissue. Furthermore, FeSO4-treated plants showed reduced shoot-to-root As ratios, which were >10-fold lower compared to Fe/EDDHA treatment. Our results highlight the role of an iron plaque formed in roots of white lupin under aerobic conditions on As immobilisation. These findings, to our knowledge, have not been addressed before for this plant and have potential implications on soil remediation (phytostabilisation) and food security (minimising As in crops). PMID:27263113

  10. Iron plaque formed under aerobic conditions efficiently immobilizes arsenic in Lupinus albus L roots.

    PubMed

    Fresno, Teresa; Peñalosa, Jesús M; Santner, Jakob; Puschenreiter, Markus; Prohaska, Thomas; Moreno-Jiménez, Eduardo

    2016-09-01

    Arsenic is a non-threshold carcinogenic metalloid. Thus, human exposure should be minimised, e.g. by chemically stabilizing As in soil. Since iron is a potential As immobiliser, it was investigated whether root iron plaque, formed under aerobic conditions, affects As uptake, metabolism and distribution in Lupinus albus plants. White lupin plants were cultivated in a continuously aerated hydroponic culture containing Fe/EDDHA or FeSO4 and exposed to arsenate (5 or 20 μM). Only FeSO4 induced surficial iron plaque in roots. LA-ICP-MS analysis accomplished on root sections corroborated the association of As to this surficial Fe. Additionally, As(V) was the predominant species in FeSO4-treated roots, suggesting less efficient As uptake in the presence of iron plaque. Fe/EDDHA-exposed roots neither showed such surficial FeAs co-localisation nor As(V) accumulation; in contrast As(III) was the predominant species in root tissue. Furthermore, FeSO4-treated plants showed reduced shoot-to-root As ratios, which were >10-fold lower compared to Fe/EDDHA treatment. Our results highlight the role of an iron plaque formed in roots of white lupin under aerobic conditions on As immobilisation. These findings, to our knowledge, have not been addressed before for this plant and have potential implications on soil remediation (phytostabilisation) and food security (minimising As in crops).

  11. Mercury contamination in free-ranging great egret nestlings (Ardea albus) from southern Florida, USA

    SciTech Connect

    Sepulveda, M.S.; Frederick, P.C.; Spalding, M.G.; Williams, G.E. Jr.

    1999-05-01

    Between March and June of 1994 and 1995, mercury (Hg) concentrations were determined from 393 blood and 164 growing scapular feathers from 252 great egret nestlings (Ardea albus). Nestlings came from eight colonies located in Water Conservation Area 3 in the Everglades region in southern Florida. The ages of these birds ranged from 1 to 44 d (bill length 1.1 to 10.2 cm). Mercury concentrations in blood and feathers of first-hatched great egret nestlings sampled during 1994 averaged 1.2 {micro}g/g (range = 0.07--3.9) wet weight and 16 {micro}g/g (4.5--40) dry weight, respectively. During 1995, first-hatched chicks had blood and feather Hg concentrations that averaged 0.8 {micro}g/g (0.2--1.7) and 9.7 {micro}g/g (2.3--26), respectively. In both years, Hg concentrations in blood and feathers were significantly correlated, and a significant correlation also was found between Hg in blood and age of the chicks. Blood and feather Hg concentrations differed significantly between years, with higher concentrations during 1994. Birds from JW1 and L67 colonies had the highest concentrations of Hg in blood and feathers. Mercury concentrations did not differ between chicks of different hatch order Mercury in feathers of great egret nestlings from southern Florida are approximately six times higher than when compared to feather Hg concentrations of nestlings wading birds sampled elsewhere.

  12. The Pied Crow (Corvus albus) is insensitive to diclofenac at concentrations present in carrion.

    PubMed

    Naidoo, Vinny; Mompati, Kefiloe Feliciity; Duncan, Neil; Taggart, Mark Anthony

    2011-10-01

    Diclofenac, a nonsteroidal anti-inflammatory drug (NSAID), kills vultures (Gyps spp.) that consume tainted carcasses. As a result, vulture populations in India, Nepal, and Pakistan have been devastated. Studies on meloxicam and ketoprofen demonstrated that the toxicity of the NSAIDs is unpredictable, thereby necessitating individual testing of all available NSAIDs. Because it is no longer practical to use vultures for toxicity testing, we evaluated the Pied Crow (Corvus albus) as a model. Pied Crows (n=6) were exposed to a dose of 0.8 and 10 mg/kg of diclofenac, with no signs of toxicity, and a rapid half-life of elimination. Using primary renal cell and hepatocyte cultures, a high tolerance was demonstrated at the cellular level. Meta-analysis of pharmacokinetic data for the Domestic Chicken (Gallus gallus) and the African White-backed (Gyps africanus), Cape Griffon (Gyps coprotheres), and Turkey Vultures (Cathartes aura) showed a trend toward toxicity when the half-life of elimination increased. We conclude that the crow is not susceptible to diclofenac and, more important, that toxicity in the Gyps species is probably related to zero-order metabolism. PMID:22102664

  13. Transcript and proteomic analysis of developing white lupin (Lupinus albus L.) roots

    PubMed Central

    Tian, Li; Peel, Gregory J; Lei, Zhentian; Aziz, Naveed; Dai, Xinbin; He, Ji; Watson, Bonnie; Zhao, Patrick X; Sumner, Lloyd W; Dixon, Richard A

    2009-01-01

    Background White lupin (Lupinus albus L.) roots efficiently take up and accumulate (heavy) metals, adapt to phosphate deficiency by forming cluster roots, and secrete antimicrobial prenylated isoflavones during development. Genomic and proteomic approaches were applied to identify candidate genes and proteins involved in antimicrobial defense and (heavy) metal uptake and translocation. Results A cDNA library was constructed from roots of white lupin seedlings. Eight thousand clones were randomly sequenced and assembled into 2,455 unigenes, which were annotated based on homologous matches in the NCBInr protein database. A reference map of developing white lupin root proteins was established through 2-D gel electrophoresis and peptide mass fingerprinting. High quality peptide mass spectra were obtained for 170 proteins. Microsomal membrane proteins were separated by 1-D gel electrophoresis and identified by LC-MS/MS. A total of 74 proteins were putatively identified by the peptide mass fingerprinting and the LC-MS/MS methods. Genomic and proteomic analyses identified candidate genes and proteins encoding metal binding and/or transport proteins, transcription factors, ABC transporters and phenylpropanoid biosynthetic enzymes. Conclusion The combined EST and protein datasets will facilitate the understanding of white lupin's response to biotic and abiotic stresses and its utility for phytoremediation. The root ESTs provided 82 perfect simple sequence repeat (SSR) markers with potential utility in breeding white lupin for enhanced agronomic traits. PMID:19123941

  14. Isolation of heat-tolerant myoglobin from Asian swamp eel Monopterus albus.

    PubMed

    Chotichayapong, Chatrachatchaya; Wiengsamut, Kittipong; Chanthai, Saksit; Sattayasai, Nison; Tamiya, Toru; Kanzawa, Nobuyuki; Tsuchiya, Takahide

    2012-10-01

    Myoglobin from Asian swamp eel Monopterus albus was purified from fish muscle using salt fractionation followed by column chromatography and molecular filtration. The purified Mb of 0.68 mg/g wet weight of muscle was determined for its molecular mass by MALDI-TOF-MS to be 15,525.18 Da. Using isoelectric focusing technique, the purified Mb showed two derivatives with pI of 6.40 and 7.12. Six peptide fragments of this protein identified by LC-MS/MS were homologous to Mbs of sea raven Hemitripterus americanus, yellowfin tuna Thunnus albacores, blue marlin Makaira nigicans, common carp Cyprinus carpio, and goldfish Carassius auratus. According to the Mb denaturation, the swamp eel Mb had thermal stability higher than walking catfish Clarias batrachus Mb and striped catfish Pangasius hypophthalmus Mb, between 30 and 60 (°)C. For the thermal stability of Mb, the swamp eel Mb showed a biphasic behavior due to the O(2) dissociation and the heme orientation disorder, with the lowest increase in both Kd(f) and Kd(s). The thermal sensitivity of swamp eel Mb was lower than those of the other Mbs for both of fast and slow reaction stages. These results suggest that the swamp eel Mb globin structure is thermally stable, which is consistent with heat-tolerant behavior of the swamp eel particularly in drought habitat.

  15. Isolation of heat-tolerant myoglobin from Asian swamp eel Monopterus albus.

    PubMed

    Chotichayapong, Chatrachatchaya; Wiengsamut, Kittipong; Chanthai, Saksit; Sattayasai, Nison; Tamiya, Toru; Kanzawa, Nobuyuki; Tsuchiya, Takahide

    2012-10-01

    Myoglobin from Asian swamp eel Monopterus albus was purified from fish muscle using salt fractionation followed by column chromatography and molecular filtration. The purified Mb of 0.68 mg/g wet weight of muscle was determined for its molecular mass by MALDI-TOF-MS to be 15,525.18 Da. Using isoelectric focusing technique, the purified Mb showed two derivatives with pI of 6.40 and 7.12. Six peptide fragments of this protein identified by LC-MS/MS were homologous to Mbs of sea raven Hemitripterus americanus, yellowfin tuna Thunnus albacores, blue marlin Makaira nigicans, common carp Cyprinus carpio, and goldfish Carassius auratus. According to the Mb denaturation, the swamp eel Mb had thermal stability higher than walking catfish Clarias batrachus Mb and striped catfish Pangasius hypophthalmus Mb, between 30 and 60 (°)C. For the thermal stability of Mb, the swamp eel Mb showed a biphasic behavior due to the O(2) dissociation and the heme orientation disorder, with the lowest increase in both Kd(f) and Kd(s). The thermal sensitivity of swamp eel Mb was lower than those of the other Mbs for both of fast and slow reaction stages. These results suggest that the swamp eel Mb globin structure is thermally stable, which is consistent with heat-tolerant behavior of the swamp eel particularly in drought habitat. PMID:22538454

  16. Characterization of an Isoflavonoid-Specific Prenyltransferase from Lupinus albus1[W][OA

    PubMed Central

    Shen, Guoan; Huhman, David; Lei, Zhentian; Snyder, John; Sumner, Lloyd W.; Dixon, Richard A.

    2012-01-01

    Prenylated flavonoids and isoflavonoids possess antimicrobial activity against fungal pathogens of plants. However, only a few plant flavonoid and isoflavonoid prenyltransferase genes have been identified to date. In this study, an isoflavonoid prenyltransferase gene, designated as LaPT1, was identified from white lupin (Lupinus albus). The deduced protein sequence of LaPT1 shared high homologies with known flavonoid and isoflavonoid prenyltransferases. The LaPT1 gene was mainly expressed in roots, a major site for constitutive accumulation of prenylated isoflavones in white lupin. LaPT1 is predicted to be a membrane-bound protein with nine transmembrane regions and conserved functional domains similar to other flavonoid and isoflavonoid prenyltransferases; it has a predicted chloroplast transit peptide and is plastid localized. A microsomal fraction containing recombinant LaPT1 prenylated the isoflavone genistein at the B-ring 3′ position to produce isowighteone. The enzyme is also active with 2′-hydroxygenistein but has no activity with other flavonoid substrates. The apparent Km of recombinant LaPT1 for the dimethylallyl diphosphate prenyl donor is in a similar range to that of other flavonoid prenyltransferases, but the apparent catalytic efficiency with genistein is considerably higher. Removal of the transit peptide increased the apparent overall activity but also increased the Km. Medicago truncatula hairy roots expressing LaPT1 accumulated isowighteone, a compound that is not naturally produced in this species, indicating a strategy for metabolic engineering of novel antimicrobial compounds in legumes. PMID:22430842

  17. Vulnerability of age-0 pallid sturgeon Scaphirhynchus albus to fish predation

    USGS Publications Warehouse

    French, William E.; Graeb, B.D.S.; Chipps, S.R.; Bertrand, K.N.; Selch, T.M.; Klumb, R.A.

    2010-01-01

    Stocking is a commonly employed conservation strategy for endangered species such as the pallid sturgeon, Scaphirhynchus albus. However, decisions about when, where and at what size pallid sturgeon should be stocked are hindered because vulnerability of pallid sturgeon to fish predation is not known. The objective of this study was to evaluate the vulnerability of age-0 pallid sturgeon to predation by two Missouri River predators under different flow regimes, and in combination with alternative prey. To document vulnerability, age-0 pallid sturgeon (<100 mm) were offered to channel catfish Ictalurus punctatus and smallmouth bass Micropterus dolomieu in laboratory experiments. Selection of pallid sturgeon by both predators was measured by offering pallid sturgeon and an alternative prey, fathead minnows Pimephales promelas, in varying prey densities. Smallmouth bass consumed more age-0 pallid sturgeon (0.95 h-1) than did channel catfish (0.13 h-1), and predation rates did not differ between water velocities supporting sustained (0 m s-1) or prolonged swimming speeds (0.15 m s-1). Neither predator positively selected pallid sturgeon when alternative prey was available. Both predator species consumed more fathead minnows than pallid sturgeon across all prey density combinations. Results indicate that the vulnerability of age-0 pallid sturgeon to predation by channel catfish and smallmouth bass is low, especially in the presence of an alternative fish prey. ?? 2009 Blackwell Verlag GmbH.

  18. Functional analysis of family GH36 α-galactosidases from Ruminococcus gnavus E1: insights into the metabolism of a plant oligosaccharide by a human gut symbiont.

    PubMed

    Cervera-Tison, M; Tailford, L E; Fuell, C; Bruel, L; Sulzenbacher, G; Henrissat, B; Berrin, J G; Fons, M; Giardina, T; Juge, N

    2012-11-01

    Ruminococcus gnavus belongs to the 57 most common species present in 90% of individuals. Previously, we identified an α-galactosidase (Aga1) belonging to glycoside hydrolase (GH) family 36 from R. gnavus E1 (M. Aguilera, H. Rakotoarivonina, A. Brutus, T. Giardina, G. Simon, and M. Fons, Res. Microbiol. 163:14-21, 2012). Here, we identified a novel GH36-encoding gene from the same strain and termed it aga2. Although aga1 showed a very simple genetic organization, aga2 is part of an operon of unique structure, including genes putatively encoding a regulator, a GH13, two phosphotransferase system (PTS) sequences, and a GH32, probably involved in extracellular and intracellular sucrose assimilation. The 727-amino-acid (aa) deduced Aga2 protein shares approximately 45% identity with Aga1. Both Aga1 and Aga2 expressed in Escherichia coli showed strict specificity for α-linked galactose. Both enzymes were active on natural substrates such as melibiose, raffinose, and stachyose. Aga1 and Aga2 occurred as homotetramers in solution, as shown by analytical ultracentrifugation. Modeling of Aga1 and Aga2 identified key amino acids which may be involved in substrate specificity and stabilization of the α-linked galactoside substrates within the active site. Furthermore, Aga1 and Aga2 were both able to perform transglycosylation reactions with α-(1,6) regioselectivity, leading to the formation of product structures up to [Hex](12) and [Hex](8), respectively. We suggest that Aga1 and Aga2 play essential roles in the metabolism of dietary oligosaccharides and could be used for the design of galacto-oligosaccharide (GOS) prebiotics, known to selectively modulate the beneficial gut microbiota.

  19. The potential of the fungus, Muscodor albus, as a microbial control agent of potato tuber moth (Lepidoptera: Gelechiidae) in stored potatoes.

    PubMed

    Lacey, Lawrence A; Neven, Lisa G

    2006-03-01

    Potato tuber moth (PTM), Phthorimaea operculella, is a serious pest of stored potato in most countries where potatoes are grown. Entomopathogens offer promise as alternatives to broad spectrum insecticides for management of this pest. The fungus Muscodor albus, which produces a mixture of antimicrobial volatile organic chemicals, was tested for its insecticidal activity against PTM. Adults and neonate larvae were exposed to volatiles generated by 15 or 30 g of M. albus rye grain culture plus water for 72 h in hermetically sealed 28.3 L chambers at 24 degrees C. Mean percent mortalities in adult moths exposed to 0, 15, and 30 g of fungal formulation were 0.9, 84.6, and 90.6%, respectively. Development to the pupal stage of PTM that were exposed as neonate larvae to 15 or 30 of M. albus culture was reduced by 61.8 and 72.8%, respectively, relative to controls.

  20. Do rhizospheric processes linked to P nutrition participate in U absorption by Lupinus albus grown in hydroponics?

    PubMed

    Tailliez, Antoine; Pierrisnard, Sylvie; Camilleri, Virginie; Keller, Catherine; Henner, Pascale

    2013-10-01

    Phosphate (P) is an essential element for plant development but is generally present in limiting amount in the soil solution. Plant species have developed different mechanisms promoting the solubilization of this element in soils to ensure a sufficient supply for their growth. One of these mechanisms is based on the ability of certain species such as L. albus to exude large amounts of citrate through specific tertiary roots called cluster-roots. Uranium (U) is an ubiquitous contaminant known firstly for its chemical toxicity and secondly for its high affinity for P with which it forms low-soluble complexes in soils. We highlight the effects of P-U interaction on the physiology of L. albus and particularly on citrate exudation, and the impact of this root process on the phytoavailability of U and its accumulation in plants in a hydroponic study. Different levels of P (1 and 100 μM) and U (0 and 20 μM) have been tested. Our results show no toxicity of U on the development of L. albus with an adequate P supply, whereas the effects of P starvation are amplified by the presence of U in the growth medium, except for the production of cluster-roots. Citrate exudation is totally inhibited by U in a low-P environment whereas it increases in the presence of U when its toxicity is lowered by the addition of P. The differences observed in terms of toxicity and accumulation are partly explained by the microphotographs obtained by electron microscopy (TEM-EDX): in the absence of P, U penetrates deep into the roots and causes lethal damages, whereas in presence of P, we observe the formation of U-P complexes which limit the internalization of the pollutant and so its toxicity.

  1. [Lupine, a contribution to the human food supply. 3. Nutritional physiological study with lupine (Lupinus albus) flour].

    PubMed

    Gross, R; Morales, E; Gross, U; von Baer, E

    1976-12-01

    Lupinus albus flour doses of 58.9 +/- 9.6 g have been given to 20 persons. This sweet lupine flour has been digestible without complications in all cases. There have been no significant changes of hemoglobine, hematocrite, total protein, urea, bilirubine, and SGOT in the blood. So the lupine may be used for improvement of protein supply in men under the criteria that (1) the alkaloid content of the seed does not exceed 0.02%, (2) the seed itself contains no secondary fungi which may cause a lupinosis.

  2. Possibilities of chemical weed control in Lupinus albus and Lupinus luteus-screening of herbicides.

    PubMed

    Dewitte, K; Latré, J; Haesaert, G

    2006-01-01

    Weed control in sweet lupins is still a problem. Especially the phytotoxicity of herbicides in sweet lupins is not enough studied. Therefore a screening with 16 selected herbicides and 4 lupin varieties has been set up. During the growing season 2005, 10 of the tested herbicides were applied in pre-emergence, 6 in post-emergence. Pre-emergence: Most of the active matters tested in pre-emergence were not phytotoxic for lupins. Pendimethalin (1000 g/ha), linuron (500 g/ha), chlorotoluron (1500 g/ha), prosulfocarb (2400 g/ha), clomazone (72 g/ha), isoxaben (100 g/ha), metamitron (1050 g/ha) and dimethenamid-P (720 g/ha) were applied without causing any significant phytotoxic symptoms. Only the lupins treated with aclonifen (1200 g/ha) showed a significant growth inhibition, 3 weeks after treatment. Significantly more chlorosis was noticed when the lupins were treated with aclonifen or with diflufenican, in preemergence. Post-emergence: In post-emergence, diflufenican (50 g/ha) did not cause any crop damage. Florasulam (5 g/ha) caused almost 100% necrosis in L. albus as well as in L. luteus. Bentazon (652 g/ha), thifensulfuron-methyl (15 g/ha) and metribuzin (175 g/ha) caused obvious necrosis and growth inhibition of the crop. The growth inhibition was significantly more severe for lupins treated with bentazon than if they were treated with thifensulfuron-methyl or metribuzin. Three weeks after treatment, clomazone (90 g/ha) and diflufenican (50 g/ha), did not cause any crop injury at all. The results indicated an interesting range of active matters which can be applied in pre-emergence, but weed control in post-emergence stays difficult.

  3. Survival of White Ibises (Eudocimus albus) in response to chronic experimental methylmercury exposure.

    PubMed

    Frederick, Peter; Campbell, Ashley; Jayasena, Nilmini; Borkhataria, Rena

    2011-03-01

    Although methylated mercury (MeHg) is known to have neurological, immunological, reproductive, and endocrine effects on vertebrates at low environmental exposure levels, effects on survival of exposed birds have not been demonstrated in the wild. Here, we report on survival of the same group of White Ibises (Eudocimus albus) during exposure to 4 levels of dietary MeHg in captivity and later as depurated free-ranging animals. Ibises were chronically exposed in captivity to dietary MeHg in groups at 0 (control), 0.05 (Low), 0.1 (Medium) and 0.3 (High) ppm MeHg ww for 43 months. No differences in annualized survival among captive MeHg groups were seen within age classes. Survival of all ages taken together was significantly lower for Control birds than for Low or Medium dosed birds, but was not different from High dosed birds. While this might be evidence of a hormetic effect, none of the captive results support the prediction that MeHg impairs survival. Using a mark-recapture analysis we found no effects of dose group or of Hg exposure on survival or resight probabilities during the first 99 days post-release to the wild. The latter results suggest that there is no lasting, post-depuration effect of even high MeHg exposure (0.3 ppm ww dietary) on survival. While these results agree with a variety of studies of survival of free-ranging birds, we suggest many survival studies have been confounded by seasonal depuration through molt, and variation in exposure rates. We suggest future studies concentrate on evaluating survival effects during nonmolting periods in species for which methylmercury exposure is relatively constant.

  4. Composition of fractional and functional properties of dietary fiber of lupines (L. luteus and L. albus).

    PubMed

    Górecka, D; Lampart-Szczapa, E; Janitz, W; Sokolowska, B

    2000-08-01

    In this study the lupine raw materials (flour and hull) of L. luteus var. Juno and L. albus var. Wat were characterized with regard to the dietary fiber content (NDF) and its fractional composition. Functional properties, i.e. water holding capacity (WHC) and cation exchange capacity (CEC) of lupine raw material were determined, with respect to various conditions existing in each part of the human digestive tract (pH-value, time of passage). Experimental products (shortcakes, ginger breads, pancakes, minced meat and dumplings filled with meat) with addition of 5, 10 or 15% of lupine flour or shell were processed and sensory evaluation was performed according to the 5-point scale. The NDF content ranged from 75.7% to 78% in the hull of the Wat and Juno lupine vars. respectively, and 28.8% to 33.4% in the flour. Cellulose was predominant in the hull's NDF while in the flour hemicellulose was major fraction. WHC of samples depended mainly on pH-value and was higher in lupine hulls (up to 5.14 g/g dry matter (d.m.) than in the flours (up to 3.83 g/g d.m.). The CEC of lupine ranged from 0.260 to 0.750 mEq/g d.m. and from 0.330 to 0.870 mEq/g d.m. in flour of the Wat and Juno varieties. The CEC of hull was lower in the Wat var. (0.290 to 0.650 mEq/g d.m.) in comparison with the Juno variety (0.150 to 0.750 mEq/g d.m.) Sensory evaluation showed that 10% addition of flour or hull of lupine to experimental products enables preparation of good quality foodstuffs.

  5. Glycomyces fuscus sp. nov. and Glycomyces albus sp. nov., actinomycetes isolated from a hypersaline habitat.

    PubMed

    Han, Xiao-Xue; Luo, Xiao-Xia; Zhang, Li-Li

    2014-07-01

    Two actinomycete strains, designated TRM 49117(T) and TRM 49136(T), were isolated from a hypersaline habitat in Xinjiang Province, north-west China and were characterized taxonomically by using a polyphasic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TRM 49117(T) had 93.93% similarity with the type strain Glycomyces halotolerans TRM 40137(T) (GenBank accession no. HQ651156) and TRM 49136(T) had 94.32% similarity with G. halotolerans TRM 40137(T). The 16S rRNA gene sequence similarity between the two new isolates was 93%. The isolates contained meso-diaminopimelic acid as the diagnostic diamino acid and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major cellular fatty acids. The predominant menaquinones of the isolates were MK-9(H4) and MK-9(H6). The whole-cell sugar patterns of these strains contained xylose and ribose, and strain TRM 49136(T) also contained arabinose. The polar lipid pattern of strain TRM 49117(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylcholine, phosphatidylinositol and three additional unknown phospholipids. The polar lipid pattern of strain TRM 49136(T) comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, glycolipids and two phosphoglycolipids of unknown composition. Genotypic and phenotypic data confirmed that strains TRM 49117(T) and TRM 49136(T) represent two novel species, clearly different from related species of the genus Glycomyces, for which the names Glycomyces fuscus sp. nov. (type strain TRM 49117(T) = CCTCC AA 2013003(T) = NRRL B-59998(T) = KACC 17682(T)) and Glycomyces albus sp. nov. (type strain TRM 49136(T) = CCTCC AA 2013004(T) = NRRL B-24927(T) = KACC 17681(T)) are proposed. PMID:24776532

  6. Exposure of great egret (Ardea albus) nestlings to mercury through diet in the Everglades ecosystem

    SciTech Connect

    Frederick, P.C.; Spalding, M.G.; Sepulveda, M.S.; Williams, G.E.; Nico, L.; Robins, R.

    1999-09-01

    The authors estimated exposure of great egret (Ardea albus) nestlings to mercury in food in the Florida Everglades, USA, by collecting regurgitated food samples during the 1993 to 1996 breeding seasons and during 1995 measured concentrations of mercury in individual prey items from those samples. Great egret nestlings had a diet composed predominantly of fish, though the species composition of fish in the diet fluctuated considerably among years. Great egrets concentrated on the larger fish available in the marsh, especially members of the Centrarchidae. The importance of all nonnative fish fluctuated from 0 to 32% of the diet by biomass and was dominated by pike killifish (Belonesox belizanus) and cichlids (Cichlidae). Total mercury concentrations in prey fish ranged from 0.04 to 1.40 mg/kg wet weight, and they found a significant relationship between mass of individual fish and mercury concentration. The authors estimated the concentration of total mercury in the diet as a whole by weighting the mercury concentration in a given fish species by the proportion of that species in the diet. They estimate that total mercury concentrations in the diets ranged among years from 0.37 to 0.47 mg/kg fish. The authors estimated total mercury exposure in great egret nestlings by combining these mercury concentrations with measurements of food intake rate, as measured over the course of the nestling period in both lab and field situations. They estimate that, at the 0.41 mg/kg level, nestlings would ingest 4.32 mg total mercury during an 80-day nestling period. Captive feeding studies reported elsewhere suggest that this level of exposure in the wild could be associated with reduced fledgling mass, increased lethargy, decreased appetite, and, possibly, poor health and juvenile survival.

  7. Glycomyces fuscus sp. nov. and Glycomyces albus sp. nov., actinomycetes isolated from a hypersaline habitat.

    PubMed

    Han, Xiao-Xue; Luo, Xiao-Xia; Zhang, Li-Li

    2014-07-01

    Two actinomycete strains, designated TRM 49117(T) and TRM 49136(T), were isolated from a hypersaline habitat in Xinjiang Province, north-west China and were characterized taxonomically by using a polyphasic study. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain TRM 49117(T) had 93.93% similarity with the type strain Glycomyces halotolerans TRM 40137(T) (GenBank accession no. HQ651156) and TRM 49136(T) had 94.32% similarity with G. halotolerans TRM 40137(T). The 16S rRNA gene sequence similarity between the two new isolates was 93%. The isolates contained meso-diaminopimelic acid as the diagnostic diamino acid and anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0 as major cellular fatty acids. The predominant menaquinones of the isolates were MK-9(H4) and MK-9(H6). The whole-cell sugar patterns of these strains contained xylose and ribose, and strain TRM 49136(T) also contained arabinose. The polar lipid pattern of strain TRM 49117(T) comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylcholine, phosphatidylinositol and three additional unknown phospholipids. The polar lipid pattern of strain TRM 49136(T) comprised phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylinositol, glycolipids and two phosphoglycolipids of unknown composition. Genotypic and phenotypic data confirmed that strains TRM 49117(T) and TRM 49136(T) represent two novel species, clearly different from related species of the genus Glycomyces, for which the names Glycomyces fuscus sp. nov. (type strain TRM 49117(T) = CCTCC AA 2013003(T) = NRRL B-59998(T) = KACC 17682(T)) and Glycomyces albus sp. nov. (type strain TRM 49136(T) = CCTCC AA 2013004(T) = NRRL B-24927(T) = KACC 17681(T)) are proposed.

  8. Exposure of great egret (Ardea albus) nestlings to mercury through diet in the Everglades ecosystem

    USGS Publications Warehouse

    Frederick, Peter C; Spalding, Marilyn G.; Sepalveda, Maria S.; Williams, Gary E.; Nico, Leo G.; Robins, Robert H.

    1999-01-01

    We estimated exposure of great egret (Ardea albus) nestlings to mercury in food in the Florida Everglades, USA, by collecting regurgitated food samples during the 1993 to 1996 breeding seasons and during 1995 measured concentrations of mercury in individual prey items from those samples. Great egret nestlings had a diet composed predominantly of fish (>95% of biomass), though the species composition of fish in the diet fluctuated considerably among years. Great egrets concentrated on the larger fish available in the marsh, especially members of the Centrarchidae. The importance of all nonnative fish fluctuated from 0 to 32% of the diet by biomass and was dominated by pike killifish (Belonesox belizanus) and cichlids (Cichlidae). Total mercury concentrations in prey fish ranged from 0.04 to 1.40 mg/kg wet weight, and we found a significant relationship between mass of individual fish and mercury concentration. We estimated the concentration of total mercury in the diet as a whole by weighting the mercury concentration in a given fish species by the proportion of that species in the diet. We estimate that total mercury concentrations in the diets ranged among years from 0.37 to 0.47 mg/kg fish (4-year mean = 0.41 mg/kg). We estimated total mercury exposure in great egret nestlings by combining these mercury concentrations with measurements of food intake rate, as measured over the course of the nestling period in both lab and field situations. We estimate that, at the 0.41 mg/kg level, nestlings would ingest 4.32 mg total mercury during an 80-day nestling period. Captive feeding studies reported elsewhere suggest that this level of exposure in the wild could be associated with reduced fledging mass, increased lethargy, decreased appetite, and, possibly, poor health and juvenile survival.

  9. Macromolecular composition of phloem exudate from white lupin (Lupinus albus L.)

    PubMed Central

    2011-01-01

    Background Members of the legume genus Lupinus exude phloem 'spontaneously' from incisions made to the vasculature. This feature was exploited to document macromolecules present in exudate of white lupin (Lupinus albus [L.] cv Kiev mutant), in particular to identify proteins and RNA molecules, including microRNA (miRNA). Results Proteomic analysis tentatively identified 86 proteins from 130 spots collected from 2D gels analysed by partial amino acid sequence determination using MS/MS. Analysis of a cDNA library constructed from exudate identified 609 unique transcripts. Both proteins and transcripts were classified into functional groups. The largest group of proteins comprised those involved in metabolism (24%), followed by protein modification/turnover (9%), redox regulation (8%), cell structural components (6%), stress and defence response (6%) with fewer in other groups. More prominent proteins were cyclophilin, ubiquitin, a glycine-rich RNA-binding protein, a group of proteins that comprise a glutathione/ascorbate-based mechanism to scavenge oxygen radicals, enzymes of glycolysis and other metabolism including methionine and ethylene synthesis. Potential signalling macromolecules such as transcripts encoding proteins mediating calcium level and the Flowering locus T (FT) protein were also identified. From around 330 small RNA clones (18-25 nt) 12 were identified as probable miRNAs by homology with those from other species. miRNA composition of exudate varied with site of collection (e.g. upward versus downward translocation streams) and nutrition (e.g. phosphorus level). Conclusions This is the first inventory of macromolecule composition of phloem exudate from a species in the Fabaceae, providing a basis to identify systemic signalling macromolecules with potential roles in regulating development, growth and stress response of legumes. PMID:21342527

  10. Metal induction of a Pisolithus albus metallothionein and its potential involvement in heavy metal tolerance during mycorrhizal symbiosis.

    PubMed

    Reddy, M Sudhakara; Kour, Manpreet; Aggarwal, Sipla; Ahuja, Shanky; Marmeisse, Roland; Fraissinet-Tachet, Laurence

    2016-09-01

    Metallothioneins (MTs) are small, cysteine-rich peptides involved in intracellular sequestration of heavy metals in eukaryotes. We examined the role in metal homeostasis and detoxification of an MT from the ectomycorrhizal fungus Pisolithus albus (PaMT1). PaMT1 encodes a 35 amino acid-long polypeptide, with 7 cysteine residues; most of them part of a C-x-C motif found in other known basidiomycete MTs. The expression levels of PaMT1 increased as a function of increased external Cu and Cd concentrations and were higher with Cu than with Cd. Heterologous complementation assays in metal-sensitive yeast mutants indicated that PaMT1 encodes a polypeptide capable of conferring higher tolerance to both Cu and Cd. Eucalyptus tereticornis plantlets colonized with P. albus grown in the presence of Cu and Cd showed better growth compared with those with non-mycorrhizal plants. Higher PaMT1 expression levels were recorded in mycorrhizal plants grown in the presence of Cu and Cd compared with those in control mycorrhizal plants not exposed to heavy metals. These data provide the first evidence to our knowledge that fungal MTs could protect ectomycorrhizal fungi from heavy metal stress and in turn help the plants to establish in metal-contaminated sites. PMID:26626627

  11. Ultrastructure and mineral distribution in the tergal cuticle of the terrestrial isopod Titanethes albus. Adaptations to a karst cave biotope.

    PubMed

    Hild, Sabine; Neues, Frank; Znidarsic, Nada; Strus, Jasna; Epple, Matthias; Marti, Othmar; Ziegler, Andreas

    2009-12-01

    Composition and spatial distribution of organic and inorganic materials within the cuticle of isopods vary between species. These variations are related to the behaviour and habitat of the animal. The troglobiotic isopod Titanethes albus lives in the complete darkness of caves in the Slovenian Karst. This habitat provides constant temperature and saturated humidity throughout the year and inconsistent food supply. These conditions should have lead to functional adaptations of arthropod cuticles. However, studies on structure and composition of cave arthropod cuticles are rare and lacking for terrestrial isopods. We therefore analysed the tergite cuticle of T. albus using transmission and field-emission electron microscopy, confocal micro-Raman spectroscopic imaging, quantitative X-ray diffractometry, thermogravimetric analysis and atomic absorption spectroscopy. The ultrastructure of the epicuticle suggests a poor resistance against water loss. A weak interconnection between the organic and mineral phase within the endo- and exocuticle, a comparatively thin apical calcite layer, and almost lack of magnesium within the calcite crystal lattice suggest that the mechanical strength of the cuticle is low in the cave isopod. This may possibly be of advantage in maintaining high cuticle flexibility and reducing metabolic expenditures. PMID:19632333

  12. Heavy Metals Uptake by Asian Swamp Eel, Monopterus albus from Paddy Fields of Kelantan, Peninsular Malaysia: Preliminary Study

    PubMed Central

    Yin, Sow Ai; Ismail, Ahmad; Zulkifli, Syaizwan Zahmir

    2012-01-01

    Swamp eel, Monopterus albus is one of the common fish in paddy fields, thus it is suitable to be a bio-monitor for heavy metals pollution studies in paddy fields. This study was conducted to assess heavy metals levels in swamp eels collected from paddy fields in Kelantan, Malaysia. The results showed zinc [Zn (86.40 μg/g dry weight)] was the highest accumulated metal in the kidney, liver, bone, gill, muscle and skin. Among the selected organs, gill had the highest concentrations of lead (Pb), cadmium (Cd) and nickel (Ni) whereas muscle showed the lowest total metal accumulation of Zn, Pb, copper (Cu), Cd and Ni. Based on the Malaysian Food Regulation, the levels of Zn and Cu in edible parts (muscle and skin) were within the safety limits. However, Cd, Pb and Ni exceeded the permissible limits. By comparing with the maximum level intake (MLI), Pb, Ni and Cd in edible parts can still be consumed. This investigation indicated that M. albus from paddy fields of Kelantan are safe for human consumption with little precaution. PMID:24575231

  13. Calcium bodies of Titanethes albus (Crustacea: Isopoda): molt-related structural dynamics and calcified matrix-associated bacteria.

    PubMed

    Vittori, Miloš; Kostanjšek, Rok; Znidaršič, Nada; Zagar, Kristina; Ceh, Miran; Strus, Jasna

    2012-10-01

    Crustaceans form a variety of calcium deposits in which they store calcium necessary for the mineralization of their exoskeletons. Calcium bodies, organs containing large amounts of calcium, have been reported in some terrestrial isopod crustaceans, but have not yet been extensively studied. We analyzed the architecture of these organs during the molt cycle in the isopod Titanethes albus. Two pairs of calcium bodies are positioned ventrolaterally in posterior pereonites of T. albus. Individual organs are epithelial sacs that contain material arranged in concentric layers delimited by thin laminae. As demonstrated by electron microscopy and fluorescence in situ hybridization, abundant bacteria are present within the calcium bodies. Regardless of the molt cycle stage, crystalline concretions are present in the central areas of the calcium bodies. Energy dispersive X-ray spectrometry of the concretions demonstrated that they are composed predominantly of calcium and phosphorus and selected area electron diffraction indicated the presence of hydroxyapatite. In molting animals, a glassy layer of mineralized matrix is formed between the envelope and the outermost lamina of the calcium body. This layer consists of an amorphous calcium mineral which contains less phosphorus than the central concretions and is resorbed after molt. Since changes in the mineralized matrix are synchronized with the molt cycle, the calcium bodies likely function as a storage compartment that complements sternal deposits as a source of calcium for the mineralization of the exoskeleton. Bacteria associated with the mineralized matrix of calcium bodies are evidently involved in calcium dynamics.

  14. Triticum aestivum shows a greater biomass response to a supply of aluminium phosphate than Lupinus albus, despite releasing fewer carboxylates into the rhizosphere.

    PubMed

    Pearse, Stuart J; Veneklaas, Erik J; Cawthray, Greg; Bolland, Mike D A; Lambers, Hans

    2006-01-01

    The relationship between carboxylate release and the ability of plants to access phosphorus from AlPO4 and to detoxify aluminium was studied by comparing species with a low and high rate of carboxylate release, Triticum aestivum (wheat) and Lupinus albus (white lupin), respectively. Species were supplied with P at 10, 20, 40 or 100 mg P kg-1 sand in the form of sparingly soluble AlPO4 or soluble KH2PO4; control plants did not receive any P. Triticum aestivum was significantly better than L. albus at accessing P from AlPO4, despite accumulating fewer carboxylates in its rhizosphere. Rhizosphere pH of L. albus did not vary with form or level of P supply, while the rhizosphere pH of T. aestivum increased with the level of P supplied. Based on the evidence in the present study, a model is proposed to explain the poor performance of L. albus, whereby the release of carboxylates and associated protons reduces the chelating ability of exuded carboxylates, thus reducing P acquisition and increasing Al toxicity.

  15. In vitro bacterial growth and in vivo ruminal microbiota populations associated with bloat in steers grazing wheat forage.

    PubMed

    Min, B R; Pinchak, W E; Anderson, R C; Hume, M E

    2006-10-01

    The role of ruminal bacteria in the frothy bloat complex common to cattle grazing winter wheat has not been previously determined. Two experiments, one in vitro and another in vivo, were designed to elucidate the effects of fresh wheat forage on bacterial growth, biofilm complexes, rumen fermentation end products, rumen bacterial diversity, and bloat potential. In Exp. 1, 6 strains of ruminal bacteria (Streptococcus bovis strain 26, Prevotella ruminicola strain 23, Eubacterium ruminantium B1C23, Ruminococcus albus SY3, Fibrobacter succinogenes ssp. S85, and Ruminococcus flavefaciens C94) were used in vitro to determine the effect of soluble plant protein from winter wheat forage on specific bacterial growth rate, biofilm complexes, VFA, and ruminal H2 and CH4 in mono or coculture with Methanobrevibacter smithii. The specific growth rate in plant protein medium containing soluble plant protein (3.27% nitrogen) was measured during a 24-h incubation at 39 degrees C in Hungate tubes under a CO2 gas phase. A monoculture of M. smithii was grown similarly, except under H2:CO2 (1:1), in a basal methanogen growth medium supplemented likewise with soluble plant protein. In Exp. 2, 6 ruminally cannulated steers grazing wheat forage were used to evaluate the influence of bloat on the production of biofilm complexes, ruminal microbial biodiversity patterns, and ruminal fluid protein fractions. In Exp. 1, cultures of R. albus (P < 0.01) and R. flavefaciens (P < 0.05) produced the most H2 among strains and resulted in greater (P < 0.01) CH4 production when cocultured with M. smithii than other coculture combinations. Cultures of S. bovis and E. ruminantium + M. smithii produced the most biofilm mass among strains. In Exp. 2, when diets changed from bermudagrass hay to wheat forage, biofilm production increased (P < 0.01). Biofilm production, concentrations of whole ruminal content (P < 0.01), and cheesecloth filtrate protein fractions (P < 0.05) in the ruminal fluid were greater

  16. Missouri River Scaphirhynchus albus (pallid sturgeon) effects analysis—Integrative report 2016

    USGS Publications Warehouse

    Jacobson, Robert B.; Annis, Mandy L.; Colvin, Michael E.; James, Daniel A.; Welker, Timothy L.; Parsley, Michael J.

    2016-07-15

    The Missouri River Pallid Sturgeon Effects Analysis was designed to carry out three components of an assessment of how Missouri River management has affected, and will affect, population dynamics of endangered Scaphirhynchus albus (pallid sturgeon): (1) collection of reliable scientific information, (2) critical assessment and synthesis of available data and analyses, and (3) analysis of the effects of actions on listed species and their habitats. This report is a synthesis of the three components emphasizing development of lines of evidence relating potential future management actions to pallid sturgeon population dynamics. We address 21 working management hypotheses that emerged from an expert opinion-based filtering process.The ability to quantify linkages from abiotic changes to pallid sturgeon population dynamics is compromised by fundamental information gaps. Although a substantial foundation of pallid sturgeon science has been developed during the past 20 years, our efforts attempt to push beyond that understanding to provide predictions of how future management actions may affect pallid sturgeon responses. For some of the 21 hypotheses, lines of evidence are limited to theoretical deduction, inference from sparse empirical datasets, or expert opinion. Useful simulation models have been developed to predict the effects of management actions on survival of drifting pallid sturgeon free embryos in the Yellowstone and Upper Missouri River complex (hereafter referred to as the “upper river”), and to assess the effects of flow and channel reconfigurations on habitat availability in the Lower Missouri River, tributaries, and Mississippi River downstream of Gavins Point Dam (hereafter referred to as the “lower river”). A population model also has been developed that can be used to assess sensitivity of the population to survival of specific life stages, assess some hypotheses related to stocking decisions, and explore a limited number of management

  17. Identification of gonadal soma-derived factor involvement in Monopterus albus (protogynous rice field eel) sex change.

    PubMed

    Zhu, Yefei; Wang, Chunlei; Chen, Xiaowu; Guan, Guijun

    2016-07-01

    We studied molecular events and potential mechanisms underlying the process of female-to-male sex transformation in the rice field eel (Monopterus albus), a protogynous hermaphrodite fish in which the gonad is initially a female ovary and transforms into male testes. We cloned and identified a novel gonadal soma derived factor (GSDF), which encodes a member of the transforming growth factor-beta superfamily. gsdf expression was measured in gonads of female, intersex and male with reverse transcription-PCR and gsdf's role in sex transformation was studied with qPCR, histological analysis and dual-color in situ hybridization assays and compared to other sex-related genes. gsdf was correlated to Sertoli cell differentiation, indicating involvement in testicular differentiation and sex transformation from female to male in this species. A unique expression pattern reveals a potential role of gsdf essential for the sex transformation of rice field eels. PMID:27230579

  18. Larval Gnathostoma spinigerum Detected in Asian Swamp Eels, Monopterus albus, Purchased from a Local Market in Yangon, Myanmar

    PubMed Central

    Chai, Jong-Yil; Sohn, Woon-Mok; Na, Byoung-Kuk; Park, Jong-Bok; Jeoung, Hoo-Gn; Hoang, Eui-Hyug; Htoon, Thi Thi; Tin, Htay Htay

    2015-01-01

    The present study was performed to determine the infection status of swamp eels with Gnathostoma sp. larvae in Myanmar. We purchased total 37 Asian swamp eels, Monopterus albus, from a local market in Yangon in June and December 2013 and 2014. All collected eels were transferred with ice to our laboratory and each of them was examined by the artificial digestion technique. A total of 401 larval gnathostomes (1-96 larvae/eel) were detected in 33 (89.2%) swamp eels. Most of the larvae (n=383; 95.5%) were found in the muscle. The remaining 18 larvae were detected in the viscera. The advanced third-stage larvae (AdL3) were 2.3-4.4 mm long and 0.25-0.425 mm wide. The characteristic head bulb (0.093 × 0.221 mm in average size) with 4 rows of hooklets, muscular long esophagus (1.025 mm), and 2 pairs of cervical sacs (0.574 mm) were observed by light microscopy. The average number of hooklets in the 1st, 2nd, 3rd, and 4th rows was 41, 45, 48, and 51, respectively. As scanning electron microscopic findings, the characteristic 4-5 rows of hooklets on the head bulb, a cervical papilla, tegumental spines regularly arranged in the transverse striations, and an anus were well observed. Based on these morphological characters, they were identified as the AdL3 of Gnathostoma spinigerum. By the present study, it has been confirmed for the first time that Asian swamp eels, M. albus, from Yangon, Myanmar are heavily infected with G. spinigerum larvae. PMID:26537042

  19. Intercropping with white lupin (Lupinus albus L.); a promising tool for phytoremediation and phytomining research

    NASA Astrophysics Data System (ADS)

    Wiche, Oliver; Székely, Balazs; Moschner, Christin; Heilmeier, Hermann

    2015-04-01

    In recent studies root-soil interactions of white lupine (Lupinus albus L.) have drawn special attention to researchers due to its particularly high potential to increase bioavailability of phosphorous (P) and trace nutrients in soils. In mixed cultures, white lupine has the ability to mobilize P and trace nutrients in soil in excess of its own need and make this excess available for other intercropped companion species. While improved acquisition of P and improved yield parameters have mostly been documented in cereal-lupine intercrops, compared to sole crops, only a few recent studies have evidenced similar effects for trace elements e.g. Fe, Zn and Mn. In this preliminary study we tried to obtain more information about the mobilization of trace elements due to intercropping under field conditions. We hypothesize, that processes that lead to a better acquisition of trace nutrients might also affect other trace elements what could be useful for phytoremediation and phytomining research. Here we report the results of a semi-field experiment were we investigated the effects of an intercropping of white lupine with oat (Avena sativa L.) on the concentrations of trace metals in shoots of oat. We investigated the effects on 12 trace elements, including 4 elements with relevance for plant nutrition (P, Fe, Mn, Zn) and 8 trace elements, belonging to the group of metalloids, lanthanides and actinides with high relevance in phytoremediation (Cd, Pb Th, U) and phytomining research (Sc, La, Nd, Ge). The experiment was carried out on a semi-field lysimer at the off-site soil recycling and remediation center in Hirschfeld (Saxony, Germany). To test the intercropping-dependent mobilization of trace metals in soil and enhanced uptake of elements by oat, white lupine and oat were cultivated on 20 plots (4 m² each) in monocultures and mixed cultures and two different white lupin /oat-ratios (11% and 33%, respectively) applying various treatments. The geometrical arrangement of

  20. Effect of water activity on the production of volatile organic compounds by Muscodor albus and their effect on three pathogens in stored potato.

    PubMed

    Corcuff, Ronan; Mercier, Julien; Tweddell, Russell; Arul, Joseph

    2011-03-01

    Muscodor albus (Xylariaceae, Ascomycetes) isolate CZ-620 produces antimicrobial volatile organic compounds (VOC), which appear to have potential for the control of various postharvest diseases. The effect of water activity (Aw) on the production of VOC by M. albus culture, and their inhibitory effects on the growth of three pathogens of potato tuber (Fusarium sambucinum, Helminthosporium solani, and Pectobacterium atrosepticum) and the development of diseases caused by the three pathogens (dry rot, silver scurf, and bacterial soft rot, respectively) were investigated. Rye grain culture of the fungus produced six alcohols, three aldehydes, five acids or esters, and two terpenoids. The most abundant VOC were: isobutyric acid; bulnesene, a sesquiterpene; an unidentified terpene; 2 and 3-methyl-1-butanol; and ethanol. However, the level of each of those VOC varied with Aw of the culture. Emission activity occurred mainly at Aw above 0.75 and high emission of most VOC occurred only at Aw above 0.90. The aldehydes (2-methyl-propanal and 3-methyl-butanal) were the only VOC produced in quantities below an Aw of 0.90. An Aw value of 0.96 favored maximum emission of acids, esters, and terpenoids. There was a higher production of alcohols and a decrease in aldehydes with increase in Aw. Isobutyric acid, which has been the main M. albus VOC monitored in previous studies as an indicator of antifungal activity, had a rather narrow optimum, peaking at Aw of 0.96 and declining sharply above 0.98. Results showed that substrate Aw affects the production dynamics of each group of VOC by the fungus, and suggest that VOC production can be prolonged by maintaining M. albus culture at a constant optimum Aw. The VOC was inhibitory to F. sambucinum, H. solani, and P. atrosepticum; and biofumigation with M. albus significantly reduced dry rot and soft rot development, and completely controlled silver scurf in inoculated tubers incubated at both 8°C and 22°C. The results show that Aw

  1. Estimation of daily age and timing of hatching of exotic Asian swamp eels Monopterus albus (Zuiew, 1793) in a backwater marsh of the Chattahoochee River, Georgia, USA

    USGS Publications Warehouse

    Long, James M.; Lafleur, C.

    2011-01-01

    Otoliths were used to estimate daily age, growth, and hatching date of the exotic Asian swamp eel (Monopterus albus) captured from a backwater marsh of the Chattahoochee River, Georgia, USA. The eels were sampled using leaf litter traps (N = 140) from 17 July to 28 August 2008. The captured (N = 15) Asian swamp eels ranged in total length from 4.9 cm to 12.2 cm, and were estimated to be from 21 to 51 days old (N = 13), and hatched from 13 June to 7 August 2008. Assuming linear growth, these individuals grew an average rate of 0.2 cm per day. To the authors' knowledge, this was the first time otoliths were used to estimate daily age, growth, and hatching date for M. albus, which can be useful for understanding the ecology of this species in the wild.

  2. Estimation of daily age and timing of hatching of exotic Asian swamp eels Monopterus albus (Zuiew, 1793) in a backwater marsh of the Chattahoochee River, Georgia, USA

    USGS Publications Warehouse

    Long, J.M.; Lafleur, C.

    2011-01-01

    Otoliths were used to estimate daily age, growth, and hatching date of the exotic Asian swamp eel (Monopterus albus) captured from a backwater marsh of the Chattahoochee River, Georgia, USA. The eels were sampled using leaf litter traps (N=140) from 17 July to 28 August 2008. The captured (N=15) Asian swamp eels ranged in total length from 4.9cm to 12.2cm, and were estimated to be from 21 to 51days old (N=13), and hatched from 13 June to 7 August 2008. Assuming linear growth, these individuals grew an average rate of 0.2cm per day. To the authors' knowledge, this was the first time otoliths were used to estimate daily age, growth, and hatching date for M. albus, which can be useful for understanding the ecology of this species in the wild. Published 2011. This article is a US Government work and is in the public domain in the USA.

  3. Increased temperature tolerance of the air-breathing Asian swamp eel Monopterus albus after high-temperature acclimation is not explained by improved cardiorespiratory performance.

    PubMed

    Lefevre, S; Findorf, I; Bayley, M; Huong, D T T; Wang, T

    2016-01-01

    This study investigated the hypothesis that in the Asian swamp eel Monopterus albus, an air-breathing fish from south-east Asia that uses the buccopharyngeal cavity for oxygen uptake, the upper critical temperature (TU) is increased by acclimation to higher temperature, and that the increased TU is associated with improved cardiovascular and respiratory function. Monopterus albus were therefore acclimated to 27° C (current average) and 32° C (current maximum temperature as well as projected average within 100-200 years), and both the effect of acclimation and acute temperature increments on cardiovascular and respiratory functions were investigated. Two weeks of heat acclimation increased upper tolerated temperature (TU ) by 2° C from 36·9 ± 0·1° C to 38·9 ± 0·1° C (mean ± s.e.). Oxygen uptake (M˙O2) increased with acclimation temperature, accommodated by increases in both aerial and aquatic respiration. Overall, M˙O2 from air (M˙O2a ) was predominant, representing 85% in 27° C acclimated fish and 80% in 32° C acclimated fish. M˙O2 increased with acute increments in temperature and this increase was entirely accommodated by an increase in air-breathing frequency and M˙O2a . Monopterus albus failed to upregulate stroke volume; rather, cardiac output was maintained through increased heart rate with rising temperature. Overall, acclimation of M. albus to 32° C did not improve its cardiovascular and respiratory performance at higher temperatures, and cardiovascular adaptations, therefore, do not appear to contribute to the observed increase in TU. PMID:26563596

  4. Increased temperature tolerance of the air-breathing Asian swamp eel Monopterus albus after high-temperature acclimation is not explained by improved cardiorespiratory performance.

    PubMed

    Lefevre, S; Findorf, I; Bayley, M; Huong, D T T; Wang, T

    2016-01-01

    This study investigated the hypothesis that in the Asian swamp eel Monopterus albus, an air-breathing fish from south-east Asia that uses the buccopharyngeal cavity for oxygen uptake, the upper critical temperature (TU) is increased by acclimation to higher temperature, and that the increased TU is associated with improved cardiovascular and respiratory function. Monopterus albus were therefore acclimated to 27° C (current average) and 32° C (current maximum temperature as well as projected average within 100-200 years), and both the effect of acclimation and acute temperature increments on cardiovascular and respiratory functions were investigated. Two weeks of heat acclimation increased upper tolerated temperature (TU ) by 2° C from 36·9 ± 0·1° C to 38·9 ± 0·1° C (mean ± s.e.). Oxygen uptake (M˙O2) increased with acclimation temperature, accommodated by increases in both aerial and aquatic respiration. Overall, M˙O2 from air (M˙O2a ) was predominant, representing 85% in 27° C acclimated fish and 80% in 32° C acclimated fish. M˙O2 increased with acute increments in temperature and this increase was entirely accommodated by an increase in air-breathing frequency and M˙O2a . Monopterus albus failed to upregulate stroke volume; rather, cardiac output was maintained through increased heart rate with rising temperature. Overall, acclimation of M. albus to 32° C did not improve its cardiovascular and respiratory performance at higher temperatures, and cardiovascular adaptations, therefore, do not appear to contribute to the observed increase in TU.

  5. Activation and silencing of secondary metabolites in Streptomyces albus and Streptomyces lividans after transformation with cosmids containing the thienamycin gene cluster from Streptomyces cattleya.

    PubMed

    Braña, Alfredo F; Rodríguez, Miriam; Pahari, Pallab; Rohr, Jurgen; García, Luis A; Blanco, Gloria

    2014-05-01

    Activation and silencing of antibiotic production was achieved in Streptomyces albus J1074 and Streptomyces lividans TK21 after introduction of genes within the thienamycin cluster from S. cattleya. Dramatic phenotypic and metabolic changes, involving activation of multiple silent secondary metabolites and silencing of others normally produced, were found in recombinant strains harbouring the thienamycin cluster in comparison to the parental strains. In S. albus, ultra-performance liquid chromatography purification and NMR structural elucidation revealed the identity of four structurally related activated compounds: the antibiotics paulomycins A, B and the paulomenols A and B. Four volatile compounds whose biosynthesis was switched off were identified by gas chromatography-mass spectrometry analyses and databases comparison as pyrazines; including tetramethylpyrazine, a compound with important clinical applications to our knowledge never reported to be produced by Streptomyces. In addition, this work revealed the potential of S. albus to produce many others secondary metabolites normally obtained from plants, including compounds of medical relevance as dihydro-β-agarofuran and of interest in perfume industry as β-patchoulene, suggesting that it might be an alternative model for their industrial production. In S. lividans, actinorhodins production was strongly activated in the recombinant strains whereas undecylprodigiosins were significantly reduced. Activation of cryptic metabolites in Streptomyces species might represent an alternative approach for pharmaceutical drug discovery.

  6. Genomics of Sponge-Associated Streptomyces spp. Closely Related to Streptomyces albus J1074: Insights into Marine Adaptation and Secondary Metabolite Biosynthesis Potential

    PubMed Central

    Ian, Elena; Malko, Dmitry B.; Sekurova, Olga N.; Bredholt, Harald; Rückert, Christian; Borisova, Marina E.; Albersmeier, Andreas; Kalinowski, Jörn; Gelfand, Mikhail S.; Zotchev, Sergey B.

    2014-01-01

    A total of 74 actinomycete isolates were cultivated from two marine sponges, Geodia barretti and Phakellia ventilabrum collected at the same spot at the bottom of the Trondheim fjord (Norway). Phylogenetic analyses of sponge-associated actinomycetes based on the 16S rRNA gene sequences demonstrated the presence of species belonging to the genera Streptomyces, Nocardiopsis, Rhodococcus, Pseudonocardia and Micromonospora. Most isolates required sea water for growth, suggesting them being adapted to the marine environment. Phylogenetic analysis of Streptomyces spp. revealed two isolates that originated from different sponges and had 99.7% identity in their 16S rRNA gene sequences, indicating that they represent very closely related strains. Sequencing, annotation, and analyses of the genomes of these Streptomyces isolates demonstrated that they are sister organisms closely related to terrestrial Streptomyces albus J1074. Unlike S. albus J1074, the two sponge streptomycetes grew and differentiated faster on the medium containing sea water. Comparative genomics revealed several genes presumably responsible for partial marine adaptation of these isolates. Genome mining targeted to secondary metabolite biosynthesis gene clusters identified several of those, which were not present in S. albus J1074, and likely to have been retained from a common ancestor, or acquired from other actinomycetes. Certain genes and gene clusters were shown to be differentially acquired or lost, supporting the hypothesis of divergent evolution of the two Streptomyces species in different sponge hosts. PMID:24819608

  7. Effects of disodium fumarate on ruminal fermentation and microbial communities in sheep fed on high-forage diets.

    PubMed

    Zhou, Y W; McSweeney, C S; Wang, J K; Liu, J X

    2012-05-01

    This study was conducted to investigate effects of disodium fumarate (DF) on fermentation characteristics and microbial populations in the rumen of Hu sheep fed on high-forage diets. Two complementary feeding trials were conducted. In Trial 1, six Hu sheep fitted with ruminal cannulae were randomly allocated to a 2 × 2 cross-over design involving dietary treatments of either 0 or 20 g DF daily. Total DNA was extracted from the fluid- and solid-associated rumen microbes, respectively. Numbers of 16S rDNA gene copies associated with rumen methanogens and bacteria, and 18S rDNA gene copies associated with rumen protozoa and fungi were measured using real-time PCR, and expressed as proportion of total rumen bacteria 16S rDNA. Ruminal pH decreased in the DF group compared with the control (P < 0.05). Total volatile fatty acids increased (P < 0.001), but butyrate decreased (P < 0.01). Addition of DF inhibited the growth of methanogens, protozoa, fungi and Ruminococcus flavefaciens in fluid samples. Both Ruminococcus albus and Butyrivibrio fibrisolvens populations increased (P < 0.001) in particle-associated samples. Trial 2 was conducted to investigate the adaptive response of rumen microbes to DF. Three cannulated sheep were fed on basal diet for 2 weeks and continuously for 4 weeks with supplementation of DF at a level of 20 g/day. Ruminal samples were collected every week to analyze fermentation parameters and microbial populations. No effects of DF were observed on pH, acetate and butyrate (P > 0.05). Populations of methanogens and R. flavefaciens decreased in the fluid samples (P < 0.001), whereas addition of DF stimulated the population of solid-associated Fibrobacter succinogenes. Population of R. albus increased in the 2nd to 4th week in fluid-associated samples and was threefold higher in the 4th week than control week in solid samples. Analysis of denaturing gradient gel electrophoresis fingerprints revealed that there were significant changes in rumen

  8. Effects of disodium fumarate on ruminal fermentation and microbial communities in sheep fed on high-forage diets.

    PubMed

    Zhou, Y W; McSweeney, C S; Wang, J K; Liu, J X

    2012-05-01

    This study was conducted to investigate effects of disodium fumarate (DF) on fermentation characteristics and microbial populations in the rumen of Hu sheep fed on high-forage diets. Two complementary feeding trials were conducted. In Trial 1, six Hu sheep fitted with ruminal cannulae were randomly allocated to a 2 × 2 cross-over design involving dietary treatments of either 0 or 20 g DF daily. Total DNA was extracted from the fluid- and solid-associated rumen microbes, respectively. Numbers of 16S rDNA gene copies associated with rumen methanogens and bacteria, and 18S rDNA gene copies associated with rumen protozoa and fungi were measured using real-time PCR, and expressed as proportion of total rumen bacteria 16S rDNA. Ruminal pH decreased in the DF group compared with the control (P < 0.05). Total volatile fatty acids increased (P < 0.001), but butyrate decreased (P < 0.01). Addition of DF inhibited the growth of methanogens, protozoa, fungi and Ruminococcus flavefaciens in fluid samples. Both Ruminococcus albus and Butyrivibrio fibrisolvens populations increased (P < 0.001) in particle-associated samples. Trial 2 was conducted to investigate the adaptive response of rumen microbes to DF. Three cannulated sheep were fed on basal diet for 2 weeks and continuously for 4 weeks with supplementation of DF at a level of 20 g/day. Ruminal samples were collected every week to analyze fermentation parameters and microbial populations. No effects of DF were observed on pH, acetate and butyrate (P > 0.05). Populations of methanogens and R. flavefaciens decreased in the fluid samples (P < 0.001), whereas addition of DF stimulated the population of solid-associated Fibrobacter succinogenes. Population of R. albus increased in the 2nd to 4th week in fluid-associated samples and was threefold higher in the 4th week than control week in solid samples. Analysis of denaturing gradient gel electrophoresis fingerprints revealed that there were significant changes in rumen

  9. Kinetics of Inactivation of Bacillus subtilis subsp. niger Spores and Staphylococcus albus on Paper by Chlorine Dioxide Gas in an Enclosed Space

    PubMed Central

    Wang, Tao; Wu, Jinhui; Hao, Limei; Yi, Ying; Zhang, Zongxing

    2016-01-01

    ABSTRACT Bacillus subtilis subsp. niger spore and Staphylococcus albus are typical biological indicators for the inactivation of airborne pathogens. The present study characterized and compared the behaviors of B. subtilis subsp. niger spores and S. albus in regard to inactivation by chlorine dioxide (ClO2) gas under different gas concentrations and relative humidity (RH) conditions. The inactivation kinetics under different ClO2 gas concentrations (1 to 5 mg/liter) were determined by first-order and Weibull models. A new model (the Weibull-H model) was established to reveal the inactivation tendency and kinetics for ClO2 gas under different RH conditions (30 to 90%). The results showed that both the gas concentration and RH were significantly (P < 0.05) and positively correlated with the inactivation of the two chosen indicators. There was a rapid improvement in the inactivation efficiency under high RH (>70%). Compared with the first-order model, the Weibull and Weibull-H models demonstrated a better fit for the experimental data, indicating nonlinear inactivation behaviors of the vegetative bacteria and spores following exposure to ClO2 gas. The times to achieve a six-log reduction of B. subtilis subsp. niger spore and S. albus were calculated based on the established models. Clarifying the kinetics of inactivation of B. subtilis subsp. niger spores and S. albus by ClO2 gas will allow the development of ClO2 gas treatments that provide an effective disinfection method. IMPORTANCE Chlorine dioxide (ClO2) gas is a novel and effective fumigation agent with strong oxidization ability and a broad biocidal spectrum. The antimicrobial efficacy of ClO2 gas has been evaluated in many previous studies. However, there are presently no published models that can be used to describe the kinetics of inactivation of airborne pathogens by ClO2 gas under different gas concentrations and RH conditions. The first-order and Weibull (Weibull-H) models established in this study can

  10. Responses in digestion, rumen fermentation and microbial populations to inhibition of methane formation by a halogenated methane analogue.

    PubMed

    Mitsumori, Makoto; Shinkai, Takumi; Takenaka, Akio; Enishi, Osamu; Higuchi, Koji; Kobayashi, Yosuke; Nonaka, Itoko; Asanuma, Narito; Denman, Stuart E; McSweeney, Christopher S

    2012-08-01

    The effects of the anti-methanogenic compound, bromochloromethane (BCM), on rumen microbial fermentation and ecology were examined in vivo. Japanese goats were fed a diet of 50 % Timothy grass and 50 % concentrate and then sequentially adapted to low, mid and high doses of BCM. The goats were placed into the respiration chambers for analysis of rumen microbial function and methane and H2 production. The levels of methane production were reduced by 5, 71 and 91 %, and H2 production was estimated at 545, 2941 and 3496 mmol/head per d, in response to low, mid and high doses of BCM, respectively, with no effect on maintenance feed intake and digestibility. Real-time PCR quantification of microbial groups showed a significant decrease relative to controls in abundance of methanogens and rumen fungi, whereas there were increases in Prevotella spp. and Fibrobacter succinogenes, a decrease in Ruminococcus albus and R. flavefaciens was unchanged. The numbers of protozoa were also unaffected. Denaturing gradient gel electrophoresis and quantitative PCR analysis revealed that several Prevotella spp. were the bacteria that increased most in response to BCM treatment. It is concluded that the methane-inhibited rumen adapts to high hydrogen levels by shifting fermentation to propionate via Prevotella spp., but the majority of metabolic hydrogen is expelled as H2 gas.

  11. Ruminal fermentation and microbial ecology of buffaloes and cattle fed the same diet.

    PubMed

    Lwin, Khin-Ohnmar; Kondo, Makoto; Ban-Tokuda, Tomomi; Lapitan, Rosalina M; Del-Barrio, Arnel N; Fujihara, Tsutomu; Matsui, Hiroki

    2012-12-01

    Although buffaloes and cattle are ruminants, their digestive capabilities and rumen microbial compositions are considered to be different. The purpose of this study was to compare the rumen microbial ecology of crossbred water buffaloes and cattle that were fed the same diet. Cattle exhibited a higher fermentation rate than buffaloes. Methane production and methanogen density were lower in buffaloes. Phylogenetic analysis of Fibrobacter succinogenes-specific 16S ribosomal RNA gene clone library showed that the diversity of groups within a species was significantly different (P < 0.05) between buffalo and cattle and most of the clones were affiliated with group 2 of the species. Population densities of F.succinogenes, Ruminococcus albus and R. flavefaciens were higher until 6 h post-feeding in cattle; however, buffaloes exhibited different traits. The population of anaerobic fungi decreased at 3 h in cattle compared to buffaloes and was similar at 0 h and 6 h. The diversity profiles of bacteria and fungi were similar in the two species. The present study showed that the profiles of the fermentation process, microbial population and diversity were similar in crossbred water buffaloes and crossbred cattle.

  12. Effects of chestnut tannins and coconut oil on growth performance, methane emission, ruminal fermentation, and microbial populations in sheep.

    PubMed

    Liu, H; Vaddella, V; Zhou, D

    2011-12-01

    This study was conducted to evaluate the effects of chestnut tannins (CT) and coconut oil (CO) on growth performance, methane (CH₄) emission, ruminal fermentation, and microbial populations in sheep. A total of 48 Rideau Arcott sheep (average body weight 31.5±1.97 kg, 16 wk old) were randomly assigned into 6 treatment groups in a 3 × 2 factorial design, with CT and CO as the main effects (8 sheep per group). The treatments were control diet (CTR), 10 or 30 g of CT/kg of diet (CT10 and CT30), 25 g of CO/kg of concentrate (CO25), and 10 or 30 g of CT/kg of diet+25 g of CO/kg of concentrate (CT10CO25 and CT30CO25). After the feeding trial (60 d), all sheep were moved to respiratory chambers to measure CH₄ emission. After CH₄ emission measurements, all sheep were slaughtered to obtain rumen fluid samples. Results showed that the addition of CT, CO, and CT+CO had no significant effects on growth performance of sheep but reduced CH₄ emission. Addition of CT reduced the NH₃-N concentration in rumen fluid in CT30. Addition of CO decreased the concentration of total volatile fatty acids in rumen fluid. No significant differences were observed in pH and molar proportion of volatile fatty acids among treatments. Addition of CT, CO, and CT+CO significantly decreased methanogen and protozoa populations. Moreover, CO decreased counts of Fibrobacter succinogenes. No significant differences were observed in populations of fungi, Ruminococcus flavefaciens, or Ruminococcus albus among treatments. In conclusion, supplementation of CT and CO seemed to be a feasible means of decreasing emissions of CH₄ from sheep by reduction of methanogen and protozoa populations with no negative effect on growth performance.

  13. Effects of Adaptation of In vitro Rumen Culture to Garlic Oil, Nitrate, and Saponin and Their Combinations on Methanogenesis, Fermentation, and Abundances and Diversity of Microbial Populations

    PubMed Central

    Patra, Amlan K.; Yu, Zhongtang

    2015-01-01

    This study investigated the effects of garlic oil (0.25 g/L), nitrate (5 mM), and quillaja saponin (0.6 g/L), alone and in binary or ternary combinations, on methanogenesis, rumen fermentation, and abundances of select microbial populations using in vitro rumen cultures. Potential adaptation to these compounds was also examined by repeated transfers of the cultures on alternate days until day 18. All treatments except saponin alone significantly decreased methanogenesis. Ternary combinations of garlic oil, nitrate, and saponin additively/synergistically suppressed methane production by 65% at day 2 and by 40% at day 18. Feed digestion was not adversely affected by any of the treatments at day 2, but was decreased by the combinations (binary and ternary) of garlic oil with the other inhibitors at days 10 and 18. Saponin, alone or in combinations, and garlic oil alone lowered ammonia concentration at day 2, while nitrate increased ammonia concentration at days 10 and 18. Total volatile fatty acid concentration was decreased by garlic oil alone or garlic oil-saponin combination. Molar proportions of acetate and propionate were affected to different extents by the different treatments. The abundances of methanogens were similar among treatments at day 2; however, garlic oil and its combination with saponin and/or nitrate at day 10 and all treatments except saponin at day 18 significantly decreased the abundances of methanogens. All the inhibitors, either alone or in combinations, did not adversely affect the abundances of total bacteria or Ruminococcus flavefaciens. However, at day 18 the abundances of Fibrobacter succinogenes and Ruminococcus albus were lowered in the presence of garlic oil and saponin, respectively. The results suggest that garlic oil-nitrate-saponin combination (at the doses used in this study) can effectively decreases methanogenesis in the rumen, but its efficacy may decrease while inhibition to feed digestion can increase over time. PMID:26733975

  14. Effects of coconut and fish oils on ruminal methanogenesis, fermentation, and abundance and diversity of microbial populations in vitro.

    PubMed

    Patra, A K; Yu, Z

    2013-03-01

    Coconut (CO) and fish (FO) oils were previously shown to inhibit rumen methanogenesis and biohydrogenation, which mitigates methane emission and helps improve beneficial fatty acids in meat and milk. This study aimed at investigating the comparative effects of CO and FO on the methanogenesis, fermentation, and microbial abundances and diversity in vitro rumen cultures containing different doses (0, 3.1, and 6.2 mL/L) of each oil and 400mg feed substrate using rumen fluid from lactating dairy cows as inocula. Increasing doses of CO and FO quadratically decreased concentrations of methane, but hydrogen concentrations were only increased quadratically by CO. Both oils linearly decreased dry matter and neutral detergent fiber digestibility of feeds but did not affect the concentration of total volatile fatty acids. However, CO reduced acetate percentage and acetate to propionate ratio and increased the percentages of propionate and butyrate to a greater extent than FO. Ammonia concentration was greater for CO than FO. As determined by quantitative real-time PCR, FO had greater inhibition to methanogens than CO, but the opposite was true for protozoal, Ruminococcus flavefaciens, and Fibrobacter succinogenes. Ruminococcus albus was not affected by either oil. Denaturing gradient gel electrophoresis (DGGE) profiles revealed that bacterial and archaeal community composition were changed differently by oil type. Based on Pareto-Lorenz evenness curve analysis of the DGGE profiles, CO noticeably changed the functional organization of archaea compared with FO. In conclusion, although both CO and FO decreased methane concentrations to a similar extent, the mode of reduction and the effect on abundances and diversity of archaeal and bacterial populations differed between the oils. Thus, the use of combination of CO and FO at a low dose may additively lower methanogenesis in the rumen while having little adverse effect on rumen fermentation. PMID:23332846

  15. Effects of dietary supplementation of rumen-protected folic acid on rumen fermentation, degradability and excretion of urinary purine derivatives in growing steers.

    PubMed

    Wang, Cong; Liu, Qiang; Guo, Gang; Huo, WenJie; Ma, Le; Zhang, YanLi; Pei, CaiXia; Zhang, ShuanLin; Wang, Hao

    2016-12-01

    The present experiment was undertaken to determine the effects of dietary addition of rumen-protected folic acid (RPFA) on ruminal fermentation, nutrient degradability, enzyme activity and the relative quantity of ruminal cellulolytic bacteria in growing beef steers. Eight rumen-cannulated Jinnan beef steers averaging 2.5 years of age and 419 ± 1.9 kg body weight were used in a replicated 4 × 4 Latin square design. The four treatments comprised supplementation levels of 0 (Control), 70, 140 and 210 mg RPFA/kg dietary dry matter (DM). On DM basis, the ration consisted of 50% corn silage, 47% concentrate and 3% soybean oil. The DM intake (averaged 8.5 kg/d) was restricted to 95% of ad libitum intake. The intake of DM, crude protein (CP) and net energy for growth was not affected by treatments. In contrast, increasing RPFA supplementation increased average daily gain and the concentration of total volatile fatty acid and reduced ruminal pH linearly. Furthermore, increasing RPFA supplementation enhanced the acetate to propionate ratio and reduced the ruminal ammonia N content linearly. The ruminal effective degradability of neutral detergent fibre from corn silage and CP from concentrate improved linearly and was highest for the highest supplementation levels. The activities of cellobiase, xylanase, pectinase and α-amylase linearly increased, but carboxymethyl-cellulase and protease were not affected by the addition of RPFA. The relative quantities of Butyrivibrio fibrisolvens, Ruminococcus albus, Ruminococcus flavefaciens and Fibrobacter succinogenes increased linearly. With increasing RPFA supplementation levels, the excretion of urinary purine derivatives was also increased linearly. The present results indicated that the supplementation of RPFA improved ruminal fermentation, nutrient degradability, activities of microbial enzymes and the relative quantity of the ruminal cellulolytic bacteria in a dose-dependent manner. According to the conditions of this

  16. Microbial perspective on fiber utilization by swine.

    PubMed

    Varel, V H; Yen, J T

    1997-10-01

    Dietary fiber may contribute up to 30% of the maintenance energy needs of growing pigs. Higher energy contributions may be obtained from dietary fiber fed to sows, along with some improvements in reproduction, health, and well-being. As long as cereal grain supplies and high-quality protein supplements are abundant, the use of fibrous feeds for swine most likely will be limited. However, as the human demand for cereal grains increases, swine producers, especially those with reproductive animals, may be economically forced to incorporate alternative feedstuffs. These feedstuffs might include lignified plant cell wall material such as grasses and legumes, and feed-milling and distillery by-products that contain a high level of fiber residues. The microflora in swine large intestine will be able to adapt to these lignified forages and by-product feeds much better than the microflora in humans. Swine microflora contain highly active ruminal cellulolytic and hemicellulolytic bacterial species, which include Fibrobacter succinogenes (intestinalis), Ruminococcus albus, Ruminococcus flavefaciens, Butyrivibrio spp., and Prevotella ruminicola. Additionally, a new highly active cellulolytic bacterium, Clostridium herbivorans, has been recently isolated from pig large intestine. The populations of these microorganisms are known to increase in response to the ingestion of diets high in plant cell wall material. The numbers of cellulolytic bacteria from adult animals are approximately 6.7 times greater than those found in growing pigs. None of these highly active cellulolytic bacterial species are found in the human large intestine. Thus, the pig large intestinal fermentation of fiber seems to more closely resemble that of ruminants than that of humans.

  17. Effects of isobutyrate supplementation on ruminal microflora, rumen enzyme activities and methane emissions in Simmental steers.

    PubMed

    Wang, C; Liu, Q; Zhang, Y L; Pei, C X; Zhang, S L; Wang, Y X; Yang, W Z; Bai, Y S; Shi, Z G; Liu, X N

    2015-02-01

    The objective of this study was to evaluate the effects of isobutyrate supplementation on rumen microflora, enzyme activities and methane emissions in Simmental steers consuming a corn stover-based diet. Eight ruminally cannulated Simmental steers were used in a replicated 4 × 4 Latin square experiment. The treatments were control (without isobutyrate), low isobutyrate (LIB), moderate isobutyrate (MIB) and high isobutyrate (HIB) with 8.4, 16.8 and 25.2 g isobutyrate per steer per day respectively. Isobutyrate was hand-mixed into the concentrate portion. Diet consisted of 60% corn stover and 40% concentrate [dry matter (DM) basis]. Dry matter intake (averaged 9 kg/day) was restricted to a maximum of 90% of ad libitum intake. Population of total bacteria, cellulolytic bacteria and anaerobic fungi were linearly increased, whereas that of protozoa and total methanogens was linearly reduced with increasing isobutyrate supplementation. Real-time PCR quantification of population of Ruminococcus albus, Ruminococcus flavefaciens, Butyrivibrio fibrisolvens and Fibrobacter succinogenes was linearly increased with increasing isobutyrate supplementation. Activities of carboxymethyl cellulase, xylanase and β-glucosidase were linearly increased, whereas that of protease was linearly reduced. Methane production was linearly decreased with increasing isobutyrate supplementation. Effective degradabilities of cellulose and hemicellulose of corn stover were linearly increased, whereas that of crude protein in diet was linearly decreased with increasing isobutyrate supplementation. The present results indicate that isobutyrate supplemented improved microflora, rumen enzyme activities and methane emissions in steers. It was suggested that the isobutyrate stimulated the digestive micro-organisms or enzymes in a dose-dependent manner. In the experimental conditions of this trial, the optimum isobutyrate dose was approximately 16.8 g isobutyrate per steer per day.

  18. Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle.

    PubMed

    Carberry, Ciara A; Kenny, David A; Han, Sukkyan; McCabe, Matthew S; Waters, Sinead M

    2012-07-01

    Feed-efficient animals have lower production costs and reduced environmental impact. Given that rumen microbial fermentation plays a pivotal role in host nutrition, the premise that rumen microbiota may contribute to host feed efficiency is gaining momentum. Since diet is a major factor in determining rumen community structure and fermentation patterns, we investigated the effect of divergence in phenotypic residual feed intake (RFI) on ruminal community structure of beef cattle across two contrasting diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were performed to profile the rumen bacterial population and to quantify the ruminal populations of Entodinium spp., protozoa, Fibrobacter succinogenes, Ruminococcus flavefaciens, Ruminococcus albus, Prevotella brevis, the genus Prevotella, and fungi in 14 low (efficient)- and 14 high (inefficient)-RFI animals offered a low-energy, high-forage diet, followed by a high-energy, low-forage diet. Canonical correspondence and Spearman correlation analyses were used to investigate associations between physiological variables and rumen microbial structure and specific microbial populations, respectively. The effect of RFI on bacterial profiles was influenced by diet, with the association between RFI group and PCR-DGGE profiles stronger for the higher forage diet. qPCR showed that Prevotella abundance was higher (P < 0.0001) in inefficient animals. A higher (P < 0.0001) abundance of Entodinium and Prevotella spp. and a lower (P < 0.0001) abundance of Fibrobacter succinogenes were observed when animals were offered the low-forage diet. Thus, differences in the ruminal microflora may contribute to host feed efficiency, although this effect may also be modulated by the diet offered.

  19. Construction of a BAC library and identification of Dmrt1 gene of the rice field eel, Monopterus albus

    SciTech Connect

    Jang Songhun; Zhou Fang; Xia Laixin; Zhao Wei; Cheng Hanhua . E-mail: hhcheng@whu.edu.cn; Zhou Rongjia . E-mail: rjzhou@whu.edu.cn

    2006-09-22

    A bacterial artificial chromosome (BAC) library was constructed using nuclear DNA from the rice field eel (Monopterus albus). The BAC library consists of a total of 33,000 clones with an average insert size of 115 kb. Based on the rice field eel haploid genome size of 600 Mb, the BAC library is estimated to contain approximately 6.3 genome equivalents and represents 99.8% of the genome of the rice field eel. This is first BAC library constructed from this species. To estimate the possibility of isolating a specific clone, high-density colony hybridization-based library screening was performed using Dmrt1 cDNA of the rice field eel as a probe. Both library screening and PCR identification results revealed three positive BAC clones which were overlapped, and formed a contig covering the Dmrt1 gene of 195 kb. By sequence comparisons with the Dmrt1 cDNA and sequencing of first four intron-exon junctions, Dmrt1 gene of the rice field eel was predicted to contain four introns and five exons. The sizes of first and second intron are 1.5 and 2.6 kb, respectively, and the sizes of last two introns were predicted to be about 20 kb. The Dmrt1 gene structure was conserved in evolution. These results also indicate that the BAC library is a useful resource for BAC contig construction and molecular isolation of functional genes.

  20. Interactions between light intensity and phosphorus nutrition affect the phosphate-mining capacity of white lupin (Lupinus albus L.).

    PubMed

    Cheng, Lingyun; Tang, Xiaoyan; Vance, Carroll P; White, Philip J; Zhang, Fusuo; Shen, Jianbo

    2014-07-01

    Light intensity affects photosynthetic carbon (C) fixation and the supply of carbon to roots. To evaluate interactions between carbon supply and phosphorus (P) supply, effects of light intensity on sucrose accumulation, root growth, cluster root formation, carboxylate exudation, and P uptake capacity were studied in white lupin (Lupinus albus L.) grown hydroponically with either 200 µmol m(-2) s(-1) or 600 µmol m(-2) s(-1) light and a sufficient (50 µM P) or deficient (1 µM P) P supply. Plant biomass and root:shoot ratio increased with increasing light intensity, particularly when plants were supplied with sufficient P. Both low P supply and increasing light intensity increased the production of cluster roots and citrate exudation. Transcripts of a phosphoenol pyruvate carboxylase gene (LaPEPC3) in cluster roots (which is related to the exudation of citrate), transcripts of a phosphate transporter gene (LaPT1), and P uptake all increased with increasing light intensity, under both P-sufficient and P-deficient conditions. Across all four experimental treatments, increased cluster root formation and carboxylate exudation were associated with lower P concentration in the shoot and greater sucrose concentration in the roots. It is suggested that C in excess of shoot growth capabilities is translocated to the roots as sucrose, which serves as both a nutritional signal and a C-substrate for carboxylate exudation and cluster root formation.

  1. Sensory prediction or motor control? Application of marr-albus type models of cerebellar function to classical conditioning.

    PubMed

    Lepora, Nathan F; Porrill, John; Yeo, Christopher H; Dean, Paul

    2010-01-01

    Marr-Albus adaptive filter models of the cerebellum have been applied successfully to a range of sensory and motor control problems. Here we analyze their properties when applied to classical conditioning of the nictitating membrane response in rabbits. We consider a system-level model of eyeblink conditioning based on the anatomy of the eyeblink circuitry, comprising an adaptive filter model of the cerebellum, a comparator model of the inferior olive and a linear dynamic model of the nictitating membrane plant. To our knowledge, this is the first model that explicitly includes all these principal components, in particular the motor plant that is vital for shaping and timing the behavioral response. Model assumptions and parameters were systematically investigated to disambiguate basic computational capacities of the model from features requiring tuning of properties and parameter values. Without such tuning, the model robustly reproduced a range of behaviors related to sensory prediction, by displaying appropriate trial-level associative learning effects for both single and multiple stimuli, including blocking and conditioned inhibition. In contrast, successful reproduction of the real-time motor behavior depended on appropriate specification of the plant, cerebellum and comparator models. Although some of these properties appear consistent with the system biology, fundamental questions remain about how the biological parameters are chosen if the cerebellar microcircuit applies a common computation to many distinct behavioral tasks. It is possible that the response profiles in classical conditioning of the eyeblink depend upon operant contingencies that have previously prevailed, for example in naturally occurring avoidance movements.

  2. Increasing capture efficiency of pallid sturgeon Scaphirhynchus albus (Forbes and Richardson, 1905) and the reliability of catch rate estimates

    USGS Publications Warehouse

    DeVries, R. J.; Hann, D. A.; Schramm, H.L.

    2015-01-01

    This study evaluated the effects of environmental parameters on the probability of capturing endangered pallid sturgeon (Scaphirhynchus albus) using trotlines in the lower Mississippi River. Pallid sturgeon were sampled by trotlines year round from 2008 to 2011. A logistic regression model indicated water temperature (T; P < 0.01) and depth (D; P = 0.03) had significant effects on capture probability (Y = −1.75 − 0.06T + 0.10D). Habitat type, surface current velocity, river stage, stage change and non-sturgeon bycatch were not significant predictors (P = 0.26–0.63). Although pallid sturgeon were caught throughout the year, the model predicted that sampling should focus on times when the water temperature is less than 12°C and in deeper water to maximize capture probability; these water temperature conditions commonly occur during November to March in the lower Mississippi River. Further, the significant effect of water temperature which varies widely over time, as well as water depth indicate that any efforts to use the catch rate to infer population trends will require the consideration of temperature and depth in standardized sampling efforts or adjustment of estimates.

  3. New disease records for hatchery-reared sturgeon. I. Expansion of frog virus 3 host range into Scaphirhynchus albus.

    PubMed

    Waltzek, Thomas B; Miller, Debra L; Gray, Matthew J; Drecktrah, Bruce; Briggler, Jeffrey T; MacConnell, Beth; Hudson, Crystal; Hopper, Lacey; Friary, John; Yun, Susan C; Malm, Kirsten V; Weber, E Scott; Hedrick, Ronald P

    2014-10-16

    In 2009, juvenile pallid sturgeon Scaphirhynchus albus, reared at the Blind Pony State Fish Hatchery (Missouri, USA) to replenish dwindling wild stocks, experienced mass mortality. Histological examination revealed extensive necrosis of the haematopoietic tissues, and a virus was isolated from affected organs in cell culture and then observed by electron microscopy. Experimental infection studies revealed that the virus is highly pathogenic to juvenile pallid sturgeon, one of several species of sturgeon currently listed as Endangered. The DNA sequence of the full length major capsid protein gene of the virus was identical to that of the species Frog virus 3 (FV3), the type species for the genus Ranavirus, originally isolated from northern leopard frog Lithobates pipiens. Although FV3 infections and epizootics in amphibians and reptiles are well documented, there is only 1 prior report of a natural infection of FV3 in fish. Our results illustrate the broad potential host range for FV3, with the known potential to cause significant mortality in poikilothermic vertebrates across 3 taxonomic classes including bony fishes, anuran and caudate amphibians, and squamate and testudine reptiles.

  4. Construction of integrated linkage map of a recombinant inbred line population of white lupin (Lupinus albus L.)

    PubMed Central

    Vipin, Cina Ann; Luckett, David J.; Harper, John D.I.; Ash, Gavin J.; Kilian, Andrzej; Ellwood, Simon R.; Phan, Huyen T.T.; Raman, Harsh

    2013-01-01

    We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an F8 recombinant inbred line population derived from Kiev Mutant/P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genic markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good genome coverage and were associated with previously identified genic and AFLP markers linked with quantitative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies. PMID:24273424

  5. New disease records for hatchery-reared sturgeon. I. Expansion of frog virus 3 host range into Scaphirhynchus albus.

    PubMed

    Waltzek, Thomas B; Miller, Debra L; Gray, Matthew J; Drecktrah, Bruce; Briggler, Jeffrey T; MacConnell, Beth; Hudson, Crystal; Hopper, Lacey; Friary, John; Yun, Susan C; Malm, Kirsten V; Weber, E Scott; Hedrick, Ronald P

    2014-10-16

    In 2009, juvenile pallid sturgeon Scaphirhynchus albus, reared at the Blind Pony State Fish Hatchery (Missouri, USA) to replenish dwindling wild stocks, experienced mass mortality. Histological examination revealed extensive necrosis of the haematopoietic tissues, and a virus was isolated from affected organs in cell culture and then observed by electron microscopy. Experimental infection studies revealed that the virus is highly pathogenic to juvenile pallid sturgeon, one of several species of sturgeon currently listed as Endangered. The DNA sequence of the full length major capsid protein gene of the virus was identical to that of the species Frog virus 3 (FV3), the type species for the genus Ranavirus, originally isolated from northern leopard frog Lithobates pipiens. Although FV3 infections and epizootics in amphibians and reptiles are well documented, there is only 1 prior report of a natural infection of FV3 in fish. Our results illustrate the broad potential host range for FV3, with the known potential to cause significant mortality in poikilothermic vertebrates across 3 taxonomic classes including bony fishes, anuran and caudate amphibians, and squamate and testudine reptiles. PMID:25320034

  6. Root Carbon Dioxide Fixation by Phosphorus-Deficient Lupinus albus (Contribution to Organic Acid Exudation by Proteoid Roots).

    PubMed Central

    Johnson, J. F.; Allan, D. L.; Vance, C. P.; Weiblen, G.

    1996-01-01

    When white lupin (Lupinus albus L.) is subjected to P deficiency lateral root development is altered and densely clustered, tertiary lateral roots (proteoid roots) are initiated. These proteoid roots exude large amounts of citrate, which increases P solubilization. In the current study plants were grown with either 1 mM P (+P-treated) or without P (-P-treated). Shoots or roots of intact plants from both P treatments were labeled independently with 14CO2 to compare the relative contribution of C fixed in each with the C exuded from roots as citrate and other organic acids. About 25-fold more acid-stable 14C, primarily in citrate and malate, was recovered in exudates from the roots of -P-treated plants compared with +P-treated plants. The rate of in vivo C fixation in roots was about 4-fold higher in -P-treated plants than in +P-treated plants. Evidence from labeling intact shoots or roots indicates that synthesis of citrate exuded by -P-treated roots is directly related to nonphotosynthetic C fixation in roots. C fixed in roots of -P-treated plants contributed about 25 and 34% of the C exuded as citrate and malate, respectively. Nonphotosynthetic C fixation in white lupin roots is an integral component in the exudation of large amounts of citrate and malate, thus increasing the P available to the plant. PMID:12226371

  7. Interactions between light intensity and phosphorus nutrition affect the phosphate-mining capacity of white lupin (Lupinus albus L.).

    PubMed

    Cheng, Lingyun; Tang, Xiaoyan; Vance, Carroll P; White, Philip J; Zhang, Fusuo; Shen, Jianbo

    2014-07-01

    Light intensity affects photosynthetic carbon (C) fixation and the supply of carbon to roots. To evaluate interactions between carbon supply and phosphorus (P) supply, effects of light intensity on sucrose accumulation, root growth, cluster root formation, carboxylate exudation, and P uptake capacity were studied in white lupin (Lupinus albus L.) grown hydroponically with either 200 µmol m(-2) s(-1) or 600 µmol m(-2) s(-1) light and a sufficient (50 µM P) or deficient (1 µM P) P supply. Plant biomass and root:shoot ratio increased with increasing light intensity, particularly when plants were supplied with sufficient P. Both low P supply and increasing light intensity increased the production of cluster roots and citrate exudation. Transcripts of a phosphoenol pyruvate carboxylase gene (LaPEPC3) in cluster roots (which is related to the exudation of citrate), transcripts of a phosphate transporter gene (LaPT1), and P uptake all increased with increasing light intensity, under both P-sufficient and P-deficient conditions. Across all four experimental treatments, increased cluster root formation and carboxylate exudation were associated with lower P concentration in the shoot and greater sucrose concentration in the roots. It is suggested that C in excess of shoot growth capabilities is translocated to the roots as sucrose, which serves as both a nutritional signal and a C-substrate for carboxylate exudation and cluster root formation. PMID:24723402

  8. Effects of methylmercury and spatial complexity on foraging behavior and foraging efficiency in juvenile white ibises (Eudocimus albus).

    PubMed

    Adams, Evan M; Frederick, Peter C

    2008-08-01

    Methylmercury is a globally distributed neurotoxin, endocrine disruptor, and teratogen, the effects of which on wildlife at environmentally relevant levels are largely unknown. In birds, foraging efficiency and learning may be sensitive endpoints for sublethal methylmercury toxicity, and these endpoints also may be biologically relevant at the population level. In the present study, groups of wild-caught, prefledgling white ibises (Eudocimus albus) were raised in a free-flight, open-air aviary on diets that approximated the measured range of methylmercury exposure in the Everglades ecosystem (0, 0.05, 0.1, and 0.3 mg/kg/d). The effect of methylmercury exposure on group foraging efficiency was examined by allowing birds to forage on 200 fathead minnows (Pimephales promelas) in artificial ponds for 15 min by straining the arenas' contents through a seine net and counting all remaining prey. Additionally, we varied the difficulty of foraging by these tactile feeding birds by adding multiple levels of structural complexity (e.g., increased vegetation and prey refugia) to the pond. Structural complexity affected both foraging efficiency and the rate of increase in efficiency over time (improvement). Methylmercury exposure affected foraging efficiency (p = 0.03). It did not affect foraging improvement in the face of increasingly challenging environments, however, and the dose-response relationship was nonlinear (e.g., the control and high-exposure groups were the least efficient foragers). Evidence for an effect of methylmercury on foraging efficiency therefore was inconclusive because of unpredicted results and no interaction with time or habitat complexity. These data suggest a nonlinear dose-response relationship at low levels of methylmercury exposure; future research is needed to verify this hypothesis. This appears to be the first experimental demonstration of the effects of habitat complexity on foraging efficiency in long-legged wading birds.

  9. Sperm-cell ultrastructure of North American sturgeons. IV. The pallid sturgeon (Scaphirhynchus albus Forbes and Richardson, 1905)

    USGS Publications Warehouse

    DiLauro, M.N.; Walsh, R.A.; Peiffer, M.; Bennett, R.M.

    2001-01-01

    Sperm-cell morphology and ultrastructure in the pallid sturgeon (Scaphirhynchus albus) were examined using transmission and scanning electron microscopy. Metrics and structure were compared with similar metrics obtained from other published descriptions of sturgeon sperm cells. General morphology was found to be similar to that of sperm cells of the white (Acipenser transmontanus), lake (A. fulvescens), stellate (A. stellatus), Chinese (A. sinensis), Russian (A. gueldenstaedti colchicus), and shortnose (A. brevirostrum) sturgeons, which all shared a gradual tapering of the nuclear diameter from posterior to anterior, unlike that of the Atlantic sturgeon (A. oxyrhynchus). The sperm cell of the pallid sturgeon was similar in size to that of the Atlantic sturgeon, being only slightly larger. The sperm cell of the pallid sturgeon differed from those of other sturgeons chiefly in the acrosomal region, where the posterolateral projections (PLP) have the shape of an acute triangle and are arranged in a spiral about the longitudinal axis of the cell. The PLP were longer than those of other sturgeons, being twice the length of those of the Atlantic sturgeon and 58% longer than those of the lake sturgeon. Also, in cross section the acrosome had the shape of a hollow cone rather than the cap of an oak tree acorn, as was found in ultrastructural studies of other sturgeons. In addition, we were able to confirm that the structural arrangement of the distal centriole of the midpiece is identical with that of the proximal centriole: nine sets of microtubular triplets around the periphery of the centriole. This information is of potential use to fishery biologists, forensic biologists, zoologists, reproductive physiologists, taxonomists, evolutionary biologists, and aquaculturists.

  10. Influence of graded inclusion of white lupin (Lupinus albus) meal on performance, nutrient digestibility and intestinal morphology of broiler chickens.

    PubMed

    Kaczmarek, S A; Hejdysz, M; Kubiś, M; Rutkowski, A

    2016-06-01

    The aim of this study was to investigate the effect of white lupin (Lupinus albus) meal (WLM) addition on the intestinal viscosity, bird performance, nutrient utilisation and villi morphology of growing broiler chicks. The experiment was conducted with 480 broiler chicks divided into 6 dietary treatments, including a maize-soybean meal control diet (CON) and 5 experimental diets containing 100, 150, 200, 250 and 300 g/kg WLM. During the period from d 0 to 35, birds fed on 200 or higher WLM/kg were characterised by lower body weight gain and feed intake than CON. The use of 150 g of WLM/kg increased feed conversion ratio (FCR) compared to CON treatment. Apparent metabolisable energy corrected to zero N balance (AMEN) and apparent ileal digestibility of dry matter, ether extract, crude protein and starch, linearly decreased as WLM increased from 0 to 300 g/kg. There was a quadratic effect of WLM dose on sialic acid excretion. A strong negative linear correlation was found between the excretion of sialic acid and AMEN. The viscosity of ileal digesta was linearly increased as WLM increased. The effect of WLM dose on ileum villus height (VH) was linear, while that on ileum villus area (VA) was quadratic. Both parameters decreased as WLM increased from 0 to 300 g/kg. In conclusion, the use of over 150 g/kg of WLM in broiler diets depressed performance results. However, depression of nutrient utilisation was only observed when 250 or 300 g/kg of WLM was used. PMID:27025275

  11. Juvenile pallid (Scaphirhynchus albus) and hybrid pallidxshovelnose (S. albusxplatorynchus) sturgeons exhibit low physiological responses to acute handling and severe confinement.

    PubMed

    Barton, B A; Bollig, H; Hauskins, B L; Jansen, C R

    2000-05-01

    Following a 7.5-h transport haul, juvenile pallid sturgeon (Scaphirhynchus albus) showed a small but significant increase in plasma cortisol to 4.7 ng ml(-1) but similar increases did not occur after fish were handled in a net held in the air for 30 s. Subsequent experiments on yearling pallid sturgeon and hybrid pallidxshovelnose (S. albusxplatorynchus) sturgeon using the same 30-s handling stressor failed to evoke increases in plasma cortisol, lactate or glucose. Plasma cortisol increased significantly from about 2 to 13-14 ng ml(-1) in both pallid and hybrid sturgeon during a 6-h severe confinement stressor with handling. Plasma cortisol in 2-year-old pallid sturgeon subjected to the same stressor demonstrated a linear pattern of increase during the initial 1 h. Plasma lactate increased from 1.11 to about 2.11 mmol l(-1) in hybrid sturgeon during the first hour of severe confinement but did not change throughout the entire confinement period in pallid sturgeon. A significant increase in plasma cortisol to 5.4 ng ml(-1) in 2-year-old pallid sturgeon 1 h after being subjected to 30 s handling at 19:00 h but not at 07:00 or 13:00 h suggests that a small diurnal variation in their stress response may exist. Although both pallid and hybrid sturgeons were responsive to stress, they exhibited very low physiological responses compared with those following equivalent stressors in most teleostean fishes or another chondrostean, the paddlefish (Polyodon spathula). Reasons for the apparent low responses to handling and confinement in scaphirhynchid sturgeons are not known but may relate to their evolutionary history, neuroendocrine mechanisms involved in their corticosteroid responses, or anatomy of their interrenal tissue structure.

  12. Bycatch of the endangered pallid sturgeon (Scaphirhynchus albus) in a commercial fishery for shovelnose sturgeon (Scaphirhynchus platorynchus)

    USGS Publications Warehouse

    Bettoli, Phillip William; Casto-Yerty, M.; Scholten, G.D.; Heist, Edward J.

    2009-01-01

    We quantified the bycatch of pallid sturgeon Scaphirhynchus albus in Tennessee's shovelnose sturgeon (Scaphirhynchus platorynchus) fishery by accompanying commercial fishers and monitoring their catch on five dates in spring 2007. Fishers were free to keep or discard any sturgeon they collected in their gillnets and trotlines and we were afforded the opportunity to collect meristic and morphometric data and tissue samples from discarded and harvested specimens. Fishers removed 327 live sturgeon from their gear in our presence, of which 93 were harvested; we also obtained the carcasses of 20 sturgeon that a fisher harvested out of our sight while we were on the water with another fisher. Two of the 113 harvested sturgeon were confirmed pallid sturgeon based on microsatellite DNA analyses. Additionally, fishers gave us five, live pallid sturgeon that they had removed from their gear. If the incidental harvest rate of pallid sturgeon (1.8% of all sturgeon harvested) was similar in the previous two commercial seasons, at least 169 adult pallid sturgeon were harvested by commercial fishers in the Tennessee waters of the Mississippi River in 2005-2007. If fishers altered their behavior because of our presence (i.e. if they were more conservative in what they harvested), the pallid sturgeon take was probably higher when they fished unaccompanied by observers. While retrieving a gill net set the previous day, a fisher we were accompanying retrieved a gillnet lost 2 days earlier; this ghost net caught 53 sturgeon whereby one fish was harvested but most fish were dead, including one confirmed pallid sturgeon.

  13. Bycatch of the endangered pallid sturgeon (Scaphirhynchus albus) in a commercial fishery for shovelnose sturgeon (Scaphirhynchus platorynchus)

    USGS Publications Warehouse

    Bettoli, P.W.; Casto-Yerty, M.; Scholten, G.D.; Heist, E.J.

    2009-01-01

    We quantified the bycatch of pallid sturgeon Scaphirhynchus albus in Tennessee's shovelnose sturgeon (Scaphirhynchus platorynchus) fishery by accompanying commercial fishers and monitoring their catch on five dates in spring 2007. Fishers were free to keep or discard any sturgeon they collected in their gillnets and trotlines and we were afforded the opportunity to collect meristic and morphometric data and tissue samples from discarded and harvested specimens. Fishers removed 327 live sturgeon from their gear in our presence, of which 93 were harvested; we also obtained the carcasses of 20 sturgeon that a fisher harvested out of our sight while we were on the water with another fisher. Two of the 113 harvested sturgeon were confirmed pallid sturgeon based on microsatellite DNA analyses. Additionally, fishers gave us five, live pallid sturgeon that they had removed from their gear. If the incidental harvest rate of pallid sturgeon (1.8% of all sturgeon harvested) was similar in the previous two commercial seasons, at least 169 adult pallid sturgeon were harvested by commercial fishers in the Tennessee waters of the Mississippi River in 2005-2007. If fishers altered their behavior because of our presence (i.e. if they were more conservative in what they harvested), the pallid sturgeon take was probably higher when they fished unaccompanied by observers. While retrieving a gill net set the previous day, a fisher we were accompanying retrieved a gillnet lost 2 days earlier; this ghost net caught 53 sturgeon whereby one fish was harvested but most fish were dead, including one confirmed pallid sturgeon. ?? 2008 Blackwell Verlag, Berlin.

  14. Migrations and swimming capabilities of endangered pallid sturgeon (Scaphirhynchus albus) to guide passage designs in the fragmented Yellowstone River

    USGS Publications Warehouse

    Braaten, P. J.; Elliott, Caroline M.; Rhoten, Jason C.; Fuller, D. B.; McElroy, Brandon J.

    2015-01-01

    Fragmentation of the Yellowstone River is hypothesized to preclude recruitment of endangered Scaphirhynchus albus (pallid sturgeon) by impeding upstream spawning migrations and access to upstream spawning areas, thereby limiting the length of free-flowing river required for survival of early life stages. Building on this hypothesis, the reach of the Yellowstone River affected by Intake Diversion Dam (IDD) is targeted for modification. Structures including a rock ramp and by-pass channel have been proposed as restoration alternatives to facilitate passage. Limited information on migrations and swimming capabilities of pallid sturgeon is available to guide engineering design specifications for the proposed structures. Migration behavior, pathways (channel routes used during migrations), and swimming capabilities of free-ranging wild adult pallid sturgeon were examined using radiotelemetry, and complemented with hydraulic data obtained along the migration pathways. Migrations of 12–26% of the telemetered pallid sturgeon population persisted to IDD, but upstream passage over the dam was not detected. Observed migration pathways occurred primarily through main channel habitats; however, migrations through side channels up to 3.9 km in length were documented. The majority of pallid sturgeon used depths of 2.2–3.4 m and mean water velocities of 0.89–1.83 m/s while migrating. Results provide inferences on depths, velocities, and habitat heterogeneity of reaches successfully negotiated by pallid sturgeon that may be used to guide designs for structures facilitating passage at IDD. Passage will provide connectivity to potential upstream spawning areas on the Yellowstone River, thereby increasing the likelihood of recruitment for this endangered species.

  15. Virgibacillus albus sp. nov., a novel moderately halophilic bacterium isolated from Lop Nur salt lake in Xinjiang province, China.

    PubMed

    Zhang, Yun-Jiao; Zhou, Yu; Ja, Man; Shi, Rong; Chun-Yu, Wei-Xun; Yang, Ling-Ling; Tang, Shu-Kun; Li, Wen-Jun

    2012-11-01

    A Gram-positive, moderately halophilic, strictly aerobic bacterium, designated YIM 93624(T), was isolated from a salt lake in Xinjiang province of China and subjected to a polyphasic taxonomic study. Strain YIM 93624(T) grew at 15-45 °C (optimum 25-30 °C), 1-17% (w/v) NaCl (optimum 5-10 %, w/v) and pH 4.0-9.0 (optimum pH 7.0). The predominant menaquinone was found to be MK-7. The major fatty acids were anteiso-C(15:0) and C(16:0). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, a glycolipid and two unidentified phospholipids. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The G+C content of the genomic DNA was 37.9 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 93624(T) was a member of the genus Virgibacillus and exhibited the highest similarity of 97.0 % to Virgibacillus koreensis KCTC 3823(T). However, the level of DNA-DNA relatedness between strain YIM 93624(T) and V. koreensis KCTC 3823(T) was 32.5 %. On the basis of phylogenetic, physiological and chemotaxonomic analysis data, the isolate is concluded to represent a novel species of the genus Virgibacillus, for which the name Virgibacillus albus sp. nov., is proposed, with type strain of YIM 93624(T) (=DSM 23711(T) = JCM 17364(T)). PMID:22622623

  16. Molecular beacons: trial of a fluorescence-based solution hybridization technique for ecological studies with ruminal bacteria.

    PubMed Central

    Schofield, P; Pell, A N; Krause, D O

    1997-01-01

    Molecular beacons are fluorescent probes developed for solution rather than membrane hybridization. We have investigated the utility of these probes to study rumen microbial ecology. Two cellulolytic species, Ruminococcus albus and Fibrobacter succinogenes, were tested. Membrane and solution hybridizations gave similar results in competition experiments with cocultures of R. albus 8 and F. succinogenes S85. PMID:9055429

  17. Glucuronoyl esterases are active on polymeric substrate, methyl esterified glucuronoxylan

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Alkali extracted beechwood glucuronoxylan methyl ester prepared by esterification of 4-O-methyl-D-glucuronic acid side residues by methanol was found to serve as substrate of microbial glucuronoyl esterases from Ruminococcus flavefaciens, Schizophyllum commune and Trichoderma reesei. The enzymatic d...

  18. Direct cloning and heterologous expression of the salinomycin biosynthetic gene cluster from Streptomyces albus DSM41398 in Streptomyces coelicolor A3(2).

    PubMed

    Yin, Jia; Hoffmann, Michael; Bian, Xiaoying; Tu, Qiang; Yan, Fu; Xia, Liqiu; Ding, Xuezhi; Stewart, A Francis; Müller, Rolf; Fu, Jun; Zhang, Youming

    2015-01-01

    Linear plus linear homologous recombination-mediated recombineering (LLHR) is ideal for obtaining natural product biosynthetic gene clusters from pre-digested bacterial genomic DNA in one or two steps of recombineering. The natural product salinomycin has a potent and selective activity against cancer stem cells and is therefore a potential anti-cancer drug. Herein, we separately isolated three fragments of the salinomycin gene cluster (salO-orf18) from Streptomyces albus (S. albus) DSM41398 using LLHR and assembled them into intact gene cluster (106 kb) by Red/ET and expressed it in the heterologous host Streptomyces coelicolor (S. coelicolor) A3(2). We are the first to report a large genomic region from a Gram-positive strain has been cloned using LLHR. The successful reconstitution and heterologous expression of the salinomycin gene cluster offer an attractive system for studying the function of the individual genes and identifying novel and potential analogues of complex natural products in the recipient strain. PMID:26459865

  19. Direct cloning and heterologous expression of the salinomycin biosynthetic gene cluster from Streptomyces albus DSM41398 in Streptomyces coelicolor A3(2)

    PubMed Central

    Yin, Jia; Hoffmann, Michael; Bian, Xiaoying; Tu, Qiang; Yan, Fu; Xia, Liqiu; Ding, Xuezhi; Francis Stewart, A.; Müller, Rolf; Fu, Jun; Zhang, Youming

    2015-01-01

    Linear plus linear homologous recombination-mediated recombineering (LLHR) is ideal for obtaining natural product biosynthetic gene clusters from pre-digested bacterial genomic DNA in one or two steps of recombineering. The natural product salinomycin has a potent and selective activity against cancer stem cells and is therefore a potential anti-cancer drug. Herein, we separately isolated three fragments of the salinomycin gene cluster (salO-orf18) from Streptomyces albus (S. albus) DSM41398 using LLHR and assembled them into intact gene cluster (106 kb) by Red/ET and expressed it in the heterologous host Streptomyces coelicolor (S. coelicolor) A3(2). We are the first to report a large genomic region from a Gram-positive strain has been cloned using LLHR. The successful reconstitution and heterologous expression of the salinomycin gene cluster offer an attractive system for studying the function of the individual genes and identifying novel and potential analogues of complex natural products in the recipient strain. PMID:26459865

  20. Glycocaulis albus sp. nov., a moderately halophilic dimorphic prosthecate bacterium isolated from petroleum-contaminated saline soil.

    PubMed

    Lv, Xiang-Lin; Xie, Bai-Sheng; Cai, Man; Geng, Shuang; Tang, Yue-Qin; Wang, Ya-Nan; Cui, Heng-Lin; Liu, Xue-Ying; Ye, Si-Yuan; Wu, Xiao-Lei

    2014-09-01

    Two novel bacterial strains, SLG210-30A1(T) and SLG210-19A2, which shared 99.9 % 16S rRNA gene sequence similarity with each other, were isolated from petroleum-contaminated saline soil in Shengli Oilfield, eastern China. Cells were Gram-stain-negative, motile, aerobic, mesophilic and moderately halophilic. They could grow chemoheterotrophically with oxygen as an electron acceptor. Morphologically, cells were typical Caulobacteria-type dimorphic prosthecate bacteria. The genomic DNA G+C contents of strains SLG210-30A1(T) and SLG210-19A2 were 61.8 mol% and 61.6 mol% respectively. Strain SLG210-30A1(T) had Q10 as the predominant respiratory ubiquinone, and C16 : 0 (28.4 %), C17 : 0 (11.6 %), C18 : 0 (22.1 %) and C18 : 1ω7c (14.0 %) as the major cellular fatty acids. The polar lipids of the two isolates were some glycolipids, a lipid, a phospholipid, an aminoglycolipid and an aminophospholipid (all unidentified). The 16S rRNA gene sequences of strains SLG210-30A1(T) and SLG210-19A2 showed the highest similarities with Glycocaulis abyssi MCS 33(T) (99.8-99.9 %), but low sequence similarities (<94.7 %) with type strains of other members of the family Hyphomonadaceae. However, the DNA-DNA relatedness of G. abyssi MCS 33(T) to strains SLG210-30A1(T) and SLG210-19A2 was 37.4±4.4 % and 36.1±1.1 %, respectively. Based on different physiological, biochemical, and phylogenetic characteristics, strains SLG210-30A1(T) and SLG210-19A2 represent a novel species of the genus Glycocaulis. The name Glycocaulis albus is therefore proposed with strain SLG210-30A1(T) ( = LMG 27741(T) = CGMCC 1.12766(T)) as the type strain. An emended description of the genus Glycocaulis is also provided.

  1. Urbanized White Ibises (Eudocimus albus) as Carriers of Salmonella enterica of Significance to Public Health and Wildlife

    PubMed Central

    Hernandez, Sonia M.; Welch, Catharine N.; Peters, Valerie E.; Lipp, Erin K.; Curry, Shannon; Yabsley, Michael J.; Sanchez, Susan; Presotto, Andrea; Gerner-Smidt, Peter; Hise, Kelley B.; Hammond, Elizabeth; Kistler, Whitney M.; Madden, Marguerite; Conway, April L.; Kwan, Tiffany; Maurer, John J.

    2016-01-01

    Worldwide, Salmonella spp. is a significant cause of disease for both humans and wildlife, with wild birds adapted to urban environments having different opportunities for pathogen exposure, infection, and transmission compared to their natural conspecifics. Food provisioning by people may influence these factors, especially when high-density mixed species flocks aggregate. White Ibises (Eudocimus albus), an iconic Everglades species in decline in Florida, are becoming increasingly common in urbanized areas of south Florida where most are hand-fed. We examined the prevalence of Salmonella shedding by ibises to determine the role of landscape characteristics where ibis forage and their behavior, on shedding rates. We also compared Salmonella isolated from ibises to human isolates to better understand non-foodborne human salmonellosis. From 2010–2013, 13% (n = 261) adult/subadult ibises and 35% (n = 72) nestlings sampled were shedding Salmonella. The prevalence of Salmonella shedding by ibises significantly decreased as the percent of Palustrine emergent wetlands and herbaceous grasslands increased, and increased as the proportion of open-developed land types (e.g. parks, lawns, golf courses) increased, suggesting that natural ecosystem land cover types supported birds with a lower prevalence of infection. A high diversity of Salmonella serotypes (n = 24) and strain types (43 PFGE types) were shed by ibises, of which 33% of the serotypes ranked in the top 20 of high significance for people in the years of the study. Importantly, 44% of the Salmonella Pulsed-Field Gel Electrophoresis patterns for ibis isolates (n = 43) matched profiles in the CDC PulseNet USA database. Of these, 20% came from Florida in the same three years we sampled ibis. Importantly, there was a negative relationship between the amount of Palustrine emergent wetland and the number of Salmonella isolates from ibises that matched human cases in the PulseNet database (p = 0.056). Together, our

  2. Changes in cell size and number and in rhizodermal development contribute to root tip swelling of Hyoscyamus albus roots subjected to iron deficiency.

    PubMed

    Kawahara, Yuki; Kitamura, Yoshie

    2015-04-01

    Root tip swelling is a common phenomenon observed when plant roots are subjected to Fe deficiency. We analysed whether an increase in cell number or an enlargement of cell width was involved in this phenomenon. Root tips of Hyoscyamus albus cultured with or without Fe were stained with fluorescent SYTO14 and analysed by confocal laser-scanning microscopy. Time-course and position-based examination revealed that the inhibition of longitudinal cell elongation and acceleration of transverse cell enlargement under Fe deficiency started from the tips and then extended towards the base during the time-course period. An increase in cell number also occurred behind the tips. In addition, the development of rhizodermal protrusions was observed on the surface of roots subjected to Fe deficiency. These results indicated that changes in cell size and number and in root hair development were all involved in root tip swelling.

  3. Differentiation and morphogenesis of the ovary and expression of gonadal development-related genes in the protogynous hermaphroditic ricefield eel Monopterus albus.

    PubMed

    He, Z; Li, Y; Wu, Y; Shi, S; Sun, C; Deng, Q; Xie, J; Wang, T; Zhang, W; Zhang, L

    2014-11-01

    The ovarian differentiation, morphogenesis and expression of some putative gonadal development-related genes were analysed in the ricefield eel Monopterus albus, a protogynous hermaphroditic teleost with a single elongate ovary. At c. 1 day post-hatching (dph), the gonadal ridge was colonized with primordial germ cells (PGCs) at the periphery and transformed into the gonadal primordium, which appeared to contain two germinal epithelia. At c. 7 dph, four ovarian cavities appeared in the gonadal tissue with two in each germinal epithelial compartment, and the indifferent gonad might have begun to differentiate into the ovary. The oocytes at the leptotene stage in meiosis I appeared at c. 14 dph, and oocytes at the diplotene stage at c. 30 dph. As development proceeded, the connective tissue separating the two germinal epithelia disappeared, and two of the four ovarian cavities collapsed into one. At 60 dph, the gonad had already taken the shape as observed in the adults. One outer and two inner ovarian cavities could be easily recognized, with slightly basophilic primary growth oocytes usually residing close to the outer ovarian cavity. The expression of cyp19a1a and erb in the early gonad was detected at 6 dph. The abundant expression of foxl2 coincided with the up-regulation of cyp19a1a at 8 dph onwards. The expression of dmrt1 isoforms was not detectable until 8 dph for dmrt1a and dmrt1b and until 33 dph for dmrt1d. The earlier appearance of cyp19a1a compared to dmrt1 transcripts in the indifferent gonad may contribute to the initial differentiation of the gonad towards the ovary in M. albus. PMID:25123578

  4. A re-assessment of sucrose signaling involved in cluster-root formation and function in phosphate-deficient white lupin (Lupinus albus).

    PubMed

    Wang, Zhengrui; Shen, Jianbo; Ludewig, Uwe; Neumann, Günter

    2015-07-01

    Apart from substrate functions, a signaling role of sucrose in root growth regulation is well established. This raised the question whether sucrose signals might also be involved in formation of cluster-roots (CRs) under phosphate (Pi) limitation, mediating exudation of phosphorus (P)-mobilizing root exudates, e.g. in Lupinus albus and members of the Proteaceae. Earlier studies demonstrated that CR formation in L. albus was mimicked to some extent by external application of high sucrose concentrations (25 mM) in the presence of extremely high P supply (1-10 mM), usually suppressing CR formation. In this study, we re-addressed this question using an axenic hydroponic culture system with normal P supply (0.1 mM) and a range of sucrose applications (0.25-25 mM). The 2.5 mM sucrose concentration was comparable with internal sucrose levels in the zone of CR initiation in first-order laterals of P-deficient plants (3.4 mM) and induced the same CR morphology. Similar to earlier studies, high sucrose concentrations (25 mM) resulted in root thickening and inhibition of root elongation, associated with a 10-fold increase of the internal sucrose level. The sucrose analog palatinose and a combination of glucose/fructose failed to stimulate CR formation under P-sufficient conditions, demonstrating a signal function of sucrose and excluding osmotic or carbon source effects. In contrast to earlier findings, sucrose was able to induce CR formation but had no effect on CR functioning with respect to citrate exudation, in vitro activity and expression of genes encoding phosphoenolpyruvate carboxylase, secretory acid phosphatase and MATE transporters, mediating P-mobilizing functions of CRs.

  5. A re-assessment of sucrose signaling involved in cluster-root formation and function in phosphate-deficient white lupin (Lupinus albus).

    PubMed

    Wang, Zhengrui; Shen, Jianbo; Ludewig, Uwe; Neumann, Günter

    2015-07-01

    Apart from substrate functions, a signaling role of sucrose in root growth regulation is well established. This raised the question whether sucrose signals might also be involved in formation of cluster-roots (CRs) under phosphate (Pi) limitation, mediating exudation of phosphorus (P)-mobilizing root exudates, e.g. in Lupinus albus and members of the Proteaceae. Earlier studies demonstrated that CR formation in L. albus was mimicked to some extent by external application of high sucrose concentrations (25 mM) in the presence of extremely high P supply (1-10 mM), usually suppressing CR formation. In this study, we re-addressed this question using an axenic hydroponic culture system with normal P supply (0.1 mM) and a range of sucrose applications (0.25-25 mM). The 2.5 mM sucrose concentration was comparable with internal sucrose levels in the zone of CR initiation in first-order laterals of P-deficient plants (3.4 mM) and induced the same CR morphology. Similar to earlier studies, high sucrose concentrations (25 mM) resulted in root thickening and inhibition of root elongation, associated with a 10-fold increase of the internal sucrose level. The sucrose analog palatinose and a combination of glucose/fructose failed to stimulate CR formation under P-sufficient conditions, demonstrating a signal function of sucrose and excluding osmotic or carbon source effects. In contrast to earlier findings, sucrose was able to induce CR formation but had no effect on CR functioning with respect to citrate exudation, in vitro activity and expression of genes encoding phosphoenolpyruvate carboxylase, secretory acid phosphatase and MATE transporters, mediating P-mobilizing functions of CRs. PMID:25412792

  6. Age estimations of wild pallid sturgeon (Scaphirhynchus albus, Forbes & Richardson 1905) based on pectoral fin spines, otoliths and bomb radiocarbon: inferences on recruitment in the dam-fragmented Missouri River

    USGS Publications Warehouse

    Braaten, P. J.; Campana, S. E.; Fuller, D. B.; Lott, R. D.; Bruch, R. M.; Jordan, G. R.

    2015-01-01

    An extant stock of wild pallid sturgeon Scaphirhynchus albus persists in the fragmented upper Missouri River basin of Montana and North Dakota. Although successful spawning and hatch of embryos has been verified, long-term catch records suggest that recruitment has not occurred for several decades as the extant stock lacks juvenile size classes and is comprised exclusively of large, presumably old individuals. Ages of 11 deceased (death years 1997–2007) wild S. albus (136–166 cm fork length) were estimated based on pectoral fin spines, sagittal otoliths and bomb radiocarbon (14C) assays of otoliths to test the hypothesis that members of this stock are old and to provide inferences on recruitment years that produced the extant stock. Age estimations based on counts of presumed annuli were about 2 years greater for otoliths (mean = 51 years, range = 43–57 years) than spines (mean = 49 years, range = 37–59 years). Based on 14C assays, confirmed birth years for all individuals occurred prior to 1957, thus establishing known longevity of at least 50 years. Estimated age based on presumed otolith annuli for one S. albus was validated to at least age 49. Although 14C assays confirmed pre-1957 birth years for all S. albus, only 56% of estimated ages from spines and 91% of estimated ages from otoliths depicted pre-1957 birth years. Both ageing structures were subject to under-ageing error (up to 15 years). Lack of or severe curtailment of S. albus recruitment in the upper Missouri River basin since the mid-1950s closely parallels the 1953–1957 timeframe when a mainstem reservoir was constructed and started to fill. This reservoir may function as a system-wide stressor to diminish recruitment success of S. albus in the upper Missouri River basin.

  7. High Brain Ammonia Tolerance and Down-Regulation of Na+:K+:2Cl- Cotransporter 1b mRNA and Protein Expression in the Brain of the Swamp Eel, Monopterus albus, Exposed to Environmental Ammonia or Terrestrial Conditions

    PubMed Central

    Ip, Yuen K.; Hou, Zhisheng; Chen, Xiu L.; Ong, Jasmine L. Y.; Chng, You R.; Ching, Biyun; Hiong, Kum C.; Chew, Shit F.

    2013-01-01

    Na+:K+:2Cl- cotransporter 1 (NKCC1) has been implicated in mediating ischemia-, trauma- or ammonia-induced astrocyte swelling/brain edema in mammals. This study aimed to determine the effects of ammonia or terrestrial exposure on ammonia concentrations in the plasma and brain, and the mRNA expression and protein abundance of nkcc/Nkcc in the brain, of the swamp eel Monopterusalbus. Ammonia exposure led to a greater increase in the ammonia concentration in the brain of M. albus than terrestrial exposure. The brain ammonia concentration of M. albus reached 4.5 µmol g-1 and 2.7 µmol g-1 after 6 days of exposure to 50 mmol l-1 NH4Cl and terrestrial conditions, respectively. The full cDNA coding sequence of nkcc1b from M. albus brain comprised 3276 bp and coded for 1092 amino acids with an estimated molecular mass of 119.6 kDa. A molecular characterization indicated that it could be activated through phosphorylation and/or glycosylation by osmotic and/or oxidative stresses. Ammonia exposure for 1 day or 6 days led to significant decreases in the nkcc1b mRNA expression and Nkcc1b protein abundance in the brain of M. albus. In comparison, a significant decrease in nkcc1b mRNA expression was observed in the brain of M. albus only after 6 days of terrestrial exposure, but both 1 day and 6 days of terrestrial exposure resulted in significant decreases in the protein abundance of Nkcc1b. These results are novel because it has been established in mammals that ammonia up-regulates NKCC1 expression in astrocytes and NKCC1 plays an important role in ammonia-induced astrocyte swelling and brain edema. By contrast, our results indicate for the first time that M. albus is able to down-regulate the mRNA and protein expression of nkcc1b/Nkcc1b in the brain when confronted with ammonia toxicity, which could be one of the contributing factors to its extraordinarily high brain ammonia tolerance. PMID:24069137

  8. Gene Cloning and mRNA Expression of Glutamate Dehydrogenase in the Liver, Brain, and Intestine of the Swamp Eel, Monopterus albus (Zuiew), Exposed to Freshwater, Terrestrial Conditions, Environmental Ammonia, or Salinity Stress

    PubMed Central

    Tok, Chia Y.; Chew, Shit F.; Ip, Yuen K.

    2011-01-01

    The swamp eel, Monopterus albus, is an obligatory air-breathing teleost which can undergo long period of emersion, has high environmental and tissue ammonia tolerance, and can survive in brackish water. We obtained a cDNA sequence of glutamate dehydrogenase (gdh), which consisted of a 133-bp 5′ UTR, a complete coding sequence region spanning 1629 bp and a 3′ UTR of approximately 717 bp, from the liver, intestine, and brain of M. albus. The translated Gdh amino acid sequence had 542 residues, and it formed a monophyletic clade with Bostrychus sinensis Gdh1a, Tetraodon nigroviridis Gdh1a, Chaenocephalus aceratus Gdh1a, Salmo salar Gdh1a1 and Gdh1a2, and O. mykiss Gdh1a. One day of exposure to terrestrial conditions or 75 mmol l−1 NH4Cl, but not to water at salinity 20, resulted in a significant increase in mRNA expression of gdh1a and Gdh amination activity in the liver of M. albus. However, exposure to brackish water, but not to terrestrial conditions or 75 mmol l−1 NH4Cl, led to a significant increase in the mRNA expression of gdh1a and Gdh amination activity in the intestine. By contrast, all the three experimental conditions had no significant effects on the mRNA expression of gdh1a in the brain of M. albus, despite a significant decrease in the Gdh amination activity in the brain of fish exposed to 75 mmol l−1 NH4Cl for 6 days. Our results indicate for the first time that the mRNA expression of gdh1a was differentially up-regulated in the liver and intestine of M. albus in response to ammonia toxicity and salinity stress, respectively. The increases in mRNA expression of gdh1a and Gdh amination activity would probably lead to an increase in glutamate production in support of increased glutamine synthesis for the purpose of ammonia detoxification or cell volume regulation under these two different environmental conditions. PMID:22319499

  9. Effects of replacing dietary starch with neutral detergent-soluble fibre on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria using the rumen simulation technique (RUSITEC).

    PubMed

    Zhao, X H; Liu, C J; Liu, Y; Li, C Y; Yao, J H

    2013-12-01

    A rumen simulation technique (RUSITEC) apparatus with eight 800 ml fermenters was used to investigate the effects of replacing dietary starch with neutral detergent-soluble fibre (NDSF) by inclusion of sugar beet pulp in diets on ruminal fermentation, microbial synthesis and populations of ruminal cellulolytic bacteria. Experimental diets contained 12.7, 16.4, 20.1 or 23.8% NDSF substituted for starch on a dry matter basis. The experiment was conducted over two independent 15-day incubation periods with the last 8 days used for data collection. There was a tendency that 16.4% NDSF in the diet increased the apparent disappearance of organic matter (OM) and neutral detergent fibre (NDF). Increasing dietary NDSF level increased carboxymethylcellulase and xylanase activity in the solid fraction and apparent disappearance of acid detergent fibre (ADF) but reduced the 16S rDNA copy numbers of Ruminococcus albus in both liquid and solid fractions and R. flavefaciens in the solid fraction. The apparent disappearance of dietary nitrogen (N) was reduced by 29.6% with increased dietary NDSF. Substituting NDSF for starch appeared to increase the ratios of acetate/propionate and methane/volatile fatty acids (VFA) (mol/mol). Replacing dietary starch with NDSF reduced the daily production of ammonia-N and increased the growth of the solid-associated microbial pellets (SAM). Total microbial N flow and efficiency of microbial synthesis (EMS), expressed as g microbial N/kg OM fermented, tended to increase with increased dietary NDSF, but the numerical increase did not continue as dietary NDSF exceeded 20.1% of diet DM. Results suggested that substituting NDSF for starch up to 16.4% of diet DM increased digestion of nutrients (except for N) and microbial synthesis, and further increases (from 16.4% to 23.8%) in dietary NDSF did not repress microbial synthesis but did significantly reduce digestion of dietary N.

  10. In vitro fermentation of lupin seeds (Lupinus albus) and broad beans (Vicia faba): dynamic modulation of the intestinal microbiota and metabolomic output.

    PubMed

    Gullón, Patricia; Gullón, Beatriz; Tavaria, Freni; Vasconcelos, Marta; Gomes, Ana Maria

    2015-10-01

    Broad beans (Vicia faba) and lupin seeds (Lupinus albus) are legumes rich in a wide range of compounds, which may represent a useful dietary approach for modulating the human gut microbiome. In this work, after in vitro digestion, legume samples were used as carbon sources in anaerobic batch cultures to evaluate their impact on the intestinal microbiota composition and on their metabolic products. The fermentations were monitored by a decrease in pH, generation of short chain fatty acids (SCFA) and lactate and the changes in the dynamic bacterial populations by fluorescence in situ hybridization (FISH). The total SCFA at the end of fermentation was 81.52 mM for lupin seeds and 78.41 mM for broad beans accompanied by a decrease of the pH for both legumes. The microbial groups that increased significantly (P < 0.05) were Bifidobacterium spp., Lactobacillus-Enterococcus, Atopobium, Bacteroides-Pretovella, Clostridium coccoides-Eubacterium rectale, Faecalibacterium prausnitzii and Roseburia intestinalis. This impact on the intestinal microbiota suggests that lupin seeds and broad beans may be used in the development of novel functional foods, which can be included in dietary strategies for human health promotion. PMID:26252418

  11. Effects of deep frying on proximate composition and micronutrient of Indian mackerel (Rastrelliger kanagurta), eel (Monopterus albus) and cockle (Anadara granosa).

    PubMed

    Rahman, M M; Zamri, M; Fadilla, N

    2012-06-15

    This study was conducted to determine the proximate composition and four micronutrients (Cd, Cu, Mn and Zn) of Indian Mackerel (Rastrelliger kanagurta), Eel (Monopterus albus) and Cockle (Anadara granosa). All fish and shellfish were purchased from local fish market in Kuantan city. All samples of each species were mixed and divided into two groups based on random selection. Each group were again divided into 3 sub-groups which were considered as replications. The first group were kept uncooked. The second group were fried in a beaker of 400 mL palm cooking oil capacity at a temperature approximately of 180 degrees C for a 15 min period. Both raw and fried samples were analysed following standard methods to determine protein, lipid, ash, moisture, carbohydrate, Cd, Cu, Mn and Zn contents. Results showed that protein content was higher in Indian mackerel and eel than cockle while overall Cd, Cu, Mn and Zn contents were higher in cockle than Indian mackerel and eel. Therefore, fish is better than shellfish in the nutritional point of view. Fried fish and shellfish had very high fat content. Therefore, frying cannot be recommended to prepare a healthy diet. More research is needed including all cooking methods of fish to know the nutritional changes by each cooking method. Fish contains many important fatty acids and amino acids which might be lost during frying. Therefore, future study should include the effects of different cooking methods on amino acids and fatty acids compositions of fish and shellfish.

  12. Molecular cloning and characterization of amh and dax1 genes and their expression during sex inversion in rice-field eel Monopterus albus

    PubMed Central

    Hu, Qing; Guo, Wei; Gao, Yu; Tang, Rong; Li, Dapeng

    2015-01-01

    The full-length cDNAs of amh and dax1 in the hermaphrodite, rice-field eel (Monopterus albus), were cloned and characterized in this study. Multiple sequence alignment revealed Dax1 was well conserved among vertebrates, whereas Amh had a low degree of similarity between different vertebrates. Their expression profiles in gonads during the course of sex inversion and tissues were investigated. The tissue distribution indicated amh was expressed mostly in gonads and was scarcely detectable in other tissues, whereas the expression of dax1 was widespread among the different tissues, especially liver and gonads. amh was scarcely detectable in ovaries whereas it was abundantly expressed in both ovotestis and testis. By contrast, dax1 was highly expressed in ovaries, especially in ♀IV (ovaries in IV stage), but it was decreased significantly in ♀/♂I (ovotestis in I stage). Its expression was increased again in ♀/♂III (ovotestis in III stage), and then decreased to a low level in testis. These significant different expression patterns of amh and dax1 suggest the increase of amh expression and the decline of dax1 expression are important for the activation of testis development, and the high level of amh and a low level of dax1 expression are necessary for maintenance of testis function. PMID:26578091

  13. In vitro fermentation of lupin seeds (Lupinus albus) and broad beans (Vicia faba): dynamic modulation of the intestinal microbiota and metabolomic output.

    PubMed

    Gullón, Patricia; Gullón, Beatriz; Tavaria, Freni; Vasconcelos, Marta; Gomes, Ana Maria

    2015-10-01

    Broad beans (Vicia faba) and lupin seeds (Lupinus albus) are legumes rich in a wide range of compounds, which may represent a useful dietary approach for modulating the human gut microbiome. In this work, after in vitro digestion, legume samples were used as carbon sources in anaerobic batch cultures to evaluate their impact on the intestinal microbiota composition and on their metabolic products. The fermentations were monitored by a decrease in pH, generation of short chain fatty acids (SCFA) and lactate and the changes in the dynamic bacterial populations by fluorescence in situ hybridization (FISH). The total SCFA at the end of fermentation was 81.52 mM for lupin seeds and 78.41 mM for broad beans accompanied by a decrease of the pH for both legumes. The microbial groups that increased significantly (P < 0.05) were Bifidobacterium spp., Lactobacillus-Enterococcus, Atopobium, Bacteroides-Pretovella, Clostridium coccoides-Eubacterium rectale, Faecalibacterium prausnitzii and Roseburia intestinalis. This impact on the intestinal microbiota suggests that lupin seeds and broad beans may be used in the development of novel functional foods, which can be included in dietary strategies for human health promotion.

  14. Nitrogen transfer from Lupinus albus L., Trifolium incarnatum L. and Vicia sativa L. contribute differently to rapeseed (Brassica napus L.) nitrogen nutrition.

    PubMed

    Génard, Thaïs; Etienne, Philippe; Laîné, Philippe; Yvin, Jean-Claude; Diquélou, Sylvain

    2016-09-01

    Nitrogen (N) transfer is well documented in legume-cereal intercropping but this is less often reported for legume-Brassica intercrops even though Brassica crops require higher levels of N fertilizers. The present study was carried out to quantify N transfer from legumes (Lupinus albus L., Trifolium incarnatum L. or Vicia sativa L.) to rapeseed (Brassica napus L.) using the split-root (15)N-labelling method. After three months we observed that legumes did not alter the growth of rapeseed. Vetch showed the lowest growth and demonstrated low (15)N shoot to root translocation and no significant N transfer to rapeseed. In contrast, significant (15)N enrichment was found in lupine and clover and (15)N was transferred to the associated rapeseed plants (around 6 and 4 mg N plant(-1), respectively), which contributed 2 to 3% of the rapeseed total N. Additionally, the data revealed that N2 fixation dominated the N nutrition in lupine despite the high N level provided in the donor compartment, suggesting a greater niche segregation between companion plants. Based on the results of this study we suggest that intercropping can be a relevant contributor to rapeseed N nutrition. Among the three legumes tested, clover and lupine seemed to be the best intercropping candidates.

  15. Unusual site-specific DNA integration into the highly active pseudo-attB of the Streptomyces albus J1074 genome.

    PubMed

    Bilyk, Bohdan; Luzhetskyy, Andriy

    2014-06-01

    The φC31-encoded recombination system has become a widely used tool for genetic analysis of streptomycetes, gene therapy and generation of transgenic animals. However, the application of this system, even in the context of its natural host genus, Streptomyces, may require a specific approach for each species. In this study, we have identified a novel pseudo-attB site, called pseB4, for integration of vectors using the φC31 system. More than 90 % of clones contained two copies of pSET152- or pOJ436-based cosmids, after their introduction into S. albus. The efficiency of the integration of φC31-based vectors into pseB4 is therefore comparable to that of the integration into attB. Moreover, in contrast with integration into the native attB, integration into pseB4 is not polar and does not require a complementary sequence in the TT-core region. Furthermore, an analysis of conjugation frequency revealed mutual inhibition of plasmid integration into either site when both the attB and pseB4 sites were present in the genome.

  16. New Deferoxamine Glycoconjugates Produced upon Overexpression of Pathway-Specific Regulatory Gene in the Marine Sponge-Derived Streptomyces albus PVA94-07.

    PubMed

    Sekurova, Olga N; Pérez-Victoria, Ignacio; Martín, Jesús; Degnes, Kristin F; Sletta, Håvard; Reyes, Fernando; Zotchev, Sergey B

    2016-01-01

    Activation of silent biosynthetic gene clusters in Streptomyces bacteria via overexpression of cluster-specific regulatory genes is a promising strategy for the discovery of novel bioactive secondary metabolites. This approach was used in an attempt to activate a cryptic gene cluster in a marine sponge-derived Streptomyces albus PVA94-07 presumably governing the biosynthesis of peptide-based secondary metabolites. While no new peptide-based metabolites were detected in the recombinant strain, it was shown to produce at least four new analogues of deferoxamine with additional acyl and sugar moieties, for which chemical structures were fully elucidated. Biological activity tests of two of the new deferoxamine analogues revealed weak activity against Escherichia coli. The gene knockout experiment in the gene cluster targeted for activation, as well as overexpression of certain genes from this cluster did not have an effect on the production of these compounds by the strain overexpressing the regulator. It seems plausible that the production of such compounds is a response to stress imposed by the production of an as-yet unidentified metabolite specified by the cryptic cluster. PMID:27618884

  17. Effects of deep frying on proximate composition and micronutrient of Indian mackerel (Rastrelliger kanagurta), eel (Monopterus albus) and cockle (Anadara granosa).

    PubMed

    Rahman, M M; Zamri, M; Fadilla, N

    2012-06-15

    This study was conducted to determine the proximate composition and four micronutrients (Cd, Cu, Mn and Zn) of Indian Mackerel (Rastrelliger kanagurta), Eel (Monopterus albus) and Cockle (Anadara granosa). All fish and shellfish were purchased from local fish market in Kuantan city. All samples of each species were mixed and divided into two groups based on random selection. Each group were again divided into 3 sub-groups which were considered as replications. The first group were kept uncooked. The second group were fried in a beaker of 400 mL palm cooking oil capacity at a temperature approximately of 180 degrees C for a 15 min period. Both raw and fried samples were analysed following standard methods to determine protein, lipid, ash, moisture, carbohydrate, Cd, Cu, Mn and Zn contents. Results showed that protein content was higher in Indian mackerel and eel than cockle while overall Cd, Cu, Mn and Zn contents were higher in cockle than Indian mackerel and eel. Therefore, fish is better than shellfish in the nutritional point of view. Fried fish and shellfish had very high fat content. Therefore, frying cannot be recommended to prepare a healthy diet. More research is needed including all cooking methods of fish to know the nutritional changes by each cooking method. Fish contains many important fatty acids and amino acids which might be lost during frying. Therefore, future study should include the effects of different cooking methods on amino acids and fatty acids compositions of fish and shellfish. PMID:24191621

  18. An experimental test and models of drift and dispersal processes of pallid sturgeon (Scaphirhynchus albus) free embryos in the Missouri River

    USGS Publications Warehouse

    Braaten, P.J.; Fuller, D.B.; Lott, R.D.; Ruggles, M.P.; Brandt, T.F.; Legare, R.G.; Holm, R.J.

    2012-01-01

    Free embryos of wild pallid sturgeon Scaphirhynchus albus were released in the Missouri River and captured at downstream sites through a 180-km reach of the river to examine ontogenetic drift and dispersal processes. Free embryos drifted primarily in the fastest portion of the river channel, and initial drift velocities for all age groups (mean = 0.66–0.70 m s−1) were only slightly slower than mean water column velocity (0.72 m s−1). During the multi-day long-distance drift period, drift velocities of all age groups declined an average of 9.7% day−1. Younger free embryos remained in the drift upon termination of the study; whereas, older age groups transitioned from drifting to settling during the study. Models based on growth of free embryos, drift behavior, size-related variations in drift rates, and channel hydraulic characteristics were developed to estimate cumulative distance drifted during ontogenetic development through a range of simulated water temperatures and velocity conditions. Those models indicated that the average free embryo would be expected to drift several hundred km during ontogenetic development. Empirical data and model results highlight the long-duration, long-distance drift and dispersal processes for pallid sturgeon early life stages. In addition, results provide a likely mechanism for lack of pallid sturgeon recruitment in fragmented river reaches where dams and reservoirs reduce the length of free-flowing river available for pallid sturgeon free embryos during ontogenetic development.

  19. Natural growth and diet of known-age pallid sturgeon (Scaphirhynchus albus) early life stages in the upper Missouri River basin, Montana and North Dakota

    USGS Publications Warehouse

    Braaten, P.J.; Fuller, D.B.; Lott, R.D.; Haddix, T.M.; Holte, L.D.; Wilson, R.H.; Bartron, M.L.; Kalie, J.A.; DeHaan, P.W.; Ardren, W.R.; Holm, R.J.; Jaeger, M.E.

    2012-01-01

    Prior to anthropogenic modifications, the historic Missouri River provided ecological conditions suitable for reproduction, growth, and survival of pallid sturgeon Scaphirhynchus albus. However, little information is available to discern whether altered conditions in the contemporary Missouri River are suitable for feeding, growth and survival of endangered pallid sturgeon during the early life stages. In 2004 and 2007, nearly 600 000 pallid sturgeon free embryos and larvae were released in the upper Missouri River and survivors from these releases were collected during 2004–2010 to quantify natural growth rates and diet composition. Based on genetic analysis and known-age at release (1–17 days post-hatch, dph), age at capture (dph, years) could be determined for each survivor. Totals of 23 and 28 survivors from the 2004 and 2007 releases, respectively, were sampled. Growth of pallid sturgeon was rapid (1.91 mm day-1) during the initial 13–48 dph, then slowed as fish approached maximum length (120–140 mm) towards the end of the first growing season. The diet of young-of-year pallid sturgeon was comprised of Diptera larvae, Diptera pupae, and Ephemeroptera nymphs. Growth of pallid sturgeon from ages 1–6 years was about 48.0 mm year-1. This study provides the first assessment of natural growth and diet of young pallid sturgeon in the wild. Results depict pallid sturgeon growth trajectories that may be expected for naturally produced wild stocks under contemporary habitat conditions in the Missouri River and Yellowstone River.

  20. Effects of intercropping of oat (Avena sativa L.) with white lupin (Lupinus albus L.) on the mobility of target elements for phytoremediation and phytomining in soil solution.

    PubMed

    Wiche, Oliver; Székely, Balazs; Kummer, Nicolai-Alexeji; Moschner, Christin; Heilmeier, Hermann

    2016-09-01

    This study aims to investigate how intercropping of oat (Avena sativa L.) with white lupin (Lupinus albus L.) affects the mobile fractions of trace metals (Fe, Mn, Pb, Cd, Th, U, Sc, La, Nd, Ge) in soil solution. Oat and white lupin were cultivated in monocultures and mixed cultures with differing oat/white lupin ratios (11% and 33% lupin, respectively). Temporal variation of soil solution chemistry was compared with the mobilization of elements in the rhizosphere of white lupin and concentrations in plant tissues. Relative to the monocrops, intercropping of oat with 11% white lupin significantly increased the concentrations of Fe, Pb, Th, La and Nd in soil solution as well as the concentrations of Fe, Pb, Th, Sc, La and Nd in tissues of oat. Enhanced mobility of the mentioned elements corresponded to a depletion of elements in the rhizosphere soil of white lupin. In mixed cultures with 33% lupin, concentrations in soil solution only slightly increased. We conclude that intercropping with 11% white lupin might be a promising tool for phytoremediation and phytomining research enhancing mobility of essential trace metals as well as elements with relevance for phytoremediation (Pb, Th) and phytomining (La, Nd, Sc) in soil.

  1. Nitrogen transfer from Lupinus albus L., Trifolium incarnatum L. and Vicia sativa L. contribute differently to rapeseed (Brassica napus L.) nitrogen nutrition.

    PubMed

    Génard, Thaïs; Etienne, Philippe; Laîné, Philippe; Yvin, Jean-Claude; Diquélou, Sylvain

    2016-09-01

    Nitrogen (N) transfer is well documented in legume-cereal intercropping but this is less often reported for legume-Brassica intercrops even though Brassica crops require higher levels of N fertilizers. The present study was carried out to quantify N transfer from legumes (Lupinus albus L., Trifolium incarnatum L. or Vicia sativa L.) to rapeseed (Brassica napus L.) using the split-root (15)N-labelling method. After three months we observed that legumes did not alter the growth of rapeseed. Vetch showed the lowest growth and demonstrated low (15)N shoot to root translocation and no significant N transfer to rapeseed. In contrast, significant (15)N enrichment was found in lupine and clover and (15)N was transferred to the associated rapeseed plants (around 6 and 4 mg N plant(-1), respectively), which contributed 2 to 3% of the rapeseed total N. Additionally, the data revealed that N2 fixation dominated the N nutrition in lupine despite the high N level provided in the donor compartment, suggesting a greater niche segregation between companion plants. Based on the results of this study we suggest that intercropping can be a relevant contributor to rapeseed N nutrition. Among the three legumes tested, clover and lupine seemed to be the best intercropping candidates. PMID:27656683

  2. Molecular cloning and characterization of amh and dax1 genes and their expression during sex inversion in rice-field eel Monopterus albus.

    PubMed

    Hu, Qing; Guo, Wei; Gao, Yu; Tang, Rong; Li, Dapeng

    2015-01-01

    The full-length cDNAs of amh and dax1 in the hermaphrodite, rice-field eel (Monopterus albus), were cloned and characterized in this study. Multiple sequence alignment revealed Dax1 was well conserved among vertebrates, whereas Amh had a low degree of similarity between different vertebrates. Their expression profiles in gonads during the course of sex inversion and tissues were investigated. The tissue distribution indicated amh was expressed mostly in gonads and was scarcely detectable in other tissues, whereas the expression of dax1 was widespread among the different tissues, especially liver and gonads. amh was scarcely detectable in ovaries whereas it was abundantly expressed in both ovotestis and testis. By contrast, dax1 was highly expressed in ovaries, especially in ♀IV (ovaries in IV stage), but it was decreased significantly in ♀/♂I (ovotestis in I stage). Its expression was increased again in ♀/♂III (ovotestis in III stage), and then decreased to a low level in testis. These significant different expression patterns of amh and dax1 suggest the increase of amh expression and the decline of dax1 expression are important for the activation of testis development, and the high level of amh and a low level of dax1 expression are necessary for maintenance of testis function. PMID:26578091

  3. New Deferoxamine Glycoconjugates Produced upon Overexpression of Pathway-Specific Regulatory Gene in the Marine Sponge-Derived Streptomyces albus PVA94-07.

    PubMed

    Sekurova, Olga N; Pérez-Victoria, Ignacio; Martín, Jesús; Degnes, Kristin F; Sletta, Håvard; Reyes, Fernando; Zotchev, Sergey B

    2016-08-27

    Activation of silent biosynthetic gene clusters in Streptomyces bacteria via overexpression of cluster-specific regulatory genes is a promising strategy for the discovery of novel bioactive secondary metabolites. This approach was used in an attempt to activate a cryptic gene cluster in a marine sponge-derived Streptomyces albus PVA94-07 presumably governing the biosynthesis of peptide-based secondary metabolites. While no new peptide-based metabolites were detected in the recombinant strain, it was shown to produce at least four new analogues of deferoxamine with additional acyl and sugar moieties, for which chemical structures were fully elucidated. Biological activity tests of two of the new deferoxamine analogues revealed weak activity against Escherichia coli. The gene knockout experiment in the gene cluster targeted for activation, as well as overexpression of certain genes from this cluster did not have an effect on the production of these compounds by the strain overexpressing the regulator. It seems plausible that the production of such compounds is a response to stress imposed by the production of an as-yet unidentified metabolite specified by the cryptic cluster.

  4. Effects of intercropping of oat (Avena sativa L.) with white lupin (Lupinus albus L.) on the mobility of target elements for phytoremediation and phytomining in soil solution.

    PubMed

    Wiche, Oliver; Székely, Balazs; Kummer, Nicolai-Alexeji; Moschner, Christin; Heilmeier, Hermann

    2016-09-01

    This study aims to investigate how intercropping of oat (Avena sativa L.) with white lupin (Lupinus albus L.) affects the mobile fractions of trace metals (Fe, Mn, Pb, Cd, Th, U, Sc, La, Nd, Ge) in soil solution. Oat and white lupin were cultivated in monocultures and mixed cultures with differing oat/white lupin ratios (11% and 33% lupin, respectively). Temporal variation of soil solution chemistry was compared with the mobilization of elements in the rhizosphere of white lupin and concentrations in plant tissues. Relative to the monocrops, intercropping of oat with 11% white lupin significantly increased the concentrations of Fe, Pb, Th, La and Nd in soil solution as well as the concentrations of Fe, Pb, Th, Sc, La and Nd in tissues of oat. Enhanced mobility of the mentioned elements corresponded to a depletion of elements in the rhizosphere soil of white lupin. In mixed cultures with 33% lupin, concentrations in soil solution only slightly increased. We conclude that intercropping with 11% white lupin might be a promising tool for phytoremediation and phytomining research enhancing mobility of essential trace metals as well as elements with relevance for phytoremediation (Pb, Th) and phytomining (La, Nd, Sc) in soil. PMID:26940160

  5. Isotherms and kinetic study of dihydrogen and hydrogen phosphate ions (H{2}PO{4}- and HPO{4}2-) adsorption onto crushed plant matter of the semi-arid zones of Morocco: Asphodelus microcarpus, Asparagus albus and Senecio anthophorbium

    NASA Astrophysics Data System (ADS)

    Chiban, M.; Benhima, H.; Saadi, B.; Nounah, A.; Sinan, F.

    2005-03-01

    In the present work H{2}PO4- and HPO42- ions adsorption onto organic matter (OM) obtained from ground dried three plants growing in arid zones of Morocco has been studied. The adsorption process is affected by various parameters such as contact time, particle size and initial concentration of phosphate solution (Ci ≤ 30 mg/l). The uptake of both ions is increased by increasing the concentration of them selves. The retention of phosphate ions by Asphodelus microcarpus, Asparagus albus are well defined by several isotherms such as the Langmuir, Temkin and Freundlich.

  6. Abyssicoccus albus gen. nov., sp. nov., a novel member of the family Staphylococcaceae isolated from marine sediment of the Indian Ocean.

    PubMed

    Jiang, Zhao; Yuan, Chang-Guo; Xiao, Min; Tian, Xin-Peng; Khan, Inam-Ullah; Kim, Chang-Jin; Zhi, Xiao-Yang; Li, Wen-Jun

    2016-08-01

    A Gram-stain positive, aerobic, non-motile, asporogenous, coccoid shaped bacterium, designated YIM M12140(T), was isolated from a marine sediment sample collected from the Indian Ocean. Phylogenetic analysis showed that strain YIM M12140(T) forms a separate clade within the family Staphylococcaceae. Strain YIM M12140(T) shares high 16S rRNA gene sequence similarity with Macrococcus brunensis DSM 19358(T) (92.9 %). The isolate was found to grow at 0-10 % (w/v) NaCl (optimum, 2-3 %), pH 6.0-10.0 (optimum, pH 8.0) and temperature 5-40 °C (optimum, 28 °C). The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid and two unidentified polar lipids. The major cellular fatty acids of the strain were identified as anteiso-C15:0, -C17:0, iso-C16:0, anteiso-C19:0 and C20:0. The respiratory menaquinones were found to be MK-6 (94 %) and MK-7 (6 %). The cell wall amino acids were found to contain Lys, Ala, Glu, Gly, Asp, Ser and Thr. Whole cell sugars were identified as mannose, ribose, rhamnose, glucose, galactose and xylose. The G+C content of the genomic DNA of strain YIM M12140(T) was determined to be 42.4 mol %. Based on phenotypic, chemotaxonomic data and phylogenetic analysis, it is proposed that strain YIM M12140(T) represents a novel species of a new genus in the family Staphylococcaceae, for which the name Abyssicoccus albus gen. nov., sp. nov. is proposed. The type strain is YIM M12140(T) (= DSM 29158(T) = CCTCC AB 2014213(T)).

  7. The regulatory network of cluster-root function and development in phosphate-deficient white lupin (Lupinus albus) identified by transcriptome sequencing.

    PubMed

    Wang, Zhengrui; Straub, Daniel; Yang, Huaiyu; Kania, Angelika; Shen, Jianbo; Ludewig, Uwe; Neumann, Günter

    2014-07-01

    Lupinus albus serves as model plant for root-induced mobilization of sparingly soluble soil phosphates via the formation of cluster-roots (CRs) that mediate secretion of protons, citrate, phenolics and acid phosphatases (APases). This study employed next-generation sequencing to investigate the molecular mechanisms behind these complex adaptive responses at the transcriptome level. We compared different stages of CR development, including pre-emergent (PE), juvenile (JU) and the mature (MA) stages. The results confirmed that the primary metabolism underwent significant modifications during CR maturation, promoting the biosynthesis of organic acids, as had been deduced from physiological studies. Citrate catabolism was downregulated, associated with citrate accumulation in MA clusters. Upregulation of the phenylpropanoid pathway reflected the accumulation of phenolics. Specific transcript expression of ALMT and MATE transporter genes correlated with the exudation of citrate and flavonoids. The expression of transcripts related to nucleotide degradation and APases in MA clusters coincided with the re-mobilization and hydrolysis of organic phosphate resources. Most interestingly, hormone-related gene expression suggested a central role of ethylene during CR maturation. This was associated with the upregulation of the iron (Fe)-deficiency regulated network that mediates ethylene-induced expression of Fe-deficiency responses in other species. Finally, transcripts related to abscisic acid and jasmonic acid were upregulated in MA clusters, while auxin- and brassinosteroid-related genes and cytokinin receptors were most strongly expressed during CR initiation. Key regulations proposed by the RNA-seq data were confirmed by quantitative real-time polymerase chain reaction (RT-qPCR) and some physiological analyses. A model for the gene network regulating CR development and function is presented. PMID:24635386

  8. Ectomycorrhizal Pisolithus albus inoculation of Acacia spirorbis and Eucalyptus globulus grown in ultramafic topsoil enhances plant growth and mineral nutrition while limits metal uptake.

    PubMed

    Jourand, Philippe; Hannibal, Laure; Majorel, Clarisse; Mengant, Stéphane; Ducousso, Marc; Lebrun, Michel

    2014-01-15

    Ectomycorrhizal fungi (ECM) isolates of Pisolithus albus (Cooke and Massee) from nickel-rich ultramafic topsoils in New Caledonia were inoculated onto Acacia spirorbis Labill. (an endemic Fabaceae) and Eucalyptus globulus Labill. (used as a Myrtaceae plant host model). The aim of the study was to analyze the growth of symbiotic ECM plants growing on the ultramafic substrate that is characterized by high and toxic metal concentrations i.e. Co, Cr, Fe, Mn and Ni, deficient concentrations of plant essential nutrients such as N, P, K, and that presents an unbalanced Ca/Mg ratio (1/19). ECM inoculation was successful with a plant level of root mycorrhization up to 6.7%. ECM symbiosis enhanced plant growth as indicated by significant increases in shoot and root biomass. Presence of ECM enhanced uptake of major elements that are deficient in ultramafic substrates; in particular P, K and Ca. On the contrary, the ECM symbioses strongly reduced transfer to plants of element in excess in soils; in particular all metals. ECM-inoculated plants released metal complexing molecules as free thiols and oxalic acid mostly at lower concentrations than in controls. Data showed that ECM symbiosis helped plant growth by supplying uptake of deficient elements while acting as a protective barrier to toxic metals, in particular for plants growing on ultramafic substrate with extreme soil conditions. Isolation of indigenous and stress-adapted beneficial ECM fungi could serve as a potential tool for inoculation of ECM endemic plants for the successful restoration of ultramafic ecosystems degraded by mining activities.

  9. Abyssicoccus albus gen. nov., sp. nov., a novel member of the family Staphylococcaceae isolated from marine sediment of the Indian Ocean.

    PubMed

    Jiang, Zhao; Yuan, Chang-Guo; Xiao, Min; Tian, Xin-Peng; Khan, Inam-Ullah; Kim, Chang-Jin; Zhi, Xiao-Yang; Li, Wen-Jun

    2016-08-01

    A Gram-stain positive, aerobic, non-motile, asporogenous, coccoid shaped bacterium, designated YIM M12140(T), was isolated from a marine sediment sample collected from the Indian Ocean. Phylogenetic analysis showed that strain YIM M12140(T) forms a separate clade within the family Staphylococcaceae. Strain YIM M12140(T) shares high 16S rRNA gene sequence similarity with Macrococcus brunensis DSM 19358(T) (92.9 %). The isolate was found to grow at 0-10 % (w/v) NaCl (optimum, 2-3 %), pH 6.0-10.0 (optimum, pH 8.0) and temperature 5-40 °C (optimum, 28 °C). The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, one unidentified aminophospholipid and two unidentified polar lipids. The major cellular fatty acids of the strain were identified as anteiso-C15:0, -C17:0, iso-C16:0, anteiso-C19:0 and C20:0. The respiratory menaquinones were found to be MK-6 (94 %) and MK-7 (6 %). The cell wall amino acids were found to contain Lys, Ala, Glu, Gly, Asp, Ser and Thr. Whole cell sugars were identified as mannose, ribose, rhamnose, glucose, galactose and xylose. The G+C content of the genomic DNA of strain YIM M12140(T) was determined to be 42.4 mol %. Based on phenotypic, chemotaxonomic data and phylogenetic analysis, it is proposed that strain YIM M12140(T) represents a novel species of a new genus in the family Staphylococcaceae, for which the name Abyssicoccus albus gen. nov., sp. nov. is proposed. The type strain is YIM M12140(T) (= DSM 29158(T) = CCTCC AB 2014213(T)). PMID:27272908

  10. Seasonal population dynamics of Pallisentis (Neosentis) celatus (Acanthocephala: Quadrigyridae) in the intestine of the rice-field eel Monopterus albus in China.

    PubMed

    Boping, Zeng; Wenbin, Wang

    2007-12-01

    Studies on the seasonal population dynamics of Pallisentis (Neosentis) celatus (Acanthocephala: Quadrigyridae) in the intestine of the rice-field eel Monopterus albus from the paddies and ditches in the Dong-ting Lake basin of China, were carried out with samples taken from June 2002 to May 2003. Prevalences were above 21% in all seasons sampled and with a distinct seasonal trend, which was highest (45.81%) in the spring and decreased by degrees. The mean intensity of infection was above 4.0 worms per fish. The maximum intensity of worms recovered from a single fish was 86 in the autumn of 2002. No significant seasonal differences were found in mean intensities, and differences in the mean abundance between winter and spring, winter and autumn were significant. Over-dispersed distributions of P. (N.) celatus in the host population, due to heterogeneity and feeding habits, were observed in all seasons. The size composition of both sexes of P. (N.) celatus showed males between 2.0 mm and 14.0 mm and females between 2.2 mm and 22.2 mm, with the main recruitment phase in the worm populations occurring in the summer and autumn, especially in the autumn, with the lowest recruitment occurring in the winter. The maturation and copulation of worms were mainly focused in the spring season. The sex ratio of female to male was both high in summer (1.09:1) and autumn (1.08:1). The higher proportion of females and the change in the worm sex ratio in summer can be attributed to the reduced longevity of male worms. As immature male worms exhibit a higher proportion of the worm population than females in all seasons, further studies are needed to determine if such a situation compensates for the shorter life span of males.

  11. Application of non-lethal stable isotope analysis to assess feeding patterns of juvenile pallid sturgeon Scaphirhynchus albus: a comparison of tissue types and sample preservation methods

    USGS Publications Warehouse

    Andvik, R.T.; VanDeHey, J.A.; Fincel, M.J.; French, William E.; Bertrand, K.N.; Chipps, Steven R.; Klumb, R.A.; Graeb, B.D.S.

    2010-01-01

    Traditional techniques for stable isotope analysis (SIA) generally require sacrificing animals to collect tissue samples; this can be problematic when studying diets of endangered species such as the pallid sturgeon Scaphirhynchus albus. Our objectives were to (i) determine if pectoral fin tissue (non-lethal) could be a substitute for muscle tissue (lethal) in SIA of juvenile pallid sturgeon, and (ii) evaluate the influence of preservation techniques on stable isotope values. In the laboratory, individual juvenile pallid sturgeon were held for up to 186 day and fed chironomids, fish, or a commercially available pellet diet. Significant, positive relationships (r² ≥ 0.8) were observed between fin and muscle tissues for both δ15N and δ13C; in all samples isotopes were enriched in fins compared to muscle tissue. Chironomid and fish based diets of juvenile pallid sturgeon were distinguishable for fast growing fish (0.3 mm day−1) using stable δ15N and δ13C isotopes. Frozen and preserved fin tissue δ15N isotopes were strongly related (r2 = 0.89) but δ13C isotopes were weakly related (r2 = 0.16). Therefore, freezing is recommended for preservation of fin clips to avoid the confounding effect of enrichment by ethanol. This study demonstrates the utility of a non-lethal technique to assess time integrated food habits of juvenile pallid sturgeon and should be applicable to other threatened or endangered species.

  12. Dietary micronized-dehulled white lupin (Lupinus albus L.) in meat-type guinea fowls and its influence on growth performance, carcass traits and meat lipid profile.

    PubMed

    Tufarelli, V; Demauro, R; Laudadio, V

    2015-10-01

    The present study aimed to evaluate the effects of dietary substitution of soybean meal (SBM) with micronized-dehulled white lupin (Lupinus albus L. cv. Multitalia) in guinea fowl broilers on their growth performance, carcass traits, and meat fatty acids composition. A total of 120 one-day-old guinea fowl females were randomly assigned to 2 treatments which were fed from hatch to 12 wk of age. Birds were fed 2 wheat middlings-based diets comprising of a control treatment which contained SBM (195 g/kg) and a test diet containing micronized-dehulled lupin (240 g/kg) as the main protein source. Replacing SBM with treated lupin had no adverse effect on growth traits, dressing percentage, or breast and thigh muscles relative to the weight of guinea fowls. A decrease (P < 0.05) of abdominal fat was found in guinea fowls fed lupin-diet. Breast muscle from birds fed lupin had higher lightness (L*) (P < 0.01) and redness (a*) (P < 0.05) scores and water-holding capacity (P < 0.05) than the SBM-control diet. Meat from guinea fowls fed lupin had less total lipids (P < 0.05) and cholesterol (P < 0.01), and higher concentrations of phospholipids (P < 0.01). Feeding treated lupin increased polyunsaturated fatty acid (PUFA) levels in breast meat and decreased saturated fatty acid (SFA) concentrations. Our findings suggest that replacing SBM as protein source with micronized-dehulled lupin in meat-type guinea fowl diet can improve carcass qualitative characteristics, enhancing also meat lipid profile with no effect on growth traits.

  13. Potential of tannin-rich plants for modulating ruminal microbes and ruminal fermentation in sheep.

    PubMed

    Rira, M; Morgavi, D P; Archimède, H; Marie-Magdeleine, C; Popova, M; Bousseboua, H; Doreau, M

    2015-01-01

    The objective of this work was to study nutritional strategies for decreasing methane production by ruminants fed tropical diets, combining in vitro and in vivo methods. The in vitro approach was used to evaluate the dose effect of condensed tannins (CT) contained in leaves of Gliricidia sepium, Leucaena leucocephala, and Manihot esculenta (39, 75, and 92 g CT/kg DM, respectively) on methane production and ruminal fermentation characteristics. Tannin-rich plants (TRP) were incubated for 24 h alone or mixed with a natural grassland hay based on Dichanthium spp. (control plant), so that proportions of TRP were 0, 0.25, 0.5, 0.75, and 1.0. Methane production, VFA concentration, and fermented OM decreased with increased proportions of TRP. Numerical differences on methane production and VFA concentration among TRP sources may be due to differences in their CT content, with greater effects for L. leucocephala and M. esculenta than for G. sepium. Independently of TRP, the response to increasing doses of CT was linear for methane production but quadratic for VFA concentration. As a result, at moderate tannin dose, methane decreased more than VFA. The in vivo trial was conducted to investigate the effect of TRP on different ruminal microbial populations. To this end, 8 rumen-cannulated sheep from 2 breeds (Texel and Blackbelly) were used in two 4 × 4 Latin square designs. Diets were fed ad libitum and were composed of the same feeds used for the in vitro trial: control plant alone or combined with pellets made from TRP leaves at 44% of the diet DM. Compared to TRP, concentration of Ruminococcus flavefaciens was greater for the control diet and concentration of Ruminococcus albus was least for the control diet. The methanogen population was greater for Texel than for Blackbelly. By contrast, TRP-containing diets did not affect protozoa or Fibrobacter succinogenes numbers. Hence, TRP showed potential for mitigating methane production by ruminants. These findings suggest

  14. Effects of Dietary Forage and Calf Starter Diet on Ruminal pH and Bacteria in Holstein Calves during Weaning Transition

    PubMed Central

    Kim, Yo-Han; Nagata, Rie; Ohtani, Natsuki; Ichijo, Toshihiro; Ikuta, Kentaro; Sato, Shigeru

    2016-01-01

    We investigated the relationship between ruminal pH and bacteria in calves fed calf starter with and without forage during weaning transition. First, 16 Holstein bull calves were obtained from dairy farms and equipped with rumen cannulas by cannulation surgery. Then, calves (73.5 ± 4.2 kg; mean ± SE) were assigned to groups fed calf starter either with forage (HAY, n = 8) or without forage (CON, n = 8), and all calves were weaned at 8 weeks of age. Ruminal pH was measured continuously, and rumen fluid samples were collected at 7, 8, 9, and 11 weeks of age, namely −1, 0, 1, and 3 weeks after weaning, respectively, to assess volatile fatty acid concentrations and bacterial DNA. The 24-h mean ruminal pH was significantly (P < 0.05) different between the two groups. Diurnal changes in the 1-h mean ruminal pH were observed throughout the study in the HAY group; however, they were not observed at 0 and 1 weeks after weaning in the CON group. Moreover, the HAY group had significantly (P < 0.05) higher proportions of acetate and butyrate and lower proportion of propionate, and significantly (P < 0.05) lower ruminal acetate-to-propionate ratios were observed in the CON group. The ruminal bacterial diversity indices decreased after −1 week in both groups and increased at 0 and 1 weeks after weaning in the HAY and CON groups, respectively. From the 454 pyrosequencing analysis, significant differences (P < 0.05) were observed in the relative abundance of several phyla (Bacteroidetes, Actinobacteria, and Tenericutes) and one genus (Prevotella) between the two groups. From quantitative real-time PCR analysis, the HAY group had the higher copy numbers of cellulolytic bacteria (Ruminococcus flavefaciens and Ruminococcus albus) compared with the CON group. This study demonstrated that feeding of dietary forage alleviates subacute ruminal acidosis due to diurnal changes in ruminal pH. Furthermore, changes in ruminal pH affect the ruminal bacterial diversity and relative

  15. Effects of dietary supplementation of rumen-protected folic acid on rumen fermentation, degradability and excretion of urinary purine derivatives in growing steers.

    PubMed

    Wang, Cong; Liu, Qiang; Guo, Gang; Huo, WenJie; Ma, Le; Zhang, YanLi; Pei, CaiXia; Zhang, ShuanLin; Wang, Hao

    2016-12-01

    The present experiment was undertaken to determine the effects of dietary addition of rumen-protected folic acid (RPFA) on ruminal fermentation, nutrient degradability, enzyme activity and the relative quantity of ruminal cellulolytic bacteria in growing beef steers. Eight rumen-cannulated Jinnan beef steers averaging 2.5 years of age and 419 ± 1.9 kg body weight were used in a replicated 4 × 4 Latin square design. The four treatments comprised supplementation levels of 0 (Control), 70, 140 and 210 mg RPFA/kg dietary dry matter (DM). On DM basis, the ration consisted of 50% corn silage, 47% concentrate and 3% soybean oil. The DM intake (averaged 8.5 kg/d) was restricted to 95% of ad libitum intake. The intake of DM, crude protein (CP) and net energy for growth was not affected by treatments. In contrast, increasing RPFA supplementation increased average daily gain and the concentration of total volatile fatty acid and reduced ruminal pH linearly. Furthermore, increasing RPFA supplementation enhanced the acetate to propionate ratio and reduced the ruminal ammonia N content linearly. The ruminal effective degradability of neutral detergent fibre from corn silage and CP from concentrate improved linearly and was highest for the highest supplementation levels. The activities of cellobiase, xylanase, pectinase and α-amylase linearly increased, but carboxymethyl-cellulase and protease were not affected by the addition of RPFA. The relative quantities of Butyrivibrio fibrisolvens, Ruminococcus albus, Ruminococcus flavefaciens and Fibrobacter succinogenes increased linearly. With increasing RPFA supplementation levels, the excretion of urinary purine derivatives was also increased linearly. The present results indicated that the supplementation of RPFA improved ruminal fermentation, nutrient degradability, activities of microbial enzymes and the relative quantity of the ruminal cellulolytic bacteria in a dose-dependent manner. According to the conditions of this

  16. Effect of tannins and saponins in Samanea saman on rumen environment, milk yield and milk composition in lactating dairy cows.

    PubMed

    Anantasook, N; Wanapat, M; Cherdthong, A; Gunun, P

    2015-04-01

    The objective of this study was to investigate the effects of tannins and saponins in Samanea saman on rumen fermentation, milk yield and milk composition in lactating dairy cows. Four multiparous early-lactating dairy cows (Holstein-Friesian cross-bred, 75%) with an initial body weight (BW) of 405 ± 40 kg and 36 ± 8 day in milk were randomly assigned to receive dietary treatments according to a 4 × 4 Latin square design. The four dietary treatments were unsupplemented (control), supplemented with rain tree pod (S. saman) meal (RPM) at 60 g/kg, supplemented with palm oil (PO) at 20 g/kg, and supplemented with RPM at 60 g/kg and PO at 20 g/kg (RPO), of total dry matter (DM) intake. Cows were fed with concentrate diets at a ratio of concentrate to milk yield of 1:2, and chopped 30 g/kg of urea-treated rice straw was fed ad libitum. The RPM contained condensed tannins and crude saponins at 88 and 141 g/kg of DM respectively. It was found that supplementation with RPM and/or PO to dairy cows diets did not show negative effect on ruminal pH, blood urea nitrogen and milk urea nitrogen concentration (p > 0.05). However, supplementation with RPM resulted in lower ammonia nitrogen (NH3 -N) concentration (p < 0.05). In addition, propionic acid and milk production increased while acetic acid, acetic to propionic ratio, methane production, methanogens and protozoal population decreased with RPM and/or PO supplementation. Furthermore, addition of PO and RPO in the diets increased milk fat while supplementation of RPM resulted in greater milk protein and Fibrobacter succinogenes numbers (p < 0.05). The population of Ruminococcus flavefaciens and Ruminococcus albus were not affected by any treatments. The findings on the present study showed that supplementation with RPM and RPO to diets of cows improved the rumen environment and increased milk yield, content of milk protein and milk fat.

  17. Rumen microorganisms, methane production, and microbial protein synthesis affected by mangosteen peel powder supplement in lactating dairy cows.

    PubMed

    Polyorach, Sineenart; Wanapat, Metha; Cherdthong, Anusorn; Kang, Sungchhang

    2016-03-01

    Four crossbred dairy cows (50 % Holstein-Friesian × 50 % Thai native), 404 ± 50.0 kg of body weight (4 years old) and 90 ± 5 day in milk with daily milk production of 9 ± 2.0 kg/day, were randomly assigned according to a 4 × 4 Latin square design to study the effect of mangosteen (Garcinia mangostana) peel powder (MSP) supplementation on rumen microorganisms, methane production, and microbial protein synthesis fed concentrate containing yeast fermented cassava chip protein (YEFECAP). The treatments were different levels of MSP supplementation at 0, 100, 200, and 300 g/head/day. Rice straw was used as a roughage source fed ad libitum, and concentrate containing YEFECAP at 200 g/kg concentrate was offered corresponding to concentrate-to-milk-yield ratio at 1:2. A quantitative real-time PCR approach was used to determine the population densities of ruminal microorganisms. The results revealed that supplementation of MSP did not affect on Fibrobactor succinogenes, Ruminococcus flavefaciens, and Ruminococcus albus (P > 0.05). However, total bacteria was linearly increased (P < 0.01) while methanogens and protozoal population were linearly decreased (P < 0.01) with increasing level of MSP supplementation. Increasing level of MSP supplement could decrease rumen methane production from 27.5 to 23.7 mmol/100 ml(3). Furthermore, cows that received MSP at 300 g/head/day had the highest microbial crude protein and efficiency of rumen microbial N synthesis (416.8 g/day and 16.2 g/kg organic matter truly digested in the rumen (OMDR), respectively). In conclusion, supplementation of MSP at 300 g/head/day with YEFECAP as a protein source in the concentrate mixture revealed an enhancement of rumen fermentation and methane reduction in lactating dairy cows.

  18. Potential of tannin-rich plants for modulating ruminal microbes and ruminal fermentation in sheep.

    PubMed

    Rira, M; Morgavi, D P; Archimède, H; Marie-Magdeleine, C; Popova, M; Bousseboua, H; Doreau, M

    2015-01-01

    The objective of this work was to study nutritional strategies for decreasing methane production by ruminants fed tropical diets, combining in vitro and in vivo methods. The in vitro approach was used to evaluate the dose effect of condensed tannins (CT) contained in leaves of Gliricidia sepium, Leucaena leucocephala, and Manihot esculenta (39, 75, and 92 g CT/kg DM, respectively) on methane production and ruminal fermentation characteristics. Tannin-rich plants (TRP) were incubated for 24 h alone or mixed with a natural grassland hay based on Dichanthium spp. (control plant), so that proportions of TRP were 0, 0.25, 0.5, 0.75, and 1.0. Methane production, VFA concentration, and fermented OM decreased with increased proportions of TRP. Numerical differences on methane production and VFA concentration among TRP sources may be due to differences in their CT content, with greater effects for L. leucocephala and M. esculenta than for G. sepium. Independently of TRP, the response to increasing doses of CT was linear for methane production but quadratic for VFA concentration. As a result, at moderate tannin dose, methane decreased more than VFA. The in vivo trial was conducted to investigate the effect of TRP on different ruminal microbial populations. To this end, 8 rumen-cannulated sheep from 2 breeds (Texel and Blackbelly) were used in two 4 × 4 Latin square designs. Diets were fed ad libitum and were composed of the same feeds used for the in vitro trial: control plant alone or combined with pellets made from TRP leaves at 44% of the diet DM. Compared to TRP, concentration of Ruminococcus flavefaciens was greater for the control diet and concentration of Ruminococcus albus was least for the control diet. The methanogen population was greater for Texel than for Blackbelly. By contrast, TRP-containing diets did not affect protozoa or Fibrobacter succinogenes numbers. Hence, TRP showed potential for mitigating methane production by ruminants. These findings suggest

  19. Effect of tannins and saponins in Samanea saman on rumen environment, milk yield and milk composition in lactating dairy cows.

    PubMed

    Anantasook, N; Wanapat, M; Cherdthong, A; Gunun, P

    2015-04-01

    The objective of this study was to investigate the effects of tannins and saponins in Samanea saman on rumen fermentation, milk yield and milk composition in lactating dairy cows. Four multiparous early-lactating dairy cows (Holstein-Friesian cross-bred, 75%) with an initial body weight (BW) of 405 ± 40 kg and 36 ± 8 day in milk were randomly assigned to receive dietary treatments according to a 4 × 4 Latin square design. The four dietary treatments were unsupplemented (control), supplemented with rain tree pod (S. saman) meal (RPM) at 60 g/kg, supplemented with palm oil (PO) at 20 g/kg, and supplemented with RPM at 60 g/kg and PO at 20 g/kg (RPO), of total dry matter (DM) intake. Cows were fed with concentrate diets at a ratio of concentrate to milk yield of 1:2, and chopped 30 g/kg of urea-treated rice straw was fed ad libitum. The RPM contained condensed tannins and crude saponins at 88 and 141 g/kg of DM respectively. It was found that supplementation with RPM and/or PO to dairy cows diets did not show negative effect on ruminal pH, blood urea nitrogen and milk urea nitrogen concentration (p > 0.05). However, supplementation with RPM resulted in lower ammonia nitrogen (NH3 -N) concentration (p < 0.05). In addition, propionic acid and milk production increased while acetic acid, acetic to propionic ratio, methane production, methanogens and protozoal population decreased with RPM and/or PO supplementation. Furthermore, addition of PO and RPO in the diets increased milk fat while supplementation of RPM resulted in greater milk protein and Fibrobacter succinogenes numbers (p < 0.05). The population of Ruminococcus flavefaciens and Ruminococcus albus were not affected by any treatments. The findings on the present study showed that supplementation with RPM and RPO to diets of cows improved the rumen environment and increased milk yield, content of milk protein and milk fat. PMID:24814291

  20. Microtus species as new herbivorous laboratory animals: reproduction; bacterial flora and fermentation in the digestive tracts; and nutritional physiology.

    PubMed

    Kudo, H; Oki, Y

    1984-05-01

    In a study of the possible introduction of Japanese field vole (Microtus montebelli ) and Hungarian voles (M. arvalis) as herbivorous experimental animals, the following biological characteristics were investigated: breeding and reproductive performance; bacterial flora and fermentation in the digestive tracts; and nutritional physiology. The animals are polyestrus , show postpartum estrus on the day of parturition, and there is little or no delay in implantation due to lactation, especially in M. arvalis. On examination of vaginal smears, Japanese field vole did not show any definite pattern, whereas most Hungarian voles showed 6- to 18- day cycles. From the esophageal sac of voles fed rations with a high fiber content, cellulolytic bacteria similar to Ruminococcus albus, Ruminococcus flavefaciens , and Bacteroides succinogenes were isolated. More than 1 000 000/g anaerobic bacteria were present in the esophageal sac and the pattern and the types of bacteria resembled those found in the rumen. Gastric fermentation took place in the esophageal sac. The pH and total VFAs were much smaller in the fundic and pyloric regions of the stomach than in the esophageal sac. Acetic and lactic acids were the major fermentation products in the esophageal sac. Following deficiency or lowering of the cellulose decomposing abilities, a decrease of VFAs and an increase in lactic acid production in the esophageal sac were observed. These effects resulted in high glucose, FFA and ketone bodies in the blood, and a higher incidence of glucosuria. Diabetes induced by administrations of drugs such as alloxan, streptozotocin and phloridzin were compared using Microtus and mice. Microtus had low sensitivity to alloxan but high sensitivity to streptozotocin. The influence of monensin on Microtus was also investigated by using diets containing 20 and 80 mg/kg monensin. Diets containing 80 mg/kg monensin led to 50 % mortality in 7 weeks and growth was hindered. Gas production from the

  1. Effects of Protein Level and Mangosteen Peel Pellets (Mago-pel) in Concentrate Diets on Rumen Fermentation and Milk Production in Lactating Dairy Crossbreds

    PubMed Central

    Norrapoke, T.; Wanapat, M.; Wanapat, S.

    2012-01-01

    Four, lactating dairy crossbreds (50%×50% Holstein Friesian×Native Zebu cattle) were randomly assigned according to a 2×2 factorial arrangement (two protein levels and two levels of mangosteen peel pellets (Mago-pel)) in a 4×4 Latin square design to receive four dietary treatments. All cows received concentrate at a proportion of 1 kg concentrate per 2 kg of milk yield, and urea-treated 5% rice straw (UTRS) was given ad libitum. It was found that total dry matter intakes, nutrient digestibility, ruminal pH and NH3-N concentrations were not affected (p>0.05) by treatments. Concentrations of ruminal pH and NH3-N were not affected by dietary treatments although the concentration of BUN varied significantly (p<0.05) between protein levels (p<0.05). The populations of rumen bacteria and fungal zoospores did not differ among treatments (p>0.05); however, the population of protozoa was decreased (p<0.05) when cows received Mago-pel supplementation. The composition of the population of bacteria, identified by real-time PCR technique, including total bacteria, methanogens, Fibrobacter succinogenes and Ruminococcus albus was similar (p>0.05) among dietary treatments (p>0.05); however, copy numbers of Ruminococcus flavefaciens was increased when protein level increased (p<0.05). Microbial protein synthesis, in terms of both quantity and efficiency, was enriched by Mago-pel supplementation. Milk yield was greatest in cows fed UTRS based diets with concentrate containing protein at 16% CP with Mago-pel, but were lowest without Mago-pel (p<0.05). In addition, protein level and supplementation of Mago-pel did not affect (p>0.05) milk composition except solids-not-fat which was higher in cows fed the diet with 19% CP. Therefore, feeding a concentrate containing 16% CP together with 300 g/hd/d Mago-pel supplementation results in changes in rumen fermentation and microbial population and improvements in milk production in lactating dairy crossbreds fed on UTRS. PMID:25049652

  2. Improved assay for quantitating adherence of ruminal bacteria to cellulose.

    PubMed Central

    Rasmussen, M A; White, B A; Hespell, R B

    1989-01-01

    A quantitative technique suitable for the determination of adherence of ruminal bacteria to cellulose was developed. This technique employs adherence of cells to cellulose disks and alleviates the problem of nonspecific cell entrapment within cellulose particles. By using this technique, it was demonstrated that the adherence of Ruminococcus flavefaciens FD1 to cellulose was inhibited by formaldehyde, methylcellulose, and carboxymethyl cellulose. Adherence was unaffected by acid hydrolysates of methylcellulose, glucose, and cellobiose. PMID:2782879

  3. Effects of extracts of lupine seed on blood glucose levels in glucose resistant mice: antihyperglycemic effects of Lupinus albus (white lupine, Egypt) and Lupinus caudatus (tailcup lupine, Mesa Verde National Park).

    PubMed

    Knecht, Kathryn T; Nguyen, Hoa; Auker, Adrienne D; Kinder, David H

    2006-01-01

    Lupine is a medicinal food plant with potential value in the management of diabetes. In white mice, extracts of seeds of the white lupine [Lupinus albus (L. termis L.)] were associated with increased tolerance to an oral glucose bolus. Antihyperglycemic activity was present in extracts of the whole seed but not extracts of the seed coat, and was not detected when glucose was administered intraperitoneally rather than orally. However, in contrast to results seen with the prescription drug, acarbose, lupine extract did not appear to increase the bulk or carbohydrate content of the feces. Antihyperglycemic activity was also seen in extracts of the tailcup lupine (L. caudatus) found in the Four Corners Region of the United States. PMID:17317651

  4. The rotation of white lupin (Lupinus albus L.) with metal-accumulating plant crops: a strategy to increase the benefits of soil phytoremediation.

    PubMed

    Fumagalli, Pietro; Comolli, Roberto; Ferrè, Chiara; Ghiani, Alessandra; Gentili, Rodolfo; Citterio, Sandra

    2014-12-01

    Most of the plants employed to remove metals from contaminated soils are annuals and have a seed-to-seed life cycle of a few months, usually over spring and summer. Consequently, for most of the year, fields are not actively cleaned but are completely bare and subject to erosion by water and wind. The objective of this study was to evaluate the benefits of using Lupinus albus as a winter crop in a rotation sequence with a summer crop ideally selected for phytoextraction, such as industrial hemp. Lupin plants were grown in two alkaline soil plots (heavy metal-contaminated and uncontaminated) of approximately 400 m(2) each after the cultivation and harvest of industrial hemp. A smaller-scale parallel pot experiment was also performed to better understand the lupin behavior in increasing concentrations of Cd, Cu, Ni and Zn. White lupin grew well in alkaline conditions, covering the soil during the winter season. In few months plants were approximately 40-50 cm high in both control and contaminated plots. In fields where the bioavailable fraction of metals was low (less than 12%), plants showed a high tolerance to these contaminants. However, their growth was affected in some pot treatments in which the concentrations of assimilable Cu, Zn and Ni were higher, ranging from approximately 40-70% of the total concentrations. The lupin's ability to absorb heavy metals and translocate them to shoots was negligible with respect to the magnitude of contamination, suggesting that this plant is not suitable for extending the period of phytoextraction. However, it is entirely exploitable as green manure, avoiding the application of chemical amendments during phytoremediation. In addition, in polluted fields, white lupin cultivation increased the soil concentration of live bacteria and the bioavailable percentage of metals. On average live bacteria counts per gram of soil were 65×10(6)±18×10(6) and 99×10(6)±22*10(6) before and after cultivation, respectively. The percentages

  5. The rotation of white lupin (Lupinus albus L.) with metal-accumulating plant crops: a strategy to increase the benefits of soil phytoremediation.

    PubMed

    Fumagalli, Pietro; Comolli, Roberto; Ferrè, Chiara; Ghiani, Alessandra; Gentili, Rodolfo; Citterio, Sandra

    2014-12-01

    Most of the plants employed to remove metals from contaminated soils are annuals and have a seed-to-seed life cycle of a few months, usually over spring and summer. Consequently, for most of the year, fields are not actively cleaned but are completely bare and subject to erosion by water and wind. The objective of this study was to evaluate the benefits of using Lupinus albus as a winter crop in a rotation sequence with a summer crop ideally selected for phytoextraction, such as industrial hemp. Lupin plants were grown in two alkaline soil plots (heavy metal-contaminated and uncontaminated) of approximately 400 m(2) each after the cultivation and harvest of industrial hemp. A smaller-scale parallel pot experiment was also performed to better understand the lupin behavior in increasing concentrations of Cd, Cu, Ni and Zn. White lupin grew well in alkaline conditions, covering the soil during the winter season. In few months plants were approximately 40-50 cm high in both control and contaminated plots. In fields where the bioavailable fraction of metals was low (less than 12%), plants showed a high tolerance to these contaminants. However, their growth was affected in some pot treatments in which the concentrations of assimilable Cu, Zn and Ni were higher, ranging from approximately 40-70% of the total concentrations. The lupin's ability to absorb heavy metals and translocate them to shoots was negligible with respect to the magnitude of contamination, suggesting that this plant is not suitable for extending the period of phytoextraction. However, it is entirely exploitable as green manure, avoiding the application of chemical amendments during phytoremediation. In addition, in polluted fields, white lupin cultivation increased the soil concentration of live bacteria and the bioavailable percentage of metals. On average live bacteria counts per gram of soil were 65×10(6)±18×10(6) and 99×10(6)±22*10(6) before and after cultivation, respectively. The percentages

  6. Effects of dehulling, steam-cooking and microwave-irradiation on digestive value of white lupin (Lupinus albus) seed meal for rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar).

    PubMed

    Saez, Patricio; Borquez, Aliro; Dantagnan, Patricio; Hernández, Adrián

    2015-01-01

    A digestibility trial was conducted to assess the effect of dehulling, steam-cooking and microwave-irradiation on the apparent digestibility of nutrients in white lupin (Lupinus albus) seed meal when fed to rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar). Six ingredients, whole lupin seed meal (LSM), dehulled LSM, dehulled LSM steam-cooked for 15 or 45 min (SC15 and SC45, respectively) and LSM microwave-irradiated at 375 or 750 W (MW375 and MW750, respectively), were evaluated for digestibility of dry matter, crude protein (CP), lipids, nitrogen-free extractives (NFE) and gross energy (GE). The diet-substitution approach was used (70% reference diet + 30% test ingredient). Faeces from each tank were collected using a settlement column. Dehulled LSM showed higher levels of proximate components (except for NFE and crude fibre), GE and phosphorus in comparison to whole LSM. Furthermore, SC15, SC45, MW375 and MW750 showed slight variations of chemical composition in comparison to dehulled LSM. Results from the digestibility trial indicated that dehulled LSM, SC15, SC45 and MW375 are suitable processing methods for the improvement of nutrients' apparent digestibility coefficient (ADC) in whole LSM. MW750 showed a lower ADC of nutrients (except for CP and lipids for rainbow trout) in comparison with MW350 for rainbow trout and Atlantic salmon, suggesting a heat damage of the ingredient when microwave-irradiation exceeded 350 W.

  7. Sensitivity of shovelnose sturgeon (Scaphirhynchus platorynchus) and pallid sturgeon (S. albus) early life stages to 3,30,4,40,5-pentachlorobiphenyl and 2,3,7,8-tetrachlorodibenzo-p-dioxin exposure

    USGS Publications Warehouse

    Buckler, Justin; Candrl, James S.; McKee, Michael J.; Papoulias, Diana M.; Tillitt, Donald E.; Galat, David L.

    2015-01-01

    Concern exists that polychlorinated biphenyls (PCBs) may be contributing to the current decline of shovelnose sturgeon (Scaphirhynchus platorynchus) and the US federally endangered pallid sturgeon (Scaphirhynchus albus). Waterborne exposures with newly fertilized eggs were used to assess developmental and morphological effects of 2 of the most potent aryl hydrocarbon receptor (AhR) agonists, 3,30,4,40,5-pentachlorobiphenyl (PCB-126) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), on early life stage shovelnose and pallid sturgeon. No dose-related effects of PCB-126 were observed on percent development or hatch in either species at concentrations as high as 1711 ng/g egg. Effects of TCDD on percent development were not assessed in shovelnose sturgeon. However, percent development was not affected by TCDD in pallid sturgeon, and percent hatch was unaffected by TCDD doses as high as 60 ng/g egg to 81 ng/g egg in either species. Morphological pathologies such as yolk sac edema and craniofacial deformities were typical of AhR agonist exposure and were similar in both species. Calculated PCB-126 50% lethal dose (LD50, 95% fiducial limits) values were 196 ng/ g egg (188–203 ng/g) for shovelnose and 159 ng/g egg (122–199 ng/g) for pallid sturgeon. Likewise, calculated TCDD LD50 values were 13 ng/g egg (11–15 ng/g) for shovelnose and 12 ng/g egg (10–14 ng/g) for pallid sturgeon. These LD50 values are among the highest recorded in early life stage fish, suggesting that early life stage Scaphirhynchus sturgeon may be comparatively insensitive to AhR agonists.

  8. Effects of different forms of white lupin (Lupinus albus) grain supplementation on feed intake, digestibility, growth performance and carcass characteristics of Washera sheep fed Rhodes grass (Chloris gayana) hay-based diets.

    PubMed

    Tefera, Gebru; Tegegne, Firew; Mekuriaw, Yeshambel; Melaku, Solomon; Tsunekawa, Atsushi

    2015-12-01

    Protein is the major limiting nutrient in feeding ruminants especially in dryland areas. Thus, looking for locally available protein sources such as white lupin (Lupinus albus) grain is commendable. The objective of this experiment was to determine effects of supplementation of different forms of white lupin grain (WLG) on feed and nutrient intake, digestibility, growth and carcass characteristics. Twenty-five yearling male Washera sheep with initial body weight (BW) of 16.26 ± 1.41 kg (mean ± SD) were used. Animals were blocked into five based on their initial BW and were randomly assigned to one of the following five dietary treatments: Rhodes grass (Chloris gayana) hay (RGH) alone (T1) or supplemented with 300 g (on dry matter (DM) basis) raw WLG (T2) or raw soaked and dehulled WLG (T3) or roasted WLG (T4) or raw soaked WLG (T5). Supplementation with WLG significantly improved total DM and nutrient intake (P < 0.001), nutrient digestibility (P < 0.01), and average daily gain (ADG) and feed conversion efficiency (FCE) (P < 0.001). Carcass quality parameters were significantly (P < 0.001) higher for supplemented sheep. However, the difference in carcass quality parameters among supplemented groups was not significant (P > 0.05). It is concluded that roasting white lupin grain can lead to a better feed and nutrient intake and consequently better carcass quality. White lupin grain can be recommended not only for maintenance but also for optimum performance of ruminants.

  9. Sensitivity of shovelnose sturgeon (Scaphirhynchus platorynchus) and pallid sturgeon (S. albus) early life stages to 3,3',4,4',5-pentachlorobiphenyl and 2,3,7,8-tetrachlorodibenzo-P-dioxin exposure.

    PubMed

    Buckler, Justin; Candrl, James S; McKee, Michael J; Papoulias, Diana M; Tillitt, Donald E; Galat, David L

    2015-06-01

    Concern exists that polychlorinated biphenyls (PCBs) may be contributing to the current decline of shovelnose sturgeon (Scaphirhynchus platorynchus) and the US federally endangered pallid sturgeon (Scaphirhynchus albus). Waterborne exposures with newly fertilized eggs were used to assess developmental and morphological effects of 2 of the most potent aryl hydrocarbon receptor (AhR) agonists, 3,3',4,4',5-pentachlorobiphenyl (PCB-126) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), on early life stage shovelnose and pallid sturgeon. No dose-related effects of PCB-126 were observed on percent development or hatch in either species at concentrations as high as 1711 ng/g egg. Effects of TCDD on percent development were not assessed in shovelnose sturgeon. However, percent development was not affected by TCDD in pallid sturgeon, and percent hatch was unaffected by TCDD doses as high as 60 ng/g egg to 81 ng/g egg in either species. Morphological pathologies such as yolk sac edema and craniofacial deformities were typical of AhR agonist exposure and were similar in both species. Calculated PCB-126 50% lethal dose (LD50, 95% fiducial limits) values were 196 ng/g egg (188-203 ng/g) for shovelnose and 159 ng/g egg (122-199 ng/g) for pallid sturgeon. Likewise, calculated TCDD LD50 values were 13 ng/g egg (11-15 ng/g) for shovelnose and 12 ng/g egg (10-14 ng/g) for pallid sturgeon. These LD50 values are among the highest recorded in early life stage fish, suggesting that early life stage Scaphirhynchus sturgeon may be comparatively insensitive to AhR agonists.

  10. Structural Characterization and Bioactivity Analysis of the Two-Component Lantibiotic Flv System from a Ruminant Bacterium.

    PubMed

    Zhao, Xiling; van der Donk, Wilfred A

    2016-02-18

    The discovery of new ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) has greatly benefitted from the influx of genomic information. The lanthipeptides are a subset of this class of compounds. Adopting the genome-mining approach revealed a novel lanthipeptide gene cluster encoded in the genome of Ruminococcus flavefaciens FD-1, an anaerobic bacterium that is an important member of the rumen microbiota of livestock. The post-translationally modified peptides were produced via heterologous expression in Escherichia coli. Subsequent structural characterization and assessment of their bioactivity revealed features reminiscent of and distinct from previously reported lanthipeptides. The lanthipeptides of R. flavefaciens FD-1 represent a unique example within two-component lanthipeptides, consisting of a highly conserved α-peptide and a diverse set of eight β-peptides. PMID:27028884

  11. Differential fermentation of cellulose allomorphs by ruminal cellulolytic bacteria.

    PubMed

    Weimer, P J; French, A D; Calamari, T A

    1991-11-01

    In addition to its usual native crystalline form (cellulose I), cellulose can exist in a variety of alternative crystalline forms (allomorphs) which differ in their unit cell dimensions, chain packing schemes, and hydrogen bonding relationships. We prepared, by various chemical treatments, four different alternative allomorphs, along with an amorphous (noncrystalline) cellulose which retained its original molecular weight. We then examined the kinetics of degradation of these materials by two species of ruminal bacteria and by inocula from two bovine rumens. Ruminococcus flavefaciens FD-1 and Fibrobacter succinogenes S85 were similar to one another in their relative rates of digestion of the different celluloses, which proceeded in the following order: amorphous > III(I) > IV(I) > III(II) > I > II. Unlike F. succinogenes, R. flavefaciens did not degrade cellulose II, even after an incubation of 3 weeks. Comparisons of the structural features of these allomorphs with their digestion kinetics suggest that degradation is enhanced by skewing of adjacent sheets in the microfibril, but is inhibited by intersheet hydrogen bonding and by antiparallelism in adjacent sheets. Mixed microflora from the bovine rumens showed in vitro digestion rates quite different from one another and from those of both of the two pure bacterial cultures, suggesting that R. flavefaciens and F. succinogenes (purportedly among the most active of the cellulolytic bacteria in the rumen) either behave differently in the ruminal ecosystem from the way they do in pure culture or did not play a major role in cellulose digestion in these ruminal samples.

  12. STUDIES ON THE METABOLIC FUNCTION OF BRANCHED-CHAIN VOLATILE FATTY ACIDS, GROWTH FACTORS FOR RUMINOCOCCI I.

    PubMed Central

    Allison, Milton J.; Bryant, Marvin P.; Doetsch, Raymond N.

    1962-01-01

    Allison, Milton J. (Dairy Cattle Research Branch, U. S. Department of Agriculture, Beltsville, Md.), M. P. Bryant, and R. N. Doetsch. Studies on the metabolic function of branched-chain volatile fatty acids, growth factors for ruminococci. I. Incorporation of isovalerate into leucine. J. Bacteriol. 83:523–532. 1962.—Ruminococcus flavefaciens strain C94, a cellulolytic rumen bacterium, requires either isobutyrate or isovalerate for growth. The organism was grown in the presence of C14-labeled isovalerate, and the metabolic fate of the labeled carbon was studied to obtain information on the functions of this growth factor. Radioactivity from isovalerate-1-C14 and isovalerate-3-C14 was found mainly in the protein and lipid fractions of the cells. The C14 in protein was all in leucine, indicating that a function of isovalerate was to serve as a carbon skeleton for leucine synthesis. As C14 in leucine synthesized from isovalerate-1-C14 was entirely in carbon 2, the intact isovalerate molecule was apparently incorporated into leucine. This is evidence that leucine was synthesized by a mechanism different from that previously demonstrated in other microorganisms. R. flavefaciens has a definite but limited ability to incorporate exogenous amino acids, including leucine. It incorporated 2% of the C14 during growth in uniformly labeled (UL) C14-Chlorella protein hydrolyzate; Escherichia coli incorporated 37% of the label under similar conditions. In another experiment, a limited amount of exogenous leucine-2-C14 was incorporated into protein of R. flavefaciens. The requirement for isovalerate was not replaced by dl-leucine or 2-ketoisocaproate. It is suggested that isovalerate or isobutyrate is required because R. flavefaciens has a limited ability to incorporate exogenous branched-chain amino acids and a limited ability to synthesize the isopropyl group found in these amino acids and in other components of the cell. Images PMID:13860621

  13. Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples.

    PubMed

    Wang, Rong-Fu; Beggs, Marjorie L; Robertson, Latriana H; Cerniglia, Carl E

    2002-08-01

    An oligonucleotide-microarray method was developed for the detection of intestinal bacteria in fecal samples collected from human subjects. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific for each bacterial species (total 60 probes) were synthesized and applied to glass slides. Cyanine5 (CY5)-labeled 16S rDNAs were amplified by polymerase chain reaction (PCR) from human fecal samples or bacterial DNA using two universal primers and were hybridized to the oligo-microarray. The 20 intestinal bacterial species tested were Bacteroides thetaiotaomicron, Bacteroides vulgatus, Bacteroides fragilis, Bacteroides distasonis, Clostridium clostridiiforme, Clostridium leptum, Fusobacterium prausnitzii, Peptostreptococcus productus, Ruminococcus obeum, Ruminococcus bromii, Ruminococcus callidus, Ruminococcus albus, Bifidobacterium longum, Bifidobacterium adolescentis, Bifidobacterium infantis, Eubacterium biforme, Eubacterium aerofaciens, Lactobacillus acidophilus, Escherichia coli, and Enterococcus faecium. The two universal primers were able to amplify full size 16S rDNA from all of the 20 bacterial species tested. The hybridization results indicated that the oligo-microarray method developed in this study is a reliable method for the detection of predominant human intestinal bacteria in the fecal samples.

  14. Bovine spongiform encephalopathy: is it an autoimmune disease due to bacteria showing molecular mimicry with brain antigens?

    PubMed Central

    Ebringer, A; Thorpe, C; Pirt, J; Wilson, C; Cunningham, P; Ettelaie, C

    1997-01-01

    Bovine spongiform encephalopathy (BSE) could be an autoimmune disease produced following exposure of cattle to feedstuffs containing bacteria showing molecular mimicry between bacterial components and bovine tissue. Analysis of molecular sequence databases (Genbank and SwissProt) shows that three bacteria (Acinetobacter calcoaceticus,Ruminococcus albus, and Agrobacter tumefaciens) share sequences with the encephalitogenic peptide of bovine myelin, while three molecules in Escherichia coli show molecular mimicry with host-encoded prion protein. Immune responses against these bacteria at both T and B cell levels may cause neurological tissue injury resembling BSE. The role of these bacteria in BSE, if any, merits further investigation. Images Figure 1. Figure 2. PMID:9370514

  15. Biogas production from brewery spent grain enhanced by bioaugmentation with hydrolytic anaerobic bacteria.

    PubMed

    Čater, Maša; Fanedl, Lijana; Malovrh, Špela; Logar, Romana Marinšek

    2015-06-01

    Lignocellulosic substrates are widely available but not easily applied in biogas production due to their poor anaerobic degradation. The effect of bioaugmentation by anaerobic hydrolytic bacteria on biogas production was determined by the biochemical methane potential assay. Microbial biomass from full scale upflow anaerobic sludge blanket reactor treating brewery wastewater was a source of active microorganisms and brewery spent grain a model lignocellulosic substrate. Ruminococcus flavefaciens 007C, Pseudobutyrivibrio xylanivorans Mz5(T), Fibrobacter succinogenes S85 and Clostridium cellulovorans as pure and mixed cultures were used to enhance the lignocellulose degradation and elevate the biogas production. P. xylanivorans Mz5(T) was the most successful in elevating methane production (+17.8%), followed by the coculture of P. xylanivorans Mz5(T) and F. succinogenes S85 (+6.9%) and the coculture of C. cellulovorans and F. succinogenes S85 (+4.9%). Changes in microbial community structure were detected by fingerprinting techniques.

  16. Biogas production from brewery spent grain enhanced by bioaugmentation with hydrolytic anaerobic bacteria.

    PubMed

    Čater, Maša; Fanedl, Lijana; Malovrh, Špela; Logar, Romana Marinšek

    2015-06-01

    Lignocellulosic substrates are widely available but not easily applied in biogas production due to their poor anaerobic degradation. The effect of bioaugmentation by anaerobic hydrolytic bacteria on biogas production was determined by the biochemical methane potential assay. Microbial biomass from full scale upflow anaerobic sludge blanket reactor treating brewery wastewater was a source of active microorganisms and brewery spent grain a model lignocellulosic substrate. Ruminococcus flavefaciens 007C, Pseudobutyrivibrio xylanivorans Mz5(T), Fibrobacter succinogenes S85 and Clostridium cellulovorans as pure and mixed cultures were used to enhance the lignocellulose degradation and elevate the biogas production. P. xylanivorans Mz5(T) was the most successful in elevating methane production (+17.8%), followed by the coculture of P. xylanivorans Mz5(T) and F. succinogenes S85 (+6.9%) and the coculture of C. cellulovorans and F. succinogenes S85 (+4.9%). Changes in microbial community structure were detected by fingerprinting techniques. PMID:25836034

  17. Degradation and utilization of xylans by the rumen anaerobe Prevotella bryantii (formerly P. ruminicola subsp. brevis) B(1)4.

    PubMed

    Miyazaki, K; Martin, J C; Marinsek-Logar, R; Flint, H J

    1997-12-01

    Freshly harvested whole cells from cultures of P. bryantii B(1)4 grown with oat spelt xylan (OSX) as an energy source showed less than 25% of the enzyme activity against OSX, and less than 15% of the activity against birchwood xylan (BWX) and carboxymethylcellulose, that was detectable in sonicated cell preparations. This indicates that much of this hydrolytic activity is either periplasmic, membrane-associated or intracellular and may be concerned with the processing of transported oligosaccharides.P. bryantii B(1)4 cultures were able to utilise up to 45% and 51% of the total pentose present in OSX and BWX, respectively, after 24 h, but could utilize 84% of a water-soluble fraction of BWX. Analysis of the xylan left undegraded after incubation with P. bryantii showed that while xylose and arabinose were removed to a similar extent, uronic acids were utilized to a greater extent than xylose. Predigestion of xylans with two cloned xylanases from the cellulolytic rumen anaerobe Ruminococcus flavefaciens gave little increase in overall pentose utilization suggesting that external P. bryantii xylanases are as effective as the cloned R. flavefaciens enzymes in releasing products that can be utilised by P. bryantii cells. The xylanase system of P. bryantiiis able to efficiently utilise not only xylo-oligosaccharides but also larger water-soluble xylan fragments. PMID:16887612

  18. Uptake of milk with and without solid feed during the monogastric phase: Effect on fibrolytic and methanogenic microorganisms in the gastrointestinal tract of calves.

    PubMed

    Guzman, Cesar E; Bereza-Malcolm, Lara T; De Groef, Bert; Franks, Ashley E

    2016-03-01

    Microbial communities are affected by diet and play a role in the successful transition from milk to a solid diet. The response of microorganisms in the gastrointestinal tract of Holstein bull calves to the uptake of milk with solid feed (control treatment; CT), or milk without solid feed (milk-only treatment; MT) during the first 3 weeks of life was investigated. Samples were collected from the rumen (fluid and tissue), abomasum (fluid), cecum (fluid and tissue) and feces at 7, 14 and 20 days of age. Calf weight was higher on days 14 and 20 in the MT than the CT. In the rumen at 14 days, the fibrolytic bacteria Fibrobacter succinogenes and Prevotella ruminicola increased in the CT and Ruminococcus flavefaciens increased in the MT. This suggests that R. flavefaciens is not strictly fibrolytic and that it might use milk as a substrate or other microbial species might supply a substrate. Diet affected methanogens, but this may have been due to an indirect effect via an association with Geobacter spp. or other syntrophic partners. The treatments also affected microorganisms in the abomasum, cecum and feces. Our results contribute to an understanding of diet, microbes in the gastrointestinal tract and weaning.

  19. The effect of fibre source on the numbers of some fibre-degrading bacteria of Arabian camel's (Camelus dromedarius) foregut origin.

    PubMed

    Samsudin, Anjas Asmara; Wright, André-Denis; Al Jassim, Rafat

    2014-10-01

    The total bacterial community of Fibrobacter succinogenes and Ruminococcus flavefaciens in fibre-enriched culture of the foregut contents of 12 adult feral camels (Camelus dromedaries) fed on native vegetation in Australia was investigated using quantitative PCR. Foregut contents were collected postmortem, pooled and filtered before divided into two fractions. One fraction was used for extraction of DNA, while the other fraction was inoculated straight away into BM 10 contained filter paper (FP), cotton thread (CT) or neutral detergent fibre (NDF) as the sole carbohydrate sources in Hungate tubes. The tubes were incubated anaerobically at 39 °C for 1 week. After a near complete degradation of the FP and CT and extensive turbidity in the NDF, media subculturing was carried out into fresh media tubes. This was repeated twice before genomic DNA was extracted and used for quantification of bacteria. Using an absolute quantification method, the numbers of cells in 1 ml of each sample ranged from 4.07 × 10(6) to 2.73 × 10(9) for total bacteria, 1.34 × 10(3) to 2.17 × 10(5) for F. succinogenes and 5.78 × 10(1) to 3.53 × 10(4) for R. flavefaciens. The mean cell number of F. succinogenes was highest in the FP enrichment medium at approximately 107-fold, whereas for the R. flavefaciens targeted primer, the NDF enrichment media had the highest mean cell number at approximately 4-fold when compared to the rumen content. The data presented here provide evidence of fibre type preference by the two main fibre-degrading bacteria and would help us understand the interaction between fibre type and fibre-degrading microorganisms, which has ramification on camel nutrition at different seasons and environments.

  20. Ruminococcal cellulosome systems from rumen to human.

    PubMed

    Ben David, Yonit; Dassa, Bareket; Borovok, Ilya; Lamed, Raphael; Koropatkin, Nicole M; Martens, Eric C; White, Bryan A; Bernalier-Donadille, Annick; Duncan, Sylvia H; Flint, Harry J; Bayer, Edward A; Moraïs, Sarah

    2015-09-01

    A cellulolytic fiber-degrading bacterium, Ruminococcus champanellensis, was isolated from human faecal samples, and its genome was recently sequenced. Bioinformatic analysis of the R. champanellensis genome revealed numerous cohesin and dockerin modules, the basic elements of the cellulosome, and manual sequencing of partially sequenced genomic segments revealed two large tandem scaffoldin-coding genes that form part of a gene cluster. Representative R. champanellensis dockerins were tested against putative cohesins, and the results revealed three different cohesin-dockerin binding profiles which implied two major types of cellulosome architectures: (i) an intricate cell-bound system and (ii) a simplistic cell-free system composed of a single cohesin-containing scaffoldin. The cell-bound system can adopt various enzymatic architectures, ranging from a single enzyme to a large enzymatic complex comprising up to 11 enzymes. The variety of cellulosomal components together with adaptor proteins may infer a very tight regulation of its components. The cellulosome system of the human gut bacterium R. champanellensis closely resembles that of the bovine rumen bacterium Ruminococcus flavefaciens. The two species contain orthologous gene clusters comprising fundamental components of cellulosome architecture. Since R. champanellensis is the only human colonic bacterium known to degrade crystalline cellulose, it may thus represent a keystone species in the human gut.

  1. Effects of Nitrate Addition on Rumen Fermentation, Bacterial Biodiversity and Abundance.

    PubMed

    Zhao, Liping; Meng, Qingxiang; Ren, Liping; Liu, Wei; Zhang, Xinzhuang; Huo, Yunlong; Zhou, Zhenming

    2015-10-01

    This study examined changes of rumen fermentation, ruminal bacteria biodiversity and abundance caused by nitrate addition with Ion Torrent sequencing and real-time polymerase chain reaction. Three rumen-fistulated steers were fed diets supplemented with 0%, 1%, and 2% nitrate (dry matter %) in succession. Nitrate supplementation linearly increased total volatile fatty acids and acetate concentration obviously (p = 0.02; p = 0.02; p<0.01), butyrate and isovalerate concentration numerically (p = 0.07). The alpha (p>0.05) and beta biodiversity of ruminal bacteria were not affected by nitrate. Nitrate increased typical efficient cellulolytic bacteria species (Ruminococcus flavefaciens, Ruminococcus ablus, and Fibrobacter succinogenes) (p<0.01; p = 0.06; p = 0.02). Ruminobactr, Sphaerochaeta, CF231, and BF311 genus were increased by 1% nitrate. Campylobacter fetus, Selenomonas ruminantium, and Mannheimia succiniciproducens were core nitrate reducing bacteria in steers and their abundance increased linearly along with nitrate addition level (p<0.01; p = 0.02; p = 0.04). Potential nitrate reducers in the rumen, Campylobacter genus and Cyanobacteria phyla were significantly increased by nitrate (p<0.01; p = 0.01). To the best of our knowledge, this was the first detailed view of changes in ruminal microbiota by nitrate. This finding would provide useful information on nitrate utilization and nitrate reducer exploration in the rumen. PMID:26194220

  2. Effects of Nitrate Addition on Rumen Fermentation, Bacterial Biodiversity and Abundance

    PubMed Central

    Zhao, Liping; Meng, Qingxiang; Ren, Liping; Liu, Wei; Zhang, Xinzhuang; Huo, Yunlong; Zhou, Zhenming

    2015-01-01

    This study examined changes of rumen fermentation, ruminal bacteria biodiversity and abundance caused by nitrate addition with Ion Torrent sequencing and real-time polymerase chain reaction. Three rumen-fistulated steers were fed diets supplemented with 0%, 1%, and 2% nitrate (dry matter %) in succession. Nitrate supplementation linearly increased total volatile fatty acids and acetate concentration obviously (p = 0.02; p = 0.02; p<0.01), butyrate and isovalerate concentration numerically (p = 0.07). The alpha (p>0.05) and beta biodiversity of ruminal bacteria were not affected by nitrate. Nitrate increased typical efficient cellulolytic bacteria species (Ruminococcus flavefaciens, Ruminococcus ablus, and Fibrobacter succinogenes) (p<0.01; p = 0.06; p = 0.02). Ruminobactr, Sphaerochaeta, CF231, and BF311 genus were increased by 1% nitrate. Campylobacter fetus, Selenomonas ruminantium, and Mannheimia succiniciproducens were core nitrate reducing bacteria in steers and their abundance increased linearly along with nitrate addition level (p<0.01; p = 0.02; p = 0.04). Potential nitrate reducers in the rumen, Campylobacter genus and Cyanobacteria phyla were significantly increased by nitrate (p<0.01; p = 0.01). To the best of our knowledge, this was the first detailed view of changes in ruminal microbiota by nitrate. This finding would provide useful information on nitrate utilization and nitrate reducer exploration in the rumen. PMID:26194220

  3. Inhibition of ruminal cellulose fermentation by extracts of the perennial legume cicer milkvetch (Astragalus cicer).

    PubMed

    Weimer, P J; Hatfield, R D; Buxton, D R

    1993-02-01

    Cicer milkvetch (Astragalus cicer L.) is a perennial legume used as a pasture or rangeland plant for ruminants. A study was undertaken to determine whether reported variations in its ruminal digestibility may be related to the presence of an antinutritive material. In vitro fermentation of neutral detergent fiber (NDF) of cicer milkvetch by mixed rumen microflora was poorer than was the fermentation of NDF in alfalfa (Medicago sativa L.). Fermentation of cicer milkvetch NDF was improved by preextraction of the ground herbage with water for 3 h at 39 degrees C. Such water extracts selectively inhibited in vitro fermentation of pure cellulose by mixed ruminal microflora and by pure cultures of the ruminal bacteria Ruminococcus flavefaciens FD-1 and Fibrobacter succinogenes S85. Inhibition of the cellulose fermentation by mixed ruminal microflora was dependent upon the concentration of cicer milkvetch extract and was overcome upon prolonged incubation. Pure cultures exposed to the extract did not recover from inhibition, even after long incubation times, unless the inhibitory agent was removed (viz., by dilution of inhibited cultures into fresh medium). The extract did not affect the fermentation of cellobiose by R. flavefaciens but did cause some inhibition of cellobiose fermentation by F. succinogenes. Moreover, the extracts did not inhibit hydrolysis of crystalline cellulose, carboxymethyl cellulose, or p-nitrophenylcellobioside by supernatants of these pure cultures of cellulolytic bacteria or by a commercial cellulase preparation from the fungus Trichoderma reesei. The agent caused cellulose-adherent cells to detach from cellulose fibers, suggesting that the agent may act, at least in part, by disrupting the glycocalyx necessary for adherence to, and rapid digestion of, cellulose.

  4. Effect of feeding palm oil by-products based diets on total bacteria, cellulolytic bacteria and methanogenic archaea in the rumen of goats.

    PubMed

    Abubakr, Abdelrahim; Alimon, Abdul Razak; Yaakub, Halimatun; Abdullah, Norhani; Ivan, Michael

    2014-01-01

    Rumen microorganisms are responsible for digestion and utilization of dietary feeds by host ruminants. Unconventional feed resources could be used as alternatives in tropical areas where feed resources are insufficient in terms of quality and quantity. The objective of the present experiment was to evaluate the effect of diets based on palm oil (PO), decanter cake (DC) or palm kernel cake (PKC) on rumen total bacteria, selected cellulolytic bacteria, and methanogenic archaea. Four diets: control diet (CD), decanter cake diet (DCD), palm kernel cake diet (PKCD) and CD plus 5% PO diet (CPOD) were fed to rumen cannulated goats and rumen samples were collected at the start of the experimental diets (day 0) and on days 4, 6, 8, 12, 18, 24 and 30 post dietary treatments. Feeding DCD and PKCD resulted in significantly higher (P<0.05) DNA copy number of total bacteria, Fibrobacter succinogenes, Ruminococcus flavefeciens, and Ruminococcus albus. Rumen methanogenic archaea was significantly lower (P<0.05) in goats fed PKCD and CPOD and the trend showed a severe reduction on days 4 and 6 post experimental diets. In conclusion, results indicated that feeding DCD and PKC increased the populations of cellulolytic bacteria and decreased the density of methanogenic archaea in the rumen of goats.

  5. Effect of Feeding Palm Oil By-Products Based Diets on Total Bacteria, Cellulolytic Bacteria and Methanogenic Archaea in the Rumen of Goats

    PubMed Central

    Abubakr, Abdelrahim; Alimon, Abdul Razak; Yaakub, Halimatun; Abdullah, Norhani; Ivan, Michael

    2014-01-01

    Rumen microorganisms are responsible for digestion and utilization of dietary feeds by host ruminants. Unconventional feed resources could be used as alternatives in tropical areas where feed resources are insufficient in terms of quality and quantity. The objective of the present experiment was to evaluate the effect of diets based on palm oil (PO), decanter cake (DC) or palm kernel cake (PKC) on rumen total bacteria, selected cellulolytic bacteria, and methanogenic archaea. Four diets: control diet (CD), decanter cake diet (DCD), palm kernel cake diet (PKCD) and CD plus 5% PO diet (CPOD) were fed to rumen cannulated goats and rumen samples were collected at the start of the experimental diets (day 0) and on days 4, 6, 8, 12, 18, 24 and 30 post dietary treatments. Feeding DCD and PKCD resulted in significantly higher (P<0.05) DNA copy number of total bacteria, Fibrobacter succinogenes, Ruminococcus flavefeciens, and Ruminococcus albus. Rumen methanogenic archaea was significantly lower (P<0.05) in goats fed PKCD and CPOD and the trend showed a severe reduction on days 4 and 6 post experimental diets. In conclusion, results indicated that feeding DCD and PKC increased the populations of cellulolytic bacteria and decreased the density of methanogenic archaea in the rumen of goats. PMID:24756125

  6. Changes in Rumen Microbial Community Composition during Adaption to an In Vitro System and the Impact of Different Forages.

    PubMed

    Lengowski, Melanie B; Zuber, Karin H R; Witzig, Maren; Möhring, Jens; Boguhn, Jeannette; Rodehutscord, Markus

    2016-01-01

    This study examined ruminal microbial community composition alterations during initial adaption to and following incubation in a rumen simulation system (Rusitec) using grass or corn silage as substrates. Samples were collected from fermenter liquids at 0, 2, 4, 12, 24, and 48 h and from feed residues at 0, 24, and 48 h after initiation of incubation (period 1) and on day 13 (period 2). Microbial DNA was extracted and real-time qPCR was used to quantify differences in the abundance of protozoa, methanogens, total bacteria, Fibrobacter succinogenes, Ruminococcus albus, Ruminobacter amylophilus, Prevotella bryantii, Selenomonas ruminantium, and Clostridium aminophilum. We found that forage source and sampling time significantly influenced the ruminal microbial community. The gene copy numbers of most microbial species (except C. aminophilum) decreased in period 1; however, adaption continued through period 2 for several species. The addition of fresh substrate in period 2 led to increasing copy numbers of all microbial species during the first 2-4 h in the fermenter liquid except protozoa, which showed a postprandial decrease. Corn silage enhanced the growth of R. amylophilus and F. succinogenes, and grass silage enhanced R. albus, P. bryantii, and C. aminophilum. No effect of forage source was detected on total bacteria, protozoa, S. ruminantium, or methanogens or on total gas production, although grass silage enhanced methane production. This study showed that the Rusitec provides a stable system after an adaption phase that should last longer than 48 h, and that the forage source influenced several microbial species. PMID:26928330

  7. Changes in Rumen Microbial Community Composition during Adaption to an In Vitro System and the Impact of Different Forages

    PubMed Central

    Lengowski, Melanie B.; Zuber, Karin H. R.; Witzig, Maren; Möhring, Jens; Boguhn, Jeannette; Rodehutscord, Markus

    2016-01-01

    This study examined ruminal microbial community composition alterations during initial adaption to and following incubation in a rumen simulation system (Rusitec) using grass or corn silage as substrates. Samples were collected from fermenter liquids at 0, 2, 4, 12, 24, and 48 h and from feed residues at 0, 24, and 48 h after initiation of incubation (period 1) and on day 13 (period 2). Microbial DNA was extracted and real-time qPCR was used to quantify differences in the abundance of protozoa, methanogens, total bacteria, Fibrobacter succinogenes, Ruminococcus albus, Ruminobacter amylophilus, Prevotella bryantii, Selenomonas ruminantium, and Clostridium aminophilum. We found that forage source and sampling time significantly influenced the ruminal microbial community. The gene copy numbers of most microbial species (except C. aminophilum) decreased in period 1; however, adaption continued through period 2 for several species. The addition of fresh substrate in period 2 led to increasing copy numbers of all microbial species during the first 2–4 h in the fermenter liquid except protozoa, which showed a postprandial decrease. Corn silage enhanced the growth of R. amylophilus and F. succinogenes, and grass silage enhanced R. albus, P. bryantii, and C. aminophilum. No effect of forage source was detected on total bacteria, protozoa, S. ruminantium, or methanogens or on total gas production, although grass silage enhanced methane production. This study showed that the Rusitec provides a stable system after an adaption phase that should last longer than 48 h, and that the forage source influenced several microbial species. PMID:26928330

  8. Co-fermentation of xylose and cellobiose by an engineered Saccharomyces cerevisiae.

    PubMed

    Aeling, Kimberly A; Salmon, Kirsty A; Laplaza, José M; Li, Ling; Headman, Jennifer R; Hutagalung, Alex H; Picataggio, Stephen

    2012-11-01

    We have integrated and coordinately expressed in Saccharomyces cerevisiae a xylose isomerase and cellobiose phosphorylase from Ruminococcus flavefaciens that enables fermentation of glucose, xylose, and cellobiose under completely anaerobic conditions. The native xylose isomerase was active in cell-free extracts from yeast transformants containing a single integrated copy of the gene. We improved the activity of the enzyme and its affinity for xylose by modifications to the 5'-end of the gene, site-directed mutagenesis, and codon optimization. The improved enzyme, designated RfCO*, demonstrated a 4.8-fold increase in activity compared to the native xylose isomerase, with a K(m) for xylose of 66.7 mM and a specific activity of 1.41 μmol/min/mg. In comparison, the native xylose isomerase was found to have a K(m) for xylose of 117.1 mM and a specific activity of 0.29 μmol/min/mg. The coordinate over-expression of RfCO* along with cellobiose phosphorylase, cellobiose transporters, the endogenous genes GAL2 and XKS1, and disruption of the native PHO13 and GRE3 genes allowed the fermentation of glucose, xylose, and cellobiose under completely anaerobic conditions. Interestingly, this strain was unable to utilize xylose or cellobiose as a sole carbon source for growth under anaerobic conditions, thus minimizing yield loss to biomass formation and maximizing ethanol yield during their fermentation. PMID:22911235

  9. Reducing methane emissions and the methanogen population in the rumen of Tibetan sheep by dietary supplementation with coconut oil.

    PubMed

    Ding, Xuezhi; Long, Ruijun; Zhang, Qian; Huang, Xiaodan; Guo, Xusheng; Mi, Jiandui

    2012-10-01

    The objective was to evaluate the effect of dietary coconut oil on methane (CH(4)) emissions and the microbial community in Tibetan sheep. Twelve animals were assigned to receive either a control diet (oaten hay) or a mixture diet containing concentrate (maize meal), in which coconut oil was supplemented at 12 g/day or not for a period of 4 weeks. CH(4) emissions were measured by using the 'tunnel' technique, and microbial communities were examined using quantitative real-time PCR. Daily CH(4) production for the control and forage-to-concentrate ratio of 6:4 was 17.8 and 15.3 g, respectively. Coconut oil was particularly effective at reducing CH(4) emissions from Tibetan sheep. The inclusion of coconut oil for the control decreased CH(4) production (in grams per day) by 61.2%. In addition, there was a positive correlation between the number of methanogens and the daily CH(4) production (R = 0.95, P < 0.001). Oaten hay diet containing maize meal (6:4) plus coconut oil supplemented at 12 g/day decreases the number of methanogens by 77% and a decreases in the ruminal fungal population (85-95%) and Fibrobacter succinogenes (50-98%) but an increase in Ruminococcus flavefaciens (25-70%). The results from our experiment suggest that adding coconut oil to the diet can reduce CH(4) emissions in Tibetan sheep and that these reductions persist for at least the 4-week feeding period.

  10. Ultrastable cellulosome-adhesion complex tightens under load

    PubMed Central

    Schoeler, Constantin; Malinowska, Klara H.; Bernardi, Rafael C.; Milles, Lukas F.; Jobst, Markus A.; Durner, Ellis; Ott, Wolfgang; Fried, Daniel B.; Bayer, Edward A.; Schulten, Klaus; Gaub, Hermann E.; Nash, Michael A.

    2014-01-01

    Challenging environments have guided nature in the development of ultrastable protein complexes. Specialized bacteria produce discrete multi-component protein networks called cellulosomes to effectively digest lignocellulosic biomass. While network assembly is enabled by protein interactions with commonplace affinities, we show that certain cellulosomal ligand–receptor interactions exhibit extreme resistance to applied force. Here, we characterize the ligand–receptor complex responsible for substrate anchoring in the Ruminococcus flavefaciens cellulosome using single-molecule force spectroscopy and steered molecular dynamics simulations. The complex withstands forces of 600–750 pN, making it one of the strongest bimolecular interactions reported, equivalent to half the mechanical strength of a covalent bond. Our findings demonstrate force activation and inter-domain stabilization of the complex, and suggest that certain network components serve as mechanical effectors for maintaining network integrity. This detailed understanding of cellulosomal network components may help in the development of biocatalysts for production of fuels and chemicals from renewable plant-derived biomass. PMID:25482395

  11. Effects of Cellulolytic Ruminal Bacteria and of Cell Extracts on Germination of Euonymus americanus L. Seeds.

    PubMed

    Howard, Gary T; Elliott, Larry P

    1988-01-01

    In past attempts, the experimental germination of the seeds of Euonymus americanus L. in vitro has had little success. However, treatment of seeds with ruminal fluid containing viable microflora has been successful in stimulating germination. In the presence of the cellulolytic ruminal bacterium, Clostridium cellobioparum ATCC 15832, seeds of E. americanus were stimulated to germinate. Subsequent studies were designed to determine whether the bacterium synthesized a cellulolytic enzyme responsible for initiating germination. The cell-free endocellulase from C. cellobioparum induced germination of the seeds. To support the hypothesis that the endocellulase from C. cellobioparum was responsible for triggering germination, a 1,4-beta-d-glucan glucanohydrolase (EC 3.2.1.4) from Penicillum funiculosum was used to treat the seeds. In addition, no germination was obtained from seeds treated with a commercial exocellulase enzyme. Also, Ruminococcus flavefaciens FD-1 was found to initiate germination of E. americanus seeds. Thus, cellulase activity is indicated in the degradation of the testa of the seed, allowing imbibition and germination.

  12. The gut microbial community in metabolic syndrome patients is modified by diet.

    PubMed

    Haro, Carmen; Garcia-Carpintero, Sonia; Alcala-Diaz, Juan F; Gomez-Delgado, Francisco; Delgado-Lista, Javier; Perez-Martinez, Pablo; Rangel Zuñiga, Oriol A; Quintana-Navarro, Gracia M; Landa, Blanca B; Clemente, Jose C; Lopez-Miranda, Jose; Camargo, Antonio; Perez-Jimenez, Francisco

    2016-01-01

    Intestinal microbiota changes may be involved in the development of metabolic syndrome (MetS), which is a multicomponent disorder frequently associated with obesity. The aim of this study was to test the effect of consuming two healthy diets: a Mediterranean diet and a low-fat high-carbohydrate diet, for 2years in the gut microbiota of MetS patients and those in the control group. We analyzed the differences in the bacterial community structure between the groups after 2years of dietary intervention (Mediterranean or low-fat diet) through quantitative polymerase chain reaction using primers, targeting specific bacterial taxa. We observed, at basal time, that the abundance of Bacteroides, Eubacterium and Lactobacillus genera is lower in the control group than in MetS patients, while Bacteroides fragilis group, Parabacteroides distasonis, Bacteroides thetaiotaomicron, Faecalibacterium prausnitzii, Fusobacterium nucleatum, Bifidobacterium longum, Bifidobacterium adolescentis, Ruminococcus flavefaciens subgroup and Eubacterium rectale are depleted in MetS patients (all P values <.05). Additionally, we found that long-term consumption of Mediterranean diet partially restores the population of P. distasonis, B. thetaiotaomicron, F. prausnitzii, B. adolescentis and B. longum in MetS patients (all P values <.05). Our results suggest that the Mediterranean diet could be a useful tool to restore potentially beneficial members of the gut microbiota, although the stability of these changes over time still remains to be assessed.

  13. Endocrine disruption in white ibises (Eudocimus albus) caused by exposure to environmentally relevant levels of methylmercury.

    PubMed

    Jayasena, Nilmini; Frederick, Peter C; Larkin, Iskande L V

    2011-10-01

    Methylmercury is a globally distributed pollutant and upper trophic level aquatic fauna are at particularly high risk of exposure. Although methylmercury is known to have a number of neurological and developmental effects, relatively little is known about effects on endocrine disruption and reproduction in aquatic fauna, particularly in response to chronic exposure at low concentrations. We experimentally exposed captive white ibises for 3.5 years (2005-2008) to dietary methylmercury at three environmentally relevant concentrations (0.05, 0.1 and 0.3 ppm wet weight in diet). We measured fecal concentrations of estradiol and testosterone metabolites in two consecutive breeding seasons (2007 and 2008). When effects were controlled for stage of breeding, this resulted in altered estradiol and testosterone concentrations in adult breeders of both sexes. Changes in endocrine expression were not consistent over both years, and a clear dose-response relationship was not always present. Endocrine changes were, however, associated at all dose levels with changes in reproductive behavior, reduced reproductive success and altered mate choice in males. Male-male pairing and altered courtship behavior in males were related both to dose treatment and, in 2008, to a demasculinized pattern of endocrine expression. Changes in hormone concentrations of dosed homosexually paired males, when present, were in the same direction but at a higher magnitude than those in heterosexual dosed males. Dosed homosexual males showed decreased testosterone during nest-building and elevated testosterone during incubation when compared with their dosed heterosexual counterparts during the 2008 breeding season. In the same year, exposed males had elevated estradiol during courtship, but had decreased estradiol during other stages in comparison with controls. Dosed females generally showed decreased estradiol and testosterone concentrations compared to controls, albeit not with a clear dose-response effect. Our findings suggest that endocrine disruption due to chronic exposure to even low concentrations of dietary methylmercury may be a widespread mechanism by which reproduction is impaired in wild bird populations.

  14. White Sweetclover (Melilotus albus) and Narrowleaf Hawksbeard (Crepis tectorum) Seed Germination after Passing Through Moose

    Technology Transfer Automated Retrieval System (TEKTRAN)

    White sweetclover and narrowleaf hawksbeard are non-indigenous invasive plant species in Alaska that are rapidly spreading, including into areas that are otherwise free of non-indigenous plants. There has been concern that native moose could be dispersing viable seed from these plants after ingestio...

  15. Evaluation of herbicide efficacy, injury and yield in white lupin (Lupinus albus L.)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    White lupin is of increasing interest in the southeastern USA as a winter legume cover crop or as mid-winter forage for ruminants. White lupins are poor weed competitors during early establishment which makes effective weed control necessary, however, only three herbicides are currently registered f...

  16. 78 FR 17600 - Banda de Lupinus albus doce (BLAD); Exemption From the Requirement of a Tolerance

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-22

    ... mutagen, and is not a developmental toxicant. There are no known effects on endocrine systems via oral... Classification System (NAICS) codes is not intended to be exhaustive, but rather provides a guide to help readers... Findings In the Federal Register of March 14, 2012 (77 FR 15012) (FRL-9335- 9), EPA issued a...

  17. Expression and ontogeny of growth hormone (Gh) in the protogynous hermaphroditic ricefield eel (Monopterus albus).

    PubMed

    Chen, Dong; Liu, Jiang; Chen, Wanping; Shi, Shuxia; Zhang, Weimin; Zhang, Lihong

    2015-12-01

    Growth hormone (GH) is a single-chain polypeptide hormone mainly secreted by somatotropes of the anterior pituitary gland and is an important regulator of somatic growth in vertebrates including teleosts. In this study, a polyclonal antiserum against ricefield eel Gh was generated and the expression of Gh at the mRNA and protein levels was analyzed. Both RT-PCR and western blot analysis showed that Gh was predominantly expressed in the pituitary glands of ricefield eels. The immunoreactive Gh signals were localized to the multicellular layers of the adenohypophysis adjacent to the neurohypophysis in ricefield eels. Ontogenetic analysis showed that immunoreactive Gh signals could be detected in the pituitary glands of ricefield eel embryos as early as 3 days post-fertilization. During the sex change from female to male, the levels of the immunoreactive Gh signals in the pituitary glands of the ricefield eels peaked at the intersexual stage. These results suggest that Gh in the pituitary glands may be associated with embryonic development before hatching, as well as with the sex change in the adult ricefield eels, possibly via the classical endocrine manner.

  18. Nodulation of Lupinus albus by Strains of Ochrobactrum lupini sp. nov.

    PubMed Central

    Trujillo, Martha E.; Willems, Anne; Abril, Adriana; Planchuelo, Ana-María; Rivas, Raúl; Ludeña, Dolores; Mateos, Pedro F.; Martínez-Molina, Eustoquio; Velázquez, Encarna

    2005-01-01

    The nodulation of legumes has for more than a century been considered an exclusive capacity of a group of microorganisms commonly known as rhizobia and belonging to the α-Proteobacteria. However, in the last 3 years four nonrhizobial species, belonging to α and β subclasses of the Proteobacteria, have been described as legume-nodulating bacteria. In the present study, two fast-growing strains, LUP21 and LUP23, were isolated from nodules of Lupinus honoratus. The phylogenetic analysis based on the 16S and 23S rRNA gene sequences showed that the isolates belong to the genus Ochrobactrum. The strains were able to reinfect Lupinus plants. A plasmid profile analysis showed the presence of three plasmids. The nodD and nifH genes were located on these plasmids, and their sequences were obtained. These sequences showed a close resemblance to the nodD and nifH genes of rhizobial species, suggesting that the nodD and nifH genes carried by strain LUP21T were acquired by horizontal gene transfer. A polyphasic study including phenotypic, chemotaxonomic, and molecular features of the strains isolated in this study showed that they belong to a new species of the genus Ochrobactrum for which we propose the name Ochrobactrum lupini sp. nov. Strain LUP21T (LMG 20667T) is the type strain. PMID:15746334

  19. Organic matter and nutrients associated with fine root turnover in a white oak stand. [Quercus albus

    SciTech Connect

    Joslin, J.D.; Henderson, G.S.

    1987-06-01

    Organic matter and nutrients cycled by fine root turnover were quantified in a mature white oak (Quercus alba L.) stand and compared to contributions from litterfall. The budget method, a revised version of the traditional repeated sampling method, was used to measure root turnover. The magnitude of the live and dead pools of three size classes of fine (<5 mm diameter) roots were monitored bimonthly for 14 months. Decomposition rates over these intervals were also measured, while production and mortality were calculated. Litterfall was collected simultaneously, and the nutrient concentrations of the various detritus components determined. Root pools fluctuated less, and total root turnover biomass (220 g m/sup -2/ yr/sup -1/) was also less than previously noted in most other stands studied. Fine root turnover accounted for 30% of the total detritus production and 20-40% of the turnover of the five macronutrients (N, P, K, Ca, Mg) studied. Differences with previous studies suggest that there may be rather large species and/or site-related differences in the amount of energy various stands allocate for fine root maintenance. For. Sci. 33(2):330-346.

  20. Effect of Exogenous Fibrolytic Enzyme Application on the Microbial Attachment and Digestion of Barley Straw In vitro

    PubMed Central

    Wang, Y.; Ramirez-Bribiesca, J. E.; Yanke, L. J.; Tsang, A.; McAllister, T. A.

    2012-01-01

    The effects of exogenous fibrolytic enzymes (EFE; a mixture of two preparations from Trichoderma spp., with predominant xylanase and β-glucanase activities, respectively) on colonization and digestion of ground barley straw and alfalfa hay by Fibrobacter succinogenes S85 and Ruminococcus flavefaciens FD1 were studied in vitro. The two levels (28 and 280 μg/ml) of EFE tested and both bacteria were effective at digesting NDF of hay and straw. With both substrates, more NDF hydrolysis (p<0.01) was achieved with EFE alone at 280 than at 28 μg/ml. A synergistic effect (p<0.01) of F. succinogenes S85 and EFE on straw digestion was observed at 28 but not 280 μg/ml of EFE. Strain R. flavefaciens FD1 digested more (p<0.01) hay and straw with higher EFE than with lower or no EFE, but the effect was additive rather than synergistic. Included in the incubation medium, EFE showed potential to improve fibre digestion by cellulolytic ruminal bacteria. In a second batch culture experiment using mixed rumen microbes, DM disappearance (DMD), gas production and incorporation of 15N into particle-associated microbial N (15N-PAMN) were higher (p<0.001) with ammoniated (5% w/w; AS) than with native (S) ground barley straw. Application of EFE to the straws increased (p<0.001) DMD and gas production at 4 and 12 h, but not at 48 h of the incubation. EFE applied onto S increased (p<0.01) 15N-PAMN at 4 h only, but EFE on AS increased (p<0.001) 15N-PAMN at all time points. Prehydrolysis increased (p<0.01) DMD from both S and AS at 4 and 12 h, but reduced (p<0.01) 15N-PAMN in the early stage (4 h) of the incubation, as compared to non-prehydrolyzed samples. Application of EFE to barley straw increased rumen bacterial colonization of the substrate, but excessive hydrolytic action of EFE prior to incubation decreased it. PMID:25049480

  1. The effect of lipid supplements on ruminal bacteria in continuous culture fermenters varies with the fatty acid composition.

    PubMed

    Potu, Ramesh B; AbuGhazaleh, Amer A; Hastings, Darcie; Jones, Karen; Ibrahim, Salam A

    2011-04-01

    A single flow continuous culture fermenter system was used in this study to investigate the influence of dietary lipid supplements varying in their fatty acid content on the DNA concentration of selected rumen bacteria. Four continuous culture fermenters were used in a 4 × 4 Latin square design with four periods of 10 d each. Treatment diets were fed at 45 g/d (DM basis) in three equal portions during the day. The diets were: 1) control (CON), 2) control with animal fat source (SAT), 3) control with soybean oil (SBO), and 4) control with fish oil (FO). Lipid supplements were added at 3% of diet DM. The concentrations of total volatile fatty acids and acetate were not affected (P>0.05) by lipid supplements. Concentrations of propionate, iso-butyrate, valerate and iso-valerate were highest (P<0.05) with the FO diet compared with the other treatment diets. The concentration of til C18:l (vaccenic acid, VA) in effluents increased (P<0.05) with SBO and FO diets and was highest with the SBO diet. The concentrations of C18:0 in effluents were lowest (P<0.05) for the FO diet compared with the other treatment diets. Concentrations of DNA for Anaerovibrio lipolytica, and Butyrivibrio proteoclasticus in fermenters were similar (P>0.05) for all diets. The DNA concentrations of Butyrivibrio fibrisolvens and Ruminococcus albus in fermenters were lowest (P<0.05) with the FO diet but were similar (P>0.05) among the other treatment diets. Selenomonas ruminantium DNA concentration in fermenters was highest (P<0.05) with the FO diet. In conclusion, SBO had no effect on bacterial DNA concentrations tested in this study and the VA accumulation in the rumen observed on the FO diet may be due in part to FO influence on B. fibrisolvens, R. albus, and S. ruminantium. PMID:21538241

  2. Comparative evaluation of rumen metagenome community using qPCR and MG-RAST.

    PubMed

    Nathani, Neelam M; Patel, Amrutlal K; Dhamannapatil, Prakash S; Kothari, Ramesh K; Singh, Krishna M; Joshi, Chaitanya G

    2013-01-01

    Microbial profiling of metagenome communities have been studied extensively using MG-RAST and other related metagenome annotation databases. Although, database based taxonomic profiling provides snapshots of the metagenome architecture, their reliability needs to be validated through more accurate methods. Here, we performed qPCR based absolute quantitation of selected rumen microbes in the liquid and solid fraction of the rumen fluid of river buffalo adapted to varying proportion of concentrate to green or dry roughages and compared with the MG-RAST based annotation of the metagenomes sequences of 16S r-DNA amplicons and high throughput shotgun sequencing. Animals were adapted to roughage-to-concentrate ratio in the proportion of 50:50, 75:25 and 100:00, respectively for six weeks. At the end of each treatment, rumen fluid was collected at 3 h post feeding. qPCR revealed that the relative abundance of Prevotella bryantii was higher, followed by the two cellulolytic bacteria Fibrobacter succinogens and Ruminococcus flavefaciens that accounted up to 1.33% and 0.78% of the total rumen bacteria, respectively. While, Selenomonas ruminantium and archaea Methanomicrobiales were lower in microbial population in the rumen of buffalo. There was no statistically significant difference between the enumerations shown by qPCR and analysis of the shotgun sequencing data by MG-RAST except for Prevotella. These results indicate the variations in abundance of different microbial species in buffalo rumen under varied feeding regimes as well as in different fractions of rumen liquor, i.e. solid and the liquid. The results also present the reliability of shotgun sequencing to describe metagenome and analysis/annotation by MG-RAST. PMID:24025701

  3. Mitigation of methane production from cattle by feeding cashew nut shell liquid.

    PubMed

    Shinkai, T; Enishi, O; Mitsumori, M; Higuchi, K; Kobayashi, Y; Takenaka, A; Nagashima, K; Mochizuki, M; Kobayashi, Y

    2012-09-01

    The effects of cashew nut shell liquid (CNSL) feeding on methane production and rumen fermentation were investigated by repeatedly using 3 Holstein nonlactating cows with rumen fistulas. The cows were fed a concentrate and hay diet (6:4 ratio) for 4 wk (control period) followed by the same diet with a CNSL-containing pellet for the next 3 wk (CNSL period). Two trials were conducted using CNSL pellets blended with only silica (trial 1) or with several other ingredients (trial 2). Each pellet type was fed to cows to allow CNSL intake at 4 g/100 kg of body weight per day. Methane production was measured in a respiration chamber system, and energy balance, nutrient digestibility, and rumen microbial changes were monitored. Methane production per unit of dry matter intake decreased by 38.3 and 19.3% in CNSL feeding trials 1 and 2, respectively. Energy loss as methane emission decreased from 9.7 to 6.1% (trial 1) and from 8.4 to 7.0% (trial 2) with CNSL feeding, whereas the loss to feces (trial 1) and heat production (trial 2) increased. Retained energy did not differ between the control and CNSL periods. Digestibility of dry matter and gross energy decreased with CNSL feeding in trial 1, but did not differ in trial 2. Feeding CNSL caused a decrease in acetate and total short-chain fatty acid levels and an increase in propionate proportion in both trials. Relative copy number of methyl coenzyme-M reductase subunit A gene and its expression decreased with CNSL feeding. The relative abundance of fibrolytic or formate-producing species such as Ruminococcus flavefaciens, Butyrivibrio fibrisolvens, and Treponema bryantii decreased, but species related to propionate production, including Prevotella ruminicolla, Selenomonas ruminantium, Anaerovibrio lipolytica, and Succinivibrio dextrinosolvens, increased. If used in a suitable formulation, CNSL acts as a potent methane-inhibiting and propionate-enhancing agent through the alteration of rumen microbiota without adversely

  4. Effects of vanillin, quillaja saponin, and essential oils on in vitro fermentation and protein-degrading microorganisms of the rumen.

    PubMed

    Patra, Amlan K; Yu, Zhongtang

    2014-01-01

    This study investigated the effects of vanillin on methanogenesis and rumen fermentation, and the responses of ruminal protein-degrading bacteria to vanillin (at concentrations of 0, 0.76 and 1.52 g/L), essential oils (clove oil, 1 g/L; origanum oil, 0.50 g/L, and peppermint oil, 1 g/L), and quillaja saponin (at concentration of 0 and 6 g/L) in vitro. Methane production, degradabilities of feed substrate, and ammonia concentration decreased linearly with increasing doses of vanillin. Concentration of total volatile fatty acids also decreased, whereas proportion of butyrate tended to increase linearly with increasing doses of vanillin. Protozoa population decreased, but abundances of Ruminococcus flavefaciens, Prevotella bryantii, Butyrivibrio fibrisolvens, Prevotella ruminicola, Clostridium aminophilum, and Ruminobacter amylophilus increased with increasing doses of vanillin. Origanum and clove oils resulted in lower ammonia concentrations compared to control and peppermint oil. All the tested essential oils decreased abundances of protozoa, Selenomonas ruminantium, R. amylophilus, P. ruminicola and P. bryantii, with the largest decrease resulted from origanum oil followed by clove oil and peppermint oil. The abundances of Megasphaera elsdenii, C. aminophilum, and Clostridium sticklandii were deceased by origanum oil while that of B. fibrisolvens was lowered by both origanum and clove oils. Saponin decreased ammonia concentration and protozoal population, but increased the abundances of S. ruminantium, R. amylophilus, P. ruminicola, and P. bryantii, though the magnitude was small (less than one log unit). The results suggest that reduction of ammonia production by vanillin and saponin may not be caused by direct inhibition of major known proteolytic bacteria, and essential oils can have different inhibitory effects on different proteolytic bacteria, resulting in varying reduction in ammonia production.

  5. Potential of novel dextran oligosaccharides as prebiotics for obesity management through in vitro experimentation.

    PubMed

    Sarbini, Shahrul R; Kolida, Sofia; Deaville, Eddie R; Gibson, Glenn R; Rastall, Robert A

    2014-10-28

    The energy-salvaging capacity of the gut microbiota from dietary ingredients has been proposed as a contributing factor for the development of obesity. This knowledge generated interest in the use of non-digestible dietary ingredients such as prebiotics to manipulate host energy homeostasis. In the present study, the in vitro response of obese human faecal microbiota to novel oligosaccharides was investigated. Dextrans of various molecular weights and degrees of branching were fermented with the faecal microbiota of healthy obese adults in pH-controlled batch cultures. Changes in bacterial populations were monitored using fluorescent in situ hybridisation and SCFA concentrations were analysed by HPLC. The rate of gas production and total volume of gas produced were also determined. In general, the novel dextrans and inulin increased the counts of bifidobacteria. Some of the dextrans were able to alter the composition of the obese human microbiota by increasing the counts of Bacteroides-Prevotella and decreasing those of Faecalibacterium prausnitzii and Ruminococcus bromii/R. flavefaciens. Considerable increases in SCFA concentrations were observed in response to all substrates. Gas production rates were similar during the fermentation of all dextrans, but significantly lower than those during the fermentation of inulin. Lower total gas production and shorter time to attain maximal gas production were observed during the fermentation of the linear 1 kDa dextran than during the fermentation of the other dextrans. The efficacy of bifidobacteria to ferment dextrans relied on the molecular weight and not on the degree of branching. In conclusion, there are no differences in the profiles between the obese and lean human faecal fermentations of dextrans.

  6. Impact of increasing fruit and vegetables and flavonoid intake on the human gut microbiota.

    PubMed

    Klinder, Annett; Shen, Qing; Heppel, Susanne; Lovegrove, Julie A; Rowland, Ian; Tuohy, Kieran M

    2016-04-01

    Epidemiological studies have shown protective effects of fruits and vegetables (F&V) in lowering the risk of developing cardiovascular diseases (CVD) and cancers. Plant-derived dietary fibre (non-digestible polysaccharides) and/or flavonoids may mediate the observed protective effects particularly through their interaction with the gut microbiota. The aim of this study was to assess the impact of fruit and vegetable (F&V) intake on gut microbiota, with an emphasis on the role of flavonoids, and further to explore relationships between microbiota and factors associated with CVD risk. In the study, a parallel design with 3 study groups, participants in the two intervention groups representing high-flavonoid (HF) and low flavonoid (LF) intakes were asked to increase their daily F&V intake by 2, 4 and 6 portions for a duration of 6 weeks each, while a third (control) group continued with their habitual diet. Faecal samples were collected at baseline and after each dose from 122 subjects. Faecal bacteria enumeration was performed by fluorescence in situ hybridisation (FISH). Correlations of dietary components, flavonoid intake and markers of CVD with bacterial numbers were also performed. A significant dose X treatment interaction was only found for Clostidium leptum-Ruminococcus bromii/flavefaciens with a significant increase after intake of 6 additional portions in the LF group. Correlation analysis of the data from all 122 subjects independent from dietary intervention indicated an inhibitory role of F&V intake, flavonoid content and sugars against the growth of potentially pathogenic clostridia. Additionally, we observed associations between certain bacterial populations and CVD risk factors including plasma TNF-α, plasma lipids and BMI/waist circumference. PMID:26757793

  7. Potential of novel dextran oligosaccharides as prebiotics for obesity management through in vitro experimentation.

    PubMed

    Sarbini, Shahrul R; Kolida, Sofia; Deaville, Eddie R; Gibson, Glenn R; Rastall, Robert A

    2014-10-28

    The energy-salvaging capacity of the gut microbiota from dietary ingredients has been proposed as a contributing factor for the development of obesity. This knowledge generated interest in the use of non-digestible dietary ingredients such as prebiotics to manipulate host energy homeostasis. In the present study, the in vitro response of obese human faecal microbiota to novel oligosaccharides was investigated. Dextrans of various molecular weights and degrees of branching were fermented with the faecal microbiota of healthy obese adults in pH-controlled batch cultures. Changes in bacterial populations were monitored using fluorescent in situ hybridisation and SCFA concentrations were analysed by HPLC. The rate of gas production and total volume of gas produced were also determined. In general, the novel dextrans and inulin increased the counts of bifidobacteria. Some of the dextrans were able to alter the composition of the obese human microbiota by increasing the counts of Bacteroides-Prevotella and decreasing those of Faecalibacterium prausnitzii and Ruminococcus bromii/R. flavefaciens. Considerable increases in SCFA concentrations were observed in response to all substrates. Gas production rates were similar during the fermentation of all dextrans, but significantly lower than those during the fermentation of inulin. Lower total gas production and shorter time to attain maximal gas production were observed during the fermentation of the linear 1 kDa dextran than during the fermentation of the other dextrans. The efficacy of bifidobacteria to ferment dextrans relied on the molecular weight and not on the degree of branching. In conclusion, there are no differences in the profiles between the obese and lean human faecal fermentations of dextrans. PMID:25196744

  8. Development of a membrane-array method for the detection of human intestinal bacteria in fecal samples.

    PubMed

    Wang, R F; Kim, S-J; Robertson, L H; Cerniglia, C E

    2002-10-01

    A membrane-array method was developed for the detection of human intestinal bacteria in fecal samples without using the expensive microarray-arrayer and laser-scanner. The 16S rDNA sequences of 20 predominant human intestinal bacterial species were used to design oligonucleotide probes. Three 40-mer oligonucleotides specific for each bacterial species (total 60 probes) were synthesized and applied to nitrocellulose membranes. Digoxigenin (DIG)-labeled 16S rDNAs were amplified by polymerase chain reaction (PCR) from human fecal samples or pure cultured bacteria using two universal primers, and were hybridized to the membrane-array. Hybridization signals were read by NBT/BCIP color development. The 20 intestinal bacterial species tested were Bacteroides thetaiotaomicron, B. vulgatus, B. fragilis, B. distasonis, Clostridium clostridiiforme, C. leptum, Fusobacterium prausnitzii, Peptostreptococcus productus, Ruminococcus obeum, R. bromii, R. callidus, R. albus, Bifidobacterium longum, B. adolescentis, B. infantis, Eubacterium biforme, E. aerofaciens, Lactobacillus acidophilus,Escherichia coli, and Enterococcus faecium. The two universal primers were able to amplify full size 16S rDNA from all of the 20 bacterial species tested. The hybridization results indicated that the membrane-array method is a reliable technique for the detection of predominant human intestinal bacteria in the fecal samples. The result was also confirmed by using specific PCR methods for these bacteria.

  9. Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes

    PubMed Central

    Azevedo, Analice C.; Bento, Cláudia B. P.; Ruiz, Jeronimo C.; Queiroz, Marisa V.

    2015-01-01

    Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides. PMID:26253660

  10. Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes.

    PubMed

    Azevedo, Analice C; Bento, Cláudia B P; Ruiz, Jeronimo C; Queiroz, Marisa V; Mantovani, Hilário C

    2015-10-01

    Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides.

  11. Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes.

    PubMed

    Azevedo, Analice C; Bento, Cláudia B P; Ruiz, Jeronimo C; Queiroz, Marisa V; Mantovani, Hilário C

    2015-10-01

    Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides. PMID:26253660

  12. The effect of replacing corn with glycerol on ruminal bacteria in continuous culture fermenters.

    PubMed

    AbuGhazaleh, A A; Abo El-Nor, S; Ibrahim, S A

    2011-06-01

    The effects of substituting corn with glycerol on DNA concentration of selected ruminal bacteria were investigated using continuous fermenters. Four continuous culture fermenters were used in a 4 × 4 Latin Square design with four 10 days consecutive periods. Treatment diets (60:40 forage to concentrate) were fed at 45 g/day dry matter (DM) in three equal portions. Glycerol (0.995 g/g glycerol) was used to replace corn in a grain mix at proportions of 0% (T0; control), 15% (T15), 30% (T30) and 45% (T45). On day 10 of each period, samples were collected from each fermenter 3 h after the morning feeding and analysed for volatile fatty acid and bacterial DNA concentration. Glycerol substitution was related to significantly higher butyrate, valerate and isovalerate concentrations. Compared with the T0 diet, acetate concentration was significantly lower with the T30 and T45 diets whilst propionate concentration was higher only with the T45 diet. The DNA concentrations for Butyrivibrio fibrisolvens and Selenomonas ruminantium decreased with the T30 and T45 diets compared with the T0 diet. No differences in the DNA concentrations for Ruminococcus albus and Succinivibrio dextrinosolvens amongst diets were observed. The findings show that substituting 15% of the dietary corn with glycerol had no substantive effects on fermentation processing or ruminal bacteria. Higher substitution levels, however, may adversely affect ruminal bacteria and negatively impact acetate production. PMID:20880288

  13. [COMPARATIVE ANALYSIS OF LIPID METABOLISM INDICES IN SOME PARASITES OF THE WHITE CHARR (SALVELINUS ALBUS) FROM THE LAKE KRINOTSKOE].

    PubMed

    Gordeev, I I; Mikryakov, D V; Silkina, N I

    2015-01-01

    Comparative study of lipid metabolism indices (total lipids, separate lipid fractions, level of the lipid peroxidation processes, and antioxidant protection) was carried out in three parasite species collected from the white char in the Lake Kronotskoe: Diphyllobothrium ditremum Crepin, 1825 (Cestoda), Philonema oncorhynchi Kuitunen-Ekbaum, 1933 (Nematoda) H Neoechinorhynchus salmonis Ching, 1984 (Acanthocephala). Acanthocephalans possessed significantly greater levels of total lipids, triacylglycerol, and malondialdehyde; nematodes, of cholesterol and sterol esters; and cestodes, in phospholipids and constants of the substrate oxidation. Dependence between lipid metabolism of helminths and their taxonomic affiliation, morpho-functional features, the stage of the life cycle, and the site of infection in the host are discussed.

  14. Development of working hypotheses linking management of the Missouri River to population dynamics of Scaphirhynchus albus (pallid sturgeon)

    USGS Publications Warehouse

    Jacobson, Robert B.; Parsley, Michael J.; Annis, Mandy L.; Colvin, Michael E.; Welker, Timothy L.; James, Daniel A.

    2016-01-01

    The initial set of candidate hypotheses provides a useful starting point for quantitative modeling and adaptive management of the river and species. We anticipate that hypotheses will change from the set of working management hypotheses as adaptive management progresses. More importantly, hypotheses that have been filtered out of our multistep process are still being considered. These filtered hypotheses are archived and if existing hypotheses are determined to be inadequate to explain observed population dynamics, new hypotheses can be created or filtered hypotheses can be reinstated.

  15. [Canning of "humitas" prepared with opaque-2 corn, supplemented with sweet lupine (Lupinus albus var. Multolupa). Nutritional and quality changes].

    PubMed

    Camacho, L; Bañados, E; Fernández, E

    1989-06-01

    The effects of opaque-2 corn and the complementation with lupin flour on the sensory quality and nutritive value of "humitas" were evaluated. Moreover, the nutritional and quality changes which occur during the retorting of the product canned in two can sizes, were studied. Hybrid and opaque-2 corn were replaced with 6%, 8%, 10% and 12% lupin flour, being 8% the complementation level with the best sensory and nutritional quality. Heat penetration studies of the product canned in N2 and N6 tin cans, were carried out. Total process time at 121 degrees C was 73 min and 147 min, respectively. "Humitas" prepared with hybrid and opaque-2 corn, with and without 8% lupin flour, prior and after sterilization, were subjected to proximate analysis, pH, titratible acidity and available lysine determinations. Biological evaluation of the protein by the net protein ratio (NPR) and digestibility, as well as organoleptic quality and acceptability analyses were also determined. It was concluded that the complementation with 8% lupin flour improves significantly the nutritional value of hybrid corn "humitas", but not that of opaque-2 corn. The canning process affected lysine availability and was directly related to the amino acid concentration, and to the retorting duration. On the other hand, the thermal processing adversely affected the biological quality of protein and some sensory attributes. The 8% lupin complementation was also detrimental for the organoleptic quality of the product. PMID:2487029

  16. Effect of different debittering processes on mineral and phytic acid content of lupin (Lupinus albus L.) seeds.

    PubMed

    Ertaş, Nilgün; Bilgiçli, Nermin

    2014-11-01

    Lupin is a valuable ancient legume which contains high amount of protein, dietary fiber, oil, minerals and different functional components. Bitter lupin seeds cannot be consumed directly since its high toxic alkaloid content. Cooking and soaking are effective processes for removing these toxic substances and antinutrients as phytic acid, trypsin inhibitors and oligosaccharides. In this study, debittering process containing cooking and soaking up to 144 h was applied to lupin seeds. Raw lupin seeds had 3.3 % ash and 41.3 % protein content. Ash and protein content of debittered seeds changed between 2.1 and 2.5 %, 39.5 and 40.9 % respectively. After debittering process, significant (p < 0.05) decreases (between % 5.7 and 75.7) were observed in calcium, phosphorus, zinc, iron, magnesium and manganese contents of the lupin seeds. Phytic acid was removed from raw lupin seeds up to 71.4 % ratio by debittering processes, and soaking in distilled water at 55 °C and long soaking time (144 h) was found the most effective methods on phytic acid loss. While more lighter (L*) seeds were obtained with soaking in distilled water at 25 °C, soaking in 0.5 % NaHCO3 solution gave more yellowish (b*) seed properties compared to other soaking methods. Soaking in 0.5 % NaHCO3 solution at 144 h gave the most liked products in terms of sensorial evaluation. PMID:26396330

  17. Enrichment of gluten-free cakes with lupin (Lupinus albus L.) or buckwheat (Fagopyrum esculentum M.) flours.

    PubMed

    Levent, Hacer; Bilgiçli, Nermin

    2011-11-01

    In the present study, the effect of debittered lupin flour (LF) and whole buckwheat flour (BF) on the nutritional and sensory quality of gluten-free cake was studied. LF (10, 20, 30 and 40%) and BF (5, 10, 15 and 20%) were partially replaced with corn starch and rice flour mixture (1:1 w/w) in the gluten-free cake recipe. LF increased the protein, calcium, iron, manganese, phosphorus and zinc contents of the cakes, while BF caused a significant increase (P < 0.05) especially in potassium and magnesium contents of the gluten-free cakes. According to the overall acceptability rating, it was concluded that gluten-free cake could be produced with satisfactory results by the addition of LF and BF up to 30% and 10%, respectively. PMID:21568822

  18. [COMPARATIVE ANALYSIS OF LIPID METABOLISM INDICES IN SOME PARASITES OF THE WHITE CHARR (SALVELINUS ALBUS) FROM THE LAKE KRINOTSKOE].

    PubMed

    Gordeev, I I; Mikryakov, D V; Silkina, N I

    2015-01-01

    Comparative study of lipid metabolism indices (total lipids, separate lipid fractions, level of the lipid peroxidation processes, and antioxidant protection) was carried out in three parasite species collected from the white char in the Lake Kronotskoe: Diphyllobothrium ditremum Crepin, 1825 (Cestoda), Philonema oncorhynchi Kuitunen-Ekbaum, 1933 (Nematoda) H Neoechinorhynchus salmonis Ching, 1984 (Acanthocephala). Acanthocephalans possessed significantly greater levels of total lipids, triacylglycerol, and malondialdehyde; nematodes, of cholesterol and sterol esters; and cestodes, in phospholipids and constants of the substrate oxidation. Dependence between lipid metabolism of helminths and their taxonomic affiliation, morpho-functional features, the stage of the life cycle, and the site of infection in the host are discussed. PMID:26314155

  19. Enrichment of gluten-free cakes with lupin (Lupinus albus L.) or buckwheat (Fagopyrum esculentum M.) flours.

    PubMed

    Levent, Hacer; Bilgiçli, Nermin

    2011-11-01

    In the present study, the effect of debittered lupin flour (LF) and whole buckwheat flour (BF) on the nutritional and sensory quality of gluten-free cake was studied. LF (10, 20, 30 and 40%) and BF (5, 10, 15 and 20%) were partially replaced with corn starch and rice flour mixture (1:1 w/w) in the gluten-free cake recipe. LF increased the protein, calcium, iron, manganese, phosphorus and zinc contents of the cakes, while BF caused a significant increase (P < 0.05) especially in potassium and magnesium contents of the gluten-free cakes. According to the overall acceptability rating, it was concluded that gluten-free cake could be produced with satisfactory results by the addition of LF and BF up to 30% and 10%, respectively.

  20. Assessment of Bioavailable Concentrations of Germanium and Rare Earth Elements in the Rhizosphere of White Lupin (Lupinus albus L.)

    NASA Astrophysics Data System (ADS)

    Wiche, Oliver; Fischer, Ronny; Moschner, Christin; Székely, Balázs

    2015-04-01

    Concentrations of Germanium (Ge) and Rare Earth Elements in soils are estimated at 1.5 mg kg -1 (Ge), 25 mg kg -1 (La) and 20 mg kg -1 (Nd), which are only roughly smaller than concentrations of Pb and Zn. Germanium and rare earth elements are thus not rare but widely dispersed in soils and therefore up to date, only a few minable deposits are available. An environmental friendly and cost-effective way for Ge and rare earth element production could be phytomining. However, the most challenging part of a phytomining of these elements is to increase bioavailable concentrations of the elements in soils. Recent studies show, that mixed cultures with white lupine or other species with a high potential to mobilize trace metals in their rhizosphere due to an acidification of the soil and release of organic acids in the root zone could be a promising tool for phytomining. Complexation of Ge and rare earth elements by organic acids might play a key role in controlling bioavailability to plants as re-adsorption on soil particles and precipitation is prevented and thus, concentrations in the root zone of white lupine increase. This may also allow the complexes to diffuse along a concentration gradient to the roots of mixed culture growing species leading to enhanced plant uptake. However, to optimize mixed cultures it would be interesting to know to which extend mobilization of trace metals is dependent from chemical speciation of elements in soil due to the interspecific interaction of roots. A method for the identification of complexes of germanium and rare earth elements with organic acids, predominantly citric acid in the rhizosphere of white lupine was developed and successfully tested. The method is based on coupling of liquid chromatography with ICP-MS using a zic-philic column (SeQuant). As a preliminary result, we were able to show that complexes of germanium with citric acid exist in the rhizosphere of white lupin, what may contribute to the bioavailability of this element. These studies have been carried out in the framework of the PhytoGerm project, financed by the Federal Ministry of Education and Research, Germany. The authors are grateful to students and laboratory assistants contributing in the field work and sample preparation.

  1. Development of working hypotheses linking management of the Missouri River to population dynamics of Scaphirhynchus albus (pallid sturgeon)

    USGS Publications Warehouse

    Jacobson, Robert B.; Parsley, Michael J.; Annis, Mandy L.; Colvin, Michael E.; Welker, Timothy L.; James, Daniel A.

    2016-01-20

    The initial set of candidate hypotheses provides a useful starting point for quantitative modeling and adaptive management of the river and species. We anticipate that hypotheses will change from the set of working management hypotheses as adaptive management progresses. More importantly, hypotheses that have been filtered out of our multistep process are still being considered. These filtered hypotheses are archived and if existing hypotheses are determined to be inadequate to explain observed population dynamics, new hypotheses can be created or filtered hypotheses can be reinstated.

  2. Water-quality requirements, tolerances, and preferences of pallid sturgeon (Scaphirhynchus albus) in the lower Missouri River

    USGS Publications Warehouse

    Blevins, Dale W.

    2011-01-01

    Additional research could be used to characterize and quantify the requirements, tolerance, and preferences of pallid sturgeon to these water-quality characteristics, especially during the egg and larval life stages. Enhancements to existing water-sampling programs are needed to quantify the exposure of pallid sturgeon to many of these water-quality stressors.

  3. Effects of Flavonoid-rich Plant Extracts on In vitro Ruminal Methanogenesis, Microbial Populations and Fermentation Characteristics

    PubMed Central

    Kim, Eun T.; Guan, Le Luo; Lee, Shin J.; Lee, Sang M.; Lee, Sang S.; Lee, Il D.; Lee, Su K.; Lee, Sung S.

    2015-01-01

    The objective of this study was to evaluate the in vitro effects of flavonoid-rich plant extracts (PE) on ruminal fermentation characteristics and methane emission by studying their effectiveness for methanogenesis in the rumen. A fistulated Holstein cow was used as a donor of rumen fluid. The PE (Punica granatum, Betula schmidtii, Ginkgo biloba, Camellia japonica, and Cudrania tricuspidata) known to have high concentrations of flavonoid were added to an in vitro fermentation incubated with rumen fluid. Total gas production and microbial growth with all PE was higher than that of the control at 24 h incubation, while the methane emission was significantly lower (p<0.05) than that of the control. The decrease in methane accumulation relative to the control was 47.6%, 39.6%, 46.7%, 47.9%, and 48.8% for Punica, Betula, Ginkgo, Camellia, and Cudrania treatments, respectively. Ciliate populations were reduced by more than 60% in flavonoid-rich PE treatments. The Fibrobacter succinogenes diversity in all added flavonoid-rich PE was shown to increase, while the Ruminoccocus albus and R. flavefaciens populations in all PE decreased as compared with the control. In particular, the F. succinogenes community with the addition of Birch extract increased to a greater extent than that of others. In conclusion, the results of this study showed that flavonoid-rich PE decreased ruminal methane emission without adversely affecting ruminal fermentation characteristics in vitro in 24 h incubation time, suggesting that the flavonoid-rich PE have potential possibility as bio-active regulator for ruminants. PMID:25656200

  4. Effects of rare earth element lanthanum on rumen methane and volatile fatty acid production and microbial flora in vitro.

    PubMed

    Zhang, T T; Zhao, G Y; Zheng, W S; Niu, W J; Wei, C; Lin, S X

    2015-06-01

    The objectives of the trial were to study the effects of rare earth element (REE) lanthanum (La) on the in vitro rumen methane (CH4 ) and volatile fatty acid (VFA) production and the microbial flora of feeds. Four feed mixtures with different levels of neutral detergent fibre (NDF), that is 20.0% (I), 31.0% (II), 41.9% (III) and 52.7% (IV), were formulated as substrates. Five levels of LaCl3 , that is 0, 0.4, 0.6, 0.8 and 1.0 mmol/kg dry matter (DM), were added to the feed mixtures, respectively, as experimental treatments in a two-factor 5 × 4 randomized design. The in vitro incubation lasted for 24 h. The results showed that supplementing LaCl3 increased the total gas (p < 0.001) production and tended to increase the total VFA production (p = 0.072) and decreased the CH4 production (p = 0.001) and the ratios of acetate/propionate (p = 0.019) and CH4 /total VFA (p < 0.001). Interactions between LaCl3 and NDF were significant in total gas production (p = 0.030) and tended to be significant in CH4 production (p = 0.071). Supplementing LaCl3 at the level of 0.8 mmol/g DM decreased the relative abundance of methanogens and protozoa in the total bacterial 16S rDNA analysed using the real-time PCR (p < 0.0001), increased F. succinogenes (p = 0.0003) and decreased R. flavefaciens (p < 0.0001) whereas did not affect R. albus and anaerobic fungi (p > 0.05). It was concluded that LaCl3 decreased the CH4 production without negatively affecting feed digestion through manipulating rumen microbial flora when feed mixtures with different levels of NDF were used as substrates.

  5. Changes of Microbial Population in the Rumen of Dairy Steers as Influenced by Plant Containing Tannins and Saponins and Roughage to Concentrate Ratio

    PubMed Central

    Anantasook, N.; Wanapat, M.; Cherdthong, A.; Gunun, P.

    2013-01-01

    The objective of this study was to investigate microbial population in the rumen of dairy steers as influenced by supplementing with dietary condensed tannins and saponins and different roughage to concentrate ratios. Four, rumen fistulated dairy steers (Bos indicus) were used in a 2×2 factorial arrangement in a 4×4 Latin square design. The main factors were two roughage to concentrate ratios (R:C, 60:40 and 40:60) and two supplementations of rain tree pod meal (RPM) (0 and 60 g/kg of total DM intake). Chopped 30 g/kg urea treated rice straw was used as a roughage source. All animals received feed according to respective R:C ratios at 25 g/kg body weight. The RPM contained crude tannins and saponins at 84 and 143 g/kg of DM, respectively. It was found that ruminal pH decreased while ruminal temperature increased by a higher concentrate ratio (R:C 40:60) (p<0.05). In contrast, total bacterial, Ruminococus albus and viable proteolytic bacteria were not affected by dietary supplementation. Numbers of fungi, cellulolytic bacteria, Fibrobactor succinogenes and Ruminococus flavefaciens were higher while amylolytic bacteria was lower when steers were fed at 400 g/kg of concentrate. The population of Fibrobactor succinogenes, was found to be higher with RPM supplementation. In addition, the use of real-time PCR technique indicated that the population of protozoa and methanogens were decreased (p<0.05) with supplementation of RPM and with an increasing concentrate ratio. Supplementation of RPM and feeding different concentrate ratios resulted in changing the rumen microbes especially, when the animals were fed at 600 g/kg of concentrate and supplemented with RPM which significantly reduced the protozoa and methanogens population. PMID:25049745

  6. Influence of Rain Tree Pod Meal Supplementation on Rice Straw Based Diets Using In vitro Gas Fermentation Technique.

    PubMed

    Anantasook, N; Wanapat, M

    2012-03-01

    The objective of this study was to determine the roughage to concentrate (R:C) ratio with rain tree pod meal (RPM) supplementation on in vitro fermentation using gas production technique. The experiment design was a 6×4 factorial arrangement in a CRD. Factor A was 6 levels of R:C ratio (100:0, 80:20, 60:40, 40:60, 20:80 and 0:100) and factor B was 4 levels of RPM (0, 4, 8 and 12 mg). It was found that gas kinetic, extent rate (c) was linearly increased (p<0.01) with an increasing level of concentrate while cumulative gas production (96 h) was higher in R:C of 40:60. In addition, interaction of R:C ratio and RPM level affected NH3-N and IVDMD and were highest in R:C of 0:100 with 0, 4 mg of RPM and 40:60 with 8 mg of RPM, respectively. Moreover, interaction of R:C ratio and RPM level significantly increased total volatile fatty acids and propionate concentration whereas lower acetate, acetate to propionate ratios and CH4 production in R:C of 20:80 with 8 mg of RPM. Moreover, the two factors, R:C ratio and RPM level influenced the protozoal population and the percentage of methanogens in the total bacteria population. In addition, the use of real-time PCR found that a high level of concentrate in the diet remarkably decreased three cellulolytic bacteria numbers (F. succinogenes, R. flavefaciens and R. albus). Based on this study, it is suggested that the ratio of R:C at 40:60 and RPM level at 12 mg could improve ruminal fluid fermentation in terms of reducing fermentation losses, thus improving VFA profiles and ruminal ecology.

  7. Effect of fiber digestibility and conservation method on feed intake and the ruminal ecosystem of growing steers.

    PubMed

    Sousa, D O; Mesquita, B S; Diniz-Magalhães, J; Bueno, I C S; Mesquita, L G; Silva, L F P

    2014-12-01

    Fiber digestibility is an important factor regulating DMI in ruminants. Additionally, the ensiling process can also affect digestibility and chemical composition of the forage. The objective of this study was to investigate effects of sugarcane NDF digestibility (NDFD) and conservation method on intake, rumen kinetics, and the ruminal ecosystem of steers. Eight ruminally cannulated Nellore steers (275±22 kg BW) were used in a replicated 4×4 Latin square design with a 2×2 factorial arrangement of treatments. Two sugarcane genotypes divergent for stalk NDFD were used: IAC86-2480 with high NDFD and SP91-1049 with low NDFD. Experimental diets were formulated with 40% sugarcane, either freshly cut or as silage, and 60% concentrate on a DM basis. Each experimental period lasted for 14 d, with the last 4 d used for determination of intake, ruminal evacuation, and ruminal fluid collection. The effect of fiber digestibility on DM and NDF intake was dependent on the forage conservation method (P=0.01). High NDFD increased (P<0.01) DMI only when sugarcane was offered as silage, having no effect (P=0.41) on DMI when offered as freshly cut. Conservation method had no effect on total ruminal mass, with only a tendency (P<0.10) for greater NDF and indigestible NDF ruminal mass in steers fed the low-NDFD genotype. The NDF turnover and passage rates were greater (P<0.05) for the genotype with high NDFD but only when offered as silage. Liquid turnover rate in the rumen was greater (P=0.02) for diets containing silage, with no effect of genotype (P=0.87). There was no effect of NDFD genotype on ruminal pH (P=0.77); however, diets containing sugarcane as silage increased (P<0.01) ruminal pH. Total concentration of short chain fatty acids (P=0.05) and proportions of propionate (P=0.01) were greater for diets containing fresh sugarcane. Diets with fresh sugarcane increased the ruminal population of Streptococcus bovis (P<0.01) and Ruminococcus albus (P=0.03). The relative population

  8. Catalytic Efficiency Diversification of Duplicate β-1,3-1,4-Glucanases from Neocallimastix patriciarum J11

    PubMed Central

    Hung, Yu-Lung; Chen, Hui-Jye; Liu, Jeng-Chen

    2012-01-01

    Four types of β-1,3-1,4 glucanase (β-glucanase, EC 3.2.1.73) genes, designated bglA13, bglA16, bglA51, and bglM2, were found in the cDNA library of Neocallimastix patriciarum J11. All were highly homologous with each other and demonstrated a close phylogenetic relationship with and a similar codon bias to Streptococcus equinus. The presence of expansion and several predicted secondary structures in the 3′ untranslated regions (3′UTRs) of bglA16 and bglM2 suggest that these two genes were duplicated recently, whereas bglA13 and bglA16, which contain very short 3′UTRs, were replicated earlier. These findings indicate that the β-glucanase genes from N. patriciarum J11 may have arisen by horizontal transfer from the bacterium and subsequent duplication in the rumen fungus. β-Glucanase genes of Streptococcus equinus, Ruminococcus albus 7, and N. patriciarum J11 were cloned and expressed by Escherichia coli. The recombinant β-glucanases cloned from S. equinus, R. albus 7, and N. patriciarum J11 were endo-acting and had similar substrate specificity, but they demonstrated different properties in other tests. The specific activities and catalytic efficiency of the bacterial β-glucanases were also significantly lower than those of the fungal β-glucanases. Our results also revealed that the activities and some characteristics of enzymes were changed during the horizontal gene transfer event. The specific activities of the fungal β-glucanases ranged from 26,529 to 41,209 U/mg of protein when barley-derived β-glucan was used as the substrate. They also demonstrated similar pH and temperature optima, substrate specificity, substrate affinity, and hydrolysis patterns. Nevertheless, BglA16 and BglM2, two recently duplicated β-glucanases, showed much higher kcat values than others. These results support the notion that duplicated β-glucanase genes, namely, bglA16 and bglM2, increase the reaction efficiency of β-glucanases and suggest that the catalytic efficiency

  9. Effect of fiber digestibility and conservation method on feed intake and the ruminal ecosystem of growing steers.

    PubMed

    Sousa, D O; Mesquita, B S; Diniz-Magalhães, J; Bueno, I C S; Mesquita, L G; Silva, L F P

    2014-12-01

    Fiber digestibility is an important factor regulating DMI in ruminants. Additionally, the ensiling process can also affect digestibility and chemical composition of the forage. The objective of this study was to investigate effects of sugarcane NDF digestibility (NDFD) and conservation method on intake, rumen kinetics, and the ruminal ecosystem of steers. Eight ruminally cannulated Nellore steers (275±22 kg BW) were used in a replicated 4×4 Latin square design with a 2×2 factorial arrangement of treatments. Two sugarcane genotypes divergent for stalk NDFD were used: IAC86-2480 with high NDFD and SP91-1049 with low NDFD. Experimental diets were formulated with 40% sugarcane, either freshly cut or as silage, and 60% concentrate on a DM basis. Each experimental period lasted for 14 d, with the last 4 d used for determination of intake, ruminal evacuation, and ruminal fluid collection. The effect of fiber digestibility on DM and NDF intake was dependent on the forage conservation method (P=0.01). High NDFD increased (P<0.01) DMI only when sugarcane was offered as silage, having no effect (P=0.41) on DMI when offered as freshly cut. Conservation method had no effect on total ruminal mass, with only a tendency (P<0.10) for greater NDF and indigestible NDF ruminal mass in steers fed the low-NDFD genotype. The NDF turnover and passage rates were greater (P<0.05) for the genotype with high NDFD but only when offered as silage. Liquid turnover rate in the rumen was greater (P=0.02) for diets containing silage, with no effect of genotype (P=0.87). There was no effect of NDFD genotype on ruminal pH (P=0.77); however, diets containing sugarcane as silage increased (P<0.01) ruminal pH. Total concentration of short chain fatty acids (P=0.05) and proportions of propionate (P=0.01) were greater for diets containing fresh sugarcane. Diets with fresh sugarcane increased the ruminal population of Streptococcus bovis (P<0.01) and Ruminococcus albus (P=0.03). The relative population

  10. The effects of active dried and killed dried yeast on subacute ruminal acidosis, ruminal fermentation, and nutrient digestibility in beef heifers.

    PubMed

    Vyas, D; Uwizeye, A; Mohammed, R; Yang, W Z; Walker, N D; Beauchemin, K A

    2014-02-01

    The study addressed the importance of yeast (Saccharomyces cerevisiae) viability for reducing the incidence of subacute ruminal acidosis (SARA) and improving total tract nutrient digestibility in beef heifers. Six ruminally cannulated beef heifers (680 ± 50 kg BW) were used in a replicated 3 × 3 Latin square design and were fed a diet consisting of 40% barley silage, 10% chopped grass hay, and 50% barley grain-based concentrate (DM basis). Treatments were 1) no yeast (Control), 2) active dried yeast (ADY; 4 g providing 10(10) cfu/g; AB Vista, Marlborough, UK), and 3) killed dried yeast (KDY; 4 g autoclaved ADY). The treatments were directly dosed via the ruminal cannula daily at the time of feeding. The periods consisted of 2 wk of adaptation (d 1 to 14) and 7 d of measurements (d 15 to 21). Ruminal pH was continuously measured (d 15 to 21) using an indwelling system. Ruminal contents were sampled on d 15 and 17 at 0, 3, 6, 9, and 12 h after feeding. Total tract nutrient digestibility was measured using an external marker (YbCl3) from d 15 to 19. No treatment difference was observed for DMI (P = 0.86). Yeast supplementation (ADY and KDY) tended to increase total tract digestibility of starch (P = 0.07) whereas no effects were observed on digestibility of other nutrients. Both ADY and KDY elevated minimum (P < 0.01) and mean ruminal pH (P = 0.02) whereas no effects were observed on maximum pH (P = 0.12). Irrespective of its viability, yeast supplementation was effective in reducing time that ruminal pH was below 5.8 (P < 0.01) and 5.6 (P < 0.01). No treatment differences were observed for the ruminal VFA profile and lactate concentration. No treatment differences were observed on the relative population size of Streptococcus bovis, Fibrobacter succinogenes, and Megasphaera elsdenii (P > 0.10); however, the proportion of Ruminococcus flavefaciens in solid fraction of digesta was greater with KDY (P = 0.05). The study demonstrates the positive effects of yeast

  11. Effect of non-starch-polysaccharide-degrading enzymes as feed additive on the rumen bacterial population in non-lactating cows quantified by real-time PCR.

    PubMed

    Zeitz, J O; Guertler, P; Pfaffl, M W; Eisenreich, R; Wiedemann, S; Schwarz, F J

    2013-12-01

    The effects of non-starch-polysaccharide-degrading enzymes, added to a maize silage- and grass silage-based total mixed ration (TMR) at least 14 h before feeding, on the rumen bacterial population were investigated. Six non-lactating Holstein Friesian cows were allocated to three treatment groups using a duplicate 3 × 3 Latin square design with three 31-day periods (29 days of adaptation and 2 days of sampling). Treatments were control TMR [69% forage and 31% concentrates on a dry matter (DM) basis] or TMR with 13.8 or 27.7 ml/kg of feed DM of Roxazyme G2 liquid with activities (U/ml enzyme preparation) of xylanase 260 000, β-glucanase 180 000 and cellulase 8000 (DSM Nutritional Products, Basel, Switzerland). The concentrations of 16S rDNA of Anaerovibrio lipolytica, Fibrobacter succinogenes, Prevotella ruminicola, Ruminococcus flavefaciens, Selenomonas ruminantium and Treponema bryantii, and their relative percentage of total bacteria in rumen samples obtained before feeding and 3 and 7 h after feeding and from two rumen fractions were determined using real-time PCR. Sampling time had only little influence, but bacterial numbers and the composition of the population differed between the transition layer between rumen fluid and the fibre mat (fraction A) and the rumen fluid (fraction B) highlighting the importance to standardize sampling. The 16S rDNA copies of total bacteria and the six bacterial species as well as the population composition were mainly unaffected by the high levels of exogenous enzymes supplemented at all sampling times and in both rumen fractions. Occasionally, the percentages of the non-fibrolytic species P. ruminicola and A. lipolytica changed in response to enzyme supplementation. Some increases in the potential degradability of the diet and decreases in lag time which occurred collaterally indicate that other factors than changes in numbers of non-particle-associated bacteria are mainly responsible for the effects of

  12. Fortification of dried distillers grains plus solubles with grape seed meal in the diet modulates methane mitigation and rumen microbiota in Rusitec.

    PubMed

    Khiaosa-Ard, R; Metzler-Zebeli, B U; Ahmed, S; Muro-Reyes, A; Deckardt, K; Chizzola, R; Böhm, J; Zebeli, Q

    2015-04-01

    The role of dried distillers grains plus solubles (DDGS) and associative effects of different levels of grape seed meal (GSM) fortified in DDGS, used as both protein and energy sources in the diet, on ruminal fermentation and microbiota were investigated using rumen-simulation technique. All diets consisted of hay and concentrate mixture with a ratio of 48:52 [dry matter (DM) basis], but were different in the concentrate composition. The control diet contained soybean meal (13.5% of diet DM) and barley grain (37%), whereas DDGS treatments, unfortified DDGS (19.5% of diet DM), or DDGS fortified with GSM, either at 1, 5, 10, or 20% were used entirely in place of soybean meal and part of barley grain at a 19.5 to 25% inclusion level. All diets had similar DM, organic matter, and crude protein contents, but consisted of increasing neutral detergent fiber and decreasing nonfiber carbohydrates levels with DDGS-GSM inclusion. Compared with the soy-based control diet, the unfortified DDGS treatment elevated ammonia concentration (19.1%) of rumen fluid associated with greater crude protein degradation (~19.5%). Methane formation decreased with increasing GSM fortification levels (≥ 5%) in DDGS by which the methane concentration significantly decreased by 18.9 to 23.4 and 12.8 to 17.6% compared with control and unfortified DDGS, respectively. Compared with control, unfortified DDGS decreased butyrate proportion, and GSM fortification in the diet further decreased this variable. The proportions of genus Prevotella and Clostridium cluster XIVa were enhanced by the presence of DDGS without any associative effect of GSM fortification. The abundance of methanogenic archaea was similar, but their composition differed among treatments; whereas Methanosphaera spp. remained unchanged, proportion of Methanobrevibacter spp. decreased in DDGS-based diets, being the lowest with 20% GSM inclusion. The abundance of Ruminococcus flavefaciens, anaerobic fungi, and protozoa were decreased

  13. Microbial ecosystem and fermentation traits in the caecum of growing rabbits given diets varying in neutral detergent soluble and insoluble fibre levels.

    PubMed

    Rodríguez-Romero, Norelys; Abecia, Leticia; Fondevila, Manuel

    2013-04-01

    The effect of the level of neutral detergent fibre (NDF: 0.35, LI and 0.42, HI) and neutral detergent soluble fibre (NDSF: 0.14, LS and 0.17, HS) in the caecal ecosystem was studied in 24 weaned (28 days of age) rabbits, weighing 630 ± 80.2 g in a 2 × 2 factorial design. After 22 days, rabbits were slaughtered and their caecal contents sampled. The caecal pH (on average 6.2) and molar volatile fatty acids (VFA) proportions were not affected by dietary treatments, but total VFA concentration tended to be lower with NDF (84.7 vs. 74.1 mmol/l; P = 0.095). The amount of total bacteria tended (P = 0.075) to increase with NDSF, but only in diets with 0.35 NDF. The caecal proportions of Ruminococcus albus and Fibrobacter succinogenes were not affected by type or level of fibre, but Butyrivibrio fibrisolvens decreased (P = 0.055) with the NDF proportion in LS diets. Denaturing gradient gel electrophoresis (DGGE) analysis showed that bacterial communities clustered according to each combination of NDF and NDSF, but did not greatly differ among diets (similarity indexes between 0.67 and 0.70), nor biodiversity was affected (average Shannon and richness indexes 3.50 and 33.1; P > 0.10). Archaeal population revealed changes in the amount and composition that were particularly evident in HS diets, decreasing in concentration (from 4.37 to 4.12 log10 gene copy number/g) and biodiversity (Shannon index from 3.14 to 2.52 and richness index from 23.7 to 13.9) compared to LS. The type and level of dietary fibre had a minor impact on caecal fermentation traits or caecal bacterial community. However, the increase in NDSF from 0.14 to 0.17 reduced concentration and diversity of methanogenic archaea.

  14. Rumen microbial abundance and fermentation profile during severe subacute ruminal acidosis and its modulation by plant derived alkaloids in vitro.

    PubMed

    Mickdam, Elsayed; Khiaosa-Ard, Ratchaneewan; Metzler-Zebeli, Barbara U; Klevenhusen, Fenja; Chizzola, Remigius; Zebeli, Qendrim

    2016-06-01

    Rumen microbiota have important metabolic functions for the host animal. This study aimed at characterizing changes in rumen microbial abundances and fermentation profiles using a severe subacute ruminal acidosis (SARA) in vitro model, and to evaluate a potential modulatory role of plant derived alkaloids (PDA), containing quaternary benzophenanthridine and protopine alkaloids, of which sanguinarine and chelerythrine were the major bioactive compounds. Induction of severe SARA strongly affected the rumen microbial composition and fermentation variables without suppressing the abundance of total bacteria. Protozoa and fungi were more sensitive to the low ruminal pH condition than bacteria. Induction of severe SARA clearly depressed degradation of fiber (P < 0.001), which came along with a decreased relative abundance of fibrolytic Ruminococcus albus and Fibrobacter succinogenes (P < 0.001). Under severe SARA conditions, the genus Prevotella, Lactobacillus group, Megasphaera elsdenii, and Entodinium spp. (P < 0.001) were more abundant, whereas Ruminobacter amylophilus was less abundant. SARA largely suppressed methane formation (-70%, P < 0.001), although total methanogenic 16S rRNA gene abundance was not affected. According to principal component analysis, Methanobrevibacter spp. correlated to methane concentration. Addition of PDA modulated ruminal fermentation under normal conditions such as enhanced (P < 0.05) concentration of total SCFA, propionate and valerate, and increased (P < 0.05) degradation of crude protein compared with the unsupplemented control diet. Our results indicate strong shifts in the microbial community during severe SARA compared to normal conditions. Supplementation of PDA positively modulates ruminal fermentation under normal ruminal pH conditions. PMID:26868619

  15. Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach.

    PubMed

    Jalali, Saakshi; Kohli, Samantha; Latka, Chitra; Bhatia, Sugandha; Vellarikal, Shamsudheen Karuthedath; Sivasubbu, Sridhar; Scaria, Vinod; Ramachandran, Srinivasan

    2015-01-01

    Fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. Paper currency notes are one of the most commonly exchanged objects and its potential to transmit pathogenic organisms has been well recognized. Approaches to identify the microbiome associated with paper currency notes have been largely limited to culture dependent approaches. Subsequent studies portrayed the use of 16S ribosomal RNA based approaches which provided insights into the taxonomical distribution of the microbiome. However, recent techniques including shotgun sequencing provides resolution at gene level and enable estimation of their copy numbers in the metagenome. We investigated the microbiome of Indian paper currency notes using a shotgun metagenome sequencing approach. Metagenomic DNA isolated from samples of frequently circulated denominations of Indian currency notes were sequenced using Illumina Hiseq sequencer. Analysis of the data revealed presence of species belonging to both eukaryotic and prokaryotic genera. The taxonomic distribution at kingdom level revealed contigs mapping to eukaryota (70%), bacteria (9%), viruses and archae (~1%). We identified 78 pathogens including Staphylococcus aureus, Corynebacterium glutamicum, Enterococcus faecalis, and 75 cellulose degrading organisms including Acidothermus cellulolyticus, Cellulomonas flavigena and Ruminococcus albus. Additionally, 78 antibiotic resistance genes were identified and 18 of these were found in all the samples. Furthermore, six out of 78 pathogens harbored at least one of the 18 common antibiotic resistance genes. To the best of our knowledge, this is the first report of shotgun metagenome sequence dataset of paper currency notes, which can be useful for future applications including as bio-surveillance of exchangeable fomites for infectious agents.

  16. Effect of yeast with bacteriocin from rumen bacteria on laying performance, blood biochemistry, faecal microbiota and egg quality of laying hens.

    PubMed

    Wang, H T; Shih, W Y; Chen, S W; Wang, S Y

    2015-12-01

    The purpose of this study was to evaluate the effect of yeast with bacteriocin from Ruminococcus albus 7 (albusin B) on physiological state and production performance of laying hens. One hundred and twenty 26-week-old Single Comb White Leghorn (Hyline) laying hens were assigned into five groups including: (i) control group, (ii) yeast control (YC), (iii) 0.125% yeast with bacteriocin (0.125B), (iv) 0.25% yeast with bacteriocin (0.25B) and (v) 0.5% yeast with bacteriocin (0.5B). All supplements were added to the experimental diets of the hens from 26 to 46 weeks of age. Samples were collected every 4 weeks. Blood samples were collected from the wing vein for blood biochemical parameters assay, and faecal samples were collected by swab for the microbiota test. The egg production performance was recorded daily, and fresh eggs were collected for quality test. The blood biochemical assay results indicated that the addition of yeast with bacteriocin decreased the AST (aspartate aminotransferase) activity and it also affects the lactate concentration in laying hen blood. The result of egg quality indicated that yeast with bacteriocin supplementation had no effect on the mass of yolk and the strength of eggshell, but it had positive effect on the laying performance under hot environment. Low concentration bacteriocin (0.125B) supplementation could decrease total yolk cholesterol. The faecal microbiota result indicated that the supplementation of bacteriocin increased the lactobacilli counts. The yeast with bacteriocin supplementation significantly decreased the clostridia counts under hot environment condition, especially in hens receiving 0.25B. Combining the data from clinic chemistry, faecal microbiota, egg production and egg quality, the 0.25B supplementation may result in the best physiological parameter and egg production performance of laying hen.

  17. Eremophila glabra reduces methane production and methanogen populations when fermented in a Rusitec.

    PubMed

    Li, XiXi; Durmic, Zoey; Liu, ShiMin; McSweeney, Chris S; Vercoe, Philip E

    2014-10-01

    Eremophila glabra Juss. (Scrophulariaceae), a native Australian shrub, has been demonstrated to have low methanogenic potential in a batch in vitro fermentation system. The present study aimed to test longer-term effects of E. glabra on rumen fermentation characteristics, particularly methane production and the methanogen population, when included as a component of a fermentation substrate in an in vitro continuous culture system (Rusitec). E. glabra was included at 150, 250, 400 g/kg DM (EG15, EG25, and EG40) with an oaten chaff and lupin-based substrate (control). Overall, the experiment lasted 33 days, with 12 days of acclimatization, followed by two periods during which fermentation characteristics (total gas, methane and VFA productions, dry matter disappearance, pH) were measured. The number of copies of genes specifically associated with total bacteria and cellulolytic bacteria (16S rRNA gene) and total ruminal methanogenic archaeal organisms (the methyl coenzyme M reductase A gene (mcrA)) was also measured during this time using quantitative real-time PCR. Total gas production, methane and volatile fatty acid concentrations were significantly reduced with addition of E. glabra. At the end of the experiment, the overall methane reduction was 32% and 45% for EG15 and EG25 respectively, compared to the control, and the reduction was in a dose-dependent manner. Total bacterial numbers did not change, but the total methanogen population decreased by up to 42.1% (EG40) when compared to the control substrate. The Fibrobacter succinogenes population was reduced at all levels of E. glabra, while Ruminococcus albus was reduced only by EG40. Our results indicate that replacing a portion of a fibrous substrate with E. glabra maintained a significant reduction in methane production and methanogen populations over three weeks in vitro, with some minor inhibition on overall fermentation at the lower inclusion levels.

  18. Screening Currency Notes for Microbial Pathogens and Antibiotic Resistance Genes Using a Shotgun Metagenomic Approach

    PubMed Central

    Jalali, Saakshi; Kohli, Samantha; Latka, Chitra; Bhatia, Sugandha; Vellarikal, Shamsudheen Karuthedath; Sivasubbu, Sridhar; Scaria, Vinod; Ramachandran, Srinivasan

    2015-01-01

    Fomites are a well-known source of microbial infections and previous studies have provided insights into the sojourning microbiome of fomites from various sources. Paper currency notes are one of the most commonly exchanged objects and its potential to transmit pathogenic organisms has been well recognized. Approaches to identify the microbiome associated with paper currency notes have been largely limited to culture dependent approaches. Subsequent studies portrayed the use of 16S ribosomal RNA based approaches which provided insights into the taxonomical distribution of the microbiome. However, recent techniques including shotgun sequencing provides resolution at gene level and enable estimation of their copy numbers in the metagenome. We investigated the microbiome of Indian paper currency notes using a shotgun metagenome sequencing approach. Metagenomic DNA isolated from samples of frequently circulated denominations of Indian currency notes were sequenced using Illumina Hiseq sequencer. Analysis of the data revealed presence of species belonging to both eukaryotic and prokaryotic genera. The taxonomic distribution at kingdom level revealed contigs mapping to eukaryota (70%), bacteria (9%), viruses and archae (~1%). We identified 78 pathogens including Staphylococcus aureus, Corynebacterium glutamicum, Enterococcus faecalis, and 75 cellulose degrading organisms including Acidothermus cellulolyticus, Cellulomonas flavigena and Ruminococcus albus. Additionally, 78 antibiotic resistance genes were identified and 18 of these were found in all the samples. Furthermore, six out of 78 pathogens harbored at least one of the 18 common antibiotic resistance genes. To the best of our knowledge, this is the first report of shotgun metagenome sequence dataset of paper currency notes, which can be useful for future applications including as bio-surveillance of exchangeable fomites for infectious agents. PMID:26035208

  19. Ontogenetic behavior, migration, and social behavior of pallid sturgeon, Scaphirhynchus albus, and shovelnose sturgeon, S. platorynchus, with notes on the adaptive significance of body color

    USGS Publications Warehouse

    Kynard, B.; Henyey, E.; Horgan, M.

    2002-01-01

    We conducted laboratory studies on the ontogenetic behavior of free embryos (first life interval after hatching) and larvae (first feeding interval) of pallid and shovelnose sturgeon. Migration styles of both species were similar for timing of migration (initiation by embryos on day 0 after hatching and cessation by larvae on days 12-13 at 236-243 cumulative temperature degree units), migration distance (about 13 km), life interval when most distance was moved (embryo), and diel behavior of embryos (diurnal). However, the species differed for two behaviors: movement characteristics of embryos (peak movement rate of pallid sturgeon was only one-half the peak rate of shovelnose sturgeon, but pallid sturgeon continued the lower rate for twice as long) and diel behavior of larvae (pallid sturgeon were diurnal and shovelnose sturgeon were nocturnal). Thus, the species used different methods to move the same distance. Migrating as poorly developed embryos suggests a migration style to avoid predation at the spawning site, but moving from spawning habitat to rearing habitat before first feeding could also be important. Migrants of both species preferred bright habitat (high illumination intensity and white substrate), a behavioral preference that may characterize the migrants of many species of sturgeon. Both species were remarkably similar for swimming height above the bottom by age, and day 7 and older migrants may swim far above the bottom and move far downstream. A migration of 12 or 13 days will probably not distribute larvae throughout the population's range, so an older life interval likely initiates a second longer downstream migration (2-step migration). By day 2, individuals of both species were a black-tail phenotype (light grey body with a black-tail that moved conspicuously during swimming). Aggregation behavior suggests that black-tail is a visual signal used for group cohesion.

  20. Integration of continuous biofumigation with Muscodor albus with pre-cooling fumigation with ozone or sulfur dioxide to control postharvest gray mold of table grapes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Sulfur dioxide (SO2) fumigation controls postharvest decay of commercially stored table grapes. To develop an alternative to SO2, fumigation with up to 10,000 micro-l/l ozone (O3) for up to 2 h was applied to control postharvest gray mold caused by Botrytis cinerea. O3 was effective when grapes were...

  1. Iron Stress and Pyoverdin Production by a Fluorescent Pseudomonad in the Rhizosphere of White Lupine (Lupinus albus L.) and Barley (Hordeum vulgare L.).

    PubMed

    Marschner, P; Crowley, D E

    1997-01-01

    Induction of high-affinity iron transport during root colonization by Pseudomonas fluorescens Pf-5 (pvd-inaZ) was examined in lupine and barley growing in microcosms. P. fluorescens Pf-5 (pvd-inaZ) contains a plasmid carrying pvd-inaZ; thus, in this strain, ice nucleation activity is regulated by pyoverdin production. Lupine or barley plants were grown for 18 or 8 days, respectively, in soil amended with 2% calcium carbonate and inoculated with P. fluorescens Pf-5 (pvd-inaZ) at a density of 4 x 10(sup8) CFU g (dry weight) of soil(sup-1). A filter paper blotting technique was used to sample cells from the rhizosphere in different root zones, and then the cells were resuspended for enumeration and measurement of ice nucleation activity. The population density of P. fluorescens Pf-5 (pvd-inaZ) in the rhizosphere decreased by one order of magnitude in both lupine and barley over time. The ice nucleation activity ranged from -3.4 to -3.0 log ice nuclei CFU(sup-1) for lupine and -3.0 to -2.8 log ice nuclei CFU(sup-1) for barley, was similar in all root zones, and did not change over time. An in vitro experiment was conducted to determine the relationship between ice nucleation activity and pyoverdin production in P. fluorescens Pf-5 (pvd-inaZ). An ice nucleation activity of approximately -3.0 log ice nuclei CFU(sup-1) was measured in the in vitro experiment at 25 to 50 (mu)M FeCl(inf3). By using the regression between ice nucleation activity and pyoverdin production determined in vitro and assuming a P. fluorescens Pf-5 (pvd-inaZ) population density of 10(sup8) CFU g of root(sup-1), the maximum possible pyoverdin accumulation by P. fluorescens Pf-5 (pvd-inaZ) in the rhizosphere was estimated to be 0.5 and 0.8 nmol g of root(sup-1) for lupine and barley, respectively. The low ice nucleation activity measured in the rhizosphere suggests that nutritional competition for iron in the rhizosphere may not be a major factor influencing root colonization by P. fluorescens Pf-5 (pvd-inaZ). PMID:16535491

  2. Ontogeny of immunoreactive Lh and Fsh cells in relation to early ovarian differentiation and development in protogynous hermaphroditic ricefield eel Monopterus albus.

    PubMed

    Wu, Yangsheng; He, Zhi; Zhang, Lihong; Jiang, He; Zhang, Weimin

    2012-03-01

    Luteinizing hormone (Lh) and follicle-stimulating hormone (Fsh) control many aspects of gonadal development and function in teleosts. In the present paper, the specific antisera against ricefield eel Lhb (Lh beta subunit), Fshb (Fsh beta subunit), and Cga (the common pituitary glycoprotein hormone alpha subunit) were generated, and the cellular localization, initial appearance, and subsequent development of gonadotrophs in relation to early ovarian differentiation and development in the ricefield eel, a protogynous sex-changing teleost, were examined with immunochemistry. Lhb- and Fshb-immunoreactive signals were identified in distinct pituitary cells that occupied primarily the peripheral regions of the adenohypophysis. During ontogeny, Lhb-immunoreactive signals were first detected in the pituitary around 40 days after hatching (dah) when the oogonia transitioned into early primary growth oocytes, and the intensity of immunoreactivity increased concomitantly with the growth of primary oocytes from 60 to 140 dah. During overwintering from 170 to 230 dah, Lhb-immunoreactive signals were significantly decreased when a large proportion of perinucleolus oocytes contained intense Balbiani bodies. In contrast, Fshb-immunoreactive signals were not detectable in the pituitary until around 230 dah (in the spring after hatching) and slightly increased from 285 dah when the late perinucleolus oocytes began to enter the secondary growth phase. Both Lhb- and Fshb-immunoreactive cells were increased when the early cortical alveoli oocytes emerged at 300 dah. The mRNA expression of lhb and fshb coincided with their immunoreactive signals. Taken together, these results suggest that only Lh is involved in primary oocyte growth in ricefield eels, but both Fsh and Lh are important for the secondary ooctye growth.

  3. Growth differentiation factor 9 (Gdf9) was localized in the female as well as male germ cells in a protogynous hermaphroditic teleost fish, ricefield eel Monopterus albus.

    PubMed

    He, Zhi; Wu, Yangsheng; Xie, Jun; Wang, Taixin; Zhang, Lihong; Zhang, Weimin

    2012-09-01

    Growth differentiation factor 9 (GDF9) is a member of the transforming growth factor beta (TGFb) superfamily. As an oocyte-derived growth factor, GDF9 plays key roles in regulating follicle development. In the present study, we identified a gdf9 homologue from the ovary of ricefield eel, and analyzed its expression both at the mRNA and protein levels. Ricefield eel Gdf9 showed high homologies with those of other teleosts, especially perciformes fish. RT-PCR analysis revealed that ricefield eel gdf9 was expressed exclusively in the ovary and testis. The mRNA levels of gdf9 in the ovary were increased significantly at the pre-vitellogenic (PV) stage and then decreased significantly along with vitellogenesis. During the natural sex change, expression of ricefield eel gdf9 was peaked at the intersexual stages. The immunoreactivity for Gdf9 was localized exclusively in the cytoplasm of the oocytes in the ovary, particularly the oocytes at early stages, but not in the oogonia. Interestingly, strong immunoreactive signals were also detected in the degenerating oocytes in the intersexual gonad. Furthermore, the Gdf9 immunoreactivity was demonstrated for the first time to be localized in the cytoplasm of spermatogonia and spermatocytes of ricefield eel, a teleost fish. Taken together, the results of present study suggested that Gdf9 may play important roles in the folliculogenesis as well as spermatogenesis in ricefield eels.

  4. [Karyological differences of the Northern Dolly Varden Salvelinus malma malma and the white char Salvelinus albus from the Kamchatka River basin].

    PubMed

    Frolov, S V

    2001-03-01

    The karyotypes of northern Dolly Varden and white char, sympathrically inhabiting the Kamchatka River basin, were studied. The karyotype of Dolly Varden was stable: 2n = 78 and NF = 98 + 2, while in white char, polymorphism and mosaicism for the chromosome number were revealed: 2n = 76-79, NF = 98 + 2. Using a routine chromosome staining technique, the karyotype of white char (2n = 78) was shown to be identical to that of Dolly Varden. In both karyotypes, similar sets of marker chromosomes were present: two pairs of submetacentric (SM), one pair of submeta-subtelocentric (SM-ST), one pair of large acrocentric (A), and one pair of large sub-telocentric (ST) chromosomes. However, the karyotypes of Dolly Varden and white char differed in the number and location of nucleolus organizer regions (NORs). In Dolly Varden, single NORs located in the telomeric regions of the marker SM-ST chromosomes were observed. In white char, NORs were multiple and located both in the telomeric regions of the marker SM-ST chromosomes and on the short and long arms of large ST chromosomes. The identical marker chromosomes indicate considerable phylogenetic relatedness between Dolly Varden and white char from the Kamchatka River basin. Variation in NORs provides evidence for the reproductive isolation of these chars and their species status.

  5. Improvement of Nutritive Value and In vitro Ruminal Fermentation of Leucaena Silage by Molasses and Urea Supplementation.

    PubMed

    Phesatcha, K; Wanapat, M

    2016-08-01

    Leucaena silage was supplemented with different levels of molasses and urea to study its nutritive value and in vitro rumen fermentation efficiency. The ensiling study was randomly assigned according to a 3×3 factorial arrangement in which the first factor was molasses (M) supplement at 0%, 1%, and 2% of crop dry matter (DM) and the second was urea (U) supplement as 0%, 0.5%, and 1% of the crop DM, respectively. After 28 days of ensiling, the silage samples were collected and analyzed for chemical composition. All the nine Leucaena silages were kept for study of rumen fermentation efficiency using in vitro gas production techniques. The present result shows that supplementation of U or M did not affect DM, organic matter, neutral detergent fiber, and acid detergent fiber content in the silage. However, increasing level of U supplementation increased crude protein content while M level did not show any effect. Moreover, the combination of U and M supplement decreased the content of mimosine concentration especially with M2U1 (molasses 2% and urea 1%) silage. The result of the in vitro study shows that gas production kinetics, cumulation gas at 96 h and in vitro true digestibility increased with the increasing level of U and M supplementation especially in the combination treatments. Supplementation of M and U resulted in increasing propionic acid and total volatile fatty acid whereas, acetic acid, butyric acid concentrations and methane production were not changed. In addition, increasing U level supplementation increased NH3-N concentration. Result from real-time polymerase chain reaction revealed a significant effect on total bacteria, whereas F. succinogenes and R. flavefaciens population while R. albus was not affected by the M and U supplementation. Based on this study, it could be concluded that M and urea U supplementation could improve the nutritive value of Leucaena silage and enhance in vitro rumen fermentation efficiency. This study also suggested that

  6. Improvement of Nutritive Value and In vitro Ruminal Fermentation of Leucaena Silage by Molasses and Urea Supplementation

    PubMed Central

    Phesatcha, K.; Wanapat, M.

    2016-01-01

    Leucaena silage was supplemented with different levels of molasses and urea to study its nutritive value and in vitro rumen fermentation efficiency. The ensiling study was randomly assigned according to a 3×3 factorial arrangement in which the first factor was molasses (M) supplement at 0%, 1%, and 2% of crop dry matter (DM) and the second was urea (U) supplement as 0%, 0.5%, and 1% of the crop DM, respectively. After 28 days of ensiling, the silage samples were collected and analyzed for chemical composition. All the nine Leucaena silages were kept for study of rumen fermentation efficiency using in vitro gas production techniques. The present result shows that supplementation of U or M did not affect DM, organic matter, neutral detergent fiber, and acid detergent fiber content in the silage. However, increasing level of U supplementation increased crude protein content while M level did not show any effect. Moreover, the combination of U and M supplement decreased the content of mimosine concentration especially with M2U1 (molasses 2% and urea 1%) silage. The result of the in vitro study shows that gas production kinetics, cumulation gas at 96 h and in vitro true digestibility increased with the increasing level of U and M supplementation especially in the combination treatments. Supplementation of M and U resulted in increasing propionic acid and total volatile fatty acid whereas, acetic acid, butyric acid concentrations and methane production were not changed. In addition, increasing U level supplementation increased NH3-N concentration. Result from real-time polymerase chain reaction revealed a significant effect on total bacteria, whereas F. succinogenes and R. flavefaciens population while R. albus was not affected by the M and U supplementation. Based on this study, it could be concluded that M and urea U supplementation could improve the nutritive value of Leucaena silage and enhance in vitro rumen fermentation efficiency. This study also suggested that

  7. Effect of different levels of concentrate on ruminal microorganisms and rumen fermentation in Nellore steers.

    PubMed

    Granja-Salcedo, Yury T; Ribeiro Júnior, Carlos S; de Jesus, Raphael B; Gomez-Insuasti, Arturo S; Rivera, Astrid R; Messana, Juliana D; Canesin, Roberta C; Berchielli, Telma T

    2016-01-01

    The aim of this study was to investigate the effect of different dietary levels of concentrate on feed intake, digestibility, ruminal fermentation and microbial population in steers. Eight Nellore steers fitted with ruminal cannulas were used in a double 4 × 4 Latin square design experiment. The dietary treatments consist of four different proportions of concentrate to roughage: 30:70, 40:60, 60:40 and 80:20% in the dry matter, resulting in Diets 30, 40, 60 and 80, respectively. The roughage was corn silage, and the concentrate was composed of corn, soybean meal and urea. Apparent digestibility of organic matter and crude protein showed a linear association with concentrate proportion (p = 0.01), but the increased concentrate levels did not affect the digestibility of fibre. The lowest ruminal pH-values were observed in animals fed with Diet 80, remaining below pH 6.0 from 6 h after feeding, while in the other diets, the ruminal pH was below 6.0 not before 12 h after feeding. After feeding Diet 80, the ammonia concentration in the rumen was significantly the highest. Higher dietary concentrate levels resulted in a linear increase of propionic acid concentrations, a linear reduction of the ratio acetic acid to propionic acid (p < 0.01) and a linear increased synthesis of microbial nitrogen (p < 0.001). The predicted production of methane was lower in diets with greater amounts of concentrate (p = 0.032). The population of methanogens, R. flavefaciens and R. albus decreased with higher concentrate levels, while the population of S. ruminantium increased (p < 0.05). The results indicate that greater amounts of concentrate do not decrease ruminal pH-values as much as expected and inhibit some cellulolytic bacteria without impairing the dry matter intake and fibre digestibility in Nellore steers.

  8. Effect of different levels of concentrate on ruminal microorganisms and rumen fermentation in Nellore steers.

    PubMed

    Granja-Salcedo, Yury T; Ribeiro Júnior, Carlos S; de Jesus, Raphael B; Gomez-Insuasti, Arturo S; Rivera, Astrid R; Messana, Juliana D; Canesin, Roberta C; Berchielli, Telma T

    2016-01-01

    The aim of this study was to investigate the effect of different dietary levels of concentrate on feed intake, digestibility, ruminal fermentation and microbial population in steers. Eight Nellore steers fitted with ruminal cannulas were used in a double 4 × 4 Latin square design experiment. The dietary treatments consist of four different proportions of concentrate to roughage: 30:70, 40:60, 60:40 and 80:20% in the dry matter, resulting in Diets 30, 40, 60 and 80, respectively. The roughage was corn silage, and the concentrate was composed of corn, soybean meal and urea. Apparent digestibility of organic matter and crude protein showed a linear association with concentrate proportion (p = 0.01), but the increased concentrate levels did not affect the digestibility of fibre. The lowest ruminal pH-values were observed in animals fed with Diet 80, remaining below pH 6.0 from 6 h after feeding, while in the other diets, the ruminal pH was below 6.0 not before 12 h after feeding. After feeding Diet 80, the ammonia concentration in the rumen was significantly the highest. Higher dietary concentrate levels resulted in a linear increase of propionic acid concentrations, a linear reduction of the ratio acetic acid to propionic acid (p < 0.01) and a linear increased synthesis of microbial nitrogen (p < 0.001). The predicted production of methane was lower in diets with greater amounts of concentrate (p = 0.032). The population of methanogens, R. flavefaciens and R. albus decreased with higher concentrate levels, while the population of S. ruminantium increased (p < 0.05). The results indicate that greater amounts of concentrate do not decrease ruminal pH-values as much as expected and inhibit some cellulolytic bacteria without impairing the dry matter intake and fibre digestibility in Nellore steers. PMID:26654381

  9. Analysis of rumen microbial populations in lactating dairy cattle fed diets varying in carbohydrate profiles and Saccharomyces cerevisiae fermentation product.

    PubMed

    Mullins, C R; Mamedova, L K; Carpenter, A J; Ying, Y; Allen, M S; Yoon, I; Bradford, B J

    2013-09-01

    The rumen microbial ecosystem is a critical factor that links diets to bovine physiology and productivity; however, information about dietary effects on microbial populations has generally been limited to small numbers of samples and qualitative assessment. To assess whether consistent shifts in microbial populations occur in response to common dietary manipulations in dairy cattle, samples of rumen contents were collected from 2 studies for analysis by quantitative real-time PCR (qPCR). In one study, lactating Holstein cows (n=8) were fed diets in which a nonforage fiber source replaced an increasing proportion of forages and concentrates in a 4×4 Latin square design, and samples of ruminal digesta were collected at 9-h intervals over 3 d at the end of each period. In the second study, lactating Holstein cows (n=15) were fed diets with or without the inclusion of a Saccharomyces cerevisiae fermentation product (SCFP) in a crossover design. In this study, rumen liquid and solid samples were collected during total rumen evacuations before and after feeding in a 42-h period. In total, 146 samples of ruminal digesta were used for microbial DNA isolation and analysis by qPCR. Validated primer sets were used to quantify total bacterial and anaerobic fungal populations as well as 12 well-studied bacterial taxa. The relative abundance of the target populations was similar to those previously reported. No significant treatment effects were observed for any target population. A significant interaction of treatment and dry matter intake was observed, however, for the abundance of Eubacterium ruminantium. Increasing dry matter intake was associated with a quadratic decrease in E. ruminantium populations in control animals but with a quadratic increase in E.ruminantium populations in cows fed SCFP. Analysis of sample time effects revealed that Fibrobacter succinogenes and fungal populations were more abundant postfeeding, whereas Ruminococcus albus tended to be more abundant

  10. Treatment of grain with organic acids at 2 different dietary phosphorus levels modulates ruminal microbial community structure and fermentation patterns in vitro.

    PubMed

    Harder, H; Khol-Parisini, A; Metzler-Zebeli, B U; Klevenhusen, F; Zebeli, Q

    2015-11-01

    Recent data indicate positive effects of treating grain with citric (CAc) or lactic acid (LAc) on the hydrolysis of phytate phosphorus (P) and fermentation products of the grain. This study used a semicontinuous rumen simulation technique to evaluate the effects of processing of barley with 50.25 g/L (wt/vol) CAc or 76.25 g/L LAc on microbial composition, metabolic fermentation profile, and nutrient degradation at low or high dietary P supply. The low P diet [3.1g of P per kg of dry matter (DM) of dietary P sources only] was not supplemented with inorganic P, whereas the high P diet was supplemented with 0.5 g of inorganic P per kg of DM through mineral premix and 870 mg of inorganic P/d per incubation fermenter via artificial saliva. Target microbes were determined using quantitative PCR. Data showed depression of total bacteria but not of total protozoa or short-chain fatty acid (SCFA) concentration with the low P diet. In addition, the low P diet lowered the relative abundance of Ruminococcus albus and decreased neutral detergent fiber (NDF) degradation and acetate proportion, but increased the abundance of several predominantly noncellulolytic bacterial species and anaerobic fungi. Treatment of grain with LAc increased the abundance of total bacteria in the low P diet only, and this effect was associated with a greater concentration of SCFA in the ruminal fluid. Interestingly, in the low P diet, CAc treatment of barley increased the most prevalent bacterial group, the genus Prevotella, in ruminal fluid and increased NDF degradation to the same extent as did inorganic P supplementation in the high P diet. Treatment with either CAc or LAc lowered the abundance of Megasphaera elsdenii but only in the low P diet. On the other hand, CAc treatment increased the proportion of acetate in the low P diet, whereas LAc treatment decreased this variable at both dietary P levels. The propionate proportion was significantly increased by LAc at both P levels, whereas butyrate

  11. Effect of dietary supplementation with resveratrol on nutrient digestibility, methanogenesis and ruminal microbial flora in sheep.

    PubMed

    Ma, T; Chen, D-D; Tu, Y; Zhang, N-F; Si, B-W; Deng, K-D; Diao, Q-Y

    2015-08-01

    Two experiments were conducted to evaluate the effect of resveratrol on methanogenesis and microbial flora in Dorper × thin-tailed Han cross-bred ewes. In experiment 1, ten ewes (67.2 ± 2.24 kg BW) were assigned to two dietary treatments, a basal diet and a basal diet supplemented with resveratrol (0.25 g/head·day), to investigate the effect of resveratrol on nutrient digestibility and nitrogen balance. In experiment 2, six ewes (64.0 ± 1.85 kg BW) with ruminal cannulae were assigned to the identical dietary treatments used in experiment 1 to investigate supplementary resveratrol on ruminal fermentation and microbial flora using qPCR. The results showed that supplementary resveratrol improved the digestibility of organic matter (OM; p < 0.001), nitrogen (N; p = 0.007), neutral detergent fibre (NDF; p < 0.001) and acid detergent fibre (ADF; p < 0.001). The excretion of faecal N was reduced (p = 0.007), whereas that of urinary N increased (p = 0.002), which led to an unchanged N retention (p = 0.157). Both CO2 and CH4 output scaled to digestible dry matter (DM) intake decreased from 602.5 to 518.7 (p = 0.039) and 68.2 to 56.6 (p < 0.001) respectively. Ruminal pH (p = 0.341), ammonia (p = 0.512) and total volatile fatty acid (VFA) (p = 0.249) were unaffected by resveratrol. The molar proportion of propionate increased from 13.1 to 17.5% (p < 0.001) while that of butyrate decreased from 11.0 to 9.55% (p < 0.001). The ratio of acetate to propionate (A/P) decreased from 5.44 to 3.96 (p < 0.001). Supplementary resveratrol increased ruminal population of Fibrobacter succinogenes, Ruminococcus albus and Butyrivibrio fibrisolvens (p < 0.001) while decreased protozoa and methanogens. In conclusion, dietary resveratrol inhibited methanogenesis without adversely affecting ruminal fermentation.

  12. Treatment of grain with organic acids at 2 different dietary phosphorus levels modulates ruminal microbial community structure and fermentation patterns in vitro.

    PubMed

    Harder, H; Khol-Parisini, A; Metzler-Zebeli, B U; Klevenhusen, F; Zebeli, Q

    2015-11-01

    Recent data indicate positive effects of treating grain with citric (CAc) or lactic acid (LAc) on the hydrolysis of phytate phosphorus (P) and fermentation products of the grain. This study used a semicontinuous rumen simulation technique to evaluate the effects of processing of barley with 50.25 g/L (wt/vol) CAc or 76.25 g/L LAc on microbial composition, metabolic fermentation profile, and nutrient degradation at low or high dietary P supply. The low P diet [3.1g of P per kg of dry matter (DM) of dietary P sources only] was not supplemented with inorganic P, whereas the high P diet was supplemented with 0.5 g of inorganic P per kg of DM through mineral premix and 870 mg of inorganic P/d per incubation fermenter via artificial saliva. Target microbes were determined using quantitative PCR. Data showed depression of total bacteria but not of total protozoa or short-chain fatty acid (SCFA) concentration with the low P diet. In addition, the low P diet lowered the relative abundance of Ruminococcus albus and decreased neutral detergent fiber (NDF) degradation and acetate proportion, but increased the abundance of several predominantly noncellulolytic bacterial species and anaerobic fungi. Treatment of grain with LAc increased the abundance of total bacteria in the low P diet only, and this effect was associated with a greater concentration of SCFA in the ruminal fluid. Interestingly, in the low P diet, CAc treatment of barley increased the most prevalent bacterial group, the genus Prevotella, in ruminal fluid and increased NDF degradation to the same extent as did inorganic P supplementation in the high P diet. Treatment with either CAc or LAc lowered the abundance of Megasphaera elsdenii but only in the low P diet. On the other hand, CAc treatment increased the proportion of acetate in the low P diet, whereas LAc treatment decreased this variable at both dietary P levels. The propionate proportion was significantly increased by LAc at both P levels, whereas butyrate

  13. Effect of exchanging Onobrychis viciifolia and Lotus corniculatus for Medicago sativa on ruminal fermentation and nitrogen turnover in dairy cows.

    PubMed

    Grosse Brinkhaus, A; Bee, G; Silacci, P; Kreuzer, M; Dohme-Meier, F

    2016-06-01

    The objective of the study was to determine the effect of feeding sainfoin (SF; Onobrychis viciifolia) and birdsfoot trefoil (BT; Lotus corniculatus), 2 temperate climate forage legumes that contain condensed tannins (CT), on ruminal fermentation and N turnover in dairy cows. Six ruminally cannulated multiparous dairy cows (milk yield=40kg/d; 36 d in milk) were used in a replicated 3×3 Latin square design. All animals were fed basal diets containing 20% pelleted SF (223g of CT/kg of dry matter), BT (30.3g of CT/kg of dry matter), or alfalfa (AL) and concentrate to meet their predicted nutrient requirements. Each experimental period consisted of a 21-d adaptation period in a tiestall, followed by a 7-d collection period in metabolic crates, where feces and urine were collected quantitatively. During the 7-d period, milk yield was recorded daily and milk samples were taken at each milking. Blood, ruminal fluid, and papillae were sampled on d 2 and 5. The relative abundance of selected bacterial strains in ruminal fluid and the gene expression of transporter genes in the papillae were determined with quantitative PCR. Total volatile fatty acids and the abundance of the cellulolytic bacteria Prevotella spp. and Ruminococcus flavefaciens decreased with SF compared with AL. The relative gene expression of the monocarboxylate transporter 1 was increased with BT compared with AL and SF. Total yields of milk, milk fat, and milk protein were similar among treatments. The proportion of 18:3n-3 in milk fat was greater and those of 22:5n-3 and 22:6n-3 were lower with SF than with BT. The contents of urea N in blood (2.71, 3.45, and 3.90mmol/L for SF, AL, and BT, respectively), milk (79.8, 100.1, and 110.9mg/kg for SF, AL, and BT, respectively), and urine were lower with SF than with AL and BT, and a trend toward a lower ruminal ammonia content occurred with SF compared with BT. Intake and excretion of N with milk were similar among treatments, but urine N was lower with SF

  14. Effect of feeding growing-fattening rabbits a diet supplemented with whole white lupin (Lupinus albus cv. Amiga) seeds on fatty acid composition and indexes related to human health in hind leg meat and perirenal fat.

    PubMed

    Volek, Zdeněk; Marounek, Milan

    2011-01-01

    A total of 20 weaned rabbits (33 days old) (10 per treatment) were fed one of two diets that included 150 g of sunflower meal (SF)/kg of diet or 120 g of whole white lupin (WL)/kg of diet for 42 days. The WL diet contained less saturated fatty acids (SFA) and polyunsaturated fatty acids (PUFA) but more monounsaturated fatty acids (MUFA) than the SF diet. The WL diet significantly decreased SFA and PUFA content, as well as the PUFA n-6/PUFA n-3 ratio and saturation, atherogenic and thrombogenic indexes in hind leg meat. The fatty acid composition in perirenal fat was similar to that of hind leg meat; however, significantly higher MUFA levels were observed in rabbits fed the WL diet. Thus, feeding rabbits the WL diet affected the fatty acid profile of hind leg meat and perirenal fat in a favourable manner.

  15. Effects of Momordica charantia Saponins on In vitro Ruminal Fermentation and Microbial Population

    PubMed Central

    Kang, Jinhe; Zeng, Bo; Tang, Shaoxun; Wang, Min; Han, Xuefeng; Zhou, Chuanshe; Yan, Qiongxian; He, Zhixiong; Liu, Jinfu; Tan, Zhiliang

    2016-01-01

    This study was conducted to investigate the effects of Momordica charantia saponin (MCS) on ruminal fermentation of maize stover and abundance of selected microbial populations in vitro. Five levels of MCS supplements (0, 0.01, 0.06, 0.30, 0.60 mg/mL) were tested. The pH, NH3-N, and volatile fatty acid were measured at 6, 24, 48 h of in vitro mixed incubation fluids, whilst the selected microbial populations were determined at 6 and 24 h. The high dose of MCS increased the initial fractional rate of degradation at t-value = 0 (FRD0) and the fractional rate of gas production (k), but decreased the theoretical maximum of gas production (VF) and the half-life (t0.5) compared with the control. The NH3-N concentration reached the lowest concentration with 0.01 mg MCS/mL at 6 h. The MSC inclusion increased (p<0.001) the molar proportion of butyrate, isovalerate at 24 h and 48 h, and the molar proportion of acetate at 24 h, but then decreased (p<0.05) them at 48 h. The molar proportion of valerate was increased (p<0.05) at 24 h. The acetate to propionate ratio (A/P; linear, p<0.01) was increased at 24 h, but reached the least value at the level of 0.30 mg/mL MCS. The MCS inclusion decreased (p<0.05) the molar proportion of propionate at 24 h and then increased it at 48 h. The concentration of total volatile fatty acid was decreased (p<0.001) at 24 h, but reached the greatest concentration at the level of 0.01 mg/mL and the least concentration at the level of 0.60 mg/mL. The relative abundance of Ruminococcus albus was increased at 6 h and 24 h, and the relative abundance of Fibrobacter succinogenes was the lowest (p<0.05) at 0.60 mg/mL at 6 h and 24 h. The relative abundance of Butyrivibrio fibrisolvens and fungus reached the greatest value (p<0.05) at low doses of MCS inclusion and the least value (p<0.05) at 0.60 mg/mL at 24 h. The present results demonstrates that a high level of MCS quickly inhibits in vitro fermentation of maize stover, while MCS at low doses has the

  16. Active dry Saccharomyces cerevisiae can alleviate the effect of subacute ruminal acidosis in lactating dairy cows.

    PubMed

    AlZahal, O; Dionissopoulos, L; Laarman, A H; Walker, N; McBride, B W

    2014-12-01

    ) and lower acetate:propionate ratio (0.26 ± 0.5 vs. 0.36 ± 0.05 for ADSC and control, respectively). Microbial analyses conducted on samples collected during wk 10 showed that cows supplemented with S. cerevisiae had a 9-fold, 2-fold, 6-fold, 1.3-fold, and 8-fold increase in S. cerevisiae, Fibrobacter succinogenes, Anaerovibrio lipolytica, Ruminococcus albus, and anaerobic fungi, respectively, which suggested an increase in cellulolytic microbes within the rumen. Cows supplemented with ADSC had 2.2-fold reduction in Prevotella albensis, which is a gram-negative bacterium predominant during SARA. Prevotella spp. are suggested to be an important source of lipopolysaccharide responsible for inflammation within the rumen. Cows supplemented with ADSC had a 2.3-fold increase in Streptococcus bovis and a 12-fold reduction in Megasphaera elsdenii. The reduction in M. elsdenii may reflect lower concentration of lactic acid within the rumen for ADSC cows. In conclusion, ADSC supplementation to dairy cows was demonstrated to alleviate the condition of SARA caused by abrupt dietary changes from HF to HG, and can potentially improve rumen function, as indicated by greater numbers of cellulolytic microorganisms within the rumen.

  17. Active dry Saccharomyces cerevisiae can alleviate the effect of subacute ruminal acidosis in lactating dairy cows.

    PubMed

    AlZahal, O; Dionissopoulos, L; Laarman, A H; Walker, N; McBride, B W

    2014-12-01

    ) and lower acetate:propionate ratio (0.26 ± 0.5 vs. 0.36 ± 0.05 for ADSC and control, respectively). Microbial analyses conducted on samples collected during wk 10 showed that cows supplemented with S. cerevisiae had a 9-fold, 2-fold, 6-fold, 1.3-fold, and 8-fold increase in S. cerevisiae, Fibrobacter succinogenes, Anaerovibrio lipolytica, Ruminococcus albus, and anaerobic fungi, respectively, which suggested an increase in cellulolytic microbes within the rumen. Cows supplemented with ADSC had 2.2-fold reduction in Prevotella albensis, which is a gram-negative bacterium predominant during SARA. Prevotella spp. are suggested to be an important source of lipopolysaccharide responsible for inflammation within the rumen. Cows supplemented with ADSC had a 2.3-fold increase in Streptococcus bovis and a 12-fold reduction in Megasphaera elsdenii. The reduction in M. elsdenii may reflect lower concentration of lactic acid within the rumen for ADSC cows. In conclusion, ADSC supplementation to dairy cows was demonstrated to alleviate the condition of SARA caused by abrupt dietary changes from HF to HG, and can potentially improve rumen function, as indicated by greater numbers of cellulolytic microorganisms within the rumen. PMID:25282426

  18. Bio-based adhesives from residues of consolidated bioprocessing of cellulosic substrates

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Anaerobic bacteria (Clostridium thermocellum or Ruminococcus species) that ferment cellulosic materials to ethanol or other low molecular weight products have been proposed to serve as a basis for single-reactor bioconversions of cellulosics in a scheme termed consolidated bioprocessing (CBP). Thes...

  19. Identification of genes induced in proteoid roots of white lupin under nitrogen and phosphorus deprivation, with functional characterization of a formamidase

    Technology Transfer Automated Retrieval System (TEKTRAN)

    White lupin (Lupinus albus L.) is considered a model system for understanding plant acclimation to nutrient deficiency. It acclimates to phosphorus (P) and iron (Fe) deficiency by the development of short, densely clustered lateral roots called proteoid (or cluster) roots; proteoid-root development ...

  20. Five Lessons of a Dumbledore Education

    ERIC Educational Resources Information Center

    Music, Rusmir; Agans, Lyndsay J.

    2007-01-01

    Hogwarts School of Witchcraft and Wizardry and the world of Harry Potter may help educators re-imagine their daily work and provide good reminders that intentional formal and informal mentoring, informed by educational theory, play an essential role in student learning and development. Mentoring principles at Hogwarts flow from Albus Dumbledore,…

  1. Glycerophosphodiester phosphodiesterases play an important role in phosphate recycling and phosphate sensing in white lupin

    Technology Transfer Automated Retrieval System (TEKTRAN)

    White lupin (Lupinus albus L.), a well adapted species to phosphate (Pi) impoverished soils, develops short, densely clustered lateral roots (cluster/proteoid roots) to increase Pi uptake. Here, we report two white lupin glycerophosphodiester phosphodiesterase (GPX-PDE) genes which share strong homo...

  2. White lupin cluster root acclimation to phosphorus deficiency and root hair development involve unique glycerophosphodiester phosphodiesterases

    Technology Transfer Automated Retrieval System (TEKTRAN)

    White lupin (Lupinus albus L.) is a phosphate (Pi) deficiency tolerant legume which develops short, densely clustered tertiary lateral roots (cluster/proteoid roots) in response to Pi limitation. In this report we characterize two glycerophosphodiester phosphodiesterase (GPX-PDE) genes (GPX-PDE1 and...

  3. Agarivorans gilvus sp. nov. Isolated From Seaweed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A novel agarase-producing, non-endospore-forming marine bacterium WH0801T was isolated from a fresh seaweed sample collected from the coast of Weihai, China. Preliminary characterization based on 16S rRNA gene sequence analysis showed that WH0801T shared 96.1% identity with Agarivorans albus MKT 10...

  4. Developing and Improving Modified Achievement Level Descriptors: Rationale, Procedures, and Tools

    ERIC Educational Resources Information Center

    Quenemoen, Rachel; Albus, Debra; Rogers, Chris; Lazarus, Sheryl

    2010-01-01

    Some states are developing alternate assessments based on modified achievement standards (AA-MAS) to measure the academic achievement of some students with disabilities (Albus, Lazarus, Thurlow, & Cormier, 2009; Lazarus, Thurlow, Christensen, & Cormier, 2007). These assessments measure the same content as the general assessment for a given…

  5. Real-time RT-PCR profiling of transcription factors including 34 MYBs and signaling components in white lupin reveals their P status dependent and organ-specific expression

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phosphorus (P) is often a limiting macronutrient because of its low availability in soils. White lupin (Lupinus albus L.) plants are well adapted to growth under P-deficient conditions. White lupin acclimation to P-deficiency includes changes in root architecture and enhanced expression of numerous ...

  6. Fish and chips? Implanted transmitters help map the endangered pallid sturgeon

    USGS Publications Warehouse

    Chojnacki, Kimberly; DeLonay, Aaron

    2011-01-01

    With a flattened snout, long slender tail and rows of bony plates lining its body, the pallid sturgeon (Scaphirhynchus albus) has a unique, almost pre-historic, appearance. This endangered fish is native to the muddy, free-flowing waters of the Missouri River.

  7. Delphi Study of Instructional Strategies for English Language Learners with Disabilities: Recommendations from Educators Nationwide. ELLs with Disabilities Report 21

    ERIC Educational Resources Information Center

    Thurlow, Martha; Shyyan, Vitaliy; Barrera, Manuel; Liu, Kristi

    2008-01-01

    This study is part of national research over the past seven years at the National Center on Educational Outcomes focused on identifying and validating instructional strategies for ELLs with disabilities (Shyyan, Thurlow, & Liu, 2008; Thurlow, Albus, Shyyan, Liu, & Barrera, 2004). In recent work (Barrera, Shyyan, Liu, & Thurlow, 2008), educators…

  8. RNA-Seq atlas of white lupin: a guide to the phosphorus deficiency response pathway in plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phosphorus (P) is one of the most limiting macronutrients in soils for plant growth and development. White lupin (Lupinus albus) has evolved unique adaptation systems for growth in P-deficient conditions (-P) in soils including: 1) development of densely clustered determinant lateral roots called pr...

  9. [Topography of the metabolic cycle of 4-aminobutyrate].

    PubMed

    Santos-Ruiz, A

    1982-01-01

    This work describes, with some detail the intervention of 4-aminobutyrate as protagonist of a derivation of tricarboxylic cycle. Its vicarial mission is emphasized in connection with its existence in microorganisms (Escherichia coli and Pseudomonas fluorescens), plants (Helianthus tuberosus. Lupinus albus and Agave americana), neoplasic cells (ascitic tumor of Ehrlich and HeLa cells) and animal tissues (adrenal medulla and brain.

  10. Fermented dairy products modulate Citrobacter rodentium-induced colonic hyperplasia.

    PubMed

    Collins, James W; Chervaux, Christian; Raymond, Benoit; Derrien, Muriel; Brazeilles, Rémi; Kosta, Artemis; Chambaud, Isabelle; Crepin, Valerie F; Frankel, Gad

    2014-10-01

    We evaluated the protective effects of fermented dairy products (FDPs) in an infection model, using the mouse pathogen Citrobacter rodentium (CR). Treatment of mice with FDP formulas A, B, and C or a control product did not affect CR colonization, organ specificity, or attaching and effacing lesion formation. Fermented dairy product A (FDP-A), but neither the supernatant from FDP-A nor β-irradiated (IR) FDP-A, caused a significant reduction in colonic crypt hyperplasia and CR-associated pathology. Profiling the gut microbiota revealed that IR-FDP-A promoted higher levels of phylotypes belonging to Alcaligenaceae and a decrease in Lachnospiraceae (Ruminococcus) during CR infection. Conversely, FDP-A prevented a decrease in Ruminococcus and increased Turicibacteraceae (Turicibacter). Importantly, loss of Ruminococcus and Turicibacter has been associated with susceptibility to dextran sodium sulfate-induced colitis. Our results demonstrate that viable bacteria in FDP-A reduced CR-induced colonic crypt hyperplasia and prevented the loss of key bacterial genera that may contribute to disease pathology.

  11. Recurrent cerebellar architecture solves the motor-error problem.

    PubMed Central

    Porrill, John; Dean, Paul; Stone, James V.

    2004-01-01

    Current views of cerebellar function have been heavily influenced by the models of Marr and Albus, who suggested that the climbing fibre input to the cerebellum acts as a teaching signal for motor learning. It is commonly assumed that this teaching signal must be motor error (the difference between actual and correct motor command), but this approach requires complex neural structures to estimate unobservable motor error from its observed sensory consequences. We have proposed elsewhere a recurrent decorrelation control architecture in which Marr-Albus models learn without requiring motor error. Here, we prove convergence for this architecture and demonstrate important advantages for the modular control of systems with multiple degrees of freedom. These results are illustrated by modelling adaptive plant compensation for the three-dimensional vestibular ocular reflex. This provides a functional role for recurrent cerebellar connectivity, which may be a generic anatomical feature of projections between regions of cerebral and cerebellar cortex. PMID:15255096

  12. Sparse distributed memory and related models

    NASA Technical Reports Server (NTRS)

    Kanerva, Pentti

    1992-01-01

    Described here is sparse distributed memory (SDM) as a neural-net associative memory. It is characterized by two weight matrices and by a large internal dimension - the number of hidden units is much larger than the number of input or output units. The first matrix, A, is fixed and possibly random, and the second matrix, C, is modifiable. The SDM is compared and contrasted to (1) computer memory, (2) correlation-matrix memory, (3) feet-forward artificial neural network, (4) cortex of the cerebellum, (5) Marr and Albus models of the cerebellum, and (6) Albus' cerebellar model arithmetic computer (CMAC). Several variations of the basic SDM design are discussed: the selected-coordinate and hyperplane designs of Jaeckel, the pseudorandom associative neural memory of Hassoun, and SDM with real-valued input variables by Prager and Fallside. SDM research conducted mainly at the Research Institute for Advanced Computer Science (RIACS) in 1986-1991 is highlighted.

  13. Genetic variability and taxonomic position of ectomycorrhizal fungus Pisolithus from India.

    PubMed

    Singla, Shaveta; Reddy, M S; Marmeisse, R; Gay, G

    2004-01-01

    Eight ectomycorrhizal fungal isolates of Pisolithus associated with Eucalyptus species in different parts of India were collected and the genetic variability of these isolates was studied by ITS-RFLP and ITS sequencing. All the isolates showed same RFLP patterns with each restriction enzyme, indicating all these isolates of Pisolithus are of the same genotype. The sequence comparison of KN6 of Indian isolate showed high sequence similarities with the isolates of Pisolithus associated with Eucalyptus from Australia. Phylogeny analysis showed that all the isolates compared in this study clustered into four main groups The Indian isolate (KN6) clustered with Pisolithus albus isolates of group I, which are associated with Eucalyptus. These results suggested that Pisolithus isolates found in India are P. albus. PMID:15462520

  14. Position-Specific Mass Shift Analysis: A Systematic Method for Investigating the EI-MS Fragmentation Mechanism of epi-Isozizaene.

    PubMed

    Rabe, Patrick; Klapschinski, Tim A; Dickschat, Jeroen S

    2016-07-15

    The EI-MS fragmentation mechanism of the bacterial sesquiterpene epi-isozizaene was investigated through enzymatic conversion of all 15 synthetic ((13) C1 )FPP isotopomers with the epi-isozizaene synthase from Streptomyces albus and GC-MS and GC-QTOF analysis including MS-MS. A systematic method, which we wish to call position-specific mass shift analysis, for the identification of the full set of fragmentation reactions was developed.

  15. A new species of Aspergillus fumigatus group and comments upon its synonymy.

    PubMed

    Varshney, J L; Sarbhoy, A K

    1981-02-13

    Aspergillus fumigatus Fries, acolumnaris Rai et al. (1) has been raised to a distinct epithet and four different varieties of A. fumigatus (1--2 & 6) viz. A. fumigatus Fries. var. albus Rai et al., A. fumigatus Fries. var. grisei-brunneus Rai and Singh, A. fumigatus Fries. mut. helvola Yuill and A. fumigatus Fries. var. sclerotiorum Rai et al. which were recognised by earlier workers, have also been merged into A. fumigatus.

  16. Position-Specific Mass Shift Analysis: A Systematic Method for Investigating the EI-MS Fragmentation Mechanism of epi-Isozizaene.

    PubMed

    Rabe, Patrick; Klapschinski, Tim A; Dickschat, Jeroen S

    2016-07-15

    The EI-MS fragmentation mechanism of the bacterial sesquiterpene epi-isozizaene was investigated through enzymatic conversion of all 15 synthetic ((13) C1 )FPP isotopomers with the epi-isozizaene synthase from Streptomyces albus and GC-MS and GC-QTOF analysis including MS-MS. A systematic method, which we wish to call position-specific mass shift analysis, for the identification of the full set of fragmentation reactions was developed. PMID:27123899

  17. Description of new species of Stenaelurillus Simon, 1886 from the Western Ghats of India with the redescription of Stenaelurillus lesserti Reimoser, 1934 and notes on mating plug in the genus (Arachnida, Araneae, Salticidae)

    PubMed Central

    Sebastian, Pothalil A.; Sankaran, Pradeep M.; Malamel, Jobi J.; Joseph, Mathew M.

    2015-01-01

    Abstract A new species of the jumping spider genus Stenaelurillus Simon, 1886, Stenaelurillus albus sp. n., is described from the Western Ghats of India, one of the biodiversity hotspots of the world. Detailed morphological descriptions, diagnostic features and illustrations of copulatory organs of both sexes are given. Detailed redescription, diagnosis and illustration of Stenaelurillus lesserti Reimoser, 1934 are provided. The occurrence of a mating plug in the genus is reported. PMID:25878537

  18. Heterogeneous detection probabilities for imperiled Missouri River fishes: implications for large-river monitoring programs

    USGS Publications Warehouse

    Schloesser, J.T.; Paukert, Craig P.; Doyle, W.J.; Hill, Tracy D.; Steffensen, K.D.; Travnichek, Vincent H.

    2012-01-01

    Occupancy modeling was used to determine (1) if detection probabilities (p) for 7 regionally imperiled Missouri River fishes (Scaphirhynchus albus, Scaphirhynchus platorynchus, Cycleptus elongatus, Sander canadensis, Macrhybopsis aestivalis, Macrhybopsis gelida, and Macrhybopsis meeki) differed among gear types (i.e. stationary gill nets, drifted trammel nets, and otter trawls), and (2) how detection probabilities were affected by habitat (i.e. pool, bar, and open water), longitudinal position (five 189 to 367 rkm long segments), sampling year (2003 to 2006), and season (July 1 to October 30 and October 31 to June 30). Adult, large-bodied fishes were best detected with gill nets (p: 0.02–0.74), but most juvenile large-bodied and all small-bodied species were best detected with otter trawls (p: 0.02–0.58). Trammel nets may be a redundant sampling gear for imperiled fishes in the lower Missouri River because most species had greater detection probabilities with gill nets or otter trawls. Detection probabilities varied with river segment for S. platorynchus, C. elongatus, and all small-bodied fishes, suggesting that changes in habitat influenced gear efficiency or abundance changes among river segments. Detection probabilities varied by habitat for adult S. albus and S. canadensis, year for juvenile S. albus, C. elongatus, and S. canadensis, and season for adult S. albus. Concentrating sampling effort on gears with the greatest detection probabilities may increase species detections to better monitor a population's response to environmental change and the effects of management actions on large-river fishes.

  19. Salmonellosis in a captive heron colony

    USGS Publications Warehouse

    Locke, L.N.; Ohlendorf, H.M.; Shillinger, R.B.; Jareed, T.

    1974-01-01

    Salmonellosis caused by Salmonella typhimurium was one of several factors responsible for losses among young herons being held at the Patuxent Wildlife Research Center. The infection was demonstrated in five black-crowned night herons (Nycticorax nycticorax), three common egrets (Casmerodius albus), two little blue herons (Florida caerulea), one cattle egret (Bubulcus ibis), one snowy egret (Leucophoyx thula) and one Louisiana heron (Hydranassa tricolor). The disease was characterized by emaciation, focal liver necrosis, and frequently by a caseo-necrotic enteritis.

  20. Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen.

    PubMed

    Dai, Xin; Tian, Yan; Li, Jinting; Luo, Yingfeng; Liu, Di; Zheng, Huajun; Wang, Jiaqi; Dong, Zhiyang; Hu, Songnian; Huang, Li

    2015-02-01

    The bovine rumen represents a highly specialized bioreactor where plant cell wall polysaccharides (PCWPs) are efficiently deconstructed via numerous enzymes produced by resident microorganisms. Although a large number of fibrolytic genes from rumen microorganisms have been identified, it remains unclear how they are expressed in a coordinated manner to efficiently degrade PCWPs. In this study, we performed a metatranscriptomic analysis of the rumen microbiomes of adult Holstein cows fed a fiber diet and obtained a total of 1,107,083 high-quality non-rRNA reads with an average length of 483 nucleotides. Transcripts encoding glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) accounted for 1% and 0.1% of the total non-rRNAs, respectively. The majority (98%) of the putative cellulases belonged to four GH families (i.e., GH5, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus and Fibrobacter. Notably, transcripts for GH48 cellobiohydrolases were relatively abundant compared to the abundance of transcripts for other cellulases. Two-thirds of the putative hemicellulases were of the GH10, GH11, and GH26 types and were produced by members of the genera Ruminococcus, Prevotella, and Fibrobacter. Most (82%) predicted oligosaccharide-degrading enzymes were GH1, GH2, GH3, and GH43 proteins and were from a diverse group of microorganisms. Transcripts for CBM10 and dockerin, key components of the cellulosome, were also relatively abundant. Our results provide metatranscriptomic evidence in support of the notion that members of the genera Ruminococcus, Fibrobacter, and Prevotella are predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen.

  1. Metatranscriptomic Analyses of Plant Cell Wall Polysaccharide Degradation by Microorganisms in the Cow Rumen

    PubMed Central

    Dai, Xin; Tian, Yan; Li, Jinting; Su, Xiaoyun; Wang, Xuewei; Zhao, Shengguo; Liu, Li; Luo, Yingfeng; Liu, Di; Zheng, Huajun; Wang, Jiaqi; Dong, Zhiyang

    2014-01-01

    The bovine rumen represents a highly specialized bioreactor where plant cell wall polysaccharides (PCWPs) are efficiently deconstructed via numerous enzymes produced by resident microorganisms. Although a large number of fibrolytic genes from rumen microorganisms have been identified, it remains unclear how they are expressed in a coordinated manner to efficiently degrade PCWPs. In this study, we performed a metatranscriptomic analysis of the rumen microbiomes of adult Holstein cows fed a fiber diet and obtained a total of 1,107,083 high-quality non-rRNA reads with an average length of 483 nucleotides. Transcripts encoding glycoside hydrolases (GHs) and carbohydrate binding modules (CBMs) accounted for ∼1% and ∼0.1% of the total non-rRNAs, respectively. The majority (∼98%) of the putative cellulases belonged to four GH families (i.e., GH5, GH9, GH45, and GH48) and were primarily synthesized by Ruminococcus and Fibrobacter. Notably, transcripts for GH48 cellobiohydrolases were relatively abundant compared to the abundance of transcripts for other cellulases. Two-thirds of the putative hemicellulases were of the GH10, GH11, and GH26 types and were produced by members of the genera Ruminococcus, Prevotella, and Fibrobacter. Most (∼82%) predicted oligosaccharide-degrading enzymes were GH1, GH2, GH3, and GH43 proteins and were from a diverse group of microorganisms. Transcripts for CBM10 and dockerin, key components of the cellulosome, were also relatively abundant. Our results provide metatranscriptomic evidence in support of the notion that members of the genera Ruminococcus, Fibrobacter, and Prevotella are predominant PCWP degraders and point to the significant contribution of GH48 cellobiohydrolases and cellulosome-like structures to efficient PCWP degradation in the cow rumen. PMID:25501482

  2. Effect of disodium fumarate on microbial abundance, ruminal fermentation and methane emission in goats under different forage: concentrate ratios.

    PubMed

    Yang, C J; Mao, S Y; Long, L M; Zhu, W Y

    2012-11-01

    This study investigated the effects of disodium fumarate (DF) on methane emission, ruminal fermentation and microbial abundance in goats under different forage (F) : concentrate (C) ratios and fed according to maintenance requirements. Four ruminally fistulated, castrated male goats were used in a 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments and the main factors being the F : C ratios (41 : 59 or 58 : 42) and DF supplementation (0 or 10 g/day). DF reduced methane production (P < 0.05) on average by 11.9%, irrespective of the F : C ratio. The concentrations of total volatile fatty acids, acetate and propionate were greater in the rumen of goats supplemented with DF (P < 0.05), whereas the abundance of methanogens was lower (P < 0.05). In high-forage diets, the abundance of Selenomonas ruminantium, a fumarate-reducing bacterium, was greater in the rumen of goats supplemented with DF. The abundance of fungi, protozoa, Ruminococus flavefaciens and Fibrobacter succinogenes were not affected by the addition of DF. Variable F : C ratios affected the abundance of methanogens, fungi and R. flavefaciens (P < 0.05), but did not affect methane emission. The result implied that DF had a beneficial effect on the in vivo rumen fermentation of the goats fed diets with different F : C ratios and that this effect were not a direct action on anaerobic fungi, protozoa and fibrolytic bacteria, the generally recognized fiber-degrading and hydrogen-producing microorganisms, but due to the stimulation of fumarate-reducing bacteria and the depression of methanogens.

  3. Gonadosomatic index and fecundity of Lower Missouri and Middle Mississippi River endangered pallid sturgeon estimated using minimally invasive techniques

    USGS Publications Warehouse

    Albers, J.L.; Wildhaber, M.L.; DeLonay, A.J.

    2013-01-01

    Minimally invasive, non-lethal methods of ultrasonography were used to assess sex, egg diameter, fecundity, gonad volume, and gonadosomatic index, as well as endoscopy to visually assess the reproductive stage of Scaphirhynchus albus. Estimated mean egg diameters of 2.202 ± 0.187 mm and mean fecundity of 44 531 ± 23 940 eggs were similar to previous studies using invasive techniques. Mean S. albus gonadosomatic indices (GSI) for reproductive and nonreproductive females were 16.16 and 1.26%, respectively, while reproductive and non-reproductive male GSI were 2.00 and 0.43%, respectively. There was no relationship between hybrid status or capture location and GSI. Mean fecundity was 48.5% higher than hatchery spawn estimates. Fecundity increased as fork length increased but did so more dramatically in the upper river kilometers of the Missouri River. By examining multiple fish over multiple years, the reproductive cycle periodicity for hatchery female S. albus was found to be 2-4 years and river dwelling males 1-4 years. The use of ultrasonic and endoscopic methods in combination was shown to be helpful in tracking individual gonad characteristics over multi-year reproductive cycles.

  4. Phenolic acid esterases, coding sequences and methods

    DOEpatents

    Blum, David L.; Kataeva, Irina; Li, Xin-Liang; Ljungdahl, Lars G.

    2002-01-01

    Described herein are four phenolic acid esterases, three of which correspond to domains of previously unknown function within bacterial xylanases, from XynY and XynZ of Clostridium thermocellum and from a xylanase of Ruminococcus. The fourth specifically exemplified xylanase is a protein encoded within the genome of Orpinomyces PC-2. The amino acids of these polypeptides and nucleotide sequences encoding them are provided. Recombinant host cells, expression vectors and methods for the recombinant production of phenolic acid esterases are also provided.

  5. Microbiome-Metabolome Responses in the Cecum and Colon of Pig to a High Resistant Starch Diet.

    PubMed

    Sun, Yue; Su, Yong; Zhu, Weiyun

    2016-01-01

    Currently, knowledge about the impact of long-term intake of high resistant starch diet on pig hindgut microbiota and metabolite profile is limited. In this study, a combination of the pyrosequencing and the mass spectrometry (MS)-based metabolomics techniques were used to investigate the effects of a raw potato starch (RPS, high in resistant starch) diet on microbial composition and microbial metabolites in the hindgut of pig. The results showed that Coprococcus, Ruminococcus, and Turicibacter increased significantly, while Sarcina and Clostridium decreased in relative abundances in the hindgut of pigs fed RPS. The metabolimic analysis revealed that RPS significantly affected starch and sucrose metabolites, amino acid turnover or protein biosynthesis, lipid metabolites, glycolysis, the pentose phosphate pathway, inositol phosphate metabolism, and nucleotide metabolism. Furthermore, a Pearson's correlation analysis showed that Ruminococcus and Coprococcus were positively correlated with glucose-6-phosphate, maltose, arachidonic acid, 9, 12-octadecadienoic acid, oleic acid, phosphate, but negatively correlated with α-aminobutyric acid. However, the correlation of Clostridium and Sarcina with these compounds was in the opposite direction. The results suggest that RPS not only alters the composition of the gut microbial community but also modulates the metabolic pathway of microbial metabolism, which may further affect the hindgut health of the host. PMID:27303373

  6. Membrane filter method to study the effects of Lactobacillus acidophilus and Bifidobacterium longum on fecal microbiota

    PubMed Central

    Shimizu, Hidenori

    2015-01-01

    ABSTRACT A large number of commensal bacteria inhabit the intestinal tract, and interbacterial communication among gut microbiota is thought to occur. In order to analyze symbiotic relationships between probiotic strains and the gut microbiota, a ring with a membrane filter fitted to the bottom was used for in vitro investigations. Test strains comprising probiotic nitto strains (Lactobacillus acidophilus NT and Bifidobacterium longum NT) and type strains (L. acidophilus JCM1132T and B. longum JCM1217T) were obtained from diluted fecal samples using the membrane filter to simulate interbacterial communication. Bifidobacterium spp., Streptococcus pasteurianus, Collinsella aerofaciens, and Clostridium spp. were the most abundant gut bacteria detected before coculture with the test strains. Results of the coculture experiments indicated that the test strains significantly promote the growth of Ruminococcus gnavus, Ruminococcus torques, and Veillonella spp. and inhibit the growth of Sutterella wadsworthensis. Differences in the relative abundances of gut bacterial strains were furthermore observed after coculture of the fecal samples with each test strain. Bifidobacterium spp., which was detected as the dominant strain in the fecal samples, was found to be unaffected by coculture with the test strains. In the present study, interbacterial communication using bacterial metabolites between the test strains and the gut microbiota was demonstrated by the coculture technique. The detailed mechanisms and effects of the complex interbacterial communications that occur among the gut microbiota are, however, still unclear. Further investigation of these relationships by coculture of several fecal samples with probiotic strains is urgently required. PMID:26486646

  7. Distribution of Genes Encoding the Trypsin-Dependent Lantibiotic Ruminococcin A among Bacteria Isolated from Human Fecal Microbiota

    PubMed Central

    Marcille, F.; Gomez, A.; Joubert, P.; Ladiré, M.; Veau, G.; Clara, A.; Gavini, F.; Willems, A.; Fons, M.

    2002-01-01

    Fourteen bacterial strains capable of producing a trypsin-dependent antimicrobial substance active against Clostridium perfringens were isolated from human fecal samples of various origins (from healthy adults and children, as well as from adults with chronic pouchitis). Identification of these strains showed that they belonged to Ruminococcus gnavus, Clostridium nexile, and Ruminococcus hansenii species or to new operational taxonomic units, all from the Clostridium coccoides phylogenetic group. In hybridization experiments with a probe specific for the structural gene encoding the trypsin-dependent lantibiotic ruminococcin A (RumA) produced by R. gnavus, seven strains gave a positive response. All of them harbored three highly conserved copies of rumA-like genes. The deduced peptide sequence was identical to or showed one amino acid difference from the hypothetical precursor of RumA. Our results indicate that the rumA-like genes have been disseminated among R. gnavus and phylogenetically related strains that can make up a significant part of the human fecal microbiota. PMID:12089024

  8. Membrane filter method to study the effects of Lactobacillus acidophilus and Bifidobacterium longum on fecal microbiota.

    PubMed

    Shimizu, Hidenori; Benno, Yoshimi

    2015-11-01

    A large number of commensal bacteria inhabit the intestinal tract, and interbacterial communication among gut microbiota is thought to occur. In order to analyze symbiotic relationships between probiotic strains and the gut microbiota, a ring with a membrane filter fitted to the bottom was used for in vitro investigations. Test strains comprising probiotic nitto strains (Lactobacillus acidophilus NT and Bifidobacterium longum NT) and type strains (L. acidophilus JCM1132(T) and B. longum JCM1217(T) ) were obtained from diluted fecal samples using the membrane filter to simulate interbacterial communication. Bifidobacterium spp., Streptococcus pasteurianus, Collinsella aerofaciens, and Clostridium spp. were the most abundant gut bacteria detected before coculture with the test strains. Results of the coculture experiments indicated that the test strains significantly promote the growth of Ruminococcus gnavus, Ruminococcus torques, and Veillonella spp. and inhibit the growth of Sutterella wadsworthensis. Differences in the relative abundances of gut bacterial strains were furthermore observed after coculture of the fecal samples with each test strain. Bifidobacterium spp., which was detected as the dominant strain in the fecal samples, was found to be unaffected by coculture with the test strains. In the present study, interbacterial communication using bacterial metabolites between the test strains and the gut microbiota was demonstrated by the coculture technique. The detailed mechanisms and effects of the complex interbacterial communications that occur among the gut microbiota are, however, still unclear. Further investigation of these relationships by coculture of several fecal samples with probiotic strains is urgently required. PMID:26486646

  9. Microbiome-Metabolome Responses in the Cecum and Colon of Pig to a High Resistant Starch Diet

    PubMed Central

    Sun, Yue; Su, Yong; Zhu, Weiyun

    2016-01-01

    Currently, knowledge about the impact of long-term intake of high resistant starch diet on pig hindgut microbiota and metabolite profile is limited. In this study, a combination of the pyrosequencing and the mass spectrometry (MS)-based metabolomics techniques were used to investigate the effects of a raw potato starch (RPS, high in resistant starch) diet on microbial composition and microbial metabolites in the hindgut of pig. The results showed that Coprococcus, Ruminococcus, and Turicibacter increased significantly, while Sarcina and Clostridium decreased in relative abundances in the hindgut of pigs fed RPS. The metabolimic analysis revealed that RPS significantly affected starch and sucrose metabolites, amino acid turnover or protein biosynthesis, lipid metabolites, glycolysis, the pentose phosphate pathway, inositol phosphate metabolism, and nucleotide metabolism. Furthermore, a Pearson's correlation analysis showed that Ruminococcus and Coprococcus were positively correlated with glucose-6-phosphate, maltose, arachidonic acid, 9, 12-octadecadienoic acid, oleic acid, phosphate, but negatively correlated with α-aminobutyric acid. However, the correlation of Clostridium and Sarcina with these compounds was in the opposite direction. The results suggest that RPS not only alters the composition of the gut microbial community but also modulates the metabolic pathway of microbial metabolism, which may further affect the hindgut health of the host. PMID:27303373

  10. Microbiome-Metabolome Responses in the Cecum and Colon of Pig to a High Resistant Starch Diet.

    PubMed

    Sun, Yue; Su, Yong; Zhu, Weiyun

    2016-01-01

    Currently, knowledge about the impact of long-term intake of high resistant starch diet on pig hindgut microbiota and metabolite profile is limited. In this study, a combination of the pyrosequencing and the mass spectrometry (MS)-based metabolomics techniques were used to investigate the effects of a raw potato starch (RPS, high in resistant starch) diet on microbial composition and microbial metabolites in the hindgut of pig. The results showed that Coprococcus, Ruminococcus, and Turicibacter increased significantly, while Sarcina and Clostridium decreased in relative abundances in the hindgut of pigs fed RPS. The metabolimic analysis revealed that RPS significantly affected starch and sucrose metabolites, amino acid turnover or protein biosynthesis, lipid metabolites, glycolysis, the pentose phosphate pathway, inositol phosphate metabolism, and nucleotide metabolism. Furthermore, a Pearson's correlation analysis showed that Ruminococcus and Coprococcus were positively correlated with glucose-6-phosphate, maltose, arachidonic acid, 9, 12-octadecadienoic acid, oleic acid, phosphate, but negatively correlated with α-aminobutyric acid. However, the correlation of Clostridium and Sarcina with these compounds was in the opposite direction. The results suggest that RPS not only alters the composition of the gut microbial community but also modulates the metabolic pathway of microbial metabolism, which may further affect the hindgut health of the host.

  11. Pollinator directionality as a response to nectar gradient: promoting outcrossing while avoiding geitonogamy.

    PubMed

    Fisogni, A; Cristofolini, G; Rossi, M; Galloni, M

    2011-11-01

    Plants with multiple flowers could be prone to autonomous self-pollination and insect-mediated geitonogamy, but physiological and ecological features have evolved preventing costs related to autogamy. We studied the rare perennial herb Dictamnus albus as a model plant, with the aim of describing the plant-pollinator system from both plant and pollinator perspectives and analysing features that promote outcrossing in an entomophilous species. The breeding system and reproductive success of D. albus were investigated in experimental and natural conditions, showing that it is potentially self-compatible, but only intra-inflorescence insect-mediated selfing is possible. Nectar analysis showed gender-biased production towards the female phase, which follows the male phase, and during flowering, full blooming is found in flowers at the bottom of the raceme. Among a wide spectrum of insect visitors, three genera (Bombus, Apis, Megachile) were found to be principal pollinators. A study of insect behaviour showed a tendency towards bottom-to-top flights for the most important pollinators Bombus spp. and Apis mellifera: upward movements on the racemes could be explained by foraging behaviour, from more to less rewarding flowers. In accordance with the 'declining reward hypothesis', bumblebees and honeybees leave the plant when gain of reward is low, after which few flowers are visited, reducing the chance of self-pollen transfer among flowers. Intra-flower self-pollination is prevented in D. albus by protandry and herkogamy, while the nectar-induced sequential pattern of pollinator visits avoids geitonogamy and tends to maximise pollen export, promoting outcrossing. All these features for preventing selfing benefit plant fitness and population genetic structure.

  12. Cluster-root formation and carboxylate release in three Lupinus species as dependent on phosphorus supply, internal phosphorus concentration and relative growth rate

    PubMed Central

    Wang, Xing; Pearse, Stuart J.; Lambers, Hans

    2013-01-01

    Background and Aims Some Lupinus species produce cluster roots in response to low plant phosphorus (P) status. The cause of variation in cluster-root formation among cluster-root-forming Lupinus species is unknown. The aim of this study was to investigate if cluster-root formation is, in part, dependent on different relative growth rates (RGRs) among Lupinus species when they show similar shoot P status. Methods Three cluster-root-forming Lupinus species, L. albus, L. pilosus and L. atlanticus, were grown in washed river sand at 0, 7·5, 15 or 40 mg P kg−1 dry sand. Plants were harvested at 34, 42 or 62 d after sowing, and fresh and dry weight of leaves, stems, cluster roots and non-cluster roots of different ages were measured. The percentage of cluster roots, tissue P concentrations, root exudates and plant RGR were determined. Key Results Phosphorus treatments had major effects on cluster-root allocation, with a significant but incomplete suppression in L. albus and L. pilosus when P supply exceeded 15 mg P kg−1 sand. Complete suppression was found in L. atlanticus at the highest P supply; this species never invested more than 20 % of its root weight in cluster roots. For L. pilosus and L. atlanticus, cluster-root formation was decreased at high internal P concentration, irrespective of RGR. For L. albus, there was a trend in the same direction, but this was not significant. Conclusions Cluster-root formation in all three Lupinus species was suppressed at high leaf P concentration, irrespective of RGR. Variation in cluster-root formation among the three species cannot be explained by species-specific variation in RGR or leaf P concentration. PMID:24061491

  13. Pollinator directionality as a response to nectar gradient: promoting outcrossing while avoiding geitonogamy.

    PubMed

    Fisogni, A; Cristofolini, G; Rossi, M; Galloni, M

    2011-11-01

    Plants with multiple flowers could be prone to autonomous self-pollination and insect-mediated geitonogamy, but physiological and ecological features have evolved preventing costs related to autogamy. We studied the rare perennial herb Dictamnus albus as a model plant, with the aim of describing the plant-pollinator system from both plant and pollinator perspectives and analysing features that promote outcrossing in an entomophilous species. The breeding system and reproductive success of D. albus were investigated in experimental and natural conditions, showing that it is potentially self-compatible, but only intra-inflorescence insect-mediated selfing is possible. Nectar analysis showed gender-biased production towards the female phase, which follows the male phase, and during flowering, full blooming is found in flowers at the bottom of the raceme. Among a wide spectrum of insect visitors, three genera (Bombus, Apis, Megachile) were found to be principal pollinators. A study of insect behaviour showed a tendency towards bottom-to-top flights for the most important pollinators Bombus spp. and Apis mellifera: upward movements on the racemes could be explained by foraging behaviour, from more to less rewarding flowers. In accordance with the 'declining reward hypothesis', bumblebees and honeybees leave the plant when gain of reward is low, after which few flowers are visited, reducing the chance of self-pollen transfer among flowers. Intra-flower self-pollination is prevented in D. albus by protandry and herkogamy, while the nectar-induced sequential pattern of pollinator visits avoids geitonogamy and tends to maximise pollen export, promoting outcrossing. All these features for preventing selfing benefit plant fitness and population genetic structure. PMID:21972840

  14. Mercury in eggs of aquatic birds, Lake St. Clair-1973

    USGS Publications Warehouse

    Stendell, R.C.; Ohlendorf, H.M.; Klaas, E.E.; Elder, J.B.

    1976-01-01

    Eggs from four species of aquatic birds inhabiting waterways of the Lake St. Clair region were collected in 1973 and analyzed for mercury. Species analyzed were mallard ducks (Anas platyrhynchos), common terns (Sterna hirundo), black-crowned night herons (Nycticorax nycticorax), and great egrets (Casmerodius albus). Mallard eggs contained relatively low residue levels, less than 0.05-0.26 ppm, and common tern eggs contained the highest residues, ranging up to 1.31 ppm. Mercury levels in the eggs were appreciably lower than those in the same species in 1970. The declines are attributed to the 1970 restrictions placed on industrial discharges of mercury into the St. Clair and Detroit Rivers.

  15. Will machines ever think

    NASA Technical Reports Server (NTRS)

    Denning, P. J.

    1986-01-01

    Artificial Intelligence research has come under fire for failing to fulfill its promises. A growing number of AI researchers are reexamining the bases of AI research and are challenging the assumption that intelligent behavior can be fully explained as manipulation of symbols by algorithms. Three recent books -- Mind over Machine (H. Dreyfus and S. Dreyfus), Understanding Computers and Cognition (T. Winograd and F. Flores), and Brains, Behavior, and Robots (J. Albus) -- explore alternatives and open the door to new architectures that may be able to learn skills.

  16. Modeling the action-potential-sensitive nonlinear-optical response of myelinated nerve fibers and short-term memory

    NASA Astrophysics Data System (ADS)

    Shneider, M. N.; Voronin, A. A.; Zheltikov, A. M.

    2011-11-01

    The Goldman-Albus treatment of the action-potential dynamics is combined with a phenomenological description of molecular hyperpolarizabilities into a closed-form model of the action-potential-sensitive second-harmonic response of myelinated nerve fibers with nodes of Ranvier. This response is shown to be sensitive to nerve demyelination, thus enabling an optical diagnosis of various demyelinating diseases, including multiple sclerosis. The model is applied to examine the nonlinear-optical response of a three-neuron reverberating circuit—the basic element of short-term memory.

  17. Evidence for microorganisms in stratosphere air samples collected at a height of 41km

    NASA Astrophysics Data System (ADS)

    Wainwright, Milton; Wickramasinghe, Nalin C.; Narlikar, J. V.; Rajaratnam, P.

    2003-02-01

    Samples of air removed from the stratosphere, at an altitude of 41km, were previously found to contain viable, but non-cultureable bacteria (cocci and rods). Here, we describe experiments aimed at growing these organisms, together with any others, present in the samples. Two bacteria (Bacillus simplex and Staphylococcus pasteuri) and a single fungus, Engyodontium albus (limber)de Hoog were isolated from the samples. Contamination can never be ruled out when space-derived samples are studied on earth, however, we are confident that the organisms isolated here originated from the stratosphere.

  18. Quantitative studies on the salivary flora

    PubMed Central

    Ross, P. W.

    1971-01-01

    In a quantitative bacteriological study of the salivary flora from 50 children the following aerobic organisms were identified and enumerated: alpha-haemolytic streptococci, beta-haemolytic streptococci, Streptococcus faecalis, pneumococci, Staphylococcus aureus, Staph. albus and Staph. citreus, Neisseria spp, N. meningitidis, corynebacteria, aerobic lactobacilli, B. subtilis, H. influenzae, coliform organisms, and Candida spp. Many of the known potentially pathogenic members were present in large numbers. It is suggested that knowledge of the relative numbers of the organisms that comprise the salivary flora will lead to a greater understanding of the ecology of the mouth and of the pathogenesis of oral infections. PMID:4399776

  19. A neural-network approach to robotic control

    NASA Technical Reports Server (NTRS)

    Graham, D. P. W.; Deleuterio, G. M. T.

    1993-01-01

    An artificial neural-network paradigm for the control of robotic systems is presented. The approach is based on the Cerebellar Model Articulation Controller created by James Albus and incorporates several extensions. First, recognizing the essential structure of multibody equations of motion, two parallel modules are used that directly reflect the dynamical characteristics of multibody systems. Second, the architecture of the proposed network is imbued with a self-organizational capability which improves efficiency and accuracy. Also, the networks can be arranged in hierarchical fashion with each subsequent network providing finer and finer resolution.

  20. Optimization and microbial community analysis for production of biogas from solid waste residues of palm oil mill industry by solid-state anaerobic digestion.

    PubMed

    Suksong, Wantanasak; Kongjan, Prawit; Prasertsan, Poonsuk; Imai, Tsuyoshi; O-Thong, Sompong

    2016-08-01

    This study investigated the improvement of biogas production from solid-state anaerobic digestion (SS-AD) of oil palm biomass by optimizing of total solids (TS) contents, feedstock to inoculum (F:I) ratios and carbon to nitrogen (C:N) ratios. Highest methane yield from EFB, OPF and OPT of 358, 280 and 324m(3)CH4ton(-1)VS, respectively, was achieved at TS content of 16%, C:N ratio of 30:1 and F:I ratio of 2:1. The main contribution to methane from biomass was the degradation of cellulose and hemicellulose. The highest methane production of 72m(3)CH4ton(-1) biomass was achieved from EFB. Bacteria community structure in SS-AD process of oil palm biomass was dominated by Ruminococcus sp. and Clostridium sp., while archaea community was dominated by Methanoculleus sp. Oil palm biomass has great potential for methane production via SS-AD.

  1. Optimization and microbial community analysis for production of biogas from solid waste residues of palm oil mill industry by solid-state anaerobic digestion.

    PubMed

    Suksong, Wantanasak; Kongjan, Prawit; Prasertsan, Poonsuk; Imai, Tsuyoshi; O-Thong, Sompong

    2016-08-01

    This study investigated the improvement of biogas production from solid-state anaerobic digestion (SS-AD) of oil palm biomass by optimizing of total solids (TS) contents, feedstock to inoculum (F:I) ratios and carbon to nitrogen (C:N) ratios. Highest methane yield from EFB, OPF and OPT of 358, 280 and 324m(3)CH4ton(-1)VS, respectively, was achieved at TS content of 16%, C:N ratio of 30:1 and F:I ratio of 2:1. The main contribution to methane from biomass was the degradation of cellulose and hemicellulose. The highest methane production of 72m(3)CH4ton(-1) biomass was achieved from EFB. Bacteria community structure in SS-AD process of oil palm biomass was dominated by Ruminococcus sp. and Clostridium sp., while archaea community was dominated by Methanoculleus sp. Oil palm biomass has great potential for methane production via SS-AD. PMID:27132224

  2. Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community.

    PubMed

    Pandit, Prabhakar D; Gulhane, Madhuri K; Khardenavis, Anshuman A; Purohit, Hemant J

    2016-09-01

    Study creates a scenario for enrichment and selection of ligno-hemicellulose degrading genotypes with anaerobic bioreactor as a model using rice straw, vegetable waste and food waste as substrates. Relative discrimination analysis showed that the hydrolytic pathways and associated microbial communities for ligno-hemicellulose degradation were dominatingly colonized with rice straw as substrate. The dominating bacteria were Caldicellulosiruptor, Fervidobacterium, Cytophaga, Ruminococcus, Thermotoga associated with hemicellulose degradation and Burkholderia, Pandorea, Sphingomonas, Spirochaeta, Pseudomonas for lignocellulose hydrolysis. This was further supported by the abundance of anaerobic aromatic compound degrading genes along with genes for xylanase and xylosidase in rice straw enriched community. The metagenome analysis data was validated by evaluation of the biochemical methane potential for these substrates. Food waste being most amenable substrate yielded 1410mL of biogas/gVS added whereas, biogas yield of 1160mL/gVS and 1080mL/gVS was observed in presence of vegetable waste and rice straw respectively.

  3. Microbial ecology in anaerobic digestion at agitated and non-agitated conditions.

    PubMed

    Tian, Zhuoli; Cabrol, Léa; Ruiz-Filippi, Gonzalo; Pullammanappallil, Pratap

    2014-01-01

    To investigate the distribution and dynamics of microbial community in anaerobic digestion at agitated and non-agitated condition, 454 pyrosequencing of 16s rRNA was conducted. It revealed the distinct community compositions between the two digesters and their progressive shifting over time. Methanogens and syntrophic bacteria were found much less abundant in the agitated digester, which was mainly attributed to the presence of bacterial genera Acetanaerobacterium and Ruminococcus with relatively high abundance. The characterization of the microbial community corroborated the digestion performance affected at the agitated condition, where lower methane yield and delayed methane production rate were observed. This was further verified by the accumulation of propionic acid in the agitated digester.

  4. Microbial Ecology in Anaerobic Digestion at Agitated and Non-Agitated Conditions

    PubMed Central

    Tian, Zhuoli; Cabrol, Léa; Ruiz-Filippi, Gonzalo; Pullammanappallil, Pratap

    2014-01-01

    To investigate the distribution and dynamics of microbial community in anaerobic digestion at agitated and non-agitated condition, 454 pyrosequencing of 16s rRNA was conducted. It revealed the distinct community compositions between the two digesters and their progressive shifting over time. Methanogens and syntrophic bacteria were found much less abundant in the agitated digester, which was mainly attributed to the presence of bacterial genera Acetanaerobacterium and Ruminococcus with relatively high abundance. The characterization of the microbial community corroborated the digestion performance affected at the agitated condition, where lower methane yield and delayed methane production rate were observed. This was further verified by the accumulation of propionic acid in the agitated digester. PMID:25313520

  5. Gut bacteria that rescue growth impairments transmitted by immature microbiota from undernourished children

    PubMed Central

    Blanton, Laura V.; Charbonneau, Mark R.; Salih, Tarek; Barratt, Michael J.; Venkatesh, Siddarth; Ilkaveya, Olga; Subramanian, Sathish; Manary, Mark J.; Trehan, Indi; Jorgensen, Josh M.; Fan, Yue-mei; Henrissat, Bernard; Leyn, Semen A.; Rodionov, Dmitry A.; Osterman, Andrei L.; Maleta, Kenneth M.; Newgard, Christopher B.; Ashorn, Per; Dewey, Kathryn G.; Gordon, Jeffrey

    2016-01-01

    Undernourished children exhibit impaired gut microbiota development. Transplanting microbiota from 6- and 18-month old healthy or undernourished Malawian donors into young germ-free mice fed a Malawian diet revealed that immature microbiota from undernourished infants/children transmit impaired growth phenotypes. The representation of several age-discriminatory taxa in recipient animals correlated with lean body mass gain, liver, muscle, and brain metabolism, plus bone morphology. Co-housing mice shortly after receiving microbiota from healthy (H) or severely stunted/underweight (Un) infants demonstrated that invasion of age-/growth-discriminatory taxa from H to Un cagemates’ microbiota ameliorates growth faltering. Adding two invasive species, Ruminococcus gnavus and Clostridium symbiosum, to the Un microbiota also ameliorated growth and metabolic abnormalities. These results provide evidence that microbiota immaturity is causally related to undernutrition, and reveal potential therapeutic targets and agents. PMID:26912898

  6. Some are more equal than others: the role of "keystone" species in the degradation of recalcitrant substrates.

    PubMed

    Ze, Xiaolei; Le Mougen, Fanny; Duncan, Sylvia H; Louis, Petra; Flint, Harry J

    2013-01-01

    The microbial communities found in the mammalian large intestine and rumen efficiently degrade many recalcitrant substrates that are resistant to the host's digestive enzymes. These communities are known from molecular profiling to be highly diverse at the species and strain level, but it may be that only certain specialized organisms ("keystone species") have the ability to initiate degradation of such substrates, thus releasing energy on which the rest of the community depends. We have recently reported that Ruminococcus bromii has a superior ability to degrade certain forms of particulate resistant starch (RS) when compared with other highly abundant species of amylolytic bacteria found in the human colon and have presented evidence that this bacterium provides an example of a keystone species within the microbial community with respect to RS fermentation. The concept of keystone species can be equally relevant to other activities, e.g., those involved in stabilizing the community. PMID:23549436

  7. A biosynthetic pathway for a prominent class of microbiota-derived bile acids

    PubMed Central

    Devlin, A. Sloan; Fischbach, Michael A.

    2015-01-01

    The gut bile acid pool is millimolar in concentration, varies widely in composition among individuals, and is linked to metabolic disease and cancer. Although these molecules derive almost exclusively from the microbiota, remarkably little is known about which bacterial species and genes are responsible for their biosynthesis. Here, we report a biosynthetic pathway for the second most abundant class in the gut, iso (3β-hydroxy) bile acids, whose levels exceed 300 µM in some humans and are absent in others. We show, for the first time, that iso bile acids are produced by Ruminococcus gnavus, a far more abundant commensal than previously known producers; and that the iso bile acid pathway detoxifies deoxycholic acid, favoring the growth of the keystone genus Bacteroides. By revealing the biosynthetic genes for an abundant class of bile acids, our work sets the stage for predicting and rationally altering the composition of the bile acid pool. PMID:26192599

  8. Gut bacterial diversity of the tribes of India and comparison with the worldwide data

    PubMed Central

    Dehingia, Madhusmita; Thangjam devi, Kanchal; Talukdar, Narayan C.; Talukdar, Rupjyoti; Reddy, Nageshwar; Mande, Sharmila S.; Deka, Manab; Khan, Mojibur R.

    2015-01-01

    The gut bacteria exert phenotypic traits to the host but the factors which determine the gut bacterial profile (GBP) is poorly understood. This study aimed to understand the effect of ethnicity and geography on GBP of Mongoloid and Proto-Australoid tribes of India. Fecal bacterial diversity was studied in fifteen tribal populations representing four geographic regions (Assam, Telangana, Manipur and Sikkim) by DGGE followed by NGS analysis on Illumina MiSeq platform. Geography and diet had significant effect on GBP of the Indian tribes which was dominated by Prevotella. The effects were more prominent with lower taxonomic levels, indicating probable functional redundancy of the core GBP. A comparison with the worldwide data revealed that GBP of the Indian population was similar to the Mongolian population (Mongolia). The bacterial genera Faecalibacterium, Eubacterium, Clostridium, Blautia, Ruminococcus and Roseburia were found to be core genera in the representative populations of the world. PMID:26689136

  9. Effects of dietary linseed oil and propionate precursors on ruminal microbial community, composition, and diversity in Yanbian yellow cattle.

    PubMed

    Li, Xiang Z; Park, Byung K; Shin, Jong S; Choi, Seong H; Smith, Stephen B; Yan, Chang G

    2015-01-01

    The rumen microbial ecosystem is a complex system where rumen fermentation processes involve interactions among microorganisms. There are important relationships between diet and the ruminal bacterial composition. Thus, we investigated the ruminal fermentation characteristics and compared ruminal bacterial communities using tag amplicon pyrosequencing analysis in Yanbian yellow steers, which were fed linseed oil (LO) and propionate precursors. We used eight ruminally cannulated Yanbian yellow steers (510 ± 5.8 kg) in a replicated 4 × 4 Latin square design with four dietary treatments. Steers were fed a basal diet that comprised 80% concentrate and 20% rice straw (DM basis, CON). The CON diet was supplemented with LO at 4%. The LO diet was also supplemented with 2% dl-malate or 2% fumarate as ruminal precursors of propionate. Dietary supplementation with LO and propionate precursors increased ruminal pH, total volatile fatty acid concentrations, and the molar proportion of propionate. The most abundant bacterial operational taxonomic units in the rumen were related to dietary treatments. Bacteroidetes dominated the ruminal bacterial community and the genus Prevotella was highly represented when steers were fed LO plus propionate precursors. However, with the CON and LO diet plus malate or fumarate, Firmicutes was the most abundant phylum and the genus Ruminococcus was predominant. In summary, supplementing the diets of ruminants with a moderate level of LO plus propionate precursors modified the ruminal fermentation pattern. The most positive responses to LO and propionate precursors supplementation were in the phyla Bacteriodetes and Firmicutes, and in the genus Ruminococcus and Prevotella. Thus, diets containing LO plus malate or fumarate have significant effects on the composition of the rumen microbial community. PMID:26024491

  10. Effect of probiotic yoghurt on animal-based diet-induced change in gut microbiota: an open, randomised, parallel-group study.

    PubMed

    Odamaki, T; Kato, K; Sugahara, H; Xiao, J Z; Abe, F; Benno, Y

    2016-09-01

    Diet has a significant influence on the intestinal environment. In this study, we assessed changes in the faecal microbiota induced by an animal-based diet and the effect of the ingestion of yoghurt supplemented with a probiotic strain on these changes. In total, 33 subjects were enrolled in an open, randomised, parallel-group study. After a seven-day pre-observation period, the subjects were allocated into three groups (11 subjects in each group). All of the subjects were provided with an animal-based diet for five days, followed by a balanced diet for 14 days. Subjects in the first group ingested dairy in the form of 200 g of yoghurt supplemented with Bifidobacterium longum during both the animal-based and balanced diet periods (YAB group). Subjects in the second group ingested yoghurt only during the balanced diet period (YB group). Subjects who did not ingest yoghurt throughout the intervention were used as the control (CTR) group. Faecal samples were collected before and after the animal-based diet was provided and after the balanced diet was provided, followed by analysis by high-throughput sequencing of amplicons derived from the V3-V4 region of the 16S rRNA gene. In the YB and CTR groups, the animal-based diet caused a significant increase in the relative abundance of Bilophila, Odoribacter, Dorea and Ruminococcus (belonging to Lachnospiraceae) and a significant decrease in the level of Bifidobacterium after five days of intake. With the exception of Ruminococcus, these changes were not observed in the YAB group. No significant effect was induced by yoghurt supplementation following an animal-based diet (YB group vs CTR group). These results suggest that the intake of yoghurt supplemented with bifidobacteria played a role in maintaining a normal microbiota composition during the ingestion of a meat-based diet. This study protocol was registered in the University Hospital Medical Information Network: UMIN000014164. PMID:27133564

  11. Effects of Lactobacillus salivarius Ren on cancer prevention and intestinal microbiota in 1, 2-dimethylhydrazine-induced rat model.

    PubMed

    Zhang, Ming; Fan, Xing; Fang, Bing; Zhu, Chengzhen; Zhu, Jun; Ren, Fazheng

    2015-06-01

    Probiotics have been suggested as a prophylactic measure in colon cancer. The aim of this study was to investigate the impact of Lactobacillus salivarius Ren (Ren) in modulating colonic microbiota structure and colon cancer incidence in a rat model after injection with 1,2-dimethyl hydrazine (DMH). The results indicated that oral administration of Ren could effectively suppress DMH-induced colonic carcinogenesis. A significant decrease in cancer incidence (87.5% to 25%) was detected in rats fed with a dose of 5 × 10(10) CFU/kg bodyweight per day. Using denaturing gradient gel electrophoresis and Real-time PCR combined with multivariate statistical methods, we demonstrated that injection with DMH significantly altered the rat gut microbiota, while Ren counteracted these DMH-induced adverse effects and promoted reversion of the gut microbiota close to the healthy state. Tvalue biplots followed by band sequencing identified 21 bacterial strains as critical variables affected by DMH and Ren. Injection of DMH significantly increased the amount of Ruminococcus species (sp.) and Clostridiales bacteria, as well as decreasing the Prevotella sp. Administration of Ren reduced the amount of Ruminococcus sp., Clostridiales bacteria, and Bacteroides dorei, and increased the amount of Prevotella. Real-time PCR results were consistent with the results derived by t-value biplots. These findings suggested that Ren is a potential agent for colon cancer prevention. In conclusion, the results in the present study suggest a potential therapeutic approach based on the modulation of intestinal microflora by probiotics may be beneficial in the prevention of colorectal carcinogenesis.

  12. Effects of dietary linseed oil and propionate precursors on ruminal microbial community, composition, and diversity in Yanbian yellow cattle.

    PubMed

    Li, Xiang Z; Park, Byung K; Shin, Jong S; Choi, Seong H; Smith, Stephen B; Yan, Chang G

    2015-01-01

    The rumen microbial ecosystem is a complex system where rumen fermentation processes involve interactions among microorganisms. There are important relationships between diet and the ruminal bacterial composition. Thus, we investigated the ruminal fermentation characteristics and compared ruminal bacterial communities using tag amplicon pyrosequencing analysis in Yanbian yellow steers, which were fed linseed oil (LO) and propionate precursors. We used eight ruminally cannulated Yanbian yellow steers (510 ± 5.8 kg) in a replicated 4 × 4 Latin square design with four dietary treatments. Steers were fed a basal diet that comprised 80% concentrate and 20% rice straw (DM basis, CON). The CON diet was supplemented with LO at 4%. The LO diet was also supplemented with 2% dl-malate or 2% fumarate as ruminal precursors of propionate. Dietary supplementation with LO and propionate precursors increased ruminal pH, total volatile fatty acid concentrations, and the molar proportion of propionate. The most abundant bacterial operational taxonomic units in the rumen were related to dietary treatments. Bacteroidetes dominated the ruminal bacterial community and the genus Prevotella was highly represented when steers were fed LO plus propionate precursors. However, with the CON and LO diet plus malate or fumarate, Firmicutes was the most abundant phylum and the genus Ruminococcus was predominant. In summary, supplementing the diets of ruminants with a moderate level of LO plus propionate precursors modified the ruminal fermentation pattern. The most positive responses to LO and propionate precursors supplementation were in the phyla Bacteriodetes and Firmicutes, and in the genus Ruminococcus and Prevotella. Thus, diets containing LO plus malate or fumarate have significant effects on the composition of the rumen microbial community.

  13. Effects of Lactobacillus salivarius Ren on cancer prevention and intestinal microbiota in 1, 2-dimethylhydrazine-induced rat model.

    PubMed

    Zhang, Ming; Fan, Xing; Fang, Bing; Zhu, Chengzhen; Zhu, Jun; Ren, Fazheng

    2015-06-01

    Probiotics have been suggested as a prophylactic measure in colon cancer. The aim of this study was to investigate the impact of Lactobacillus salivarius Ren (Ren) in modulating colonic microbiota structure and colon cancer incidence in a rat model after injection with 1,2-dimethyl hydrazine (DMH). The results indicated that oral administration of Ren could effectively suppress DMH-induced colonic carcinogenesis. A significant decrease in cancer incidence (87.5% to 25%) was detected in rats fed with a dose of 5 × 10(10) CFU/kg bodyweight per day. Using denaturing gradient gel electrophoresis and Real-time PCR combined with multivariate statistical methods, we demonstrated that injection with DMH significantly altered the rat gut microbiota, while Ren counteracted these DMH-induced adverse effects and promoted reversion of the gut microbiota close to the healthy state. Tvalue biplots followed by band sequencing identified 21 bacterial strains as critical variables affected by DMH and Ren. Injection of DMH significantly increased the amount of Ruminococcus species (sp.) and Clostridiales bacteria, as well as decreasing the Prevotella sp. Administration of Ren reduced the amount of Ruminococcus sp., Clostridiales bacteria, and Bacteroides dorei, and increased the amount of Prevotella. Real-time PCR results were consistent with the results derived by t-value biplots. These findings suggested that Ren is a potential agent for colon cancer prevention. In conclusion, the results in the present study suggest a potential therapeutic approach based on the modulation of intestinal microflora by probiotics may be beneficial in the prevention of colorectal carcinogenesis. PMID:26025172

  14. Significant differences in fecal microbiota are associated with various stages of glucose tolerance in African American male veterans.

    PubMed

    Ciubotaru, Irina; Green, Stefan J; Kukreja, Subhash; Barengolts, Elena

    2015-11-01

    The importance of gut microbiota in pathogenesis of diabetes remains unknown. This study investigated the relationship between microbiota and metabolic markers in African American men (AAM) with prediabetes and hypovitaminosis D. The study was ancillary to a randomized trial of vitamin D supplementation with weekly ergocalciferol (50,000 IU) conducted in AAM veterans over 12 months (D Intervention in Veterans Affairs). Glycemic groups (Gr) were characterized based on changes in oral glucose tolerance between baseline and exit. Subjects with stable normal glucose tolerance were assigned to Gr-1 and those with stable prediabetes (impaired glucose tolerance and impaired fasting glucose) to Gr-2. Microbiota composition was analyzed in stool collected at the exit (n = 115) and compared between Gr-1 and Gr-2, as well as between the lowest and highest quartiles of dietary intake of energy and fat, hemoglobin A1c, and serum 25-hydroxyvitamin D (25[OH]D) level. Differences between Gr-1 and Gr-2 included the Bacteroidetes/Firmicutes and Bacteroidales/Clostridia ratios and differences in genera such as Ruminococcus and Dialister. Changes in specific taxa associated with the lowest and highest quartiles of 25(OH)D (eg, Ruminococcus, Roseburia, Blautia, Dorea) were clearly distinct from those of dietary intake (eg, Bacteroides, Bacteroides/Prevotella ratio) or A1c (eg, Faecalibacterium, Catenibacterium, Streptococcus). These findings suggest a novel interaction between microbiota and vitamin D and a role for microbiota in early stages of diabetes development. Although results suggest that specific taxa are associated with glycemic stability over time, a causative relationship between microbiota makeup and dysglycemia is still to be demonstrated. PMID:26209747

  15. Lupine inhalation induced asthma in a child.

    PubMed

    Moreno-Ancillo, Alvaro; Gil-Adrados, Ana C; Domínguez-Noche, Carmen; Cosmes, Pedro M

    2005-09-01

    The ingestion of lupine seed flour has been reported as a cause of allergic reactions. There is some evidence of its allergenic potential after inhalation. An 8-year-old asthmatic child, who was allergic to peanut, was studied in our clinic with the suspicion of an adverse drug reaction due to salbutamol. He suffered an asthma attack while playing with his brother, who had been eating lupine seed as snack; surprisingly, the asthma attack worsened with salbutamol. The skin tests showed a positive result with Lupinus albus extract, peanut, garbanzo bean, navy bean, pea, green bean, lentil, soy, Olea europea pollen, grass pollen and Plantago lanceolata pollen. The prick-by-prick tests both from dried seeds and those preserved in salt and water were strongly positive. Serum specific IgE antibodies were positive to Lupine albus (1.43 kU/l), peanut (4.32 kU/l), soy (2.15 kU/l), lentil (3.12 kU/l) and garbanzo (0.7 kU/l). After informed consent salbutamol was well tolerated but the patient had asthma in 5 min of manipulation of the lupine seeds. In our case, reactivity with other legumes was also demonstrated, but only peanut allergy was relevant because boiled legumes were tolerated. It is also notorious that anamnesis is so important to assess the true etiological agents of asthma.

  16. [Genetics in methylotrophic bacteria]. Progress report, July 1, 1992--June 30, 1995

    SciTech Connect

    1998-09-01

    The focus of this project has been to identify and characterize mox genes and other methylotrophy genes in both methane- and methanol-utilizing bacteria, and study expression of those genes. In the last three years of support, the project has focused on identifying methylotrophy genes and the regions involved in their expression for comparative purposes, and has begun the process of analyzing the genes involved in transcriptional regulation of the mox system in the strain for which the authors have the most information, M. extorquens AM1. In order to carry out comparative studies of the transcription of methylotrophy genes, they have cloned and characterized genes involved in methanol oxidation (mox genes) from two Type I methanotrophs, Methylobacter marinus A45 (formerly Methylomonas sp A45) and Methylobacter albus BG8 (formerly Methylomonas albus BG8). In both cases, the organization of the genes was found to be identical, and the transcriptional start sites upstream of the mxaF genes were mapped. Other methylotrophy genes have been cloned and characterized from these methanotrophs, including mxaAKL and fdh. The rest of this project has focused on the regulatory network for the mox system in M. extorquens AM1. The authors have sequenced two mox regulatory genes, mxbD and mxbM and they show identify with a specific group of sensor-kinase/response regulator pair systems.

  17. The potential of oil-utilizing bacterial consortia associated with legume root nodules for cleaning oily soils.

    PubMed

    Dashti, N; Khanafer, M; El-Nemr, I; Sorkhoh, N; Ali, N; Radwan, S

    2009-03-01

    The surfaces of root nodules of Vicia faba and Lupinus albus (legume crops), were colonized with bacterial consortia which utilized oil and fixed nitrogen. Such combined activities apparently make those periphytic consortia efficient contributors to bioremediation of oily nitrogen-poor desert soils. This was confirmed experimentally in this study. Thus, cultivating V. faba, L. albus and, for comparison, Solanum melongena, a nonlegume crop, separately in oily sand samples resulted in more oil attenuation than in an uncultivated sample. This effect was more pronounced with the legume crops than with the nonlegume crop. Furthermore, in flask cultures, V. faba plants with nodulated roots exhibited a higher potential for oil attenuation in the surrounding water than plants with nodule-free roots. Denaturation gradient gel electrophoresis (DGGE) of polymerase chain reaction amplified 16S rRNA coding genes revealed that periphytic bacteria had DGGE bands not matching those of the oil-utilizing rhizospheric bacteria. Legume nodules also contained endophytic bacteria whose 16S rDNA bands did not match those of Rhizobium nor those of all other individual periphytic and rhizospheric strains. It was concluded that legume crops host on their roots bacterial consortia with a satisfactory potential for oil phytoremediation.

  18. Distribution species abundance and nesting site use of Atlantic coast colonies of herons and their allies

    USGS Publications Warehouse

    Custer, T.W.; Osborn, R.G.; Stout, W.F.

    1980-01-01

    In 1975 and 1976, 8 teams of investigators located 262 colonies of nesting herons and their allies along the Atlantic coast from Florida to Maine [USA]. Fourteen species [Ajaia ajaja, Plegadis falcinellus, Nycticorax nycticorax, Ardea herodias, Eudocimus albus, Egretta thula, Hydranassa tricolor, Bubulcus ibis, Casmerodius albus, Butorides striatus, Florida caerulea, Dichromanassa rufescens, Nyctanassa violacea and Mycteria americana] were found in Florida, numbers decreasing to 7 in Maine. Colonies censused in the extreme south and north of the study area were lower in number of species and number of adults than those in the intermediate area. More than 90% of the colony sites surveyed in 1975 were active in 1976. The total number of nesting adults per colony, number of species per colony and number of nesting adults of each species per colony in 1976 were significantly correlated with their respective values for 1975. Abandoned and new colonies may be satellites of nearby reused colonies; they had fewer individuals and species than reused colonies and were closer to reused colonies than reused colonies were to each other. [This study was part of an attempt to examine colonially nesting herons as biological indicators of environmental quality.

  19. Co-electrospinning of bacteria and viruses

    NASA Astrophysics Data System (ADS)

    Salalha, Wael; Kuhn, Jonathan; Chervinsky, Shmuel; Zussman, Eyal

    2006-03-01

    Co-electrospinning provides a novel and highly versatile approach towards composite fibers with diameters ranging from a few hundred nm down to 30 nm with embedded elements. In the present work, co-electrospinning of poly(vinyl alcohol) (PVA) and viruses (T7, T4, λ) or bacteria (Escherichia coli, Staphylococcus albus) was carried out. These preparations should have applications for tissue engineering, gene therapy, phage therapy and biosensing. The average diameter of the co-spun nanofibers was about 300 nm. We found that the encapsulated viruses and bacteria manage to survive the electrospinning process, its pressure buildup in the core of the fiber and the electrostatic field in the co-electrospinning process. Approximately 10% of the Escherichia coli and 20% of Staphylococcus albus cells are viable after spinning. Approximately 5% of the bacterial viruses were also viable after the electrospinning. It should be noted that the encapsulated cells and viruses remain stable for two months without a further decrease in number. These results demonstrate the potential of the co-electrospinning process for the encapsulation and immobilization of bio-objects and the possibility of adapting them to technical applications (e.g., bio-chips).

  20. Shell thinning and pesticide residues in Texas aquatic bird eggs, 1970

    USGS Publications Warehouse

    King, K.A.; Flickinger, Edward L.; Hildebrand, H.H.

    1978-01-01

    Significant decreases in eggshell thickness were found in 15 of 22 species of aquatic birds in Texas in 1970. Shell thickness reductions of 9 to 15 percent were found in white pelicans (Pelecanus erythrorhynchos), brown pelicans (P .occidentalis), and great blue herons (Ardea herodias). DDT family compounds were found in all eggs, and mean residues ranged from 0.4 ppm in white ibis (Eudocimus albus) to 23.2 ppm in great egrets (Casmerodius albus). GDDT residues were negatively correlated with shell thickness in five species; PCBs were negatively correlated in two. Residues in marine birds were generally lower and more uniform than levels in birds feeding in fresh and brackish water. DDT and dieldrin residues were higher in eggs from colonies near agricultural areas where these insecticides were heavily used; higher PCB residues were consistently associated with urban and industrial areas. Populations of five species have declined and deserve continued study: brown pelican, reddish egret (Dichromanassa rufescens), white-faced ibis (Plegadis chihi), laughing gull (Larus atricilla), and Forster's tern (Sterna forsteri). Population trends of four other species were undetermined and should be followed closely in future years.

  1. Wading birds as biological indicators 1975 colony survey

    USGS Publications Warehouse

    Custer, T.W.; Osborn, R.G.

    1977-01-01

    The suitability of wading birds (herons and their allies) as biological indicators in the coastal environment were studied in 1975 by 8 teams of investigators which located and censused 198 colonies along the Atlantic coast from Maine to Florida [USA]. Over 1/4 million breeding birds [Ardea herodias, Butorides virescens, Florida caerulea, Bubulcus ibis, Dichromanassa rufescens, Casmerodius albus, Egretta thula, Hydranassa tricolor, Nycticorax nycticorax, Nyctanassa violacea, Mycteria americana, Plegadis falcinellus, Eudocimus albus and Ajaia ajaja] were censused. The number of species in colonies ranged from 1-11. The number of 1- and 2-spp. colonies increased from Florida to Maine. Colony size decreased from Florida to Maine. Wading bird colony sites are generally active each year and the number of colonies may have recently increased in some areas of the coast. Species composition and total population of colonies fluctuate from year to year. The breeding population of wading birds was correlated with the area of coastal wetlands by state. Five teams of investigators studied the reproductive biology of 9 spp. in 13 colonies. Mean clutch size, the percentage of nests in which 1 or more eggs hatched and the overall percentage of eggs that hatched differed among colonies for some species, but no latitudinal gradient was found in any of these characteristics for any species. The use of wading birds to their full potential as biological indicators requires further exploration: survey and reproductive success methods need to be tested, the survey of colonies repeated, available historical information assembled and habitat requirements measured.

  2. Qualitative identification of volatile metabolites from two fungi and three bacteria species cultivated on two media.

    PubMed

    Kiviranta, H; Tuomainen, A; Reiman, M; Laitinen, S; Liesivuori, J; Nevalainen, A

    1998-11-01

    Two fungal species, Aspergillus fumigatus and Penicillium brevicompactum and three bacteria, Klebsiella pneumoniae, Enterobacter agglomerans and Streptomyces albus were cultivated on two media, malt extract agar and dichloran glycerol agar. The volatile metabolite samples from the cultures were adsorbed on Tenax TA and analyzed qualitatively by thermal desorption gas chromatography and with a mass selective detector. Various hydrocarbons, alcohols, ketones, esters and terpenes were identified. The production was highly dependent on both the medium and the microbial species. 2-Methyl-1-propanol, 2-methyl-1-butanol and 3-methyl-1-butanol were the most commonly produced substances. The bacterial species did not produce any hydrocarbons that were characteristic to the fungi (e.g. methyl-1,3-pentadiene, 1-octene and 1,3-octadiene or 8-carbon alcohols 1-octen-3-ol and 3-octanol). Instead, K. pneumoniae and E. agglomerans produced 3-hydroxy-2-butanone and 1-hydroxy-2-propanone, which were not produced by the fungi. Geosmin and a large number of sesquiterpenes were produced by S. albus.

  3. Feeding habitat use by colonially breeding herons egrets and ibises in North Carolina USA

    USGS Publications Warehouse

    Custer, T.W.; Osborn, R.G.

    1978-01-01

    Nine species of herons, egrets and ibises [Egretta thula, Florida caerula, Hydranassa tricolor, Eudocimus albus, Bubulcus ibis, Casmerodius albus, Nycticorax nycticorax, Plegadis falcinellus and Nyctanassa violacea] were followed by airplane from a nesting colony near Beaufort, North Carolina to their feeding sites. Except for cattle egrets, which flew exclusively to fields and dumps, the birds few mainly to saltmarsh habitat. The selection of feeding habitats by great egrets and Louisiana herons was directly related to tidal depth. The great egret was the only species that effectively used eelgrass [Zostera marina] beds, and its use of this habitat was restricted to between 1.5 h before and after low tide. Shorter-legged herons probably did not use eelgrass regularly because the water was too deep. Most great egrets, white ibises, Louisiana herons and snowy egrets used areas near the colony (< 4 km). Great egrets, black-crowned night herons and white ibises flew farther from the colony at high than at low tide. Great egrets traveled farther from the colony when they used thermals and the rate of travel to feeding sites was the same, whether or not thermals were used. Aggressive encounters were observed at the landing sites of great egrets, Louisiana herons, snowy egrets and black-crowned night herons. Cattle egrets and white ibises often flew in groups to feeding sites. Colonies may act as information centers, where unsuccessful birds follow successful ones to better feeding locations.

  4. Gender identification of shovelnose sturgeon using ultrasonic and endoscopic imagery and the application of the method to the pallid sturgeon

    USGS Publications Warehouse

    Wildhaber, M.L.; Papoulias, D.M.; DeLonay, A.J.; Tillitt, D.E.; Bryan, J.L.; Annis, M.L.; Allert, J.A.

    2005-01-01

    Monthly sampling of shovelnose sturgeon Scaphirhynchus platorynchus, a biological surrogate for the endangered pallid sturgeon Scaphirhynchus albus, was conducted to develop a multiseasonal profile of reproductive stages. Data collected included histological characteristics of gonads from wild caught fish and laboratory and field ultrasonic and endoscopic images. These data were used to compare effectiveness of ultrasonic and endoscopic techniques at identifying gender of adult shovelnose sturgeon at different reproductive stages. The least invasive method (i.e. ultrasound) was least effective while the most invasive (i.e. endoscope through an abdominal incision) was the most effective at identifying shovelnose sturgeon gender. In most cases, success rate for identifying males was greater than females, with success at identifying both genders greater in more advanced reproductive stages. Concomitantly, for most months average reproductive stage was more advanced for males than females. April and May were the months with the most advanced reproductive stage, and were the months when ultrasound was most effective. Methods were also applied in the Upper Missouri River to validate their use on pallid sturgeon Scaphirhynchus albus. Ultrasound was successful at identifying pallid sturgeon gender, however, endoscopic examination through the urogenital duct was only successful at identifying pallid sturgeon gender when the urogenital duct was not opaque. ?? 2005 The Fisheries Society of the British Isles.

  5. A revision of the Rutilus complex from Mediterranean Europe with description of a new genus, Sarmarutilus, and a new species, Rutilus stoumboudae (Teleostei: Cyprinidae).

    PubMed

    Bianco, Pier Giorgio; Ketmaier, Valerio

    2014-01-01

    By combining morphology, ecology, biology, and biogeography with the available molecular (sequence variation of the entire mitochondrial cytochrome b gene; cyt-b) and karyology data, the taxonomy of several species of the Rutilus complex inhabiting southern Europe is revised. Rutilus stoumboudae, new species, is described from Lake Volvi, Greece. It differs from Rutilus rutilus in possessing more total GR and less branched rays in both dorsal and anal fins and in its placement in the cyt-b based phylogeny of the genus. The resurrected genus Leucos Heckel, 1843 (type species Leucos aula, Bonaparte, 1841), which according to molecular data diverged from Rutilus more than 5 million years ago, during the Messinian salinity crisis, includes five species of small size, without spinous tubercles on scales and head in reproductive males, pharyngeal teeth formula 5-5, and all show a preference for still waters. Leucos aula is the Italian species endemic in the Padany-Venetian district: L. basak is widespread in Croatia, Albania, Montenegro and former Yugoslav Republic of Macedonia (FYROM); L. albus, recently described from Lake Skadar, Montenegro, is also found in rivers Moraca and Zeta (Montenegro). L. albus differs from L. basak, its closest relative, in having more scales on the LL and less anal-fin rays; L. panosi is endemic to the western-Greece district, and L. ylikiensis is endemic to lakes Yliki and Paralimni in eastern Greece (introduced in Lake Volvi). Among the nominal species examined, Rutilus karamani, R. ohridanus, R. prespensis and R. prespensis vukovici are all junior synonyms of Leucos basak. Rutilus vegariticus is definitively regarded as junior synonym for R. rutilus. Sarmarutilus n.gen. is a monotypic genus, with Sarmarutilus rubilio as the type species. According to phylogenetic data, Sarmarutilus rubilio is basal to a cluster of species that includes Leucos basak, L. albus, L. aula, L. panosi and L. ylikiensis. Sarmarutilus possibly evolved in pre

  6. Glycocaulis alkaliphilus sp. nov., a dimorphic prosthecate bacterium isolated from crude oil.

    PubMed

    Geng, Shuang; Pan, Xin-Chi; Mei, Ran; Wang, Ya-Nan; Liu, Xue-Ying; Wang, Xing-Biao; Tang, Yue-Qin; Wu, Xiao-Lei

    2015-03-01

    A bacterial strain designated 6B-8(T) was isolated from crude oil from Daqing oilfield, China. Cells of strain 6B-8(T) were Gram-negative, aerobic, dimorphic and reproduced by means of binary fission. Strain 6B-8(T) could grow at 20-37 °C, pH 8-10 and 1-5 % (w/v) NaCl. Its genomic DNA G+C content was 62.0 mol%. The predominant cellular fatty acids were C18 : 1ω7c, C17 : 0, C18 : 0 and 11-methyl C18 : 1ω7c and the main hydroxy fatty acids were C12 : 0 3-OH and C12 : 1 3-OH when grown on marine agar 2216. The major quinone was Q-10 and the major polar lipids were three unidentified glycolipids. Phylogenetic analysis revealed that strain 6B-8(T) was a member of the family Hyphomonadaceae, sharing 99.6 and 99.4 % 16S rRNA gene sequence similarity with Glycocaulis abyssi LMG 27140(T) and Glycocaulis albus SLG210-30A1(T), respectively, and less than 94.4 % similarity with the type strains of other members of the family Hyphomonadaceae. However, the DNA-DNA relatedness between strain 6B-8(T) and related strains G. abyssi LMG 27140(T) and G. albus SLG210-30A1(T) was 36±5 and 42±5 %, respectively. In addition, several phenotypic and genotypic features allowed differentiation of strain 6B-8(T) from G. abyssi LMG 27140(T) and G. albus SLG210-30A1(T). Therefore, strain 6B-8(T) represents a novel species of genus Glycocaulis, for which the name Glycocaulis alkaliphilus sp. nov. is proposed. The type strain is 6B-8(T) ( = CGMCC 1.12428(T) = LMG 27410(T)). PMID:25500458

  7. Determination of hatching date for eggs of black-crowned night-herons, snowy egrets and great egrets

    USGS Publications Warehouse

    Custer, T.W.; Pendleton, G.W.; Roach, R.W.

    1992-01-01

    Floatation of eggs in water and specific gravity of eggs of Black-crowned Night-Herons (Nycticorax nycticorax ), Snowy Egrets (Egretta thula ) and Great Egrets (Casmerodius albus ) were evaluated as methods to determine date of hatching. Although specific gravity was a better predictor of hatching date than egg flotation, both techniques were imprecise. The regression between specific gravity and the number of days before hatching differed among clutches, but not among eggs within clutches. Specific gravity of eggs predicted hatching date only to within 3.8 d for Snowy Egrets, and 4.7 d for Black-crowned Night-Herons and Great Egrets. The mean incubation period was 27.3 d for Great Egrets, 23.7 d for Snowy Egrets and 22.8 d for Black-crowned Night- Herons. For all three species, the A egg (first egg laid) had a longer incubation period than the B or C egg.

  8. Molecular basis for chloronium-mediated meroterpene cyclization: cloning, sequencing, and heterologous expression of the napyradiomycin biosynthetic gene cluster.

    PubMed

    Winter, Jaclyn M; Moffitt, Michelle C; Zazopoulos, Emmanuel; McAlpine, James B; Dorrestein, Pieter C; Moore, Bradley S

    2007-06-01

    Structural inspection of the bacterial meroterpenoid antibiotics belonging to the napyradiomycin family of chlorinated dihydroquinones suggests that the biosynthetic cyclization of their terpenoid subunits is initiated via a chloronium ion. The vanadium-dependent haloperoxidases that catalyze such reactions are distributed in fungi and marine algae and have yet to be characterized from bacteria. The cloning and sequence analysis of the 43-kb napyradiomycin biosynthetic cluster (nap) from Streptomyces aculeolatus NRRL 18422 and from the undescribed marine sediment-derived Streptomyces sp. CNQ-525 revealed 33 open reading frames, three of which putatively encode vanadium-dependent chloroperoxidases. Heterologous expression of the CNQ-525-based nap biosynthetic cluster in Streptomyces albus produced at least seven napyradiomycins, including the new analog 2-deschloro-2-hydroxy-A80915C. These data not only revealed the molecular basis behind the biosynthesis of these novel meroterpenoid natural products but also resulted in the first in vivo verification of vanadium-dependent haloperoxidases.

  9. Three new genera and three new species of Nearctic Lasiopteridi (Diptera: Cecidomyiidae: Cecidomyiinae) from Asteraceae and Caprifoliaceae, and the tribe Rhopalomyiini subsumed under Oligotrophini.

    PubMed

    Gagné, Raymond J

    2016-01-01

    Three new Nearctic genera of gall midges (Diptera: Cecidomyiidae), each with a new species, are described: Helianthecis Gagné for Helianthecis capitum Gagné, new species, that lives in flower heads of Helianthus spp. (Asteraceae) from North Dakota to Texas; Lonicerae Gagné for Lonicerae russoi Gagné, new species, and Lonicerae lonicera (Felt), new combination, that form bud galls on Lonicera spp. (Caprifoliaceae) in California; and Chiosperma Gagné for Chiosperma turgidum Gagné, new species, that forms a bud gall on Symphoricarpos albus (L.) S.F. Blake (Caprifoliaceae) in Washington. The three new genera belong to the supertribe Lasiopteridi and are placed in the tribe Oligotrophini. The tribes Oligotrophini and Rhopalomyiini are combined. PMID:27615893

  10. Organization, structure and symbiotic function of Rhizobium meliloti nodulation genes determining host specificity for alfalfa.

    PubMed

    Horvath, B; Kondorosi, E; John, M; Schmidt, J; Török, I; Györgypal, Z; Barabas, I; Wieneke, U; Schell, J; Kondorosi, A

    1986-08-01

    In R. meliloti we have identified four nodulation genes determining plant host-range specificity and have designated them hsnABC and D. The genes code for 9.7, 41.7, 26.7, and 28.6 kd proteins, respectively, and are organized into two transcriptional units. Mutations in these genes affect nodulation of their natural plant hosts Medicago sativa and Melilotus albus to different extents and hsnD mutants have an altered host-range. These Nod- mutations are not complementable by nodulation genes of other Rhizobium species such as R. leguminosarum. The hsn genes determine plant-specific infection through root hairs: hsnD is required for host-specific root hair curling and nodule initiation while the hsnABC genes control infection thread growth from the root hairs.

  11. Proteomic characterization of seeds from yellow lupin (Lupinus luteus L.).

    PubMed

    Ogura, Takahiro; Ogihara, Jun; Sunairi, Michio; Takeishi, Hidetaka; Aizawa, Tomoko; Olivos-Trujillo, Marcos R; Maureira-Butler, Iván J; Salvo-Garrido, Haroldo E

    2014-06-01

    Yellow lupin (Lupinus luteus L.) is a legume crop containing a large amount of protein in its seeds. In this study, we constructed a seed-protein catalog to provide a foundation for further study of the seeds. A total of 736 proteins were identified in 341 2DE spots by nano-LC-MS/MS. Eight storage proteins were found as multiple spots in the 2DE gels. The 736 proteins correspond to 152 unique proteins as shown by UniRef50 clustering. Sixty-seven of the 152 proteins were associated with KEGG-defined pathways. Of the remaining proteins, 57 were classified according to a GO term. The functions of the remaining 28 proteins have yet to be determined. This is the first yellow lupin seed-protein catalog, and it contains considerably more data than previously reported for white lupin (L. albus L.).

  12. Brain cholinesterase activity of nestling great egrets, snowy egrets, and black-crowned night-herons

    USGS Publications Warehouse

    Custer, T.W.; Ohlendorf, H.M.

    1989-01-01

    Inhibition of brain cholinesterase (ChE) activity in birds is often used to diagnose exposure or death from organophosphorus or carbmate pesticides. Brain ChE activity in the young of altricial species increase with age; however, this relationship has only been demonstrated in the European starling (Sturnus vulgaris). Brain ChE activity of nestling great egrets (Casmerodius albus) collected from a colony in Texas increased significantly with age and did not differ among individuals from different nests. Brain ChE activity of nestling snowy egrets (Egretta thula) and black-crowned night -herons (Nycticorax nycticorax) collected in one colony each from Rhode Island, Texas, and California also increased significantly with age and did not differ among individuals from different nests or colonies. This study further demonstrates that age must be considered when evaluating exposure of nestling altricial birds to ChE inhibitors.

  13. Brain cholinesterase activity of nestling great egrets snowy egrets and black-crowned night-herons

    USGS Publications Warehouse

    Custer, T.W.; Ohlendorf, H.M.

    1989-01-01

    Inhibition of brain cholinesterase (ChE) activity in birds is often used to diagnose exposure or death from organophosphorus or carbamate pesticides. Brain ChE activity in the young of altricial species increases with age; however, this relationship has only been demonstrated in the European starling (Sturnus vulgaris). Brain ChE activity of nestling great egrets (Casmerodius albus) collected from a colony in Texas (USA) increased significantly with age and did not differ among individuals from different nests. Brain ChE activity of nestling snowy egrets (Egretta thula) and black-crowned night-herons (Nycticorax nycticorax) collected in one colony each from Rhode Island, Texas and California (USA) also increased significantly with age and did not differ among individuals from different nests or colonies. This study further demonstrates that age must be considered when evaluating exposure of nestling altricial birds to ChE inhibitors.

  14. Natural Product Discovery through Improved Functional Metagenomics in Streptomyces.

    PubMed

    Iqbal, Hala A; Low-Beinart, Lila; Obiajulu, Joseph U; Brady, Sean F

    2016-08-01

    Because the majority of environmental bacteria are not easily culturable, access to many bacterially encoded secondary metabolites will be dependent on the development of improved functional metagenomic screening methods. In this study, we examined a collection of diverse Streptomyces species for the best innate ability to heterologously express biosynthetic gene clusters. We then optimized methods for constructing high quality metagenomic cosmid libraries in the best Streptomyces host. An initial screen of a 1.5 million-membered metagenomic library constructed in Streptomyces albus, the species that exhibited the highest propensity for heterologous expression of gene clusters, led to the identification of the novel natural product metatricycloene (1). Metatricycloene is a tricyclic polyene encoded by a reductive, iterative polyketide-like gene cluster. Related gene clusters found in sequenced genomes appear to encode a largely unexplored collection of structurally diverse, polyene-based metabolites. PMID:27447056

  15. Brain cholinesterase activity of nestling great egrets, snowy egrets and black-crowned night-herons.

    PubMed

    Custer, T W; Ohlendorf, H M

    1989-07-01

    inhibition of brain cholinesterase (ChE) activity in birds is often used to diagnose exposure or death from organophosphorus or carbamate pesticides. Brain ChE activity in the young of altricial species increases with age; however, this relationship has only been demonstrated in the European starling (Sturnus vulgaris). Brain ChE activity of nestling great egrets (Casmerodius albus) collected from a colony in Texas (USA) increased significantly with age and did not differ among individuals from different nests. Brain ChE activity of nestling snowy egrets (Egretta thula) and black-crowned night-herons (Nycticorax nycticorax) collected in one colony each from Rhode Island, Texas and California (USA) also increased significantly with age and did not differ among individuals from different nests or colonies. This study further demonstrates that age must be considered when evaluating exposure of nestling altricial birds to ChE inhibitors.

  16. Carbofuran poisoning in herons: diagnosis using cholinesterase reactivation techniques.

    PubMed

    Hunt, K A; Hooper, M J; Littrell, E E

    1995-04-01

    Exposure to the carbamate insecticide carbofuran was detected using brain cholinesterase (ChE) reactivation techniques in heron carcasses collected from a potential pesticide exposure incident. Great egrets (Nycticorax nycticorax), great blue herons (Ardea herodias), and black-crowned night herons (Casmerodius albus) were exposed to carbofuran (2,3-dihydro-2,2-dimethyl-7-benzofuranyl methylcarbamate) either by dermal exposure while wading or through ingestion of contaminated food items. Carcasses may have been in the field up to 5 days prior to collection. Brain ChE, substantially inhibited in most samples, increased 7.9-208% in the reactivation assay after 4 to 96 hours at 37 C, providing evidence of exposure to a carbamate pesticide. Crayfish (Procambarus clarkii) identified in the crops of some herons contained carbofuran residues of up to 0.6 parts per million wet weight, providing additional evidence of exposure. Reactivated brain ChE in several samples approached the range of control values.

  17. Chirostylidae of Australia's western continental margin (Crustacea : Decapoda: Anomura), with the description of five new species.

    PubMed

    Mccallum, Anna W; Poore, Gary C B

    2013-01-01

    Five new species from the squat lobster family Chirostylidae are described from the continental margin of western Australia: Uroptychus albus sp. nov., Uroptychus bardi sp. nov., Uroptychus jawi sp. nov., Uroptychus taylorae sp. nov., and Uroptychus worrorra sp. nov. New records of Indo-West Pacific species for Australia are: Gastroptychus brachyterus Baba, 2005, Gastroptychus investigatoris Alcock, 1899, Uroptychodes grandirostris (Yokoya, 1933), Uroptychodes inortenseni (Van Dam, 1939), Uroptychus scandens Benedict, 1902, Uroptychus ciliatus (Van Dam, 1933) and Uroptychus vandamae Baba, 1988. New distributional records are given for species previously recorded from Australia: Uroptychus flindersi Ahyong & Poore, 2004, Uroptychus hesperius Ahyong & Poore, 2004, Uroptychusjoloensis Van Dam, 1939, Uroptychus nigricapillis Alcock, 1901, and Uroptychus spinirostris (Ahyong & Poore, 2004). These new records expand the number of chirostylid species in Australia from 34 to 46. Keys to Australian species of the genera Gastroptychus, Uroptychodes and Uroptychus are provided. PMID:26266295

  18. Chirostylidae of Australia's western continental margin (Crustacea : Decapoda: Anomura), with the description of five new species.

    PubMed

    Mccallum, Anna W; Poore, Gary C B

    2013-01-01

    Five new species from the squat lobster family Chirostylidae are described from the continental margin of western Australia: Uroptychus albus sp. nov., Uroptychus bardi sp. nov., Uroptychus jawi sp. nov., Uroptychus taylorae sp. nov., and Uroptychus worrorra sp. nov. New records of Indo-West Pacific species for Australia are: Gastroptychus brachyterus Baba, 2005, Gastroptychus investigatoris Alcock, 1899, Uroptychodes grandirostris (Yokoya, 1933), Uroptychodes inortenseni (Van Dam, 1939), Uroptychus scandens Benedict, 1902, Uroptychus ciliatus (Van Dam, 1933) and Uroptychus vandamae Baba, 1988. New distributional records are given for species previously recorded from Australia: Uroptychus flindersi Ahyong & Poore, 2004, Uroptychus hesperius Ahyong & Poore, 2004, Uroptychusjoloensis Van Dam, 1939, Uroptychus nigricapillis Alcock, 1901, and Uroptychus spinirostris (Ahyong & Poore, 2004). These new records expand the number of chirostylid species in Australia from 34 to 46. Keys to Australian species of the genera Gastroptychus, Uroptychodes and Uroptychus are provided.

  19. Exploiting composting biodiversity: study of the persistent and biotechnologically relevant microorganisms from lignocellulose-based composting.

    PubMed

    Jurado, Macarena; López, María J; Suárez-Estrella, Francisca; Vargas-García, María C; López-González, Juan A; Moreno, Joaquín

    2014-06-01

    The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. This work analyzes the identity of microbial community that persists throughout lignocellulose-based composting, evaluates their metabolic activities and studies the capability of selected isolates for composting bioaugmentation. Bacterial species of the phyla Firmicutes, Actinobacteria and Proteobacteria and fungi of the phylum Ascomycota were ubiquitous throughout the composting. The species Arthrobacter russicus, Microbacterium gubbeenense, Ochrocladosporium frigidarii and Cladosporium lignicola are detected for the first time in this ecosystem. In addition, several bacterial and fungal isolates exhibited a wide range of metabolic capabilities such as polymers (lignocellulose, protein, lipids, pectin and starch) breakdown and phosphate-solubilization that may find many biotechnological applications. In particular, Streptomyces albus BM292, Gibellulopsis nigrescens FM1397 and FM1411, Bacillus licheniformis BT575, Bacillus smithii AT907 and Alternaria tenuissima FM1385 exhibited a great potential as inoculants for composting bioaugmentation.

  20. Physical and hormonal examination of Missouri River shovelnose sturgeon reproductive stage: A reference guide

    USGS Publications Warehouse

    Wildhaber, M.L.; Papoulias, D.M.; DeLonay, A.J.; Tillitt, D.E.; Bryan, J.L.; Annis, M.L.

    2007-01-01

    From May 2001 to June 2002 Wildhaber et al. (2005) conducted monthly sampling of Lower Missouri River shovelnose sturgeon (Scaphirhynchus platorynchus) to develop methods for determination of sex and the reproductive stage of sturgeons in the field. Shovelnose sturgeon were collected from the Missouri River and ultrasonic and endoscopic imagery and blood and gonadal tissue samples were taken. The full set of data was used to develop monthly reproductive stage profiles for S. platorynchus that could be compared to data collected on pallid sturgeon (Scaphirhynchus albus). This paper presents a comprehensive reference set of images, sex steroids, and vitellogenin (VTG, an egg protein precursor) data for assessing shovelnose sturgeon sex and reproductive stage. This reference set includes ultrasonic, endoscopic, histologic, and internal images of male and female gonads of shovelnose sturgeon at each reproductive stage along with complementary data on average 17-?? estradiol, 11-ketotestosterone, VTG, gonadosomatic index, and polarization index. ?? 2007 Blackwell Verlag.

  1. Genetic factors that influence moenomycin production in streptomycetes

    PubMed Central

    Makitrynskyy, Roman; Rebets, Yuriy; Ostash, Bohdan; Zaburannyi, Nestor; Rabyk, Mariia; Walker, Suzanne; Fedorenko, Victor

    2010-01-01

    Moenomycin, a natural phosphoglycolipid product that has long history of use in animal nutrition, is currently considered attractive starting point for the development of novel antibiotics. We recently reconstituted the biosynthesis of this natural product in a heterologous host, Streptomyces lividans TK24, but production levels were too low to be useful. We have examined several other streptomycetes strains as hosts and have also explored the overexpression of two pleiotropic regulatory genes, afsS and relA, on moenomycin production. A moenomycin-resistant derivative of S. albus J1074 was found to give the highest titers of moenomycin and production was improved by overexpressing relA. Partial duplication of moe cluster 1 in S. ghanaensis also increased average moenomycin production. The results reported here suggest that rational manipulations of global regulators combined with increased moe gene dosage could be a useful for improvement of moenomycin biosynthesis. PMID:20204454

  2. Genetic factors that influence moenomycin production in streptomycetes.

    PubMed

    Makitrynskyy, Roman; Rebets, Yuriy; Ostash, Bohdan; Zaburannyi, Nestor; Rabyk, Mariia; Walker, Suzanne; Fedorenko, Victor

    2010-06-01

    Moenomycin, a natural phosphoglycolipid product that has a long history of use in animal nutrition, is currently considered an attractive starting point for the development of novel antibiotics. We recently reconstituted the biosynthesis of this natural product in a heterologous host, Streptomyces lividans TK24, but production levels were too low to be useful. We have examined several other streptomycetes strains as hosts and have also explored the overexpression of two pleiotropic regulatory genes, afsS and relA, on moenomycin production. A moenomycin-resistant derivative of S. albus J1074 was found to give the highest titers of moenomycin, and production was improved by overexpressing relA. Partial duplication of the moe cluster 1 in S. ghanaensis also increased average moenomycin production. The results reported here suggest that rational manipulation of global regulators combined with increased moe gene dosage could be a useful technique for improvement of moenomycin biosynthesis.

  3. [Development of a high content protein beverage from Chilean mesquite, lupine and quinoa for the diet of pre-schoolers].

    PubMed

    Cerezal Mezquita, P; Acosta Barrientos, E; Rojas Valdivia, G; Romero Palacios, N; Arcos Zavala, R

    2012-01-01

    This research was aimed at developing a high content protein beverage from the mixture of liquid extracts of a pseudocereal, quinoa (Chenopodium quinoa Willd) and two legumes: mesquite (Prosopis chilensis (Mol.) Stunz) and lupine (Lupinus albus L.), native from the Andean highlands of the Chilean northern macro-zone, flavored with raspberry pulp, to help in the feeding of children between 2 and 5 years of lower socioeconomic status with nutritional deficiencies. The formulation was defined by linear programming, its composition was determined by proximate analysis and physical, microbiological and sensory acceptance tests were performed. After 90 days of storage time, the beverage got a protein content of 1.36%, being tryptophan the limiting amino acid; for its part, the chromaticity coordinates of CIEL*a*b* color space showed no statistical significant differences (p < 0.05) maintaining the "dark pink" tonality, the viscosity and the sensory evaluation were acceptable for drinking.

  4. A new jumping spider of the genus Stenaelurillus Simon, 1886 from India (Araneae: Salticidae: Aelurillina).

    PubMed

    Caleb, John T D; Mathai, Manu Thomas

    2016-01-01

    The genus Stenaelurillus Simon, 1886 is known from 35 species worldwide, including 27 species from Africa and eight from Asia (four species known from India, one from Iran, one from China, one from Tibet and one from Vietnam) (World Spider Catalog 2016). The four species known from India are S. albus Sebastian et al., 2015, S. jagannathae Das, Malik & Vidhel, 2015, S. lesserti Reimoser, 1934 and S. sarojinae Caleb & Mathai, 2014 (Prószyński 2015; World Spider Catalog 2016). The present paper contains description of Stenaelurillus metallicus sp. nov., discovered from scrub jungle remnants of tropical dry evergreen forests, a unique habitat found in Madras Christian College campus, Chennai, Tamil Nadu, India. PMID:27394630

  5. Genomic characterization and taxonomic position of a rhabdovirus from a hybrid snakehead.

    PubMed

    Zeng, Weiwei; Wang, Qing; Wang, Yingying; Liu, Cun; Liang, Hongru; Fang, Xiang; Wu, Shuqin

    2014-09-01

    A new rhabdovirus, tentatively designated as hybrid snakehead rhabdovirus C1207 (HSHRV-C1207), was first isolated from a moribund hybrid snakehead (Channa maculata×Channa argus) in China. We present the complete genome sequence of HSHRV-C1207 and a comprehensive sequence comparison between HSHRV-C1207 and other rhabdoviruses. Sequence alignment and phylogenetic analysis revealed that HSHRV-C1207 shared the highest degree of homology with Monopterus albus rhabdovirus and Siniperca chuatsi rhabdovirus. All three viruses clustered into a single group that was distinct from the recognized genera in the family Rhabdoviridae. Our analysis suggests that HSHRV-C1207, as well as MARV and SCRV, should be assigned to a new rhabdovirus genus.

  6. Identifying structural elements needed for development of a predictive life-history model for pallid and shovelnose sturgeons

    USGS Publications Warehouse

    Wildhaber, Mark L.; DeLonay, A.J.; Papoulias, D.M.; Galat, D.L.; Jacobson, R.B.; Simpkins, D.G.; Braaten, P.J.; Korschgen, C.E.; Mac, M.J.

    2011-01-01

    Intensive management of the Missouri and Mississippi Rivers has resulted in dramatic changes to the river systems and their biota. These changes have been implicated in the decline of the pallid sturgeon (Scaphirhynchus albus), which has been listed as a United States federal endangered species. The sympatric shovelnose sturgeon (S. platorynchus) is more common and widespread but has also been in decline. The decline of pallid sturgeon is considered symptomatic of poor reproductive success and low or no recruitment. In order to organize information about these species and provide a basis for future development of a predictive model to help guide recovery efforts, we present an expert-vetted, conceptual life-history framework that incorporates the factors that affect reproduction, growth, and survival of shovelnose and pallid sturgeons.

  7. Physical Aquatic Habitat Assessment, Fort Randall Segment of the Missouri River, Nebraska and South Dakota

    USGS Publications Warehouse

    Elliott, Caroline M.; Jacobson, Robert B.; DeLonay, Aaron J.

    2004-01-01

    This study addressed habitat availability and use by endangered pallid sturgeon (Scaphirhynchus albus) in the Fort Randall segment of the Missouri River. Physical aquatic habitat - depth, velocity, and substrate - was mapped in 15 sites in Augsust and October of 2002. Habitat assessments were compared with fish locations using radio telemetry. Results indicate that pallid sturgeon preferentially use locations in the Fort Randall segment deeper than the average available habitat, with prominent usage peaks aat 3.5-4.0 m and 6-6.5 m, compared to the modal availability at 3-3.5 m. The fish use habitats with a modal velocity of 80 cm/s; the used velocities appear to be in proportion to their availability. Fish located preferentially over sand substrate and seemed to avoid mud and submerged vegetation.

  8. Cloning and Heterologous Expression of the Grecocycline Biosynthetic Gene Cluster

    PubMed Central

    Bilyk, Oksana; Sekurova, Olga N.; Zotchev, Sergey B.; Luzhetskyy, Andriy

    2016-01-01

    Transformation-associated recombination (TAR) in yeast is a rapid and inexpensive method for cloning and assembly of large DNA fragments, which relies on natural homologous recombination. Two vectors, based on p15a and F-factor replicons that can be maintained in yeast, E. coli and streptomycetes have been constructed. These vectors have been successfully employed for assembly of the grecocycline biosynthetic gene cluster from Streptomyces sp. Acta 1362. Fragments of the cluster were obtained by PCR and transformed together with the “capture” vector into the yeast cells, yielding a construct carrying the entire gene cluster. The obtained construct was heterologously expressed in S. albus J1074, yielding several grecocycline congeners. Grecocyclines have unique structural moieties such as a dissacharide side chain, an additional amino sugar at the C-5 position and a thiol group. Enzymes from this pathway may be used for the derivatization of known active angucyclines in order to improve their desired biological properties. PMID:27410036

  9. A microbiological study of bottled mineral water marketed in Ludhiana.

    PubMed

    Lal, M; Kaur, H

    2006-01-01

    The microbiological quality of bottled mineral water marketed in Ludhiana was examined, Twenty three brands were analyzed for presumptive coliform count by multiple tube tests, and E. coli count was confirmed by Eijkman test. Bacterial and fungal loads were tested by membrane filtration test. Out of 23 only one sample (4.4%) showed the presumptive coliform count to be 460 most probable number (MPN)l 1 00ml,and 1 was found to be positive when tested by Eijkman test for Ecoli. In the membrane filtration test three samples (13%) showed more than two types of bacteria. Different types of bacteria isolated included Bacillus sp (19/23). Pseudomonas spp (13123), Ecoli, Klebsiella sp and S.albus one each Fungi was isolated from five of twenty three. (22%) samples. Only one brand of mineral water was unfit for human consumption. The rest of the samples were contaminated with non pathogenic flora. PMID:17193757

  10. Detectability of lupine seeds by ELISA and PCR may be strongly influenced by potential differences between cultivars.

    PubMed

    Röder, Martin; Kleiner, Kornelia; Sachs, Andrea; Keil, Nicole; Holzhauser, Thomas

    2013-06-26

    Accurate methods for allergen detection are needed for the verification of allergen labeling and the avoidance of hidden allergens. But systematic data on the influence of different cultivars of allergenic crop species on their detectability in enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) are lacking. As one example, seeds of 14 different cultivars of lupine (Lupinus albus, Lupinus angustifolius, Lupinus luteus) were investigated for total protein according to a Kjeldahl method, and for their relative quantitative detectability in three commercial lupine-specific ELISA tests and four lupine-specific PCR methods. Total Kjeldahl nitrogen allowed an accurate quantification of total protein. Relative differences in quantitative response between cultivars of 390-5050% and 480-13,600% were observed between ELISA kits and PCR methods, respectively. Hence, quantitative results of selected ELISA and PCR methods may be strongly influenced by the examined lupine cultivar.

  11. Upper boundary of the biosphere.

    PubMed Central

    Imshenetsky, A A; Lysenko, S V; Kazakov, G A

    1978-01-01

    By using meterological rockets fitted with specially designed analyzers, samples for microbiological investigation have been taken. The analyzer design prevented extraneous microorganisms from penetrating into the analyzer. Before being used, the analyzers were sterilized with high gamma-ray doses. For the first time microorganisms have been detected in the mesosphere at an altitude of 48 to 77 km. The microorganisms are microscopic fungi having black conidia or spores (Circinella muscae, Aspergillus niger, Papulaspora anomala) and one species forming green conidia (Penicillium notatum). Colonies of Mycobacterium luteum and Micrococcus albus have also grown. Five of the six species have synthesized pigments. The presence of pigmented microbial forms leads us to believe that natural selection is occurring in the mesosphere because cells possessing chromogenous pigments (carotenoids, melanins) are more resistant to ultraviolet-ray action. A greater number of microorganisms have been registered in the mesosphere during dust storms than in the absence of strong winds. Images PMID:623455

  12. Cloning and Heterologous Expression of the Grecocycline Biosynthetic Gene Cluster.

    PubMed

    Bilyk, Oksana; Sekurova, Olga N; Zotchev, Sergey B; Luzhetskyy, Andriy

    2016-01-01

    Transformation-associated recombination (TAR) in yeast is a rapid and inexpensive method for cloning and assembly of large DNA fragments, which relies on natural homologous recombination. Two vectors, based on p15a and F-factor replicons that can be maintained in yeast, E. coli and streptomycetes have been constructed. These vectors have been successfully employed for assembly of the grecocycline biosynthetic gene cluster from Streptomyces sp. Acta 1362. Fragments of the cluster were obtained by PCR and transformed together with the "capture" vector into the yeast cells, yielding a construct carrying the entire gene cluster. The obtained construct was heterologously expressed in S. albus J1074, yielding several grecocycline congeners. Grecocyclines have unique structural moieties such as a dissacharide side chain, an additional amino sugar at the C-5 position and a thiol group. Enzymes from this pathway may be used for the derivatization of known active angucyclines in order to improve their desired biological properties. PMID:27410036

  13. A microbiological study of bottled mineral water marketed in Ludhiana.

    PubMed

    Lal, M; Kaur, H

    2006-01-01

    The microbiological quality of bottled mineral water marketed in Ludhiana was examined, Twenty three brands were analyzed for presumptive coliform count by multiple tube tests, and E. coli count was confirmed by Eijkman test. Bacterial and fungal loads were tested by membrane filtration test. Out of 23 only one sample (4.4%) showed the presumptive coliform count to be 460 most probable number (MPN)l 1 00ml,and 1 was found to be positive when tested by Eijkman test for Ecoli. In the membrane filtration test three samples (13%) showed more than two types of bacteria. Different types of bacteria isolated included Bacillus sp (19/23). Pseudomonas spp (13123), Ecoli, Klebsiella sp and S.albus one each Fungi was isolated from five of twenty three. (22%) samples. Only one brand of mineral water was unfit for human consumption. The rest of the samples were contaminated with non pathogenic flora.

  14. Identification and analysis of the paulomycin biosynthetic gene cluster and titer improvement of the paulomycins in Streptomyces paulus NRRL 8115.

    PubMed

    Li, Jine; Xie, Zhoujie; Wang, Min; Ai, Guomin; Chen, Yihua

    2015-01-01

    The paulomycins are a group of glycosylated compounds featuring a unique paulic acid moiety. To locate their biosynthetic gene clusters, the genomes of two paulomycin producers, Streptomyces paulus NRRL 8115 and Streptomyces sp. YN86, were sequenced. The paulomycin biosynthetic gene clusters were defined by comparative analyses of the two genomes together with the genome of the third paulomycin producer Streptomyces albus J1074. Subsequently, the identity of the paulomycin biosynthetic gene cluster was confirmed by inactivation of two genes involved in biosynthesis of the paulomycose branched chain (pau11) and the ring A moiety (pau18) in Streptomyces paulus NRRL 8115. After determining the gene cluster boundaries, a convergent biosynthetic model was proposed for paulomycin based on the deduced functions of the pau genes. Finally, a paulomycin high-producing strain was constructed by expressing an activator-encoding gene (pau13) in S. paulus, setting the stage for future investigations. PMID:25822496

  15. Inhibition of Vibrio biofilm formation by a marine actinomycete strain A66.

    PubMed

    You, JianLan; Xue, XiaoLi; Cao, LiXiang; Lu, Xin; Wang, Jian; Zhang, LiXin; Zhou, ShiNing

    2007-10-01

    China remains by far the largest aquaculture producer in the world. However, biofilms formed by pathogenic Vibrio strains pose serious problems to marine aquaculture. To provide a strategy for biofilm prevention, control, and eradication, extracts from 88 marine actinomycetes were screened. Thirty-five inhibited the biofilm formation of Vibrio harveyi, Vibrio vulnificus, and Vibrio anguillarum at a concentration of 2.5% (v/v). Thirty-three of the actinomycete extracts dispersed the mature biofilm. Six extracts inhibited the quorum-sensing system of V. harveyi by attenuating the signal molecules N-acylated homoserine lactones' activity. Strain A66, which was identified as Streptomyces albus, both attenuated the biofilms and inhibited their quorum-sensing system. It is suggested that strain A66 is a promising candidate to be used in future marine aquaculture. PMID:17624525

  16. A new species of Dentiphilometra (Nematoda: Philometridae) from the musculature of the gray snapper Lutjanus griseus (osteichthyes) off the Caribbean coast of Mexico.

    PubMed

    González-Solís, David; Moravec, Frantisek; Paredes, Vielka M Tuz

    2007-10-01

    A new nematode, Dentiphilometra lutjani n. sp. (Philometridae), is described from gravid females (the male is unknown) collected from the body musculature of the marine perciform fish gray snapper, Lutjanus griseus (Lutjanidae), from the Bay of Chetumal and southern coast of Quintana Roo, off the Caribbean coast of Mexico. The new species differs from the only other congener, Dentiphilometra monopteri, from the swamp eel Monopterus albus in China, mainly in the body length of gravid female (15.40-53.21 mm), the shape of the posterior body end (not markedly narrowed, with low caudal projections), the esophageal gland (maximum width near its posterior end), and the length (344-483 microm) of larvae from the uterus; both species also differ in their host types (marine perciform fish vs. freshwater swamp eel) and geographical distribution (Mexico vs. China).

  17. Nylon Filter Arrays Reveal Differential Gene Expression in Proteoid Roots of White Lupin in Response to Phosphorus Deficiency

    PubMed Central

    Uhde-Stone, Claudia; Zinn, Kelly E.; Ramirez-Yáñez, Mario; Li, Aiguo; Vance, Carroll P.; Allan, Deborah L.

    2003-01-01

    White lupin (Lupinus albus) adapts to phosphorus deficiency (−P) by the development of short, densely clustered lateral roots called proteoid (or cluster) roots. In an effort to better understand the molecular events mediating these adaptive responses, we have isolated and sequenced 2,102 expressed sequence tags (ESTs) from cDNA libraries prepared with RNA isolated at different stages of proteoid root development. Determination of overlapping regions revealed 322 contigs (redundant copy transcripts) and 1,126 singletons (single-copy transcripts) that compile to a total of 1,448 unique genes (unigenes). Nylon filter arrays with these 2,102 ESTs from proteoid roots were performed to evaluate global aspects of gene expression in response to −P stress. ESTs differentially expressed in P-deficient proteoid roots compared with +P and −P normal roots include genes involved in carbon metabolism, secondary metabolism, P scavenging and remobilization, plant hormone metabolism, and signal transduction. PMID:12644659

  18. Structural Diversification of Lyngbyatoxin A by Host-Dependent Heterologous Expression of the tleABC Biosynthetic Gene Cluster.

    PubMed

    Zhang, Lihan; Hoshino, Shotaro; Awakawa, Takayoshi; Wakimoto, Toshiyuki; Abe, Ikuro

    2016-08-01

    Natural products have enormous structural diversity, yet little is known about how such diversity is achieved in nature. Here we report the structural diversification of a cyanotoxin-lyngbyatoxin A-and its biosynthetic intermediates by heterologous expression of the Streptomyces-derived tleABC biosynthetic gene cluster in three different Streptomyces hosts: S. lividans, S. albus, and S. avermitilis. Notably, the isolated lyngbyatoxin derivatives, including four new natural products, were biosynthesized by crosstalk between the heterologous tleABC gene cluster and the endogenous host enzymes. The simple strategy described here has expanded the structural diversity of lyngbyatoxin A and its biosynthetic intermediates, and provides opportunities for investigation of the currently underestimated hidden biosynthetic crosstalk.

  19. Conditional capture probability for Scaphirhynchus spp. in drifting trammel nets

    SciTech Connect

    Guy, Christopher S.; Oldenburg, Eric W.; Gerrity, Paul C.

    2009-06-01

    Pallid sturgeon Scaphirhynchus albus and shovelnose sturgeon Scaphirhynchus platorynchus are commonly sampled using drifting-trammel nets in the Missouri River basin. Despite that drifting trammel nets have been used for decades to sample these species, little is known about the capture efficiency of this gear. We estimated conditional capture probability and gear efficiency for drifting trammel nets. In addition we examined several abiotic variables that were assumed to influence the success of capturing a pallid sturgeon or shovelnose sturgeon in a drifting trammel net. Conditional capture probability varied from 0.36 on the first attempt to 0.50 on the second attempt. Drifting trammel nets are relatively efficient and we suggest that they continue to be used to sample in large turbid rivers. The high variability associated with sampling pallid sturgeon and shovelnose sturgeon using drifting trammel nets is likely related to low abundance and patchy distributions. Thus, we suggest using more appropriate sampling designs for rare species.

  20. Isocoumarin derivatives and benzofurans from a sponge-derived Penicillium sp. fungus.

    PubMed

    Qi, Jun; Shao, Chang-Lun; Li, Zhi-Yong; Gan, Li-She; Fu, Xiu-Mei; Bian, Wen-Tao; Zhao, Hong-Ying; Wang, Chang-Yun

    2013-04-26

    Ten new fungal metabolites, including three hydroisocoumarins, penicimarins A-C (1-3), three isocoumarins, penicimarins D-F (6-8), and four benzofurans, penicifurans A-D (11-14), together with four known isocoumarin derivatives (4, 5, 9, 10), were obtained from the sponge-derived fungus Penicillium sp. MWZ14-4, collected from the South China Sea. Their planar structures and relative configurations were elucidated by detailed analysis of spectroscopic data and by comparison with related known compounds. The absolute configurations of 1-4 were assigned by the modified Mosher's method and TDDFT ECD calculations together with comparison of their CD spectra. Compound 1 represents a rare naturally occurring isocoumarin derivative with 4-substitution, but no substituent at the 3-position. These compounds were evaluated for antibacterial activities and cytotoxic activities in vitro. Among them, penicifuran A (11) exhibited inhibitory activity against Staphylococcus albus with an MIC value of 3.13 μM.

  1. Chemical and plant tests to assess the viability of amendments to reduce metal availability in mine soils and tailings.

    PubMed

    Rodríguez, Luis; Gómez, Rocío; Sánchez, Virtudes; Alonso-Azcárate, Jacinto

    2016-04-01

    The goal of this research was to assess the potential of several industrial wastes to immobilise metals in two polluted soils deriving from an old Pb/Zn mine. Two different approaches were used to assess the performance of different amendments: a chemical one, using extraction by ethylenediaminetetraacetic acid (EDTA), and a biological one, using Lupinus albus as a bio-indicator. Four amendments were used: inorganic sugar production waste (named 'sugar foam', SF), sludge from a drinking water treatment sludge (DWS), organic waste from olive mill waste (OMW) and paper mill sludge (PMS). Amendment to soil ratios ranged from 0.1 to 0.3 (w/w). All the amendments were capable of significantly decreasing (p < 0.05) EDTA-extractable Pb, Zn and Cu concentrations in the two soils used, with decreases in ranges 21-100, 25-100 and 2-100 % for Pb, Zn and Cu, respectively. The amendments tested were also effective in reducing the bioavailability of Pb and Zn for L. albus, which gave rise to a decrease in shoot metal accumulation by the lupine plants compared to that found in the control soil. That decrease reached up to 5.6 and 2.8 times for Pb and Zn, respectively, being statistically significant in most cases. Moreover, application of the OMW, DWS and SF amendments led to higher average values of plant biomass (up to 71%) than those obtained in the control soil. The results obtained showed the technology put forward to be a viable means of remediating mine soils as it led to a decrease in the availability and toxicity of metals and, thus, facilitated the growth of a vegetation layer. PMID:25772873

  2. Influence of 3,4-dichloroaniline (3,4-DCA) on benthic invertebrates in indoor experimental streams.

    PubMed

    Schmitz, A; Nagel, R

    1995-02-01

    The influence of 3,4-dichloroaniline (3,4-DCA) on benthic invertebrates has been examined. Acute toxicity tests were carried out with the following species: Pristina longiseta, Aelosoma variegatum (Oligochaeta), Hydrozetes lacustris (Acarina), Planorbarius corneus, and Gyraulus albus (Planorbidae). LC50 values (96 hr) were obtained for Pri. longiseta (2.5 mg/liter) and for Hy. lacustris (4.7 mg/liter). For all other species ranges of toxicity (maximal concentration with 0% dead to minimum concentration with 100% dead) were determined. These ranges were 0.8-20 mg/liter 3,4-DCA for Pri. longiseta, 1.6-20 mg/liter, 3,4-DCA for Hy. lacustris, 10-20 mg/liter 3,4-DCA for G. albus, 50-100 mg/liter 3,4-DCA for Pl. corneus, and 10 mg/liter 3,4-DCA (maximal concentration with 0% dead; minimum concentration with 100% dead was not determined) for Ae. variegatum. In two experimental streams, the recolonization of benthic organisms into defined sample areas was studied. Therefore, a phase without chemical treatment was compared with a following exposure phase. Test concentrations were 0.2 and 1.4 mg/liter 3,4-DCA (nominal concentrations). Significant effects were the complete extinction of Pri. longiseta in 0.2 mg/liter 3,4-DCA within the first 3 weeks of exposure, as well as the reduction of immigrating individuals of another species of Pristina in both test concentrations, and of Hy. lacustris and Stentor sp. in 1.4 mg/liter 3,4-DCA.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7540538

  3. Morphometric variation among spawning cisco aggregations in the Laurentian Great Lakes: are historic forms still present?

    USGS Publications Warehouse

    Yule, Daniel L.; Moore, Seth A.; Ebener, Mark P.; Claramunt, Randall M.; Pratt, Thomas C.; Salawater, Lorrie L.; Connerton, Michael J.

    2013-01-01

    Cisco (Coregonus artedi Leseur, formerly lake herring Leucichthys artedi Leseur) populations in each of the Laurentian Great Lakes collapsed between the late 1920s and early 1960s following a multitude of stressors, and never recovered in Lakes Michigan, Erie and Ontario. Prior to their collapse, Koelz (1929) studied Leucichthys spp. in the Great Lakes basin and provided a description of their diversity. Three cisco morphotypes were described; a ‘slim terete’morphotype (L. artedi artedi), a ‘deep compressed’ morphotype (L. artedi albus), and a deep-bodied form resembling tullibee in western Canadian lakes (L. artedi manitoulinus). Based on body measurements of 159 individuals (Koelz 1929), we used discriminant function analysis (DFA) to discriminate historic morphotypes. Shapes of historic morphotypes were found to vary significantly (Pillai’s trace = 1.16, P < 0.0001). The final DFA model used nine body measurements and correctly classified 90% of the historic cisco. Important discriminating measurements included body depth, eye diameter, and dorsal fin base and height. Between October-November of 2007-2011, we sampled cisco from 16 Great Lakes sites collecting digital photographs of over 1, 700 individuals. We applied the DFA model to their body measurements and classified each individual to a morphotype. Contemporary cisco from Lakes Superior, Ontario and Michigan were predominantly classified as artedi, while the most common classifications from northern Lake Huron were albus and manitoulinus. Finding historic morphotypes is encouraging because it suggests that the morphological variation present prior to their collapse still exists. We conclude that contemporary cisco having shapes matching the missing historic morphotypes in the lower lakes warrant special consideration as potential donor populations in reestablishment efforts.

  4. Imported Asian swamp eels (Synbranchidae: Monopterus) in North American live food markets: Potential vectors of non-native parasites

    USGS Publications Warehouse

    Nico, Leo G.; Sharp, Paul; Collins, Timothy M.

    2011-01-01

    Since the 1990s, possibly earlier, large numbers of Asian swamp eels (Synbranchidae: Monopterus spp.), some wild-caught, have been imported live from various countries in Asia and sold in ethnic food markets in cities throughout the USA and parts of Canada. Such markets are the likely introduction pathway of some, perhaps most, of the five known wild populations of Asian swamp eels present in the continental United States. This paper presents results of a pilot study intended to gather baseline data on the occurrence and abundance of internal macroparasites infecting swamp eels imported from Asia to North American retail food markets. These data are important in assessing the potential role that imported swamp eels may play as possible vectors of non-native parasites. Examination of the gastrointestinal tracts and associated tissues of 19 adult-sized swamp eels—identified as M. albus "Clade C"—imported from Vietnam and present in a U.S. retail food market revealed that 18 (95%) contained macroparasites. The 394 individual parasites recovered included a mix of nematodes, acanthocephalans, cestodes, digeneans, and pentastomes. The findings raise concern because of the likelihood that some parasites infecting market swamp eels imported from Asia are themselves Asian taxa, some possibly new to North America. The ecological risk is exacerbated because swamp eels sold in food markets are occasionally retained live by customers and a few reportedly released into the wild. For comparative purposes, M. albus "Clade C" swamp eels from a non-native population in Florida (USA) were also examined and most (84%) were found to be infected with internal macroparasites. The current level of analysis does not allow us to confirm whether these are non-native parasites.

  5. Stereochemistry and Mechanism of Undecylprodigiosin Oxidative Carbocyclization to Streptorubin B by the Rieske Oxygenase RedG.

    PubMed

    Withall, David M; Haynes, Stuart W; Challis, Gregory L

    2015-06-24

    The prodiginines are a group of specialized metabolites that share a 4-methoxypyrrolyldipyrromethene core structure. Streptorubin B is a structurally remarkable member of the prodiginine group produced by Streptomyces coelicolor A3(2) and other actinobacteria. It is biosynthesized from undecylprodigiosin by an oxidative carbocyclization catalyzed by the Rieske oxygenase-like enzyme RedG. Undecylprodigiosin derives from the RedH-catalyzed condensation of 2-undecylpyrrole and 4-methoxy-2, 2'-bipyrrole-5-carboxaldehyde (MBC). To probe the mechanism of the RedG-catalyzed reaction, we synthesized 2-(5-pentoxypentyl)-pyrrole, an analogue of 2-undecylpyrrole with an oxygen atom next to the site of C-C bond formation, and fed it, along with synthetic MBC, to Streptomyces albus expressing redH and redG. This resulted in the production of the 6'-oxa analogue of undecylprodigiosin. In addition, a small amount of a derivative of this analogue lacking the n-pentyl group was produced, consistent with a RedG catalytic mechanism involving hydrogen abstraction from the alkyl chain of undecylprodigiosin prior to pyrrole functionalization. To investigate the stereochemistry of the RedG-catalyzed oxidative carbocyclization, [7'-(2)H](7'R)-2-undecylpyrrole and [7'-(2)H](7'S)-2-undecylpyrrole were synthesized and fed separately, along with MBC, to S. albus expressing redH and redG. Analysis of the extent of deuterium incorporation into the streptorubin B produced in these experiments showed that the pro-R hydrogen atom is abstracted from C-7' of undecylprodigiosin and that the reaction proceeds with inversion of configuration at C-7'. This contrasts sharply with oxidative heterocyclization reactions catalyzed by other nonheme iron-dependent oxygenase-like enzymes, such as isopenicillin N synthase and clavaminate synthase, which proceed with retention of configuration at the carbon center undergoing functionalization.

  6. Effect of Gynosaponin on Rumen In vitro Methanogenesis under Different Forage-Concentrate Ratios

    PubMed Central

    Manatbay, Bakhetgul; Cheng, Yanfen; Mao, Shengyong; Zhu, Weiyun

    2014-01-01

    The study aimed to investigate the effects of gynosaponin on in vitro methanogenesis under different forage-concentrate ratios (F:C ratios). Experiment was conducted with two kinds of F:C ratios (F:C = 7:3 and F:C = 3:7) and gynosaponin addition (0 mg and 16 mg) in a 2×2 double factorial design. In the presence of gynosaponin, methane production and acetate concentration were significantly decreased, whereas concentration of propionate tended to be increased resulting in a significant reduction (p<0.05) of acetate:propionate ratio (A:P ratio), in high-forage substrate. Gynosaponin treatment increased (p<0.05) the butyrate concentration in both F:C ratios. Denaturing gradient gel electrophoresis (DGGE) analysis showed there was no apparent shift in the composition of total bacteria, protozoa and methanogens after treated by gynosaponin under both F:C ratios. The real-time polymerase chain reaction (PCR) analysis indicated that variable F:C ratios significantly affected the abundances of Fibrobacter succinogenes, Rumninococcus flavefaciens, total fungi and counts of protozoa (p<0.05), but did not affect the mcrA gene copies of methanogens and abundance of total bacteria. Counts of protozoa and abundance of F.succinogenes were decreased significantly (p<0.05), whereas mcrA gene copies of methanogens were decreased slightly (p<0.10) in high-forage substrate after treated by gynosaponin. However, gynosaponin treatment under high-concentrate level did not affect the methanogenesis, fermentation characteristics and tested microbes. Accordingly, overall results suggested that gynosaponin supplementation reduced the in vitro methanogenesis and improved rumen fermentation under high-forage condition by changing the abundances of related rumen microbes. PMID:25083102

  7. Improving rumen ecology and microbial population by dried rumen digesta in beef cattle.

    PubMed

    Cherdthong, Anusorn; Wanapat, Metha; Saenkamsorn, Anuthida; Supapong, Chanadol; Anantasook, Nirawan; Gunun, Pongsatorn

    2015-06-01

    Four Thai native beef cattle with initial body weight (BW) of 91.8 ± 4.75 kg were randomly assigned according to a 4 × 4 Latin square design to receive four concentrates replacement levels of soybean meal (SBM) by dried rumen digesta (DRD) at 0, 33, 67, and 100 % on dry matter (DM) basis. All cattle were fed rice straw ad libitum while additional concentrate was fed at 0.5 % BW daily. The experiment was conducted for four periods of 21 days. Rumen fluid was analyzed for predominant cellulolytic bacterial population by using real-time PCR technique. Increasing levels of DRD did not alter total feed intake, ruminal pH and temperature, and plasma urea nitrogen (P > 0.05). Protozoa and fungal population were not differed by DRD supplementation while population of bacteria at 4 h post feeding was increased when SBM was replaced with DRD at 66 and 100 % DM. Population of total bacteria and R. flavefaciens at 4 h post feeding were significantly highest with inclusion of 100 % of DRD in the ration. The experimental diets has no effect on excretion and absorption of purine derivatives (P > 0.05), while microbial crude protein and efficiency of microbial N synthesis were significantly increased with DRD inclusion in the diet and highest with 100 % DRD replacement (P > 0.05). Replacement of SBM by DRD at 100 % DM improved the rumen ecology and microbial population in beef cattle fed on rice straw.

  8. Parameters of fermentation and rumen microbiota of Nellore steers fed with different proportions of concentrate in fresh sugarcane containing diets.

    PubMed

    Ribeiro Júnior, Carlos S; Messana, Juliana D; Granja-Salcedo, Yury T; Canesin, Roberta C; Fiorentini, Giovani; San Vito, Elias; Furlan, Luiz R; Reis, Ricardo A; Berchielli, Telma T

    2016-10-01

    The objective of this study was to evaluate the effect of a fresh sugarcane-based diet and different roughage-to-concentrate ratios (70:30, 60:40, 40:60 and 20:80) on the rumen microbiota associated with rumen fermentation parameters and the intake and apparent digestibility of nutrients in Nellore steers. Eight rumen-cannulated Nellore steers (331 ± 8 kg BW) were distributed in a double 4 × 4 Latin square design balanced for the control of the residual effect. The ruminal pH decreased (p < 0.01) and the concentrations of N-NH3, isovaleric and valeric acids increased linearly (p < 0.05) with an increase dietary concentrate level. Furthermore, an increased concentrate proportion reduced the population of Fibrobacter succinogenes and Ruminococus flavefaciens (p < 0.01) and increased the population of Selenomonas ruminantium and Megasphaera elsdenii (p < 0.01). The protozoa count revealed a predominance of the genus Entodinium. The synthesis of microbial N [g/d] and the efficiency of microbial synthesis [g of microbial N/kg of organic matter apparently digested in the rumen] increased as the proportion of concentrate was increased (p < 0.05). Therefore, it can be concluded that an increasing proportion of concentrate in sugarcane-containing diets enhances the synthesis of microbial protein and does not alter the fibre digestibility, although the population of fibre fermenting bacteria was reduced. PMID:27415825

  9. Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers

    PubMed Central

    Niu, Yuhong; Meng, Qingxiang; Li, Shengli; Ren, Liping; Zhou, Bo; Schonewille, Thomas; Zhou, Zhenming

    2016-01-01

    This study investigated the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on the ruminal bacterial and archaeal community composition of finishing steers. Corn grain- and cotton meal-based concentrate was partially replaced with EML or SMFP. The diets had similar crude protein (CP), neutral detergent fiber (NDF), and metabolizable energy. Following the feeding trial, the steers were slaughtered and ruminal liquid samples were collected to study the ruminal microbiome. Extraction of DNA, amplification of the V4 region of the 16S rRNA gene, and Illumina MiSeq pyrosequencing were performed for each sample. Following sequence de-noising, chimera checking, and quality trimming, an average of 209,610 sequences were generated per sample. Quantitative real-time PCR was performed to examine the selected bacterial species in the rumen. Our results showed that the predominant phyla were Bacteroidetes (43.90%), Firmicutes (39.06%), Proteobacteria (4.31%), and Tenericutes (2.04%), and the predominant genera included Prevotella (13.82%), Ruminococcus (2.51%), Butyrivibrio (2.38%), and Succiniclasticum (2.26%). Compared to the control group, EML and SMFP groups had a higher abundance of total bacteria (p < 0.001); however, the bacterial community composition was similar among the three groups. At the phylum level, there were no significant differences in Firmicutes (p = 0.7932), Bacteroidetes (p = 0.2330), Tenericutes (p = 0.2811), or Proteobacteria (p = 0.0680) levels among the three groups; however, Fibrobacteres decreased in EML (p = 0.0431). At the genus level, there were no differences in Prevotella (p = 0.4280), Ruminococcus (p = 0.2639), Butyrivibrio (p = 0.4433), or Succiniclasticum (p = 0.0431) levels among the groups. Additionally, the dietary treatments had no significant effects on the archaeal community composition in the rumen. Therefore, EML and SMFP supplementation had no significant effects on the ruminal bacterial or

  10. Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers.

    PubMed

    Niu, Yuhong; Meng, Qingxiang; Li, Shengli; Ren, Liping; Zhou, Bo; Schonewille, Thomas; Zhou, Zhenming

    2016-01-01

    This study investigated the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on the ruminal bacterial and archaeal community composition of finishing steers. Corn grain- and cotton meal-based concentrate was partially replaced with EML or SMFP. The diets had similar crude protein (CP), neutral detergent fiber (NDF), and metabolizable energy. Following the feeding trial, the steers were slaughtered and ruminal liquid samples were collected to study the ruminal microbiome. Extraction of DNA, amplification of the V4 region of the 16S rRNA gene, and Illumina MiSeq pyrosequencing were performed for each sample. Following sequence de-noising, chimera checking, and quality trimming, an average of 209,610 sequences were generated per sample. Quantitative real-time PCR was performed to examine the selected bacterial species in the rumen. Our results showed that the predominant phyla were Bacteroidetes (43.90%), Firmicutes (39.06%), Proteobacteria (4.31%), and Tenericutes (2.04%), and the predominant genera included Prevotella (13.82%), Ruminococcus (2.51%), Butyrivibrio (2.38%), and Succiniclasticum (2.26%). Compared to the control group, EML and SMFP groups had a higher abundance of total bacteria (p < 0.001); however, the bacterial community composition was similar among the three groups. At the phylum level, there were no significant differences in Firmicutes (p = 0.7932), Bacteroidetes (p = 0.2330), Tenericutes (p = 0.2811), or Proteobacteria (p = 0.0680) levels among the three groups; however, Fibrobacteres decreased in EML (p = 0.0431). At the genus level, there were no differences in Prevotella (p = 0.4280), Ruminococcus (p = 0.2639), Butyrivibrio (p = 0.4433), or Succiniclasticum (p = 0.0431) levels among the groups. Additionally, the dietary treatments had no significant effects on the archaeal community composition in the rumen. Therefore, EML and SMFP supplementation had no significant effects on the ruminal bacterial or

  11. Effects of Diets Supplemented with Ensiled Mulberry Leaves and Sun-Dried Mulberry Fruit Pomace on the Ruminal Bacterial and Archaeal Community Composition of Finishing Steers.

    PubMed

    Niu, Yuhong; Meng, Qingxiang; Li, Shengli; Ren, Liping; Zhou, Bo; Schonewille, Thomas; Zhou, Zhenming

    2016-01-01

    This study investigated the effects of ensiled mulberry leaves (EML) and sun-dried mulberry fruit pomace (SMFP) on the ruminal bacterial and archaeal community composition of finishing steers. Corn grain- and cotton meal-based concentrate was partially replaced with EML or SMFP. The diets had similar crude protein (CP), neutral detergent fiber (NDF), and metabolizable energy. Following the feeding trial, the steers were slaughtered and ruminal liquid samples were collected to study the ruminal microbiome. Extraction of DNA, amplification of the V4 region of the 16S rRNA gene, and Illumina MiSeq pyrosequencing were performed for each sample. Following sequence de-noising, chimera checking, and quality trimming, an average of 209,610 sequences were generated per sample. Quantitative real-time PCR was performed to examine the selected bacterial species in the rumen. Our results showed that the predominant phyla were Bacteroidetes (43.90%), Firmicutes (39.06%), Proteobacteria (4.31%), and Tenericutes (2.04%), and the predominant genera included Prevotella (13.82%), Ruminococcus (2.51%), Butyrivibrio (2.38%), and Succiniclasticum (2.26%). Compared to the control group, EML and SMFP groups had a higher abundance of total bacteria (p < 0.001); however, the bacterial community composition was similar among the three groups. At the phylum level, there were no significant differences in Firmicutes (p = 0.7932), Bacteroidetes (p = 0.2330), Tenericutes (p = 0.2811), or Proteobacteria (p = 0.0680) levels among the three groups; however, Fibrobacteres decreased in EML (p = 0.0431). At the genus level, there were no differences in Prevotella (p = 0.4280), Ruminococcus (p = 0.2639), Butyrivibrio (p = 0.4433), or Succiniclasticum (p = 0.0431) levels among the groups. Additionally, the dietary treatments had no significant effects on the archaeal community composition in the rumen. Therefore, EML and SMFP supplementation had no significant effects on the ruminal bacterial or

  12. Real-time analysis of gut flora in Entamoeba histolytica infected patients of Northern India

    PubMed Central

    2012-01-01

    Background Amebic dysentery is caused by the protozoan parasite Entamoeba histolytica and the ingestion of quadrinucleate cyst of E. histolytica from fecally contaminated food or water initiates infection. Excystation occurs in the lumen of small intestine, where motile and potentially invasive trophozoites germinate from cysts. The ability of trophozoites to interact and digest gut bacteria is apparently important for multiplication of the parasite and its pathogenicity; however the contribution of resident bacterial flora is not well understood. We quantified the population of Bacteroides, Bifidobacterium, Ruminococcus, Lactobacillus, Clostridium leptum subgroup, Clostridium coccoides subgroup, Eubacterium, Campylobacter, Methanobrevibacter smithii and Sulphur reducing bacteria using genus specific primers in healthy (N = 22) vs amebic patients (E. histolytica positive, N = 17) stool samples by Real-time PCR. Results Absolute quantification of Bacteroides (p = .001), Closrtridium coccoides subgroup (p = 0.002), Clostridium leptum subgroup (p = 0.0001), Lactobacillus (p = 0.037), Campylobacter (p = 0.0014) and Eubacterium (p = 0.038) show significant drop in their population however, significant increase in Bifdobacterium (p = 0.009) was observed where as the population of Ruminococcus (p = 0.33) remained unaltered in healthy vs amebic patients (E. histolytica positive). We also report high prevalence of nimE gene in stool samples of both healthy volunteers and amebic patients. No significant decrease in nimE gene copy number was observed before and after the treatment with antiamebic drug. Conclusions Our results show significant alteration in predominant gut bacteria in E. histolytica infected individuals. The frequent episodes of intestinal amoebic dysentery thus result in depletion of few predominant genera in gut that may lead to poor digestion and absorption of food in intestine. It further disturbs the homeostasis

  13. Schisandra chinensis fruit modulates the gut microbiota composition in association with metabolic markers in obese women: a randomized, double-blind placebo-controlled study.

    PubMed

    Song, Mi-young; Wang, Jing-hua; Eom, Taewoong; Kim, Hojun

    2015-08-01

    Schisandra chinensis fruit (SCF) is known to have beneficial effects on metabolic diseases, including obesity, and to affect gut microbiota in in vivo studies. However, in human research, there have been a few studies in terms of its clinical roles in lipid metabolism and modulation of gut microbiota. A double-blind, placebo-controlled study with 28 obese women with SCF or placebo was conducted for 12 weeks. Anthropometry and blood and fecal sampling were performed before and after treatment. Analysis of the gut microbiota in feces was performed using denaturing gradient gel electrophoresis and quantitative polymerase chain reaction. Although the values did not differ significantly between the 2 groups, the SCF group tended to show a greater decrease in waist circumference, fat mass, fasting blood glucose, triglycerides, aspartate aminotransferase, and alanine aminotransferase than the placebo group. Clustering of the denaturing gradient gel electrophoresis fingerprints for total bacteria before and after treatment indicated more separate clustering in SCF group than placebo. In correlation analysis, Bacteroides and Bacteroidetes (both increased by SCF) showed significant negative correlation with fat mass, aspartate aminotransferase, and/or alanine aminotransferase, respectively. Ruminococcus (decreased by SCF) showed negative correlation with high-density lipoprotein cholesterol and fasting blood glucose. In conclusion, administration of SCF for 12 weeks resulted in modulation of the gut microbiota composition in Korean obese women, and significant correlations with some bacterial genera and metabolic parameters were noted. However, in general, SCF was not sufficient to induce significant changes in obesity-related parameters compared with placebo.

  14. Assembly of minicellulosomes on the surface of Bacillus subtilis.

    PubMed

    Anderson, Timothy D; Robson, Scott A; Jiang, Xiao Wen; Malmirchegini, G Reza; Fierobe, Henri-Pierre; Lazazzera, Beth A; Clubb, Robert T

    2011-07-01

    To cost-efficiently produce biofuels, new methods are needed to convert lignocellulosic biomass into fermentable sugars. One promising approach is to degrade biomass using cellulosomes, which are surface-displayed multicellulase-containing complexes present in cellulolytic Clostridium and Ruminococcus species. In this study we created cellulolytic strains of Bacillus subtilis that display one or more cellulase enzymes. Proteins containing the appropriate cell wall sorting signal are covalently anchored to the peptidoglycan by coexpressing them with the Bacillus anthracis sortase A (SrtA) transpeptidase. This approach was used to covalently attach the Cel8A endoglucanase from Clostridium thermocellum to the cell wall. In addition, a Cel8A-dockerin fusion protein was anchored on the surface of B. subtilis via noncovalent interactions with a cell wall-attached cohesin module. We also demonstrate that it is possible to assemble multienzyme complexes on the cell surface. A three-enzyme-containing minicellulosome was displayed on the cell surface; it consisted of a cell wall-attached scaffoldin protein noncovalently bound to three cellulase-dockerin fusion proteins that were produced in Escherichia coli. B. subtilis has a robust genetic system and is currently used in a wide range of industrial processes. Thus, grafting larger, more elaborate minicellulosomes onto the surface of B. subtilis may yield cellulolytic bacteria with increased potency that can be used to degrade biomass.

  15. [Progress in the knowledge of the intestinal human microbiota].

    PubMed

    Robles-Alonso, Virginia; Guarner, Francisco

    2013-01-01

    New sequencing technologies together with the development of bio-informatics allow a description of the full spectrum of the microbial communities that inhabit the human intestinal tract, as well as their functional contributions to host health. Most community members belong to the domain Bacteria, but Archaea, Eukaryotes (yeasts and protists), and Viruses are also present. Only 7 to 9 of the 55 known divisions or phyla of the domain Bacteria are detected in faecal or mucosal samples from the human gut. Most taxa belong to just two divisions: Bacteroidetes and Firmicutes, and the other divisions that have been consistently found are Proteobacteria, Actinobacteria, Fusobacteria, and Verrucomicrobia. Bacteroides, Faecalibacterium and Bifidobacterium are the most abundant genera but their relative proportion is highly variable across individuals. Full metagenomic analysis has identified more than 5 million non-redundant microbial genes encoding up to 20,000 biological functions related with life in the intestinal habitat. The overall structure of predominant genera in the human gut can be assigned into three robust clusters, which are known as "enterotypes". Each of the three enterotypes is identifiable by the levels of one of three genera: Bacteroides (enterotype 1), Prevotella (enterotype 2) and Ruminococcus (enterotype 3). This suggests that microbiota variations across individuals are stratified, not continuous. Next steps include the identification of changes that may play a role in certain disease states. A better knowledge of the contributions of microbial symbionts to host health will help in the design of interventions to improve symbiosis and combat disease.

  16. Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

    PubMed Central

    Dowd, Scot E; Callaway, Todd R; Wolcott, Randall D; Sun, Yan; McKeehan, Trevor; Hagevoort, Robert G; Edrington, Thomas S

    2008-01-01

    Background The microbiota of an animal's intestinal tract plays important roles in the animal's overall health, productivity and well-being. There is still a scarcity of information on the microbial diversity in the gut of livestock species such as cattle. The primary reason for this lack of data relates to the expense of methods needed to generate such data. Here we have utilized a bacterial tag-encoded FLX 16s rDNA amplicon pyrosequencing (bTEFAP) approach that is able to perform diversity analyses of gastrointestinal populations. bTEFAP is relatively inexpensive in terms of both time and labor due to the implementation of a novel tag priming method and an efficient bioinformatics pipeline. We have evaluated the microbiome from the feces of 20 commercial, lactating dairy cows. Results Ubiquitous bacteria detected from the cattle feces included Clostridium, Bacteroides, Porpyhyromonas, Ruminococcus, Alistipes, Lachnospiraceae, Prevotella, Lachnospira, Enterococcus, Oscillospira, Cytophage, Anaerotruncus, and Acidaminococcus spp. Foodborne pathogenic bacteria were detected in several of the cattle, a total of 4 cows were found to be positive for Salmonella spp (tentative enterica) and 6 cows were positive for Campylobacter spp. (tentative lanienae). Conclusion Using bTEFAP we have examined the microbiota in the feces of cattle. As these methods continue to mature we will better understand the ecology of the major populations of bacteria the lower intestinal tract. This in turn will allow for a better understanding of ways in which the intestinal microbiome contributes to animal health, productivity and wellbeing. PMID:18652685

  17. Changes in cecal microbiota and mucosal gene expression revealed new aspects of epizootic rabbit enteropathy.

    PubMed

    Bäuerl, Christine; Collado, M Carmen; Zúñiga, Manuel; Blas, Enrique; Pérez Martínez, Gaspar

    2014-01-01

    Epizootic Rabbit Enteropathy (ERE) is a severe disease of unknown aetiology that mainly affects post-weaning animals. Its incidence can be prevented by antibiotic treatment suggesting that bacterial elements are crucial for the development of the disease. Microbial dynamics and host responses during the disease were studied. Cecal microbiota was characterized in three rabbit groups (ERE-affected, healthy and healthy pretreated with antibiotics), followed by transcriptional analysis of cytokines and mucins in the cecal mucosa and vermix by q-rtPCR. In healthy animals, cecal microbiota with or without antibiotic pretreatment was very similar and dominated by Alistipes and Ruminococcus. Proportions of both genera decreased in ERE rabbits whereas Bacteroides, Akkermansia and Rikenella increased, as well as Clostridium, γ-Proteobacteria and other opportunistic and pathogenic species. The ERE group displayed remarkable dysbiosis and reduced taxonomic diversity. Transcription rate of mucins and inflammatory cytokines was very high in ERE rabbits, except IL-2, and its analysis revealed the existence of two clearly different gene expression patterns corresponding to Inflammatory and (mucin) Secretory Profiles. Furthermore, these profiles were associated to different bacterial species, suggesting that they may correspond to different stages of the disease. Other data obtained in this work reinforced the notion that ERE morbidity and mortality is possibly caused by an overgrowth of different pathogens in the gut of animals whose immune defence mechanisms seem not to be adequately responding. PMID:25147938

  18. Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes.

    PubMed

    Poirier, Simon; Desmond-Le Quéméner, Elie; Madigou, Céline; Bouchez, Théodore; Chapleur, Olivier

    2016-05-01

    Ammonia inhibition represents a major operational issue for anaerobic digestion (AD). In order to get more insights into AD microbiota resistance, anaerobic batch reactors performances were investigated under a wide range of Total Ammonia Nitrogen (TAN) concentrations up to 50.0g/L at 35°C. The half maximal inhibitory concentration (IC50) value was determined to be 19.0g/L. Microbial community dynamics revealed that above a TAN concentration of 10.0g/L, remarkable modifications within archaeal and bacterial communities occurred. 16S rRNA gene sequencing analysis showed a gradual methanogenic shift between two OTUs from genus Methanosarcina when TAN concentration increased up to 25.0g/L. Proportion of potential syntrophic microorganisms such as Methanoculleus and Treponema progressively raised with increasing TAN up to 10.0 and 25.0g/L respectively, while Syntrophomonas and Ruminococcus groups declined. In 25.0g/L assays, Caldicoprobacter were dominant. This study highlights the emergence of AD key phylotypes at extreme ammonia concentrations.

  19. Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions.

    PubMed

    Upadhyaya, Bijaya; McCormack, Lacey; Fardin-Kia, Ali Reza; Juenemann, Robert; Nichenametla, Sailendra; Clapper, Jeffrey; Specker, Bonny; Dey, Moul

    2016-01-01

    Dietary modulation of the gut microbiota impacts human health. Here we investigated the hitherto unknown effects of resistant starch type 4 (RS4) enriched diet on gut microbiota composition and short-chain fatty acid (SCFA) concentrations in parallel with host immunometabolic functions in twenty individuals with signs of metabolic syndrome (MetS). Cholesterols, fasting glucose, glycosylated haemoglobin, and proinflammatory markers in the blood as well as waist circumference and % body fat were lower post intervention in the RS4 group compared with the control group. 16S-rRNA gene sequencing revealed a differential abundance of 71 bacterial operational taxonomic units, including the enrichment of three Bacteroides species and one each of Parabacteroides, Oscillospira, Blautia, Ruminococcus, Eubacterium, and Christensenella species in the RS4 group. Gas chromatography-mass spectrometry revealed higher faecal SCFAs, including butyrate, propionate, valerate, isovalerate, and hexanoate after RS4-intake. Bivariate analyses showed RS4-specific associations of the gut microbiota with the host metabolic functions and SCFA levels. Here we show that dietary RS4 induced changes in the gut microbiota are linked to its biological activity in individuals with signs of MetS. These findings have potential implications for dietary guidelines in metabolic health management. PMID:27356770

  20. Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts.

    PubMed

    Kohl, Kevin D; Amaya, James; Passement, Celeste A; Dearing, M Denise; McCue, Marshall D

    2014-12-01

    Many animals face unpredictable food sources and periods of prolonged fasting, which likely present significant challenges to gut microorganisms. While several studies have demonstrated that fasting impacts the gut microbiota, experiments have not been carried out in a comparative context. We used 16S rRNA gene sequencing to document changes in colonic and cecal microbiomes of animals representing five classes of vertebrates at four time points through prolonged fasting: tilapia, toads, geckos, quail, and mice. We found differences in the starvation-induced changes in the microbiome across host species and across gut regions. Microbial phylogenetic diversity increased as a result of fasting in the colons of fish, toads, and mice, while quail exhibited a decrease in diversity; geckos exhibited no change. Microbial diversity in the cecum decreased in fish and exhibited no change in mice. Alterations in relative abundances of microbial taxa varied across hosts. Fish exhibited the most significant changes due to fasting, while geckos maintained a stable community over 28 days of fasting. We uncovered several shared responses of the microbiota across hosts. For example, all tetrapods exhibited decreases in the abundances of Coprobacillus and Ruminococcus in response to fasting. We also discuss host-mediated physiological mechanisms that may underlie these community changes.

  1. Effects of bitter melon (Momordica charantia L.) on the gut microbiota in high fat diet and low dose streptozocin-induced rats.

    PubMed

    Zhu, Ying; Bai, Juan; Zhang, Yi; Xiao, Xiang; Dong, Ying

    2016-09-01

    The effects on gut microbiota of type 2 diabetic rats fed a bitter melon formulation (BLSP, a lyophilized superfine powder) were investigated. BLSP treatment significantly reduced fasting blood glucose levels (p < 0.05) and serum insulin levels (p < 0.05) of the diabetic rats. The gut microbiota of treated and control rats were profiled by PCR amplification and pyrosequencing of 16S rRNA genes (V3-V9 region). BLSP significantly reduced the ratio of Firmicutes to Bacteroidetes in diabetic rats, while the relative abundances of Ruminococcaceae, Bacteroides and Ruminococcus were significantly lowered in BLSP-treated rats compared to diabetic rats. Additionally, BLSP significantly suppressed the activation of MAPK (JNK and p38). The results indicate that BLSP can significantly modify the proportions of particular gut microbiota in diabetic rats without disturbing the normal population diversity. By suppressing the activation of MAPK signaling pathway, a BLSP containing diet may ameliorate type 2 diabetes. PMID:27352776

  2. Insulin Resistance, Microbiota, and Fat Distribution Changes by a New Model of Vertical Sleeve Gastrectomy in Obese Rats.

    PubMed

    Basso, Nicola; Soricelli, Emanuele; Castagneto-Gissey, Lidia; Casella, Giovanni; Albanese, Davide; Fava, Francesca; Donati, Claudio; Tuohy, Kieran; Angelini, Giulia; La Neve, Federica; Severino, Anna; Kamvissi-Lorenz, Virginia; Birkenfeld, Andrea L; Bornstein, Stefan; Manco, Melania; Mingrone, Geltrude

    2016-10-01

    Metabolic surgery improves insulin resistance and type 2 diabetes possibly because of weight loss. We performed a novel sleeve gastrectomy in rats that resects ∼80% of the glandular portion, leaving the forestomach almost intact (glandular gastrectomy [GG]) and compared subsequent metabolic remodeling with a sham operation. GG did not affect body weight, at least after 10 weeks; improved hepatic and peripheral insulin sensitivity likely through increased Akt, glycogen synthase kinase 3, and AMPK phosphorylation; and reduced ectopic fat deposition and hepatic glycogen overaccumulation. Body adipose tissue was redistributed, with reduction of intraabdominal fat. We found a reduction of circulating ghrelin levels, increased GLP-1 plasma concentration, and remodeling of gut microbiome diversity characterized by a lower relative abundance of Ruminococcus and a higher relative abundance of Lactobacillus and Collinsella These data suggest that at least in rat, the glandular stomach plays a central role in the improvement of insulin resistance, even if obesity persists. GG provides a new model of the metabolically healthy obese phenotype. PMID:27431457

  3. Characterization of the gut microbiota of Kawasaki disease patients by metagenomic analysis

    PubMed Central

    Kinumaki, Akiko; Sekizuka, Tsuyoshi; Hamada, Hiromichi; Kato, Kengo; Yamashita, Akifumi; Kuroda, Makoto

    2015-01-01

    Kawasaki disease (KD) is an acute febrile illness of early childhood. Previous reports have suggested that genetic disease susceptibility factors, together with a triggering infectious agent, could be involved in KD pathogenesis; however, the precise etiology of this disease remains unknown. Additionally, previous culture-based studies have suggested a possible role of intestinal microbiota in KD pathogenesis. In this study, we performed metagenomic analysis to comprehensively assess the longitudinal variation in the intestinal microbiota of 28 KD patients. Several notable bacterial genera were commonly extracted during the acute phase, whereas a relative increase in the number of Ruminococcus bacteria was observed during the non-acute phase of KD. The metagenomic analysis results based on bacterial species classification suggested that the number of sequencing reads with similarity to five Streptococcus spp. (S. pneumonia, pseudopneumoniae, oralis, gordonii, and sanguinis), in addition to patient-derived Streptococcus isolates, markedly increased during the acute phase in most patients. Streptococci include a variety of pathogenic bacteria and probiotic bacteria that promote human health; therefore, this further species discrimination could comprehensively illuminate the KD-associated microbiota. The findings of this study suggest that KD-related Streptococci might be involved in the pathogenesis of this disease. PMID:26322033

  4. Effect of Whole-Grain Barley on the Human Fecal Microbiota and Metabolome

    PubMed Central

    De Angelis, Maria; Montemurno, Eustacchio; Vannini, Lucia; Cosola, Carmela; Cavallo, Noemi; Gozzi, Giorgia; Maranzano, Valentina; Di Cagno, Raffaella; Gesualdo, Loreto

    2015-01-01

    In this study, we compared the fecal microbiota and metabolomes of 26 healthy subjects before (HS) and after (HSB) 2 months of diet intervention based on the administration of durum wheat flour and whole-grain barley pasta containing the minimum recommended daily intake (3 g) of barley β-glucans. Metabolically active bacteria were analyzed through pyrosequencing of the 16S rRNA gene and community-level catabolic profiles. Pyrosequencing data showed that levels of Clostridiaceae (Clostridium orbiscindens and Clostridium sp.), Roseburia hominis, and Ruminococcus sp. increased, while levels of other Firmicutes and Fusobacteria decreased, from the HSB samples to the HS fecal samples. Community-level catabolic profiles were lower in HSB samples. Compared to the results for HS samples, cultivable lactobacilli increased in HSB fecal samples, while the numbers of Enterobacteriaceae, total coliforms, and Bacteroides, Porphyromonas, Prevotella, Pseudomonas, Alcaligenes, and Aeromonas bacteria decreased. Metabolome analyses were performed using an amino acid analyzer and gas chromatography-mass spectrometry solid-phase microextraction. A marked increase in short-chain fatty acids (SCFA), such as 2-methyl-propanoic, acetic, butyric, and propionic acids, was found in HSB samples with respect to the HS fecal samples. Durum wheat flour and whole-grain barley pasta containing 3% barley β-glucans appeared to be effective in modulating the composition and metabolic pathways of the intestinal microbiota, leading to an increased level of SCFA in the HSB samples. PMID:26386056

  5. Massive parallel 16S rRNA gene pyrosequencing reveals highly diverse fecal bacterial and fungal communities in healthy dogs and cats.

    PubMed

    Handl, Stefanie; Dowd, Scot E; Garcia-Mazcorro, Jose F; Steiner, Jörg M; Suchodolski, Jan S

    2011-05-01

    This study evaluated the fecal microbiota of 12 healthy pet dogs and 12 pet cats using bacterial and fungal tag-encoded FLX-Titanium amplicon pyrosequencing. A total of 120,406 pyrosequencing reads for bacteria (mean 5017) and 5359 sequences (one pool each for dogs and cats) for fungi were analyzed. Additionally, group-specific 16S rRNA gene clone libraries for Bifidobacterium spp. and lactic acid-producing bacteria (LAB) were constructed. The most abundant bacterial phylum was Firmicutes, followed by Bacteroidetes in dogs and Actinobacteria in cats. The most prevalent bacterial class in dogs and cats was Clostridia, dominated by the genera Clostridium (clusters XIVa and XI) and Ruminococcus. At the genus level, 85 operational taxonomic units (OTUs) were identified in dogs and 113 OTUs in cats. Seventeen LAB and eight Bifidobacterium spp. were detected in canine feces. Ascomycota was the only fungal phylum detected in cats, while Ascomycota, Basidiomycota, Glomeromycota, and Zygomycota were identified in dogs. Nacaseomyces was the most abundant fungal genus in dogs; Saccharomyces and Aspergillus were predominant in cats. At the genus level, 33 different fungal OTUs were observed in dogs and 17 OTUs in cats. In conclusion, this study revealed a highly diverse bacterial and fungal microbiota in canine and feline feces.

  6. Organoheterotrophic Bacterial Abundance Associates with Zinc Removal in Lignocellulose-Based Sulfate-Reducing Systems.

    PubMed

    Drennan, Dina M; Almstrand, Robert; Lee, Ilsu; Landkamer, Lee; Figueroa, Linda; Sharp, Jonathan O

    2016-01-01

    Syntrophic relationships between fermentative and sulfate-reducing bacteria are essential to lignocellulose-based systems applied to the passive remediation of mining-influenced waters. In this study, seven pilot-scale sulfate-reducing bioreactor columns containing varying ratios of alfalfa hay, pine woodchips, and sawdust were analyzed over ∼500 days to investigate the influence of substrate composition on zinc removal and microbial community structure. Columns amended with >10% alfalfa removed significantly more sulfate and zinc than did wood-based columns. Enumeration of sulfate reducers by functional signatures (dsrA) and their putative identification from 16S rRNA genes did not reveal significant correlations with zinc removal, suggesting limitations in this directed approach. In contrast, a strong indicator of zinc removal was discerned in comparing the relative abundance of core microorganisms shared by all reactors (>80% of total community), many of which had little direct involvement in metal or sulfate respiration. The relative abundance of Desulfosporosinus, the dominant putative sulfate reducer within these reactors, correlated to representatives of this core microbiome. A subset of these clades, including Treponema, Weissella, and Anaerolinea, was associated with alfalfa and zinc removal, and the inverse was found for a second subset whose abundance was associated with wood-based columns, including Ruminococcus, Dysgonomonas, and Azospira. The construction of a putative metabolic flowchart delineated syntrophic interactions supporting sulfate reduction and suggests that the production of and competition for secondary fermentation byproducts, such as lactate scavenging, influence bacterial community composition and reactor efficacy. PMID:26605699

  7. Identification and Characterization of Potential Performance-Related Gut Microbiotas in Broiler Chickens across Various Feeding Trials▿†

    PubMed Central

    Torok, Valeria A.; Hughes, Robert J.; Mikkelsen, Lene L.; Perez-Maldonado, Rider; Balding, Katherine; MacAlpine, Ron; Percy, Nigel J.; Ophel-Keller, Kathy

    2011-01-01

    Three broiler feeding trials were investigated in order to identify gut bacteria consistently linked with improvements in bird performance as measured by feed efficiency. Trials were done in various geographic locations and varied in diet composition, broiler breed, and bird age. Gut microbial communities were investigated using microbial profiling. Eight common performance-linked operational taxonomic units (OTUs) were identified within both the ilea (180, 492, and 564–566) and ceca (140–142, 218–220, 284–286, 312, and 482) across trials. OTU 564–566 was associated with lower performance, while OTUs 140–142, 482, and 492 were associated with improved performance. Targeted cloning and sequencing of these eight OTUs revealed that they represented 26 bacterial species or phylotypes which clustered phylogenetically into seven groups related to Lactobacillus spp., Ruminococcaceae, Clostridiales, Gammaproteobacteria, Bacteroidales, Clostridiales/Lachnospiraceae, and unclassified bacteria/clostridia. Where bacteria were identifiable to the phylum level, they belonged predominantly to the Firmicutes, with Bacteroidetes and Proteobacteria also identified. Some of the potential performance-related phylotypes showed high sequence identity with classified bacteria (Lactobacillus salivarius, Lactobacillus aviarius, Lactobacillus crispatus, Faecalibacterium prausnitzii, Escherichia coli, Gallibacterium anatis, Clostridium lactatifermentans, Ruminococcus torques, Bacteroides vulgatus, and Alistipes finegoldii). The 16S rRNA gene sequence information generated will allow quantitative assays to be developed which will enable elucidations of which of these phylotypes are truly performance related. This information could be used to monitor strategies to improve feed efficiency and feed formulation for optimal gut health. PMID:21742925

  8. Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans.

    PubMed

    Ushida, Kazunari; Segawa, Takahiro; Tsuchida, Sayaka; Murata, Koichi

    2016-02-01

    Preservation of indigenous gastrointestinal microbiota is deemed to be critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we investigated cecal bacterial communities in wild Japanese rock ptarmigans (Lagopus muta japonica) and compared them with those in Svalbard rock ptarmigans (L. m. hyperborea) in captivity. Ultra-deep sequencing of 16S rRNA gene indicated that the community structure of cecal microbiota in wild rock ptarmigans was remarkably different from that in captive Svalbard rock ptarmigans. Fundamental differences between bacterial communities in the two groups of birds were detected at the phylum level. Firmicutes, Actinobacteria, Bacteroidetes and Synergistetes were the major phyla detected in wild Japanese rock ptarmigans, whereas Firmicutes alone occupied more than 80% of abundance in captive Svalbard rock ptarmigans. Furthermore, unclassified genera of Coriobacteriaceae, Synergistaceae, Bacteroidaceae, Actinomycetaceae, Veillonellaceae and Clostridiales were the major taxa detected in wild individuals, whereas in zoo-reared birds, major genera were Ruminococcus, Blautia, Faecalibacterium and Akkermansia. Zoo-reared birds seemed to lack almost all rock ptarmigan-specific bacteria in their intestine, which may explain the relatively high rate of pathogenic infections affecting them. We show evidence that preservation and reconstitution of indigenous cecal microflora are critical for successful ex situ conservation and future re-introduction plan for the Japanese rock ptarmigan.

  9. Epithelial Sel1L is required for the maintenance of intestinal homeostasis

    PubMed Central

    Sun, Shengyi; Lourie, Rohan; Cohen, Sara B.; Ji, Yewei; Goodrich, Julia K.; Poole, Angela C.; Ley, Ruth E.; Denkers, Eric Y.; McGuckin, Michael A.; Long, Qiaoming; Duhamel, Gerald E.; Simpson, Kenneth W.; Qi, Ling

    2016-01-01

    Inflammatory bowel disease (IBD) is an incurable chronic idiopathic disease that drastically decreases quality of life. Endoplasmic reticulum (ER)–associated degradation (ERAD) is responsible for the clearance of misfolded proteins; however, its role in disease pathogenesis remains largely unexplored. Here we show that the expression of SEL1L and HRD1, the most conserved branch of mammalian ERAD, is significantly reduced in ileal Crohn’s disease (CD). Consistent with this observation, laboratory mice with enterocyte-specific Sel1L deficiency (Sel1LΔIEC) develop spontaneous enteritis and have increased susceptibility to Toxoplasma gondii–induced ileitis. This is associated with profound defects in Paneth cells and a disproportionate increase of Ruminococcus gnavus, a mucolytic bacterium with known association with CD. Surprisingly, whereas both ER stress sensor IRE1α and effector CHOP are activated in the small intestine of Sel1LΔIEC mice, they are not solely responsible for ERAD deficiency–associated lesions seen in the small intestine. Thus our study points to a constitutive role of Sel1L-Hrd1 ERAD in epithelial cell biology and the pathogenesis of intestinal inflammation in CD. PMID:26631554

  10. Association between Polycystic Ovary Syndrome and Gut Microbiota

    PubMed Central

    Guo, Yanjie; Qi, Yane; Yang, Xuefei; Zhao, Lihui; Wen, Shu; Liu, Yinhui; Tang, Li

    2016-01-01

    Polycystic ovary syndrome (PCOS) is the most frequent endocrinopathy in women of reproductive age. It is difficult to treat PCOS because of its complex etiology and pathogenesis. Here, we characterized the roles of gut microbiota on the pathogenesis and treatments in letrozole (a nonsteroidal aromatase inhibitor) induced PCOS rat model. Changes in estrous cycles, hormonal levels, ovarian morphology and gut microbiota by PCR-DGGE and real-time PCR were determined. The results showed that PCOS rats displayed abnormal estrous cycles with increasing androgen biosynthesis and exhibited multiple large cysts with diminished granulosa layers in ovarian tissues. Meanwhile, the composition of gut microbiota in letrozole-treated rats was different from that in the controls. Lactobacillus, Ruminococcus and Clostridium were lower while Prevotella was higher in PCOS rats when compared with control rats. After treating PCOS rats with Lactobacillus and fecal microbiota transplantation (FMT) from healthy rats, it was found that the estrous cycles were improved in all 8 rats in FMT group, and in 6 of the 8 rats in Lactobacillus transplantation group with decreasing androgen biosynthesis. Their ovarian morphologies normalized. The composition of gut microbiota restored in both FMT and Lactobacillus treated groups with increasing of Lactobacillus and Clostridium, and decreasing of Prevotella. These results indicated that dysbiosis of gut microbiota was associated with the pathogenesis of PCOS. Microbiota interventions through FMT and Lactobacillus transplantation were beneficial for the treatments of PCOS rats. PMID:27093642

  11. Ecophysiological consequences of alcoholism on human gut microbiota: implications for ethanol-related pathogenesis of colon cancer.

    PubMed

    Tsuruya, Atsuki; Kuwahara, Akika; Saito, Yuta; Yamaguchi, Haruhiko; Tsubo, Takahisa; Suga, Shogo; Inai, Makoto; Aoki, Yuichi; Takahashi, Seiji; Tsutsumi, Eri; Suwa, Yoshihide; Morita, Hidetoshi; Kinoshita, Kenji; Totsuka, Yukari; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Mizukami, Takeshi; Yokoyama, Akira; Shimoyama, Takefumi; Nakayama, Toru

    2016-01-01

    Chronic consumption of excess ethanol increases the risk of colorectal cancer. The pathogenesis of ethanol-related colorectal cancer (ER-CRC) is thought to be partly mediated by gut microbes. Specifically, bacteria in the colon and rectum convert ethanol to acetaldehyde (AcH), which is carcinogenic. However, the effects of chronic ethanol consumption on the human gut microbiome are poorly understood, and the role of gut microbes in the proposed AcH-mediated pathogenesis of ER-CRC remains to be elaborated. Here we analyse and compare the gut microbiota structures of non-alcoholics and alcoholics. The gut microbiotas of alcoholics were diminished in dominant obligate anaerobes (e.g., Bacteroides and Ruminococcus) and enriched in Streptococcus and other minor species. This alteration might be exacerbated by habitual smoking. These observations could at least partly be explained by the susceptibility of obligate anaerobes to reactive oxygen species, which are increased by chronic exposure of the gut mucosa to ethanol. The AcH productivity from ethanol was much lower in the faeces of alcoholic patients than in faeces of non-alcoholic subjects. The faecal phenotype of the alcoholics could be rationalised based on their gut microbiota structures and the ability of gut bacteria to accumulate AcH from ethanol. PMID:27295340

  12. Production of poly(hydroxybutyrate-hydroxyvalerate) from waste organics by the two-stage process: focus on the intermediate volatile fatty acids.

    PubMed

    Shen, Liang; Hu, Hongyou; Ji, Hongfang; Cai, Jiyuan; He, Ning; Li, Qingbiao; Wang, Yuanpeng

    2014-08-01

    The two-stage process, coupling volatile fatty acids (VFAs) fermentation and poly(hydroxybutyrate-hydroxyvalerate) (P(HB/HV)) biosynthesis, was investigated for five waste organic materials. The overall conversion efficiencies were glycerol>starch>molasses>waste sludge>protein, meanwhile the maximum P(HB/HV) (1.674 g/L) was obtained from waste starch. Altering the waste type brought more effects on VFAs composition other than the yield in the first stage, which in turn greatly changed the yield in the second stage. Further study showed that even-number carbon VFAs (or odd-number ones) had a good positive linear relationship with P(HB/HV) content of HB (or HV). Additionally, VFA producing microbiota was analyzed by pyrosequencing methods for five wastes, which indicated that specific species (e.g., Lactobacillus for protein; Ethanoligenens for starch; Ruminococcus and Limnobacter for glycerol) were dominant in the community for VFAs production. Potential competition among acidogenic bacteria specially involved to produce some VFA was proposed as well.

  13. Association between Polycystic Ovary Syndrome and Gut Microbiota.

    PubMed

    Guo, Yanjie; Qi, Yane; Yang, Xuefei; Zhao, Lihui; Wen, Shu; Liu, Yinhui; Tang, Li

    2016-01-01

    Polycystic ovary syndrome (PCOS) is the most frequent endocrinopathy in women of reproductive age. It is difficult to treat PCOS because of its complex etiology and pathogenesis. Here, we characterized the roles of gut microbiota on the pathogenesis and treatments in letrozole (a nonsteroidal aromatase inhibitor) induced PCOS rat model. Changes in estrous cycles, hormonal levels, ovarian morphology and gut microbiota by PCR-DGGE and real-time PCR were determined. The results showed that PCOS rats displayed abnormal estrous cycles with increasing androgen biosynthesis and exhibited multiple large cysts with diminished granulosa layers in ovarian tissues. Meanwhile, the composition of gut microbiota in letrozole-treated rats was different from that in the controls. Lactobacillus, Ruminococcus and Clostridium were lower while Prevotella was higher in PCOS rats when compared with control rats. After treating PCOS rats with Lactobacillus and fecal microbiota transplantation (FMT) from healthy rats, it was found that the estrous cycles were improved in all 8 rats in FMT group, and in 6 of the 8 rats in Lactobacillus transplantation group with decreasing androgen biosynthesis. Their ovarian morphologies normalized. The composition of gut microbiota restored in both FMT and Lactobacillus treated groups with increasing of Lactobacillus and Clostridium, and decreasing of Prevotella. These results indicated that dysbiosis of gut microbiota was associated with the pathogenesis of PCOS. Microbiota interventions through FMT and Lactobacillus transplantation were beneficial for the treatments of PCOS rats. PMID:27093642

  14. Lactobacillus rhamnosus GG Intake Modifies Preschool Children’s Intestinal Microbiota, Alleviates Penicillin-Associated Changes, and Reduces Antibiotic Use

    PubMed Central

    Korpela, Katri; Salonen, Anne; Virta, Lauri J.; Kumpu, Minna; Kekkonen, Riina A.; de Vos, Willem M.

    2016-01-01

    Antibiotic use is considered among the most severe causes of disturbance to children’s developing intestinal microbiota, and frequently causes adverse gastrointestinal effects ranging from mild and transient diarrhoea to life-threatening infections. Probiotics are commonly advocated to help in preventing antibiotic-associated gastrointestinal symptoms. However, it is currently unknown whether probiotics alleviate the antibiotic-associated changes in children’s microbiota. Furthermore, it is not known how long-term probiotic consumption influences the developing microbiota of children. We analysed the influence of long-term Lactobacillus rhamnosus GG intake on preschool children’s antibiotic use, and antibiotic-associated gastrointestinal complaints in a double blind, randomized placebo-controlled trial with 231 children aged 2–7. In addition, we analysed the effect of L. rhanmosus GG on the intestinal microbiota in a subset of 88 children. The results show that long-term L. rhamnosus GG supplementation has an influence on the composition of the intestinal microbiota in children, causing an increase in the abundance of Prevotella, Lactococcus, and Ruminococcus, and a decrease in Escherichia. The treatment appeared to prevent some of the changes in the microbiota associated with penicillin use, but not those associated with macrolide use. The treatment, however, did reduce the frequency of gastrointestinal complaints after a macrolide course. Finally, the treatment appeared to prevent certain bacterial infections for up to 3 years after the trial, as indicated by reduced antibiotic use. Trial Registration: ClinicalTrials.gov NCT01014676 PMID:27111772

  15. Phenylketonuria and Gut Microbiota: A Controlled Study Based on Next-Generation Sequencing

    PubMed Central

    Pinheiro de Oliveira, Felipe; Mendes, Roberta Hack; Dobbler, Priscila Thiago; Mai, Volker; Pylro, Victor Salter; Waugh, Sheldon G; Vairo, Filippo; Refosco, Lilia Farret; Schwartz, Ida Vanessa Doederlein

    2016-01-01

    Phenylketonuria (PKU) is an inborn error of metabolism associated with high blood levels of phenylalanine (Phe). A Phe-restricted diet supplemented with L-amino acids is the main treatment strategy for this disease; if started early, most neurological abnormalities can be prevented. The healthy human gut contains trillions of commensal bacteria, often referred to as the gut microbiota. The composition of the gut microbiota is known to be modulated by environmental factors, including diet. In this study, we compared the gut microbiota of 8 PKU patients on Phe-restricted dietary treatment with that of 10 healthy individuals. The microbiota were characterized by 16S rRNA sequencing using the Ion Torrent™ platform. The most dominant phyla detected in both groups were Bacteroidetes and Firmicutes. PKU patients showed reduced abundance of the Clostridiaceae, Erysipelotrichaceae, and Lachnospiraceae families, Clostridiales class, Coprococcus, Dorea, Lachnospira, Odoribacter, Ruminococcus and Veillonella genera, and enrichment of Prevotella, Akkermansia, and Peptostreptococcaceae. Microbial function prediction suggested significant differences in starch/glucose and amino acid metabolism between PKU patients and controls. Together, our results suggest the presence of distinct taxonomic groups within the gut microbiome of PKU patients, which may be modulated by their plasma Phe concentration. Whether our findings represent an effect of the disease itself, or a consequence of the modified diet is unclear. PMID:27336782

  16. Mining of hemicellulose and lignin degrading genes from differentially enriched methane producing microbial community.

    PubMed

    Pandit, Prabhakar D; Gulhane, Madhuri K; Khardenavis, Anshuman A; Purohit, Hemant J

    2016-09-01

    Study creates a scenario for enrichment and selection of ligno-hemicellulose degrading genotypes with anaerobic bioreactor as a model using rice straw, vegetable waste and food waste as substrates. Relative discrimination analysis showed that the hydrolytic pathways and associated microbial communities for ligno-hemicellulose degradation were dominatingly colonized with rice straw as substrate. The dominating bacteria were Caldicellulosiruptor, Fervidobacterium, Cytophaga, Ruminococcus, Thermotoga associated with hemicellulose degradation and Burkholderia, Pandorea, Sphingomonas, Spirochaeta, Pseudomonas for lignocellulose hydrolysis. This was further supported by the abundance of anaerobic aromatic compound degrading genes along with genes for xylanase and xylosidase in rice straw enriched community. The metagenome analysis data was validated by evaluation of the biochemical methane potential for these substrates. Food waste being most amenable substrate yielded 1410mL of biogas/gVS added whereas, biogas yield of 1160mL/gVS and 1080mL/gVS was observed in presence of vegetable waste and rice straw respectively. PMID:27323244

  17. Transfer of intestinal bacterial components to mammary secretions in the cow

    PubMed Central

    Young, Wayne; Hine, Brad C.; Wallace, Olivia A.M.; Callaghan, Megan

    2015-01-01

    Results from large multicentre epidemiological studies suggest an association between the consumption of raw milk and a reduced incidence of allergy and asthma in children. Although the underlying mechanisms for this association are yet to be confirmed, researchers have investigated whether bacteria or bacterial components that naturally occur in cow’s milk are responsible for modulating the immune system to reduce the risk of allergic diseases. Previous research in human and mice suggests that bacterial components derived from the maternal intestine are transported to breast milk through the bloodstream. The aim of our study was to assess whether a similar mechanism of bacterial trafficking could occur in the cow. Through the application of culture-independent methodology, we investigated the microbial composition and diversity of milk, blood and feces of healthy lactating cows. We found that a small number of bacterial OTUs belonging to the genera Ruminococcus and Bifidobacterium, and the Peptostreptococcaceae family were present in all three samples from the same individual animals. Although these results do not confirm the hypothesis that trafficking of intestinal bacteria into mammary secretions does occur in the cow, they support the existence of an endogenous entero-mammary pathway for some bacterial components during lactation in the cow. Further research is required to define the specific mechanisms by which gut bacteria are transported into the mammary gland of the cow, and the health implications of such bacteria being present in milk. PMID:25922791

  18. Early diet impacts infant rhesus gut microbiome, immunity, and metabolism.

    PubMed

    O'Sullivan, Aifric; He, Xuan; McNiven, Elizabeth M S; Haggarty, Neill W; Lönnerdal, Bo; Slupsky, Carolyn M

    2013-06-01

    Epidemiological research has indicated a relationship between infant formula feeding and increased risk of chronic diseases later in life including obesity, type-2 diabetes, and cardiovascular disease. The present study used an infant rhesus monkey model to compare the comprehensive metabolic implications of formula- and breast-feeding practices using NMR spectroscopy to characterize metabolite fingerprints from urine and serum, in combination with anthropometric measurements, fecal microbial profiling, and cytokine measurements. Here we show that formula-fed infants are larger than their breast-fed counterparts and have a different gut microbiome that includes higher levels of bacteria from the Ruminococcus genus and lower levels of bacteria from the Lactobacillus genus. In addition, formula-fed infants have higher serum insulin coupled with higher amino acid levels, while amino acid degradation products were higher in breast-fed infants. Increases in serum and urine galactose and urine galactitol were observed in the second month of life in formula-fed infants, along with higher levels of TNFα, IFN-γ, IL-1β, IL-4, and other cytokines and growth factors at week 4. These results demonstrate that metabolic and gut microbiome development of formula-fed infants is different from breast-fed infants and that the choice of infant feeding may hold future health consequences.

  19. Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans.

    PubMed

    Ushida, Kazunari; Segawa, Takahiro; Tsuchida, Sayaka; Murata, Koichi

    2016-02-01

    Preservation of indigenous gastrointestinal microbiota is deemed to be critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we investigated cecal bacterial communities in wild Japanese rock ptarmigans (Lagopus muta japonica) and compared them with those in Svalbard rock ptarmigans (L. m. hyperborea) in captivity. Ultra-deep sequencing of 16S rRNA gene indicated that the community structure of cecal microbiota in wild rock ptarmigans was remarkably different from that in captive Svalbard rock ptarmigans. Fundamental differences between bacterial communities in the two groups of birds were detected at the phylum level. Firmicutes, Actinobacteria, Bacteroidetes and Synergistetes were the major phyla detected in wild Japanese rock ptarmigans, whereas Firmicutes alone occupied more than 80% of abundance in captive Svalbard rock ptarmigans. Furthermore, unclassified genera of Coriobacteriaceae, Synergistaceae, Bacteroidaceae, Actinomycetaceae, Veillonellaceae and Clostridiales were the major taxa detected in wild individuals, whereas in zoo-reared birds, major genera were Ruminococcus, Blautia, Faecalibacterium and Akkermansia. Zoo-reared birds seemed to lack almost all rock ptarmigan-specific bacteria in their intestine, which may explain the relatively high rate of pathogenic infections affecting them. We show evidence that preservation and reconstitution of indigenous cecal microflora are critical for successful ex situ conservation and future re-introduction plan for the Japanese rock ptarmigan. PMID:26468217

  20. Diet rapidly and reproducibly alters the human gut microbiome.

    PubMed

    David, Lawrence A; Maurice, Corinne F; Carmody, Rachel N; Gootenberg, David B; Button, Julie E; Wolfe, Benjamin E; Ling, Alisha V; Devlin, A Sloan; Varma, Yug; Fischbach, Michael A; Biddinger, Sudha B; Dutton, Rachel J; Turnbaugh, Peter J

    2014-01-23

    Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles.

  1. Detection of Sialic Acid-Utilising Bacteria in a Caecal Community Batch Culture Using RNA-Based Stable Isotope Probing

    PubMed Central

    Young, Wayne; Egert, Markus; Bassett, Shalome A.; Bibiloni, Rodrigo

    2015-01-01

    Sialic acids are monosaccharides typically found on cell surfaces and attached to soluble proteins, or as essential components of ganglioside structures that play a critical role in brain development and neural transmission. Human milk also contains sialic acid conjugated to oligosaccharides, glycolipids, and glycoproteins. These nutrients can reach the large bowel where they may be metabolised by the microbiota. However, little is known about the members of the microbiota involved in this function. To identify intestinal bacteria that utilise sialic acid within a complex intestinal community, we cultured the caecal microbiota from piglets in the presence of 13C-labelled sialic acid. Using RNA-based stable isotope probing, we identified bacteria that consumed 13C-sialic acid by fractionating total RNA in isopycnic buoyant density gradients followed by 16S rRNA gene analysis. Addition of sialic acid caused significant microbial community changes. A relative rise in Prevotella and Lactobacillus species was accompanied by a corresponding reduction in the genera Escherichia/Shigella, Ruminococcus and Eubacterium. Inspection of isotopically labelled RNA sequences suggests that the labelled sialic acid was consumed by a wide range of bacteria. However, species affiliated with the genus Prevotella were clearly identified as the most prolific users, as solely their RNA showed significantly higher relative shares among the most labelled RNA species. Given the relevance of sialic acid in nutrition, this study contributes to a better understanding of their microbial transformation in the intestinal tract with potential implications for human health. PMID:25816158

  2. Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation

    PubMed Central

    Tailford, Louise E.; Owen, C. David; Walshaw, John; Crost, Emmanuelle H.; Hardy-Goddard, Jemma; Le Gall, Gwenaelle; de Vos, Willem M.; Taylor, Garry L.; Juge, Nathalie

    2015-01-01

    The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut. Alterations in mucosal carbohydrate availability impact on the composition of microbial species. Ruminococcus gnavus is a commensal anaerobe present in the gastrointestinal tract of >90% of humans and overrepresented in inflammatory bowel diseases (IBD). Using a combination of genomics, enzymology and crystallography, we show that the mucin-degrader R. gnavus ATCC 29149 strain produces an intramolecular trans-sialidase (IT-sialidase) that cleaves off terminal α2-3-linked sialic acid from glycoproteins, releasing 2,7-anhydro-Neu5Ac instead of sialic acid. Evidence of IT-sialidases in human metagenomes indicates that this enzyme occurs in healthy subjects but is more prevalent in IBD metagenomes. Our results uncover a previously unrecognized enzymatic activity in the gut microbiota, which may contribute to the adaptation of intestinal bacteria to the mucosal environment in health and disease. PMID:26154892

  3. Impact of subacute ruminal acidosis (SARA) adaptation on rumen microbiota in dairy cattle using pyrosequencing.

    PubMed

    Mao, S Y; Zhang, R Y; Wang, D S; Zhu, W Y

    2013-12-01

    The objective of this study was to evaluate the changes in bacterial populations in the rumen of dairy cattle following adaptation to subacute ruminal acidosis (SARA) using 16S rRNA gene pyrosequencing. Rumen contents were collected from four cattle adapted to either a 40% (control diet, COD) or 70% (SARA induction diet, SAID) concentrate feeds. DNA was extracted from each of the samples. Bacterial 16S rRNA genes of ruminal DNA extracts were PCR amplified with 2 bar coded primer sets and sequenced by 454 pyrosequencing. At a high taxonomic level, the percentage of Proteobacteria and Bacteroidetes were reduced by SAID feeding, whereas Firmicutes and Actinobacteria were more abundant in the SAID than in the COD group. At the genus level, as compared with the COD group, the abundances of Prevotella, Treponema, Anaeroplasma, Papillibacter, Acinetobacter and unclassified populations including unclassified Lentisphaerae, and unclassified bacteria were lower (P < 0.05), while the percentages of Ruminococcus, Atopobium, unclassified Clostridiales and Bifidobacterium were increased (P < 0.05) in the SAID group. Feeding of SAID reduced (P < 0.001) the diversity of the rumen microbial community. Taken together, our findings provide a comprehensive picture of current knowledge of the community structure of the rumen bacterial ecosystem during SARA, and enhance our understanding about the ruminal microbial ecology that may be useful in the prevention of ruminal acidosis.

  4. A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms

    PubMed Central

    Indugu, Nagaraju; Bittinger, Kyle; Kumar, Sanjay; Vecchiarelli, Bonnie

    2016-01-01

    Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M2 = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed. PMID:26870608

  5. Seasonal changes in the adherent microflora of the rumen in high-arctic Svalbard reindeer.

    PubMed

    Cheng, K J; McAllister, T A; Mathiesen, S D; Blix, A S; Orpin, C G; Costerton, J W

    1993-01-01

    Seasonal changes in bacterial colonization of the epithelial tissue were examined in the rumen of high-arctic Svalbard reindeer. Samples of tissue were collected from eight sites in the rumen of reindeer during summer and winter and bacterial colonization was examined using scanning and transmission electron microscopy. At two of these sites, colonization by adherent bacteria was estimated to cover approximately 30% of the ruminal epithelium in specimens collected from reindeer during summer. Bacteria at these sites resembled Ruminococcus sp. and were surrounded by large amounts of glycocalyx. In winter specimens, less than 10% of the epithelial surface was covered by adherent bacteria. Those bacteria that did colonize the epithelial surface were smaller and had virtually no glycocalyx on their surface. Bacteria attached to plant cell wall material in summer samples of reindeer ingesta contained large intracellular glycogen deposits, whereas feed particle-associated bacteria in ingesta collected in winter contained no intracellular glycogen. These data demonstrate that the ruminal bacterial population responds to seasonal changes in feed intake and quality. It is yet to be determined if these bacterial changes enhance the ability of Svalbard reindeer to survive in the hostile environment of the high Arctic.

  6. Discovery of intramolecular trans-sialidases in human gut microbiota suggests novel mechanisms of mucosal adaptation

    NASA Astrophysics Data System (ADS)

    Tailford, Louise E.; Owen, C. David; Walshaw, John; Crost, Emmanuelle H.; Hardy-Goddard, Jemma; Le Gall, Gwenaelle; de Vos, Willem M.; Taylor, Garry L.; Juge, Nathalie

    2015-07-01

    The gastrointestinal mucus layer is colonized by a dense community of microbes catabolizing dietary and host carbohydrates during their expansion in the gut. Alterations in mucosal carbohydrate availability impact on the composition of microbial species. Ruminococcus gnavus is a commensal anaerobe present in the gastrointestinal tract of >90% of humans and overrepresented in inflammatory bowel diseases (IBD). Using a combination of genomics, enzymology and crystallography, we show that the mucin-degrader R. gnavus ATCC 29149 strain produces an intramolecular trans-sialidase (IT-sialidase) that cleaves off terminal α2-3-linked sialic acid from glycoproteins, releasing 2,7-anhydro-Neu5Ac instead of sialic acid. Evidence of IT-sialidases in human metagenomes indicates that this enzyme occurs in healthy subjects but is more prevalent in IBD metagenomes. Our results uncover a previously unrecognized enzymatic activity in the gut microbiota, which may contribute to the adaptation of intestinal bacteria to the mucosal environment in health and disease.

  7. Rescue of Fructose-Induced Metabolic Syndrome by Antibiotics or Faecal Transplantation in a Rat Model of Obesity

    PubMed Central

    Mazzoli, Arianna; Cigliano, Luisa; Venditti, Paola; Walser, Jean-Claude; Widmer, Alex; Baccigalupi, Loredana; Ricca, Ezio; Iossa, Susanna

    2015-01-01

    A fructose-rich diet can induce metabolic syndrome, a combination of health disorders that increases the risk of diabetes and cardiovascular diseases. Diet is also known to alter the microbial composition of the gut, although it is not clear whether such alteration contributes to the development of metabolic syndrome. The aim of this work was to assess the possible link between the gut microbiota and the development of diet-induced metabolic syndrome in a rat model of obesity. Rats were fed either a standard or high-fructose diet. Groups of fructose-fed rats were treated with either antibiotics or faecal samples from control rats by oral gavage. Body composition, plasma metabolic parameters and markers of tissue oxidative stress were measured in all groups. A 16S DNA-sequencing approach was used to evaluate the bacterial composition of the gut of animals under different diets. The fructose-rich diet induced markers of metabolic syndrome, inflammation and oxidative stress, that were all significantly reduced when the animals were treated with antibiotic or faecal samples. The number of members of two bacterial genera, Coprococcus and Ruminococcus, was increased by the fructose-rich diet and reduced by both antibiotic and faecal treatments, pointing to a correlation between their abundance and the development of the metabolic syndrome. Our data indicate that in rats fed a fructose-rich diet the development of metabolic syndrome is directly correlated with variations of the gut content of specific bacterial taxa. PMID:26244577

  8. Does our food (environment) change our gut microbiome ('in-vironment'): a potential role for inflammatory bowel disease?

    PubMed

    de Wouters, Tomas; Doré, Joël; Lepage, Patricia

    2012-01-01

    Human biology can only be fully assessed by combining an analysis of both the host and its surrounding environment. As a part of the environment, the human gastrointestinal tract hosts more than 100 trillion bacteria making up the gut microbiota. The human host provides a nutrient-rich environment while the microbiota provides indispensable functions that humans cannot exert themselves. Shifts in the bacterial makeup of the human gut microbiota have been associated with disorders such as inflammatory bowel disease (IBD), irritable bowel syndrome and obesity. However, since most bacteria inhabiting our gut are not cultivable to date, until recently little was known about their individual functions. Metagenomics, i.e. the analysis of the collective genomes present in a defined ecosystem, gives insight into these specific functions. The first extensive catalogue of the intestinal metagenome outnumbers the size of the human genome by a factor of 150. Recently, 3 distinct 'types' of gut composition within the human population have been highlighted. These so-called 'enterotypes' are characterized by the dominant genera (Bacteroides, Prevotella and Ruminococcus) and their co-occurring phylogenetic groups. In accordance with the previously described impact of nutritional behavior (diet, probiotics and prebiotics) on specific bacterial populations, an association has been observed between long-term dietary habits and enterotypes. This recent discovery, i.e. that belonging to one or the other enterotype might be modulated by the diet opens up new perspectives in the fields of IBD, nutrition and therapeutic strategies.

  9. Phenylketonuria and Gut Microbiota: A Controlled Study Based on Next-Generation Sequencing.

    PubMed

    Pinheiro de Oliveira, Felipe; Mendes, Roberta Hack; Dobbler, Priscila Thiago; Mai, Volker; Pylro, Victor Salter; Waugh, Sheldon G; Vairo, Filippo; Refosco, Lilia Farret; Roesch, Luiz Fernando Würdig; Schwartz, Ida Vanessa Doederlein

    2016-01-01

    Phenylketonuria (PKU) is an inborn error of metabolism associated with high blood levels of phenylalanine (Phe). A Phe-restricted diet supplemented with L-amino acids is the main treatment strategy for this disease; if started early, most neurological abnormalities can be prevented. The healthy human gut contains trillions of commensal bacteria, often referred to as the gut microbiota. The composition of the gut microbiota is known to be modulated by environmental factors, including diet. In this study, we compared the gut microbiota of 8 PKU patients on Phe-restricted dietary treatment with that of 10 healthy individuals. The microbiota were characterized by 16S rRNA sequencing using the Ion Torrent™ platform. The most dominant phyla detected in both groups were Bacteroidetes and Firmicutes. PKU patients showed reduced abundance of the Clostridiaceae, Erysipelotrichaceae, and Lachnospiraceae families, Clostridiales class, Coprococcus, Dorea, Lachnospira, Odoribacter, Ruminococcus and Veillonella genera, and enrichment of Prevotella, Akkermansia, and Peptostreptococcaceae. Microbial function prediction suggested significant differences in starch/glucose and amino acid metabolism between PKU patients and controls. Together, our results suggest the presence of distinct taxonomic groups within the gut microbiome of PKU patients, which may be modulated by their plasma Phe concentration. Whether our findings represent an effect of the disease itself, or a consequence of the modified diet is unclear. PMID:27336782

  10. Collateral damage from oral ciprofloxacin versus nitrofurantoin in outpatients with urinary tract infections: a culture-free analysis of gut microbiota.

    PubMed

    Stewardson, A J; Gaïa, N; François, P; Malhotra-Kumar, S; Delémont, C; Martinez de Tejada, B; Schrenzel, J; Harbarth, S; Lazarevic, V

    2015-04-01

    Recent treatment guidelines for uncomplicated urinary tract infections (UTIs) discourage fluoroquinolone prescription because of collateral damage to commensal microbiota, but the ecologic impact of alternative agents has not been evaluated by culture-free techniques. We prospectively collected faecal samples at three time points from ambulatory patients with UTIs treated with ciprofloxacin or nitrofurantoin, patients not requiring antibiotics and household contacts of ciprofloxacin-treated patients. We described changes in gut microbiota using a culture-independent approach based on pyrosequencing of the V3-V4 region of the bacterial 16S rRNA gene. All groups were similar at baseline. Ciprofloxacin had a significant global impact on the gut microbiota whereas nitrofurantoin did not. The end of ciprofloxacin treatment correlated with a reduced proportion of Bifidobacterium (Actinobacteria), Alistipes (Bacteroidetes) and four genera from the phylum Firmicutes (Faecalibacterium, Oscillospira, Ruminococcus and Dialister) and an increased relative abundance of Bacteroides (Bacteroidetes) and the Firmicutes genera Blautia, Eubacterium and Roseburia. Substantial recovery had occurred 4 weeks later. Nitrofurantoin treatment correlated with a reduced relative proportion of the genus Clostridium and an increased proportion of the genus Faecalibacterium. This study supports use of nitrofurantoin over fluoroquinolones for treatment of uncomplicated UTIs to minimize perturbation of intestinal microbiota. PMID:25658522

  11. Association between Polycystic Ovary Syndrome and Gut Microbiota.

    PubMed

    Guo, Yanjie; Qi, Yane; Yang, Xuefei; Zhao, Lihui; Wen, Shu; Liu, Yinhui; Tang, Li

    2016-01-01

    Polycystic ovary syndrome (PCOS) is the most frequent endocrinopathy in women of reproductive age. It is difficult to treat PCOS because of its complex etiology and pathogenesis. Here, we characterized the roles of gut microbiota on the pathogenesis and treatments in letrozole (a nonsteroidal aromatase inhibitor) induced PCOS rat model. Changes in estrous cycles, hormonal levels, ovarian morphology and gut microbiota by PCR-DGGE and real-time PCR were determined. The results showed that PCOS rats displayed abnormal estrous cycles with increasing androgen biosynthesis and exhibited multiple large cysts with diminished granulosa layers in ovarian tissues. Meanwhile, the composition of gut microbiota in letrozole-treated rats was different from that in the controls. Lactobacillus, Ruminococcus and Clostridium were lower while Prevotella was higher in PCOS rats when compared with control rats. After treating PCOS rats with Lactobacillus and fecal microbiota transplantation (FMT) from healthy rats, it was found that the estrous cycles were improved in all 8 rats in FMT group, and in 6 of the 8 rats in Lactobacillus transplantation group with decreasing androgen biosynthesis. Their ovarian morphologies normalized. The composition of gut microbiota restored in both FMT and Lactobacillus treated groups with increasing of Lactobacillus and Clostridium, and decreasing of Prevotella. These results indicated that dysbiosis of gut microbiota was associated with the pathogenesis of PCOS. Microbiota interventions through FMT and Lactobacillus transplantation were beneficial for the treatments of PCOS rats.

  12. Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass.

    PubMed

    Huws, Sharon A; Edwards, Joan E; Creevey, Christopher J; Rees Stevens, Pauline; Lin, Wanchang; Girdwood, Susan E; Pachebat, Justin A; Kingston-Smith, Alison H

    2016-01-01

    This study investigated successional colonization of fresh perennial ryegrass (PRG) by the rumen microbiota over time. Fresh PRG was incubated in sacco in the rumens of three Holstein × Friesian cows over a period of 8 h, with samples recovered at various times. The diversity of attached bacteria was assessed using 454 pyrosequencing of 16S rRNA (cDNA). Results showed that plant epiphytic communities either decreased to low relative abundances or disappeared following rumen incubation, and that temporal colonization of the PRG by the rumen bacteria was biphasic with primary (1 and 2 h) and secondary (4-8 h) events evident with the transition period being with 2-4 h. A decrease in sequence reads pertaining to Succinivibrio spp. and increases in Pseudobutyrivibrio, Roseburia and Ruminococcus spp. (the latter all order Clostridiales) were evident during secondary colonization. Irrespective of temporal changes, the continually high abundances of Butyrivibrio, Fibrobacter, Olsenella and Prevotella suggest that they play a major role in the degradation of the plant. It is clear that a temporal understanding of the functional roles of these microbiota within the rumen is now required to unravel the role of these bacteria in the ruminal degradation of fresh PRG.

  13. Cecal bacterial communities in wild Japanese rock ptarmigans and captive Svalbard rock ptarmigans

    PubMed Central

    USHIDA, Kazunari; SEGAWA, Takahiro; TSUCHIDA, Sayaka; MURATA, Koichi

    2015-01-01

    Preservation of indigenous gastrointestinal microbiota is deemed to be critical for successful captive breeding of endangered wild animals, yet its biology is poorly understood. Here, we investigated cecal bacterial communities in wild Japanese rock ptarmigans (Lagopus muta japonica) and compared them with those in Svalbard rock ptarmigans (L. m. hyperborea) in captivity. Ultra-deep sequencing of 16S rRNA gene indicated that the community structure of cecal microbiota in wild rock ptarmigans was remarkably different from that in captive Svalbard rock ptarmigans. Fundamental differences between bacterial communities in the two groups of birds were detected at the phylum level. Firmicutes, Actinobacteria, Bacteroidetes and Synergistetes were the major phyla detected in wild Japanese rock ptarmigans, whereas Firmicutes alone occupied more than 80% of abundance in captive Svalbard rock ptarmigans. Furthermore, unclassified genera of Coriobacteriaceae, Synergistaceae, Bacteroidaceae, Actinomycetaceae, Veillonellaceae and Clostridiales were the major taxa detected in wild individuals, whereas in zoo-reared birds, major genera were Ruminococcus, Blautia, Faecalibacterium and Akkermansia. Zoo-reared birds seemed to lack almost all rock ptarmigan-specific bacteria in their intestine, which may explain the relatively high rate of pathogenic infections affecting them. We show evidence that preservation and reconstitution of indigenous cecal microflora are critical for successful ex situ conservation and future re-introduction plan for the Japanese rock ptarmigan. PMID:26468217

  14. Response of the rumen archaeal and bacterial populations to anti-methanogenic organosulphur compounds in continuous-culture fermenters.

    PubMed

    Martínez-Fernández, Gonzalo; Abecia, Leticia; Martín-García, A Ignacio; Ramos-Morales, Eva; Denman, Stuart E; Newbold, Charles J; Molina-Alcaide, Eduarda; Yáñez-Ruiz, David R

    2015-08-01

    Study of the efficacy of methanogenesis inhibitors in the rumen has given inconsistent results, mainly due to poorly understood effects on the key microbial groups involved in pathways for methane (CH4) synthesis. The experiment described in this report was designed to assess the effect of propyl propane thiosulfinate (PTS), diallyl disulfide (DDS) and bromochloromethane (BCM) on rumen fermentation, methane production and microbial populations in continuous culture fermenters. No effects on total volatile fatty acids (VFA) were observed with PTS or DDS, but VFA were decreased with BCM. Amylase activity increased with BCM as compared with the other treatments. A decrease in methane production was observed with PTS (48%) and BCM (94%) as compared with control values. The concentration of methanogenic archaea decreased with BCM from day 4 onward and with PTS on days 4 and 8. Pyrosequencing analysis revealed that PTS and BCM decreased the relative abundance of Methanomicrobiales and increased that of Methanobrevibacter and Methanosphaera. The total concentration of bacteria was not modified by any treatment, although treatment with BCM increased the relative abundance of Prevotella and decreased that of Ruminococcus. These results suggest that the inhibition of methane production in the rumen by PTS and BCM is associated with a shift in archaeal biodiversity and changes in the bacterial community with BCM. PMID:26183917

  15. Temporal dynamics of the metabolically active rumen bacteria colonizing fresh perennial ryegrass.

    PubMed

    Huws, Sharon A; Edwards, Joan E; Creevey, Christopher J; Rees Stevens, Pauline; Lin, Wanchang; Girdwood, Susan E; Pachebat, Justin A; Kingston-Smith, Alison H

    2016-01-01

    This study investigated successional colonization of fresh perennial ryegrass (PRG) by the rumen microbiota over time. Fresh PRG was incubated in sacco in the rumens of three Holstein × Friesian cows over a period of 8 h, with samples recovered at various times. The diversity of attached bacteria was assessed using 454 pyrosequencing of 16S rRNA (cDNA). Results showed that plant epiphytic communities either decreased to low relative abundances or disappeared following rumen incubation, and that temporal colonization of the PRG by the rumen bacteria was biphasic with primary (1 and 2 h) and secondary (4-8 h) events evident with the transition period being with 2-4 h. A decrease in sequence reads pertaining to Succinivibrio spp. and increases in Pseudobutyrivibrio, Roseburia and Ruminococcus spp. (the latter all order Clostridiales) were evident during secondary colonization. Irrespective of temporal changes, the continually high abundances of Butyrivibrio, Fibrobacter, Olsenella and Prevotella suggest that they play a major role in the degradation of the plant. It is clear that a temporal understanding of the functional roles of these microbiota within the rumen is now required to unravel the role of these bacteria in the ruminal degradation of fresh PRG. PMID:26542074

  16. Mining of luxS genes from rumen microbial consortia by metagenomic and metatranscriptomic approaches.

    PubMed

    Ghali, Ines; Shinkai, Takumi; Mitsumori, Makoto

    2016-05-01

    Although rumen bacterial communities vary depending on many factors such as diet, age and physiological conditions, a core microbiota exists within the rumen. In many natural environments, some bacteria use a quorum-sensing (QS) system to regulate their physiological activities. However, very limited information is available about QS systems in rumen. To investigate the autoinducer 2 (AI-2)-mediated QS system in rumen, we detected genes (luxS) encoding the AI-2 synthase (LuxS), from three datasets embedded in metagenomics RAST server (MG-RAST) and from a metatranscriptome dataset. We collected 135 luxS genes from the metagenomic datasets, which were presumed to originate from Bacteroidetes, Firmicutes, Fusobacteria and Actinobacteria, and 34 luxS genes from the metatranscriptome dataset, which probably originated from Bacteroidetes, Firmicutes and Spirochaetes. Because the essential amino acids for LuxS activity were conserved in the LuxS homologues predicted from luxS gene sequences from both datasets, the LuxS homologues probably function in the rumen. Since the largest number of sequences of luxS genes were collected from the genera Prevotella, Ruminococcus and Eubacterium, which include many fibrolytic bacteria and constituent members of biofilm on feed particles, an AI-2-mediated QS system is likely involved in biofilm formation and fibrolytic activity in the rumen. PMID:26277986

  17. A comparison of rumen microbial profiles in dairy cows as retrieved by 454 Roche and Ion Torrent (PGM) sequencing platforms.

    PubMed

    Indugu, Nagaraju; Bittinger, Kyle; Kumar, Sanjay; Vecchiarelli, Bonnie; Pitta, Dipti

    2016-01-01

    Next generation sequencing (NGS) technology is a widely accepted tool used by microbial ecologists to explore complex microbial communities in different ecosystems. As new NGS platforms continue to become available, it becomes imperative to compare data obtained from different platforms and analyze their effect on microbial community structure. In the present study, we compared sequencing data from both the 454 and Ion Torrent (PGM) platforms on the same DNA samples obtained from the rumen of dairy cows during their transition period. Despite the substantial difference in the number of reads, error rate and length of reads among both platforms, we identified similar community composition between the two data sets. Procrustes analysis revealed similar correlations (M (2) = 0.319; P = 0.001) in the microbial community composition between the two platforms. Both platforms revealed the abundance of the same bacterial phyla which were Bacteroidetes and Firmicutes; however, PGM recovered an additional four phyla. Comparisons made at the genus level by each platforms revealed differences in only a few genera such as Prevotella, Ruminococcus, Succiniclasticum and Treponema (p < 0.05; chi square test). Collectively, we conclude that the output generated from PGM and 454 yielded concurrent results, provided stringent bioinformatics pipelines are employed. PMID:26870608

  18. Microbial and Carbohydrate Active Enzyme profile of buffalo rumen metagenome and their alteration in response to variation in the diet.

    PubMed

    Patel, Dishita D; Patel, Amrutlal K; Parmar, Nidhi R; Shah, Tejas M; Patel, Jethabhai B; Pandya, Paresh R; Joshi, Chaitanya G

    2014-07-15

    Rumen microbiome represents rich source of enzymes degrading complex plant polysaccharides. We describe here analysis of Carbohydrate Active Enzymes (CAZymes) from 3.5 gigabase sequences of metagenomic data from rumen samples of Mehsani buffaloes fed on different proportions of green or dry roughages to concentrate ration. A total of 2597 contigs encoding putative CAZymes were identified by CAZyme Analysis Toolkit (CAT). The phylogenetic analysis of these contigs by MG-RAST revealed predominance of Bacteroidetes, followed by Firmicutes, Proteobacteria, and Actinobacteria phyla. Moreover, a higher abundance of oligosaccharide degrading and debranching enzymes in buffalo rumen metagenome and that of cellulases and hemicellulases in termite hindgut was observed when we compared glycoside hydrolase (GH) profile of buffalo rumen metagenome with cow rumen, termite hindgut and chicken caecum metagenome. Further, comparison of microbial profile of green or dry roughage fed animals showed significantly higher abundance (p-value<0.05) of various polysaccharide degrading bacterial genera like Fibrobacter, Prevotella, Bacteroides, Clostridium and Ruminococcus in green roughage fed animals. In addition, we found a significantly higher abundance (p-value<0.05) of enzymes associated with pectin digestion such as pectin lyase (PL) 1, PL10 and GH28 in green roughage fed animals. Our study outlines CAZyme profile of buffalo rumen metagenome and provides a scope to study the role of abundant enzyme families (oligosaccharide degrading and debranching enzymes) in digestion of coarse feed. PMID:24797613

  19. Extensive Set of 16S rRNA-Based Probes for Detection of Bacteria in Human Feces

    PubMed Central

    Harmsen, Hermie J. M.; Raangs, Gerwin C.; He, Tao; Degener, John E.; Welling, Gjalt W.

    2002-01-01

    For the detection of six groups of anaerobic bacteria in human feces, we designed seven new 16S rRNA-based oligonucleotide probes. This set of probes extends the current set of probes and gives more data on the composition of the human gut flora. Probes were designed for Phascolarctobacterium and relatives (Phasco741), Veillonella (Veil223), Eubacterium hallii and relatives (Ehal1469), Lachnospira and relatives (Lach571), and Eubacterium cylindroides and relatives (Ecyl387), and two probes were designed for Ruminococcus and relatives (Rbro730 and Rfla729). The hybridization conditions for the new probes were optimized for fluorescent in situ hybridization, and the probes were validated against a set of reference organisms. The probes were applied to fecal samples of 11 volunteers to enumerate their target bacterial groups. The Phasco741 and Veil223 probes both detected average numbers below 1% of the total number of bacteria as determined with the bacterial kingdom-specific Bact338 probe. The Ecyl387 probe detected about 1.4%, the Lach571 and Ehal1469 probes detected 3.8 and 3.6%, respectively, and a combination of the Rbro730 and Rfla729 probes detected 10.3%. A set of 15 probes consisting of probes previously described and those presented here were evaluated in hybridization with the fecal samples of the same volunteers. Together, the group-specific probes detected 90% of the total bacterial cells. PMID:12039758

  20. Identification and characterization of an anaerobic ethanol-producing cellulolytic bacterial consortium from Great Basin hot springs with agricultural residues and energy crops.

    PubMed

    Zhao, Chao; Deng, Yunjin; Wang, Xingna; Li, Qiuzhe; Huang, Yifan; Liu, Bin

    2014-09-01

    In order to obtain the cellulolytic bacterial consortia, sediments from Great Basin hot springs (Nevada, USA) were sampled and enriched with cellulosic biomass as the sole carbon source. The bacterial composition of the resulting anaerobic ethanol-producing celluloytic bacterial consortium, named SV79, was analyzed. With methods of the full-length 16S rRNA librarybased analysis and denaturing gradient gel electrophoresis, 21 bacteria belonging to eight genera were detected from this consortium. Clones with closest relation to the genera Acetivibrio, Clostridium, Cellulosilyticum, Ruminococcus, and Sporomusa were predominant. The cellulase activities and ethanol productions of consortium SV79 using different agricultural residues (sugarcane bagasse and spent mushroom substrate) and energy crops (Spartina anglica, Miscanthus floridulus, and Pennisetum sinese Roxb) were studied. During cultivation, consortium SV79 produced the maximum filter paper activity (FPase, 9.41 U/ml), carboxymethylcellulase activity (CMCase, 6.35 U/ml), and xylanase activity (4.28 U/ml) with sugarcane bagasse, spent mushroom substrate, and S. anglica, respectively. The ethanol production using M. floridulus as substrate was up to 2.63 mM ethanol/g using gas chromatography analysis. It has high potential to be a new candidate for producing ethanol with cellulosic biomass under anoxic conditions in natural environments.

  1. Co-expression of D-glucose isomerase and D-psicose 3-epimerase: development of an efficient one-step production of D-psicose.

    PubMed

    Men, Yan; Zhu, Yueming; Zeng, Yan; Izumori, Ken; Sun, Yuanxia; Ma, Yanhe

    2014-10-01

    D-Psicose has been attracting attention in recent years because of its alimentary activities and is used as an ingredient in a range of foods and dietary supplements. To develop a one-step enzymatic process of D-psicose production, thermoactive D-glucose isomerase and the D-psicose 3-epimerase obtained from Bacillus sp. and Ruminococcus sp., respectively, were successfully co-expressed in Escherichia coli BL21 strain. The substrate of one-step enzymatic process was D-glucose. The co-expression system exhibited maximum activity at 65 °C and pH 7.0. Mg(2+) could enhance the output of D-psicose by 2.32 fold to 1.6 g/L from 10 g/L of D-glucose. When using high-fructose corn syrup (HFCS) as substrate, 135 g/L D-psicose was produced under optimum conditions. The mass ratio of D-glucose, D-fructose, and D-psicose was almost 3.0:2.7:1.0, when the reaction reached equilibrium after an 8h incubation time. This co-expression system approaching to produce D-psicose has potential application in food and beverage products, especially softdrinks. PMID:25152409

  2. Organoheterotrophic Bacterial Abundance Associates with Zinc Removal in Lignocellulose-Based Sulfate-Reducing Systems.

    PubMed

    Drennan, Dina M; Almstrand, Robert; Lee, Ilsu; Landkamer, Lee; Figueroa, Linda; Sharp, Jonathan O

    2016-01-01

    Syntrophic relationships between fermentative and sulfate-reducing bacteria are essential to lignocellulose-based systems applied to the passive remediation of mining-influenced waters. In this study, seven pilot-scale sulfate-reducing bioreactor columns containing varying ratios of alfalfa hay, pine woodchips, and sawdust were analyzed over ∼500 days to investigate the influence of substrate composition on zinc removal and microbial community structure. Columns amended with >10% alfalfa removed significantly more sulfate and zinc than did wood-based columns. Enumeration of sulfate reducers by functional signatures (dsrA) and their putative identification from 16S rRNA genes did not reveal significant correlations with zinc removal, suggesting limitations in this directed approach. In contrast, a strong indicator of zinc removal was discerned in comparing the relative abundance of core microorganisms shared by all reactors (>80% of total community), many of which had little direct involvement in metal or sulfate respiration. The relative abundance of Desulfosporosinus, the dominant putative sulfate reducer within these reactors, correlated to representatives of this core microbiome. A subset of these clades, including Treponema, Weissella, and Anaerolinea, was associated with alfalfa and zinc removal, and the inverse was found for a second subset whose abundance was associated with wood-based columns, including Ruminococcus, Dysgonomonas, and Azospira. The construction of a putative metabolic flowchart delineated syntrophic interactions supporting sulfate reduction and suggests that the production of and competition for secondary fermentation byproducts, such as lactate scavenging, influence bacterial community composition and reactor efficacy.

  3. Mongolians core gut microbiota and its correlation with seasonal dietary changes

    PubMed Central

    Zhang, Jiachao; Guo, Zhuang; Lim, Angela An Qi; Zheng, Yi; Koh, Eileen Y.; Ho, Danliang; Qiao, Jianmin; Huo, Dongxue; Hou, Qiangchuan; Huang, Weiqiang; Wang, Lifeng; Javzandulam, Chimedsuren; Narangerel, Choijilsuren; Jirimutu; Menghebilige; Lee, Yuan-Kun; Zhang, Heping

    2014-01-01

    Historically, the Mongol Empire ranks among the world's largest contiguous empires, and the Mongolians developed their unique lifestyle and diet over thousands of years. In this study, the intestinal microbiota of Mongolians residing in Ulan Bator, TUW province and the Khentii pasturing area were studied using 454 pyrosequencing and q-PCR technology. We explored the impacts of lifestyle and seasonal dietary changes on the Mongolians' gut microbes. At the phylum level, the Mongolians's gut populations were marked by a dominance of Bacteroidetes (55.56%) and a low Firmicutes to Bacteroidetes ratio (0.71). Analysis based on the operational taxonomic unit (OTU) level revealed that the Mongolian core intestinal microbiota comprised the genera Prevotella, Bacteroides, Faecalibacterium, Ruminococcus, Subdoligranulum and Coprococcus. Urbanisation and life-style may have modified the compositions of the gut microbiota of Mongolians from Ulan Bator, TUW and Khentii. Based on a food frequency questionnaire, we found that the dietary structure was diverse and stable throughout the year in Ulan Bator and TUW, but was simple and varied during the year in Khentii. Accordingly, seasonal effects on intestinal microbiota were more distinct in Khentii residents than in TUW or Ulan Bator residents. PMID:24833488

  4. Changes in Cecal Microbiota and Mucosal Gene Expression Revealed New Aspects of Epizootic Rabbit Enteropathy

    PubMed Central

    Zúñiga, Manuel; Blas, Enrique; Pérez Martínez, Gaspar

    2014-01-01

    Epizootic Rabbit Enteropathy (ERE) is a severe disease of unknown aetiology that mainly affects post-weaning animals. Its incidence can be prevented by antibiotic treatment suggesting that bacterial elements are crucial for the development of the disease. Microbial dynamics and host responses during the disease were studied. Cecal microbiota was characterized in three rabbit groups (ERE-affected, healthy and healthy pretreated with antibiotics), followed by transcriptional analysis of cytokines and mucins in the cecal mucosa and vermix by q-rtPCR. In healthy animals, cecal microbiota with or without antibiotic pretreatment was very similar and dominated by Alistipes and Ruminococcus. Proportions of both genera decreased in ERE rabbits whereas Bacteroides, Akkermansia and Rikenella increased, as well as Clostridium, γ-Proteobacteria and other opportunistic and pathogenic species. The ERE group displayed remarkable dysbiosis and reduced taxonomic diversity. Transcription rate of mucins and inflammatory cytokines was very high in ERE rabbits, except IL-2, and its analysis revealed the existence of two clearly different gene expression patterns corresponding to Inflammatory and (mucin) Secretory Profiles. Furthermore, these profiles were associated to different bacterial species, suggesting that they may correspond to different stages of the disease. Other data obtained in this work reinforced the notion that ERE morbidity and mortality is possibly caused by an overgrowth of different pathogens in the gut of animals whose immune defence mechanisms seem not to be adequately responding. PMID:25147938

  5. Ecophysiological consequences of alcoholism on human gut microbiota: implications for ethanol-related pathogenesis of colon cancer

    PubMed Central

    Tsuruya, Atsuki; Kuwahara, Akika; Saito, Yuta; Yamaguchi, Haruhiko; Tsubo, Takahisa; Suga, Shogo; Inai, Makoto; Aoki, Yuichi; Takahashi, Seiji; Tsutsumi, Eri; Suwa, Yoshihide; Morita, Hidetoshi; Kinoshita, Kenji; Totsuka, Yukari; Suda, Wataru; Oshima, Kenshiro; Hattori, Masahira; Mizukami, Takeshi; Yokoyama, Akira; Shimoyama, Takefumi; Nakayama, Toru

    2016-01-01

    Chronic consumption of excess ethanol increases the risk of colorectal cancer. The pathogenesis of ethanol-related colorectal cancer (ER-CRC) is thought to be partly mediated by gut microbes. Specifically, bacteria in the colon and rectum convert ethanol to acetaldehyde (AcH), which is carcinogenic. However, the effects of chronic ethanol consumption on the human gut microbiome are poorly understood, and the role of gut microbes in the proposed AcH-mediated pathogenesis of ER-CRC remains to be elaborated. Here we analyse and compare the gut microbiota structures of non-alcoholics and alcoholics. The gut microbiotas of alcoholics were diminished in dominant obligate anaerobes (e.g., Bacteroides and Ruminococcus) and enriched in Streptococcus and other minor species. This alteration might be exacerbated by habitual smoking. These observations could at least partly be explained by the susceptibility of obligate anaerobes to reactive oxygen species, which are increased by chronic exposure of the gut mucosa to ethanol. The AcH productivity from ethanol was much lower in the faeces of alcoholic patients than in faeces of non-alcoholic subjects. The faecal phenotype of the alcoholics could be rationalised based on their gut microbiota structures and the ability of gut bacteria to accumulate AcH from ethanol. PMID:27295340

  6. Pilot Dietary Intervention with Heat-Stabilized Rice Bran Modulates Stool Microbiota and Metabolites in Healthy Adults

    PubMed Central

    Sheflin, Amy M.; Borresen, Erica C.; Wdowik, Melissa J.; Rao, Sangeeta; Brown, Regina J.; Heuberger, Adam L.; Broeckling, Corey D.; Weir, Tiffany L.; Ryan, Elizabeth P.

    2015-01-01

    Heat-stabilized rice bran (SRB) has been shown to regulate blood lipids and glucose, modulate gut mucosal immunity and inhibit colorectal cancer in animal and human studies. However, SRB’s effects on gut microbial composition and metabolism and the resulting implications for health remain largely unknown. A pilot, randomized-controlled trial was developed to investigate the effects of eating 30 g/day SRB on the stool microbiome and metabolome. Seven healthy participants consumed a study meal and snack daily for 28 days. The microbiome and metabolome were characterized using 454 pyrosequencing and gas chromatography-mass spectrometry (GC-MS) at baseline, two and four weeks post-intervention. Increases in eight operational taxonomic units (OTUs), including three from Bifidobacterium and Ruminococcus genera, were observed after two and four weeks of SRB consumption (p < 0.01). Branched chain fatty acids, secondary bile acids and eleven other putative microbial metabolites were significantly elevated in the SRB group after four weeks. The largest metabolite change was a rice bran component, indole-2-carboxylic acid, which showed a mean 12% increase with SRB consumption. These data support the feasibility of dietary SRB intervention in adults and support that SRB consumption can affect gut microbial metabolism. These findings warrant future investigations of larger cohorts evaluating SRB’s effects on intestinal health. PMID:25690418

  7. Changes in cecal microbiota and mucosal gene expression revealed new aspects of epizootic rabbit enteropathy.

    PubMed

    Bäuerl, Christine; Collado, M Carmen; Zúñiga, Manuel; Blas, Enrique; Pérez Martínez, Gaspar

    2014-01-01

    Epizootic Rabbit Enteropathy (ERE) is a severe disease of unknown aetiology that mainly affects post-weaning animals. Its incidence can be prevented by antibiotic treatment suggesting that bacterial elements are crucial for the development of the disease. Microbial dynamics and host responses during the disease were studied. Cecal microbiota was characterized in three rabbit groups (ERE-affected, healthy and healthy pretreated with antibiotics), followed by transcriptional analysis of cytokines and mucins in the cecal mucosa and vermix by q-rtPCR. In healthy animals, cecal microbiota with or without antibiotic pretreatment was very similar and dominated by Alistipes and Ruminococcus. Proportions of both genera decreased in ERE rabbits whereas Bacteroides, Akkermansia and Rikenella increased, as well as Clostridium, γ-Proteobacteria and other opportunistic and pathogenic species. The ERE group displayed remarkable dysbiosis and reduced taxonomic diversity. Transcription rate of mucins and inflammatory cytokines was very high in ERE rabbits, except IL-2, and its analysis revealed the existence of two clearly different gene expression patterns corresponding to Inflammatory and (mucin) Secretory Profiles. Furthermore, these profiles were associated to different bacterial species, suggesting that they may correspond to different stages of the disease. Other data obtained in this work reinforced the notion that ERE morbidity and mortality is possibly caused by an overgrowth of different pathogens in the gut of animals whose immune defence mechanisms seem not to be adequately responding.

  8. Diet rapidly and reproducibly alters the human gut microbiome.

    PubMed

    David, Lawrence A; Maurice, Corinne F; Carmody, Rachel N; Gootenberg, David B; Button, Julie E; Wolfe, Benjamin E; Ling, Alisha V; Devlin, A Sloan; Varma, Yug; Fischbach, Michael A; Biddinger, Sudha B; Dutton, Rachel J; Turnbaugh, Peter J

    2014-01-23

    Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles. PMID:24336217

  9. Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts.

    PubMed

    Kohl, Kevin D; Amaya, James; Passement, Celeste A; Dearing, M Denise; McCue, Marshall D

    2014-12-01

    Many animals face unpredictable food sources and periods of prolonged fasting, which likely present significant challenges to gut microorganisms. While several studies have demonstrated that fasting impacts the gut microbiota, experiments have not been carried out in a comparative context. We used 16S rRNA gene sequencing to document changes in colonic and cecal microbiomes of animals representing five classes of vertebrates at four time points through prolonged fasting: tilapia, toads, geckos, quail, and mice. We found differences in the starvation-induced changes in the microbiome across host species and across gut regions. Microbial phylogenetic diversity increased as a result of fasting in the colons of fish, toads, and mice, while quail exhibited a decrease in diversity; geckos exhibited no change. Microbial diversity in the cecum decreased in fish and exhibited no change in mice. Alterations in relative abundances of microbial taxa varied across hosts. Fish exhibited the most significant changes due to fasting, while geckos maintained a stable community over 28 days of fasting. We uncovered several shared responses of the microbiota across hosts. For example, all tetrapods exhibited decreases in the abundances of Coprobacillus and Ruminococcus in response to fasting. We also discuss host-mediated physiological mechanisms that may underlie these community changes. PMID:25319042

  10. α-Galactosidase/sucrose kinase (AgaSK), a novel bifunctional enzyme from the human microbiome coupling galactosidase and kinase activities.

    PubMed

    Bruel, Laëtitia; Sulzenbacher, Gerlind; Cervera Tison, Marine; Pujol, Ange; Nicoletti, Cendrine; Perrier, Josette; Galinier, Anne; Ropartz, David; Fons, Michel; Pompeo, Frédérique; Giardina, Thierry

    2011-11-25

    α-Galactosides are non-digestible carbohydrates widely distributed in plants. They are a potential source of energy in our daily food, and their assimilation by microbiota may play a role in obesity. In the intestinal tract, they are degraded by microbial glycosidases, which are often modular enzymes with catalytic domains linked to carbohydrate-binding modules. Here we introduce a bifunctional enzyme from the human intestinal bacterium Ruminococcus gnavus E1, α-galactosidase/sucrose kinase (AgaSK). Sequence analysis showed that AgaSK is composed of two domains: one closely related to α-galactosidases from glycoside hydrolase family GH36 and the other containing a nucleotide-binding motif. Its biochemical characterization showed that AgaSK is able to hydrolyze melibiose and raffinose to galactose and either glucose or sucrose, respectively, and to specifically phosphorylate sucrose on the C6 position of glucose in the presence of ATP. The production of sucrose-6-P directly from raffinose points toward a glycolytic pathway in bacteria, not described so far. The crystal structures of the galactosidase domain in the apo form and in complex with the product shed light onto the reaction and substrate recognition mechanisms and highlight an oligomeric state necessary for efficient substrate binding and suggesting a cross-talk between the galactose and kinase domains.

  11. Microorganisms linked to inflammatory bowel disease-associated dysbiosis differentially impact host physiology in gnotobiotic mice.

    PubMed

    Hoffmann, Thomas W; Pham, Hang-Phuong; Bridonneau, Chantal; Aubry, Camille; Lamas, Bruno; Martin-Gallausiaux, Camille; Moroldo, Marco; Rainteau, Dominique; Lapaque, Nicolas; Six, Adrien; Richard, Mathias L; Fargier, Emilie; Le Guern, Marie-Emmanuelle; Langella, Philippe; Sokol, Harry

    2016-02-01

    Studying host-microbiota interactions are fundamental to understanding the mechanisms involved in intestinal homeostasis and inflammation. In this work, we analyzed these interactions in mice that were mono-associated with six microorganisms that are representative of inflammatory bowel disease (IBD)-associated dysbiosis: the bacteria Bacteroides thetaiotaomicron, adhesive-invasive Escherichia coli (AIEC), Ruminococcus gnavus and Roseburia intestinalis; a yeast used as a probiotic drug, Saccharomyces boulardii CNCM I-745; and another yeast, Candida albicans. Extensive ex vivo analyses including colon transcriptomics, histology, immune response, bile acid metabolism and short-chain fatty acid production were studied. We showed that B. thetaiotaomicron had the highest impact on the immune system because it was almost able to recapitulate the effects of the entire conventional microbiota and notably induced Treg pathways. Furthermore, these analyses uncovered the effects of E. coli AIEC LF82 on indoleamine 2,3-dioxygenase expression and of S. boulardii CNCM I-745 on angiogenesis. These results were confirmed in vitro in human cell lines. Finally, our results suggested that R. gnavus has major effects on metabolism, and notably on tryptophan metabolism. This work therefore reveals that microorganisms with a potential role in intestinal homeostasis and inflammation have specific impacts on the host, and it suggests several tracks to follow to understand intestinal homeostasis and IBD pathogenesis better, providing new insights to identify novel therapeutic targets.

  12. Co-expression of D-glucose isomerase and D-psicose 3-epimerase: development of an efficient one-step production of D-psicose.

    PubMed

    Men, Yan; Zhu, Yueming; Zeng, Yan; Izumori, Ken; Sun, Yuanxia; Ma, Yanhe

    2014-10-01

    D-Psicose has been attracting attention in recent years because of its alimentary activities and is used as an ingredient in a range of foods and dietary supplements. To develop a one-step enzymatic process of D-psicose production, thermoactive D-glucose isomerase and the D-psicose 3-epimerase obtained from Bacillus sp. and Ruminococcus sp., respectively, were successfully co-expressed in Escherichia coli BL21 strain. The substrate of one-step enzymatic process was D-glucose. The co-expression system exhibited maximum activity at 65 °C and pH 7.0. Mg(2+) could enhance the output of D-psicose by 2.32 fold to 1.6 g/L from 10 g/L of D-glucose. When using high-fructose corn syrup (HFCS) as substrate, 135 g/L D-psicose was produced under optimum conditions. The mass ratio of D-glucose, D-fructose, and D-psicose was almost 3.0:2.7:1.0, when the reaction reached equilibrium after an 8h incubation time. This co-expression system approaching to produce D-psicose has potential application in food and beverage products, especially softdrinks.

  13. Diet rapidly and reproducibly alters the human gut microbiome

    PubMed Central

    David, Lawrence A.; Maurice, Corinne F.; Carmody, Rachel N.; Gootenberg, David B.; Button, Julie E.; Wolfe, Benjamin E.; Ling, Alisha V.; Devlin, A. Sloan; Varma, Yug; Fischbach, Michael A.; Biddinger, Sudha B.; Dutton, Rachel J.; Turnbaugh, Peter J.

    2013-01-01

    Long-term diet influences the structure and activity of the trillions of microorganisms residing in the human gut1–5, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here, we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila, and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale, and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals2, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi, and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids, and the outgrowth of microorganisms capable of triggering inflammatory bowel disease6. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles. PMID:24336217

  14. Rescue of Fructose-Induced Metabolic Syndrome by Antibiotics or Faecal Transplantation in a Rat Model of Obesity.

    PubMed

    Di Luccia, Blanda; Crescenzo, Raffaella; Mazzoli, Arianna; Cigliano, Luisa; Venditti, Paola; Walser, Jean-Claude; Widmer, Alex; Baccigalupi, Loredana; Ricca, Ezio; Iossa, Susanna

    2015-01-01

    A fructose-rich diet can induce metabolic syndrome, a combination of health disorders that increases the risk of diabetes and cardiovascular diseases. Diet is also known to alter the microbial composition of the gut, although it is not clear whether such alteration contributes to the development of metabolic syndrome. The aim of this work was to assess the possible link between the gut microbiota and the development of diet-induced metabolic syndrome in a rat model of obesity. Rats were fed either a standard or high-fructose diet. Groups of fructose-fed rats were treated with either antibiotics or faecal samples from control rats by oral gavage. Body composition, plasma metabolic parameters and markers of tissue oxidative stress were measured in all groups. A 16S DNA-sequencing approach was used to evaluate the bacterial composition of the gut of animals under different diets. The fructose-rich diet induced markers of metabolic syndrome, inflammation and oxidative stress, that were all significantly reduced when the animals were treated with antibiotic or faecal samples. The number of members of two bacterial genera, Coprococcus and Ruminococcus, was increased by the fructose-rich diet and reduced by both antibiotic and faecal treatments, pointing to a correlation between their abundance and the development of the metabolic syndrome. Our data indicate that in rats fed a fructose-rich diet the development of metabolic syndrome is directly correlated with variations of the gut content of specific bacterial taxa.

  15. Insulin Resistance, Microbiota, and Fat Distribution Changes by a New Model of Vertical Sleeve Gastrectomy in Obese Rats.

    PubMed

    Basso, Nicola; Soricelli, Emanuele; Castagneto-Gissey, Lidia; Casella, Giovanni; Albanese, Davide; Fava, Francesca; Donati, Claudio; Tuohy, Kieran; Angelini, Giulia; La Neve, Federica; Severino, Anna; Kamvissi-Lorenz, Virginia; Birkenfeld, Andrea L; Bornstein, Stefan; Manco, Melania; Mingrone, Geltrude

    2016-10-01

    Metabolic surgery improves insulin resistance and type 2 diabetes possibly because of weight loss. We performed a novel sleeve gastrectomy in rats that resects ∼80% of the glandular portion, leaving the forestomach almost intact (glandular gastrectomy [GG]) and compared subsequent metabolic remodeling with a sham operation. GG did not affect body weight, at least after 10 weeks; improved hepatic and peripheral insulin sensitivity likely through increased Akt, glycogen synthase kinase 3, and AMPK phosphorylation; and reduced ectopic fat deposition and hepatic glycogen overaccumulation. Body adipose tissue was redistributed, with reduction of intraabdominal fat. We found a reduction of circulating ghrelin levels, increased GLP-1 plasma concentration, and remodeling of gut microbiome diversity characterized by a lower relative abundance of Ruminococcus and a higher relative abundance of Lactobacillus and Collinsella These data suggest that at least in rat, the glandular stomach plays a central role in the improvement of insulin resistance, even if obesity persists. GG provides a new model of the metabolically healthy obese phenotype.

  16. Novel {alpha}-glucosidase from human gut microbiome : substrate specificities and their switch.

    SciTech Connect

    Tan, K.; Tesar, C.; Wilton, R.; Keigher, L.; Babnigg, G.; Joachimiak, A.; Biosciences Division

    2010-01-01

    The human intestine harbors a large number of microbes forming a complex microbial community that greatly affects the physiology and pathology of the host. In the human gut microbiome, the enrichment in certain protein gene families appears to be widespread. They include enzymes involved in carbohydrate metabolism such as glucoside hydrolases of dietary polysaccharides and glycoconjugates. We report the crystal structures (wild type, 2 mutants, and a mutant/substrate complex) and the enzymatic activity of a recombinant {alpha}-glucosidase from human gut bacterium Ruminococcus obeum. The first ever protein structures from this bacterium reveal a structural homologue to human intestinal maltase-glucoamylase with a highly conserved catalytic domain and reduced auxiliary domains. The {alpha}-glucosidase, a member of GH31 family, shows substrate preference for {alpha}(1-6) over {alpha}(1-4) glycosidic linkages and produces glucose from isomaltose as well as maltose. The preference can be switched by a single mutation at its active site, suggestive of widespread adaptation to utilization of a variety of polysaccharides by intestinal micro-organisms as energy resources. Novel {alpha}-glucosidase from human gut microbiome: substrate specificities and their switch.

  17. Dairy and plant based food intakes are associated with altered faecal microbiota in 2 to 3 year old Australian children

    PubMed Central

    Smith-Brown, P.; Morrison, M.; Krause, L.; Davies, P. S. W.

    2016-01-01

    The first 1000 days (conception to 24 months) is when gut microbiota composition and eating patterns are established, and a critical period influencing lifelong health. The aim of this study is to examine the associations between food intakes and microbiota composition at the end of this period. Diet was quantified for 37 well-nourished Australian children aged between 2 to 3 years by using a food frequency questionnaire and 24 hr recalls. Both dairy and plant-based (fruit, vegetables, soy, pulses and nuts) food intakes were associated with distinct microbiota profiles. Dairy intake was positively associated with the Firmicutes:Bacteroidetes ratio, and in particular Erysipelatoclostridium spp., but negatively associated with species richness and diversity. Vegetable intake was positively associated with the relative abundance of the Lachnospira genus, while soy, pulse and nut intake was positively associated with the relative abundance of bacteria related to Bacteroides xylanisolvens. Fruit intake, especially apples and pears, were negatively associated with the relative abundance of bacteria related to Ruminococcus gnavus. In this cohort of young children dairy and plant based food intakes were found to be associated with altered microbiota composition. Further exploration is needed to elucidate the effect of these dietary and microbial differences on host phenotype. PMID:27694811

  18. Impact of dietary resistant starch type 4 on human gut microbiota and immunometabolic functions

    PubMed Central

    Upadhyaya, Bijaya; McCormack, Lacey; Fardin-Kia, Ali Reza; Juenemann, Robert; Nichenametla, Sailendra; Clapper, Jeffrey; Specker, Bonny; Dey, Moul

    2016-01-01

    Dietary modulation of the gut microbiota impacts human health. Here we investigated the hitherto unknown effects of resistant starch type 4 (RS4) enriched diet on gut microbiota composition and short-chain fatty acid (SCFA) concentrations in parallel with host immunometabolic functions in twenty individuals with signs of metabolic syndrome (MetS). Cholesterols, fasting glucose, glycosylated haemoglobin, and proinflammatory markers in the blood as well as waist circumference and % body fat were lower post intervention in the RS4 group compared with the control group. 16S-rRNA gene sequencing revealed a differential abundance of 71 bacterial operational taxonomic units, including the enrichment of three Bacteroides species and one each of Parabacteroides, Oscillospira, Blautia, Ruminococcus, Eubacterium, and Christensenella species in the RS4 group. Gas chromatography–mass spectrometry revealed higher faecal SCFAs, including butyrate, propionate, valerate, isovalerate, and hexanoate after RS4-intake. Bivariate analyses showed RS4-specific associations of the gut microbiota with the host metabolic functions and SCFA levels. Here we show that dietary RS4 induced changes in the gut microbiota are linked to its biological activity in individuals with signs of MetS. These findings have potential implications for dietary guidelines in metabolic health management. PMID:27356770

  19. Intestinal Microbiota of Broiler Chickens As Affected by Litter Management Regimens.

    PubMed

    Wang, Lingling; Lilburn, Mike; Yu, Zhongtang

    2016-01-01

    Poultry litter is a mixture of bedding materials and enteric bacteria excreted by chickens, and it is typically reused for multiple growth cycles in commercial broiler production. Thus, bacteria can be transmitted from one growth cycle to the next via litter. However, it remains poorly understood how litter reuse affects development and composition of chicken gut microbiota. In this study, the effect of litter reuse on the microbiota in litter and in chicken gut was investigated using 2 litter management regimens: fresh vs. reused litter. Samples of ileal mucosa and cecal digesta were collected from young chicks (10 days of age) and mature birds (35 days of age). Based on analysis using DGGE and pyrosequencing of bacterial 16S rRNA gene amplicons, the microbiota of both the ileal mucosa and the cecal contents was affected by both litter management regimen and age of birds. Faecalibacterium, Oscillospira, Butyricicoccus, and one unclassified candidate genus closely related to Ruminococcus were most predominant in the cecal samples, while Lactobacillus was predominant in the ileal samples at both ages and in the cecal samples collected at day 10. At days 10 and 35, 8 and 3 genera, respectively, in the cecal luminal microbiota differed significantly in relative abundance between the 2 litter management regimens. Compared to the fresh litter, reused litter increased predominance of halotolerant/alkaliphilic bacteria and Faecalibacterium prausnitzii, a butyrate-producing gut bacterium. This study suggests that litter management regimens affect the chicken GI microbiota, which may impact the host nutritional status and intestinal health.

  20. Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness

    PubMed Central

    Yang, Hui; Huang, Xiaochang; Fang, Shaoming; Xin, Wenshui; Huang, Lusheng; Chen, Congying

    2016-01-01

    Uncovering the phylogenetic composition of microbial community and the potential functional capacity of microbiome in different gut locations is of great importance to pig production. Here we performed a comparative analysis of gut microbiota and metagenomics among jejunum, ileum and cecum in pigs with distinct fatness. 16S rRNA gene sequencing revealed dramatic differences of microbial composition, diversity and species abundance between small intestine and cecum. Clostridium and SMB53 were enriched in the small intestine, while Prevotella, Treponema, Ruminococcus and Faecalibacterium showed a higher abundance in the cecum. Functional capacity analysis of gut microbiome revealed that the microbiome of small intestine plays important roles in the metabolism of small molecule nutrients, while the microbiome of cecum has the stronger ability to degrade xylan, pectin and cellulose. We identified tens of fatness associated-bacterial species including Escherichia spp. that showed a notable increase of relative abundance in all three gut locations of high fatness pigs. We further suggested that the potential pathogens, inflammation process, and microbial metabolism and nutrient sensing are involved in the high fatness of pigs. These results improve our knowledge about microbiota compositions in different gut locations, and give an insight into the effect of gut microbiota on porcine fatness. PMID:27255518

  1. Detection of sialic acid-utilising bacteria in a caecal community batch culture using RNA-based stable isotope probing.

    PubMed

    Young, Wayne; Egert, Markus; Bassett, Shalome A; Bibiloni, Rodrigo

    2015-03-25

    Sialic acids are monosaccharides typically found on cell surfaces and attached to soluble proteins, or as essential components of ganglioside structures that play a critical role in brain development and neural transmission. Human milk also contains sialic acid conjugated to oligosaccharides, glycolipids, and glycoproteins. These nutrients can reach the large bowel where they may be metabolised by the microbiota. However, little is known about the members of the microbiota involved in this function. To identify intestinal bacteria that utilise sialic acid within a complex intestinal community, we cultured the caecal microbiota from piglets in the presence of 13C-labelled sialic acid. Using RNA-based stable isotope probing, we identified bacteria that consumed 13C-sialic acid by fractionating total RNA in isopycnic buoyant density gradients followed by 16S rRNA gene analysis. Addition of sialic acid caused significant microbial community changes. A relative rise in Prevotella and Lactobacillus species was accompanied by a corresponding reduction in the genera Escherichia/Shigella, Ruminococcus and Eubacterium. Inspection of isotopically labelled RNA sequences suggests that the labelled sialic acid was consumed by a wide range of bacteria. However, species affiliated with the genus Prevotella were clearly identified as the most prolific users, as solely their RNA showed significantly higher relative shares among the most labelled RNA species. Given the relevance of sialic acid in nutrition, this study contributes to a better understanding of their microbial transformation in the intestinal tract with potential implications for human health.

  2. Fecal Transplantation Treatment of Antibiotic-Induced, Noninfectious Colitis and Long-Term Microbiota Follow-Up

    PubMed Central

    Mattila, Eero; Jalanka, Jonna; de Vos, Willem M.; Arkkila, Perttu

    2014-01-01

    Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection (CDI) and is considered as a treatment for other gastrointestinal (GI) diseases. We followed up the relief of symptoms and long-term, over-a-year microbiota stabilization in a 46-year-old man, who underwent FMT for antibiotic-induced, non-CDI colitis nine months after being treated for CDI by FMT. Fecal and mucosal microbiota was analyzed before the second FMT and during 14 months after FMT by using a high-throughput phylogenetic microarray. FMT resolved the symptoms and restored normal GI-function. Microbiota analysis revealed increased bacterial diversity in the rectal mucosa and a stable fecal microbiota up to three months after FMT. A number of mucosa-associated bacteria increased after FMT and some of these bacteria remained increased in feces up to 14 months. Notably, the increased bacteria included Bifidobacterium spp. and various representatives of Clostridium clusters IV and XIVa, such as Clostridium leptum, Oscillospira guillermondii, Sporobacter termitidis, Anaerotruncus colihominis, Ruminococcus callidus, R. bromii, Lachnospira pectinoschiza, and C. colinum, which are presumed to be anti-inflammatory. The presented case suggests a possible role of microbiota in restoring and maintaining normal GI-functionality and improves our knowledge on the etiology of antibiotic-induced, noninfectious colitis. PMID:25548572

  3. Does our food (environment) change our gut microbiome ('in-vironment'): a potential role for inflammatory bowel disease?

    PubMed

    de Wouters, Tomas; Doré, Joël; Lepage, Patricia

    2012-01-01

    Human biology can only be fully assessed by combining an analysis of both the host and its surrounding environment. As a part of the environment, the human gastrointestinal tract hosts more than 100 trillion bacteria making up the gut microbiota. The human host provides a nutrient-rich environment while the microbiota provides indispensable functions that humans cannot exert themselves. Shifts in the bacterial makeup of the human gut microbiota have been associated with disorders such as inflammatory bowel disease (IBD), irritable bowel syndrome and obesity. However, since most bacteria inhabiting our gut are not cultivable to date, until recently little was known about their individual functions. Metagenomics, i.e. the analysis of the collective genomes present in a defined ecosystem, gives insight into these specific functions. The first extensive catalogue of the intestinal metagenome outnumbers the size of the human genome by a factor of 150. Recently, 3 distinct 'types' of gut composition within the human population have been highlighted. These so-called 'enterotypes' are characterized by the dominant genera (Bacteroides, Prevotella and Ruminococcus) and their co-occurring phylogenetic groups. In accordance with the previously described impact of nutritional behavior (diet, probiotics and prebiotics) on specific bacterial populations, an association has been observed between long-term dietary habits and enterotypes. This recent discovery, i.e. that belonging to one or the other enterotype might be modulated by the diet opens up new perspectives in the fields of IBD, nutrition and therapeutic strategies. PMID:23295690

  4. Soil pH determines microbial diversity and composition in the park grass experiment.

    PubMed

    Zhalnina, Kateryna; Dias, Raquel; de Quadros, Patricia Dörr; Davis-Richardson, Austin; Camargo, Flavio A O; Clark, Ian M; McGrath, Steve P; Hirsch, Penny R; Triplett, Eric W

    2015-02-01

    The Park Grass experiment (PGE) in the UK has been ongoing since 1856. Its purpose is to study the response of biological communities to the long-term treatments and associated changes in soil parameters, particularly soil pH. In this study, soil samples were collected across pH gradient (pH 3.6-7) and a range of fertilizers (nitrogen as ammonium sulfate, nitrogen as sodium nitrate, phosphorous) to evaluate the effects nutrients have on soil parameters and microbial community structure. Illumina 16S ribosomal RNA (rRNA) amplicon sequencing was used to determine the relative abundances and diversity of bacterial and archaeal taxa. Relationships between treatments, measured soil parameters, and microbial communities were evaluated. Clostridium, Bacteroides, Bradyrhizobium, Mycobacterium, Ruminococcus, Paenibacillus, and Rhodoplanes were the most abundant genera found at the PGE. The main soil parameter that determined microbial composition, diversity, and biomass in the PGE soil was pH. The most probable mechanism of the pH impact on microbial community may include mediation of nutrient availability in the soil. Addition of nitrogen to the PGE plots as ammonium sulfate decreases soil pH through increased nitrification, which causes buildup of soil carbon, and hence increases C/N ratio. Plant species richness and plant productivity did not reveal significant relationships with microbial diversity; however, plant species richness was positively correlated with soil microbial biomass. Plants responded to the nitrogen treatments with an increase in productivity and a decrease in the species richness.

  5. A retrospective metagenomics approach to studying Blastocystis.

    PubMed

    Andersen, Lee O'Brien; Bonde, Ida; Nielsen, Henrik Bjørn; Stensvold, Christen Rune

    2015-07-01

    Blastocystis is a common single-celled intestinal parasitic genus, comprising several subtypes. Here, we screened data obtained by metagenomic analysis of faecal DNA for Blastocystis by searching for subtype-specific genes in coabundance gene groups, which are groups of genes that covary across a selection of 316 human faecal samples, hence representing genes originating from a single subtype. The 316 faecal samples were from 236 healthy individuals, 13 patients with Crohn's disease (CD) and 67 patients with ulcerative colitis (UC). The prevalence of Blastocystis was 20.3% in the healthy individuals and 14.9% in patients with UC. Meanwhile, Blastocystis was absent in patients with CD. Individuals with intestinal microbiota dominated by Bacteroides were much less prone to having Blastocystis-positive stool (Matthew's correlation coefficient = -0.25, P < 0.0001) than individuals with Ruminococcus- and Prevotella-driven enterotypes. This is the first study to investigate the relationship between Blastocystis and communities of gut bacteria using a metagenomics approach. The study serves as an example of how it is possible to retrospectively investigate microbial eukaryotic communities in the gut using metagenomic datasets targeting the bacterial component of the intestinal microbiome and the interplay between these microbial communities.

  6. Competition for Ammonia Influences the Structure of Chemotrophic Communities in Geothermal Springs

    PubMed Central

    Hamilton, Trinity L.; Koonce, Evangeline; Howells, Alta; Havig, Jeff R.; Jewell, Talia; de la Torre, José R.; Peters, John W.

    2014-01-01

    Source waters sampled from Perpetual Spouter hot spring (pH 7.03, 86.4°C), Yellowstone National Park, WY, have low concentrations of total ammonia, nitrite, and nitrate, suggesting nitrogen (N) limitation and/or tight coupling of N cycling processes. Dominant small-subunit rRNA sequences in Perpetual Spouter source sediments are closely affiliated with the ammonia-oxidizing archaeon “Candidatus Nitrosocaldus yellowstonii” and the putatively nitrogen-fixing (diazotrophic) bacterium Thermocrinis albus, respectively, suggesting that these populations may interact at the level of the bioavailable N pool, specifically, ammonia. This hypothesis was evaluated by using a combination of geochemical, physiological, and transcriptomic analyses of sediment microcosms. Amendment of microcosms with allylthiourea, an inhibitor of ammonia oxidation, decreased rates of acetylene reduction (a proxy for N2 fixation) and nitrite production (a proxy for ammonia oxidation) and decreased transcript levels of structural genes involved in both nitrogen fixation (nifH) and ammonia oxidation (amoA). In contrast, amendment of microcosms with ammonia stimulated nitrite production and increased amoA transcript levels while it suppressed rates of acetylene reduction and decreased nifH transcript levels. Sequencing of amplified nifH and amoA transcripts from native sediments, as well as microcosms, at 2 and 4 h postamendment, indicates that the dominant and responsive populations involved in ammonia oxidation and N2 fixation are closely affiliated with Ca. Nitrosocaldus yellowstonii and T. albus, respectively. Collectively, these results suggest that ammonia-oxidizing archaea, such as Ca. Nitrosocaldus yellowstonii, have an apparent affinity for ammonia that is higher than that of the diazotrophs present in this ecosystem. Depletion of the bioavailable N pool through the activity of ammonia-oxidizing archaea likely represents a strong selective pressure for the inclusion of organisms capable

  7. Competition for ammonia influences the structure of chemotrophic communities in geothermal springs.

    PubMed

    Hamilton, Trinity L; Koonce, Evangeline; Howells, Alta; Havig, Jeff R; Jewell, Talia; de la Torre, José R; Peters, John W; Boyd, Eric S

    2014-01-01

    Source waters sampled from Perpetual Spouter hot spring (pH 7.03, 86.4°C), Yellowstone National Park, WY, have low concentrations of total ammonia, nitrite, and nitrate, suggesting nitrogen (N) limitation and/or tight coupling of N cycling processes. Dominant small-subunit rRNA sequences in Perpetual Spouter source sediments are closely affiliated with the ammonia-oxidizing archaeon "Candidatus Nitrosocaldus yellowstonii" and the putatively nitrogen-fixing (diazotrophic) bacterium Thermocrinis albus, respectively, suggesting that these populations may interact at the level of the bioavailable N pool, specifically, ammonia. This hypothesis was evaluated by using a combination of geochemical, physiological, and transcriptomic analyses of sediment microcosms. Amendment of microcosms with allylthiourea, an inhibitor of ammonia oxidation, decreased rates of acetylene reduction (a proxy for N2 fixation) and nitrite production (a proxy for ammonia oxidation) and decreased transcript levels of structural genes involved in both nitrogen fixation (nifH) and ammonia oxidation (amoA). In contrast, amendment of microcosms with ammonia stimulated nitrite production and increased amoA transcript levels while it suppressed rates of acetylene reduction and decreased nifH transcript levels. Sequencing of amplified nifH and amoA transcripts from native sediments, as well as microcosms, at 2 and 4 h postamendment, indicates that the dominant and responsive populations involved in ammonia oxidation and N2 fixation are closely affiliated with Ca. Nitrosocaldus yellowstonii and T. albus, respectively. Collectively, these results suggest that ammonia-oxidizing archaea, such as Ca. Nitrosocaldus yellowstonii, have an apparent affinity for ammonia that is higher than that of the diazotrophs present in this ecosystem. Depletion of the bioavailable N pool through the activity of ammonia-oxidizing archaea likely represents a strong selective pressure for the inclusion of organisms capable of

  8. Accumulation of germanium and rare earth elements in functional groups of selected energy crops cultivated on two different soils

    NASA Astrophysics Data System (ADS)

    Wiche, Oliver; Székely, Balázs

    2016-04-01

    A field experiment was conducted to investigate the uptake of Ge and selected REEs in functional groups of selected crop species. Five species belonging to the functional group of grasses (Hordeum vulgare, Zea mays, Avena sativa, Panicum miliaceum and Phalaris arundinacea) and four species from the group of herbs (Lupinus albus, Lupinus angustifolius, Fagopyrum esculentum and Brassica napus) were cultivated in parallel on two soils with slightly alkaline (soil A: pH = 7.8) and slightly acidic (soil B: pH = 6.8) conditions. After harvest, concentrations of Ge, La, Nd, Gd, Er, P, Fe, Mn and Si in shoot tissues were determined with ICP-MS. Concentrations of Ge were significantly higher in grasses than in herbs. Conversely, concentrations of La and Nd were significantly higher in herbs, than in grasses. Highest concentrations were measured in Brassica napus (REEs) and Zea mays (Ge). Concentrations of Ge significantly correlated with that of Si in the shoots showing low concentrations in herbs and high concentrations in grasses, indicating a common mechanism during the uptake in grasses. Concentrations of REEs correlated significantly with that of Fe, indicating increasing concentrations of REEs with increasing concentrations of Fe. Cultivation of species on the slightly acidic soil significantly increased the uptake Ge in Lupinus albus and Phalaris arundinacea and the uptake of La and Nd in all species except of Phalaris arundinacea. This study demonstrated that commonly used field crops could be regarded as suitable candidates for a phytomining of Ge and REEs, since these species develop high yields of shoots, high concentrations of elements and are widely used in agricultural practice. Under soil conditions where bioavailability of Ge and REEs is expected to be low (soil A) accumulation can be