Characterization of the xylan-degrading microbial community from human faeces

Chassard, Christophe; Goumy, Vanessa; Leclerc, Marion; Del’Homme, Christophe; Bernalier-Donadille, Annick

doi:10.1111/j.1574-6941.2007.00314.x

Cited by 136 publications

(107 citation statements)

References 38 publications

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“…smithii in turn favors the communities that degrade cellulose. 48 Moreover, (2) increasing the retention time led to the decrease of one major competitor group of methanogenic archaea, the sulfate-reducing bacteria (disappeared in the T96 reactor), where Clostridium cl. XIV is increased the most.…”

Section: Discussionmentioning

confidence: 99%

Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence

Tottey

Féria-Gervasio

Gaci

et al. 2017

J Neurogastroenterol Motil

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Background/AimsHuman gut microbiota harbors numerous metabolic properties essential for the host's health. Increased intestinal transit time affects a part of the population and is notably observed with human aging, which also corresponds to modifications of the gut microbiota. Thus we tested the metabolic and compositional changes of a human gut microbiota induced by an increased transit time simulated in vitro. MethodsThe in vitro system, Environmental Control System for Intestinal Microbiota, was used to simulate the environmental conditions of 3 different anatomical parts of the human colon in a continuous process. The retention times of the chemostat conditions were established to correspond to a typical transit time of 48 hours next increased to 96 hours. The bacterial communities, short chain fatty acids and metabolite fingerprints were determined. ResultsIncrease of transit time resulted in a decrease of biomass and of diversity in the more distal compartments. Short chain fatty acid analyses and metabolite fingerprinting revealed increased activity corresponding to carbohydrate fermentation in the proximal compartments while protein fermentations were increased in the lower parts. ConclusionsThis study provides the evidence that the increase of transit time, independently of other factors, affects the composition and metabolism of the gut microbiota. The transit time is one of the factors that explain some of the modifications seen in the gut microbiota of the elderly, as well as patients with slow transit time.

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Section: Discussionmentioning

confidence: 99%

Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence

Tottey

Féria-Gervasio

Gaci

et al. 2017

J Neurogastroenterol Motil

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“…Thus, these libraries were not useful for analyzing differential gene expression, but they did contain information on transcript coverage and were included in the transcriptome assembly. The reads were filtered for adaptor sequences and assembled into contiguous sequences (contigs) using ABySS version 1.0.12 with k-mer lengths of 25,30,35,40,45, and 50. Twenty five 2.83-GHz cores, on a cluster with 200 processors with 16 gigabytes per 8 cores, were used for each k-mer assembly.…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic Analyses of Xylan Degradation by Prevotella bryantii and Insights into Energy Acquisition by Xylanolytic Bacteroidetes

Dodd

Moon

Swaminathan

et al. 2010

Journal of Biological Chemistry

112

101

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Enzymatic depolymerization of lignocellulose by microbes in the bovine rumen and the human colon is critical to gut health and function within the host. Prevotella bryantii B 1 4 is a rumen bacterium that efficiently degrades soluble xylan. To identify the genes harnessed by this bacterium to degrade xylan, the transcriptomes of P. bryantii cultured on either wheat arabinoxylan or a mixture of its monosaccharide components were compared by DNA microarray and RNA sequencing approaches. The most highly induced genes formed a cluster that contained putative outer membrane proteins analogous to the starch utilization system identified in the prominent human gut symbiont Bacteroides thetaiotaomicron. The arrangement of genes in the cluster was highly conserved in other xylanolytic Bacteroidetes, suggesting that the mechanism employed by xylan utilizers in this phylum is conserved. A number of genes encoding proteins with unassigned function were also induced on wheat arabinoxylan. Among these proteins, a hypothetical protein with low similarity to glycoside hydrolases was shown to possess endoxylanase activity and subsequently assigned to glycoside hydrolase family 5. The enzyme was designated PbXyn5A. Two of the most similar proteins to PbXyn5A were hypothetical proteins from human colonic Bacteroides spp., and when expressed each protein exhibited endoxylanase activity. By using site-directed mutagenesis, we identified two amino acid residues that likely serve as the catalytic acid/base and nucleophile as in other GH5 proteins. This study therefore provides insights into capture of energy by xylanolytic Bacteroidetes and the application of their enzymes as a resource in the biofuel industry.

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“…are the most numerically dominant xylanolytic bacteria (8,9). Past studies have identified Bacteroides eggerthii, B. ovatus, B. fragilis, B. vulgatus, B. intestinalis, B. cellulosilyticus, and B. xylanisolvens as the major xylanolytic members of this genus (10)(11)(12)(13)(14)(15)(16)(17).…”

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confidence: 99%

Two New Xylanases with Different Substrate Specificities from the Human Gut Bacterium Bacteroides intestinalis DSM 17393

Hong

Iakiviak

Dodd

et al. 2014

Appl Environ Microbiol

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Xylan is an abundant plant cell wall polysaccharide and is a dominant component of dietary fiber. Bacteria in the distal human gastrointestinal tract produce xylanase enzymes to initiate the degradation of this complex heteropolymer. These xylanases typically derive from glycoside hydrolase (GH) families 10 and 11; however, analysis of the genome sequence of the xylan-degrading human gut bacterium Bacteroides intestinalis DSM 17393 revealed the presence of two putative GH8 xylanases. In the current study, we demonstrate that the two genes encode enzymes that differ in activity. The xyn8A gene encodes an endoxylanase (Xyn8A), and rex8A encodes a reducing-end xylose-releasing exo-oligoxylanase (Rex8A). Xyn8A hydrolyzed both xylopentaose (X 5 ) and xylohexaose (X 6 ) to a mixture of xylobiose (X 2 ) and xylotriose (X 3 ), while Rex8A hydrolyzed X 3 through X 6 to a mixture of xylose (X 1 ) and X 2 . Moreover, rex8A is located downstream of a GH3 gene (xyl3A) that was demonstrated to exhibit ␤-xylosidase activity and would be able to further hydrolyze X 2 to X 1 . Mutational analyses of putative active site residues of both Xyn8A and Rex8A confirm their importance in catalysis by these enzymes. Recent genome sequences of gut bacteria reveal an increase in GH8 Rex enzymes, especially among the Bacteroidetes, indicating that these genes contribute to xylan utilization in the human gut.

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Characterization of the xylan-degrading microbial community from human faeces

Cited by 136 publications

References 38 publications

Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence

Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence

Transcriptomic Analyses of Xylan Degradation by Prevotella bryantii and Insights into Energy Acquisition by Xylanolytic Bacteroidetes

Two New Xylanases with Different Substrate Specificities from the Human Gut Bacterium Bacteroides intestinalis DSM 17393

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