Quantitative Proteomic Analysis of Four Protein Components from Bacteroides thetaiotaomicron
Ontology highlight
ABSTRACT:
ORGANISM(S): Bacteroides Thetaiotaomicron Vpi-5482
SUBMITTER: 
Junhua Xie
PROVIDER: PXD075652 | iProX | Sat Mar 14 00:00:00 GMT 2026
REPOSITORIES: iProX
Similar Datasets
Project description:The adult human gut microbial community is typically dominated by two bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from E. rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the former possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole genome transcriptional profiling of both organisms in their distal gut (cecal) habitat as well as host responses, high resolution proteomic analysis of cecal contents, and biochemical assays of carbohydrate metabolism. B. thetaiotaomicron adapts to E. rectale by upregulating expression of a variety of polysaccharide utilization loci (PULs) encoding numerous glycoside hydrolase gene families, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is utilized by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of major gut bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability. We assessed how E. rectale and B. thetaiotaomicron were affected by changes in host diet. Groups of age- and gender-matched co-colonized mice were fed one of three diets that varied primarily in their carbohydrate and fat content: (i) the standard low-fat, plant polysaccharide-rich diet used for the experiments described above (abbreviated âLF/PPâ for low-fat/plant polysaccharide), (ii) a high-fat, âhigh-sugarâ Western-type diet (abbreviated HF/HS) that contained sucrose, maltodextrin, corn starch as well as complex polysaccharides (primarily cellulose) that were not digestible by B. thetaiotaomicron or E. rectale, and (iii) a control diet that was similar to (ii) except that the fat content was 4-fold lower (âLF/HSâ for low-fat, high-sugar; n=5 mice per group).
2010-05-22 | E-GEOD-14709 | biostudies-arrayexpress
Project description:The adult human gut microbial community is typically dominated by two bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from E. rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the former possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole genome transcriptional profiling of both organisms in their distal gut (cecal) habitat as well as host responses, high resolution proteomic analysis of cecal contents, and biochemical assays of carbohydrate metabolism. B. thetaiotaomicron adapts to E. rectale by upregulating expression of a variety of polysaccharide utilization loci (PULs) encoding numerous glycoside hydrolase gene families, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is utilized by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of major gut bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability. Experiment Overall Design: four biological replicates per group. NMRI mice, males (12-14 weeks old).
2009-03-07 | E-GEOD-14686 | biostudies-arrayexpress
Project description:The adult human gut microbial community is typically dominated by two bacterial phyla (divisions), the Firmicutes and the Bacteroidetes. Little is known about the factors that govern the interactions between their members. Here we examine the niches of representatives of both phyla in vivo. Finished genome sequences were generated from E. rectale and E. eligens, which belong to Clostridium Cluster XIVa, one of the most common gut Firmicute clades. Comparison of these and 25 other gut Firmicutes and Bacteroidetes indicated that the former possess smaller genomes and a disproportionately smaller number of glycan-degrading enzymes. Germ-free mice were then colonized with E. rectale and/or a prominent human gut Bacteroidetes, Bacteroides thetaiotaomicron, followed by whole genome transcriptional profiling of both organisms in their distal gut (cecal) habitat as well as host responses, high resolution proteomic analysis of cecal contents, and biochemical assays of carbohydrate metabolism. B. thetaiotaomicron adapts to E. rectale by upregulating expression of a variety of polysaccharide utilization loci (PULs) encoding numerous glycoside hydrolase gene families, and by signaling the host to produce mucosal glycans that it, but not E. rectale, can access. E. rectale adapts to B. thetaiotaomicron by decreasing production of its glycan-degrading enzymes, increasing expression of selected amino acid and sugar transporters, and facilitating glycolysis by reducing levels of NADH, in part via generation of butyrate from acetate, which in turn is utilized by the gut epithelium. This simplified model of the human gut microbiota illustrates niche specialization and functional redundancy within members of major gut bacterial phyla, and the importance of host glycans as a nutrient foundation that ensures ecosystem stability. The interactions between E. rectale and B. thetaiotaomicron were characterized by performing whole genome transcriptional profiling of each species after colonization of gnotobiotic mice with each organism alone, or in combination. E. rectale was also profiled during in vitro growth.
2010-05-22 | E-GEOD-14737 | biostudies-arrayexpress
Project description:The gut microbiota is essential for several aspects of host physiology such as metabolism, epithelial barrier function and immunity. Previous studies have revealed that host immune system as well as diet and other environmental factors have a strong impact on the composition and activity of gut microbiota, but the molecular requirements for such functional regulation remain unknown. We show that the bacteria belonging to phylum Bacteroidetes acquire their symbiotic activity in the colonic mucus, depending on a newly characterized molecular family encoded within the polysaccharide utilization loci (PUL), which we have named Mucus-Associated Functional Factor (MAFF).
2018-06-25 | GSE115814 | GEO
Project description:The gut microbiota is essential for several aspects of host physiology such as metabolism, epithelial barrier function and immunity. Previous studies have revealed that host immune system as well as diet and other environmental factors have a strong impact on the composition and activity of gut microbiota, but the molecular requirements for such functional regulation remain unknown. We show that the bacteria belonging to phylum Bacteroidetes acquire their symbiotic activity in the colonic mucus, depending on a newly characterized molecular family encoded within the polysaccharide utilization loci (PUL), which we have named Mucus-Associated Functional Factor (MAFF).
2018-06-25 | GSE115902 | GEO
Project description:The indigenous human gut microbiota is a major contributor to the human superorganism with established roles in modulating nutritional status, immunity, and systemic health including diabetes and obesity. The complexity of the gut microbiota consisting of over 1012 residents and approximately 1000 species has thus far eluded systematic analyses of the precise effects of individual microbial residents on human health. In contrast, health benefits have been shown upon ingestion of certain so-called probiotic Lactobacillus strains in food products and nutritional supplements, thereby providing a unique opportunity to study the global responses of a gut-adapted microorganism in the human gut and to identify the molecular mechanisms underlying microbial modulation of intestinal physiology, which might involve alterations in the intestinal physico-chemical environment, modifications in the gut microbiota, and/or direct interaction with mucosal epithelia and immune cells. Here we show by transcriptome analysis using DNA microarrays that the established probiotic bacterium, L. plantarum 299v, adapts its metabolic capacity in the human digestive tract for carbohydrate acquisition and expression of exo-polysaccharide and proteinaceous cell surface compounds. This report constitutes the first application of global gene expression profiling of a gut-adapted commensal microorganism in the human gut. Comparisons of the transcript profiles to those obtained for L. plantarum WCFS1 in germ-free mice revealed conserved L. plantarum responses indicative of a core transcriptome expressed in the mammalian gut and provide new molecular targets for determining microbial-host interactions affecting human health. Hybridization of the samples against a common reference of gDNA isolated from L. plantarum 299v
2010-05-16 | E-GEOD-17634 | biostudies-arrayexpress
Project description:Dietary fiber degradation is a key function of the human gut microbiota. The aim of this study was to increase our knowledge on the degradation of plant cell wall polysaccharide degradation by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. These loci or PUL ("Polysaccharide Utilization Loci") are known to encode enzyme systems in Bacteroides that are specific to a particular polysaccharide.
2015-10-28 | GSE74379 | GEO
Project description:Dietary fiber degradation is a key function of the human gut microbiota. The aim of this study was to increase our knowledge on the degradation of plant cell wall polysaccharide degradation by a prominent human gut bacterial species, Bacteroides xylanisolvens. The transcriptome analysis of B. xylanisolvens XB1AT revealed the existence of six and two genomic loci dedicated to the degradation of pectins and xylan, respectively. These loci or PUL ("Polysaccharide Utilization Loci") are known to encode enzyme systems in Bacteroides that are specific to a particular polysaccharide. Simple two-way comparisons between pectin or xylan sources (treatment) and glucose or xylose (control), collected during mid- and late-log phase. Three replicates per condition.
2015-10-28 | E-GEOD-74379 | biostudies-arrayexpress
Project description:The human gut microbiota is an important metabolic organ, yet little is known about how its individual species interact, establish dominant positions, and respond to changes in environmental factors such as diet. In this study, gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced human gut bacterial species and fed oscillating diets of disparate composition. Rapid, reproducible, and reversible changes in the structure of this assemblage were observed. Time-series microbial RNA-Seq analyses revealed staggered functional responses to diet shifts throughout the assemblage that were heavily focused on carbohydrate and amino acid metabolism. High-resolution shotgun metaproteomics confirmed many of these responses at a protein level. One member, Bacteroides cellulosilyticus WH2, proved exceptionally fit regardless of diet. Its genome encoded more carbohydrate active enzymes than any previously sequenced member of the Bacteroidetes. Transcriptional profiling indicated that B. cellulosilyticus WH2 is an adaptive forager that tailors its versatile carbohydrate utilization strategy to available dietary polysaccharides, with a strong emphasis on plant-derived xylans abundant in dietary staples like cereal grains. Two highly expressed, diet-specific polysaccharide utilization loci (PULs) in B. cellulosilyticus WH2 were identified, one with characteristics of xylan utilization systems. Introduction of a B. cellulosilyticus WH2 library comprising >90,000 isogenic transposon mutants into gnotobiotic mice, along with the other artificial community members, confirmed that these loci represent critical diet-specific fitness determinants. Carbohydrates that trigger dramatic increases in expression of these two loci and many of the organism’s 111 other predicted PULs were identified by RNA-Seq during in vitro growth on 31 distinct carbohydrate substrates, allowing us to better interpret in vivo RNA-Seq and proteomics data. These results offer insight into how gut microbes adapt to dietary perturbations at both a community level and from the perspective of a well-adapted symbiont with exceptional saccharolytic capabilities, and illustrate the value of artificial communities. 116 samples total. In 26 of these samples, we evaluated community-wide gene expression using RNA isolated from the feces of a gnotobiotic mouse harboring an artificial community comprised of 12 human gut microbes. For these samples, we sought to determine the extent to which community gene expression is altered as a result of dietary oscillation. In the other 90 samples, we evaluated gene expression in a single species (B. cellulosilyticus WH2) grown in a defined medium supplemented with a single mono-, oligo-, or polysaccharide. For these samples, we sought to identify genes (particularly polysaccharide utilization loci) whose expression was significantly increased as a result of exposure to particular carbohydrates.
2013-08-20 | E-GEOD-48993 | biostudies-arrayexpress
Project description:The gut microbiota is essential for several aspects of host physiology such as metabolism, epithelial barrier function and immunity. Previous studies have revealed that host immune system as well as diet and other environmental factors have a strong impact on the composition and activity of gut microbiota, but the molecular requirements for such functional regulation remain unknown. We show that the bacteria belonging to phylum Bacteroidetes acquire their symbiotic activity in the colonic mucus, depending on a newly characterized molecular family encoded within the polysaccharide utilization loci (PUL), which we have named Mucus-Associated Functional Factor (MAFF). We used microarray analysis of colonic epithlial cells to determin the impact of MAFF genes on colonic homeostasis.
2018-04-02 | GSE97504 | GEO