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Fitness advantage of Bacteroides thetaiotaomicron capsular polysaccharide is dependent on the resident microbiota

ABSTRACT: Population dynamics of Bacteroides thetaiotaomicron during the early colonization of the murine gut

PROVIDER: PRJEB57876 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10618000_1.fastq.gz	Fastqsanger.gz
	ERR10618000_2.fastq.gz	Fastqsanger.gz
	ERR10618700_1.fastq.gz	Fastqsanger.gz
	ERR10618700_2.fastq.gz	Fastqsanger.gz
	ERR10618001_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Fitness advantage of <i>Bacteroides thetaiotaomicron</i> capsular polysaccharide in the mouse gut depends on the resident microbiota.

Project description:Many microbiota-based therapeutics rely on our ability to introduce a microbe of choice into an already-colonized intestine. In this study, we used genetically barcoded Bacteroides thetaiotaomicron (B. theta) strains to quantify population bottlenecks experienced by a B. theta population during colonization of the mouse gut. As expected, this reveals an inverse relationship between microbiota complexity and the probability that an individual wildtype B. theta clone will colonize the gut. The polysaccharide capsule of B. theta is important for resistance against attacks from other bacteria, phage, and the host immune system, and correspondingly acapsular B. theta loses in competitive colonization against the wildtype strain. Surprisingly, the acapsular strain did not show a colonization defect in mice with a low-complexity microbiota, as we found that acapsular strains have an indistinguishable colonization probability to the wildtype strain on single-strain colonization. This discrepancy could be resolved by tracking in vivo growth dynamics of both strains: acapsular B.theta shows a longer lag phase in the gut lumen as well as a slightly slower net growth rate. Therefore, as long as there is no niche competitor for the acapsular strain, this has only a small influence on colonization probability. However, the presence of a strong niche competitor (i.e., wildtype B. theta, SPF microbiota) rapidly excludes the acapsular strain during competitive colonization. Correspondingly, the acapsular strain shows a similarly low colonization probability in the context of a co-colonization with the wildtype strain or a complete microbiota. In summary, neutral tagging and detailed analysis of bacterial growth kinetics can therefore quantify the mechanisms of colonization resistance in differently-colonized animals.

| S-EPMC10014078 | biostudies-literature

Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats

Project description:We used Affymetrix GeneChips to determine the physiological differences between biofilm and planktonic cells of Bacteroides thetaiotaomicron strain VPI-5482 (ATCC 29148) by comparing gene expression. For this purpose, B. thetaiotaomicron cells were grown in sterile, continuous flow bioreactors fed with tryptone, yeast extract, glucose (TYG) medium. The bioreactors were controlled at a temperature of 37C using a water jacket and a recirculating water heater. After 8 hours post-inoculation, planktonic cells were harvested from the bulk solution in the bioreactor, and after 8 days post-inoculation, the biofilm was scraped from the carbon paper. RNA was harvested from both biofilm and planktonic populations. RNA was extracted by a phenol:chloroform method and purified with a Qiagen RNA Easy mini-kit.

2014-01-01 | GSE38534 | GEO

Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats

2014-01-01 | E-GEOD-38534 | biostudies-arrayexpress

Bacteroides thetaiotaomicron ameliorates colon inflammation in preclinical models of Crohn’s Disease [Bacteroides]

Project description:Analysis of the Bacteroides thetaiotaomicron(BT) transcriptome during co-culture with Caco-2 intestinal epithelial cells To identify potential bacterial protein(s) involved in the anti-inflammatory effect of BT in colitis, BT was incubated with Caco-2 human intestinal epithelial cells for 2 hours, and bacterial gene expression was assessed on a Bacteroides thetaiotaomicron VPI-5482 specific microarray. Forty-three BT genes were up-regulated by five-fold or more and of these, twenty genes encoded hypothetical proteins.

2019-03-06 | GSE118525 | GEO

Genome-wide RNA-seq of Bacteroides thetaiotaomicron VPI-5482 with Bacteroides phage challenge

Project description:Purpose: Examining the transcriptome of Bacteroides thetaiotaomicron VPI-5482 challenged with Bacteroides phage to assess surface molecule expression changes Methods: Bacteroides thetaiotaomicron was grown in BPRM in vitro or Germ-Free mice were monocolonized with Bacteroides thetaiotaomicron and gavaged with ARB25 phage. Fold change was calculated as live phage versus heat-killed phage treated samples with n=3 biological replicates. Once cells reached an optical density corresponding to mid-log phase growth (absorbance between 0.4-0.5), RNA was isolated and rRNA depleted. Samples were multiplexed for sequencing on the Illumina HiSeq platform at the University of Michigan Sequencing Core. Data was analyzed using Arraystar software (DNASTAR, Inc.) using DEseq2 normalization with default parameters. Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >5-fold and with at least 2/3 biological replicates with a normalized expression level >1% of the overall average, and a p-value < 0.05 (t test with Benjamini-Hochberg correction) Results: Specific capsule expression was increased in wild-type B. thetaiotaomicron during phage infection in vitro and in vivo. Many corresponding in vivo genes were upregulated as well as other surface layer proteins.

2020-05-01 | GSE147071 | GEO

Comparative Proteomic Analysis of Fucosylated Glycoproteins in Bacteroides thetaiotaomicron under Different Polysaccharide Nutrition Conditions

Project description:Bacteroides thetaiotaomicron, one of the most eminent representative gut commensal Bacteroides species, is able to use the L-fucose in host-derived and dietary polysaccharides to modify its capsular polysaccharides and glycoproteins through a mammalian-like salvage metabolic pathway. This process is essential for the colonization of the bacteria and for symbiosis with the host. However, despite the importance of fucosylated proteins (FGPs) in Bacteroide thetaiotaomicron, their types, distribution, and functions remain unclear. In this project, the effects of different saccharide (glucose, corn starch, mucin, and fucoidan) nutrition conditions on FGP expressions and fucosylation are investigated using a chemical biological method based on metabolic labeling and bioorthogonal reaction. According to the results of label-free quantification, 559 FGPs (205 downregulated and 354 upregulated) are affected by the dietary conditions. Of these differentially expressed proteins, 65 proteins show extremely sensitive fucosylation levels. Specifically, the fucosylation of the chondroitin sulfate ABC enzyme, Sus proteins, and cationic efflux system proteins varies significantly upon the addition of mucin, corn starch, or fucoidan. Moreover, these polysaccharides can trigger an appreciable increase in the fucosylation level of the two-component system and ammonium transport proteins. These results highlight the efficiency of the combined metabolic glycan labeling and bio-orthogonal reaction in enriching the intestinal Bacteroide glycoproteins. Moreover, it emphasize the sensitivity of Bacteroides fucosylation to polysaccharide nutrition conditions, which allows for the regulation of bacterial growth.

2022-02-08 | PXD023756 | Pride

Bacteroides thetaiotaomicron OMV proteomics

Project description:Comparative proteomics of Bacteroides thetaiotaomicron samples comparing the total membrane (TM) and outer membrane vesicles (OMV) of WT B. thetaiotaomicron and delta 4364

2024-10-15 | PXD043219 | Pride

The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron

Project description:Paramount to human health, symbiotic bacteria in the gastrointestinal tract rely on the breakdown of complex polysaccharides to thrive in this sugar-deprived environment. Gut Bacteroides are metabolic generalists and deploy dozens of polysaccharide utilization loci (PULs) to forage diverse dietary and host-derived glycans. The expression of the multi-protein PUL complexes is tightly regulated at the transcriptional level. However, how PULs are orchestrated at translational level in response to the fluctuating levels of their cognate substrates is unknown. Here, we identify the RNA-binding protein RbpB and a family of noncoding RNAs as key players in post-transcriptional PUL regulation. We demonstrate that RbpB interacts with numerous cellular transcripts, including a paralogous noncoding RNA family comprised of 14 members, the FopS (family of paralogous sRNAs). Through a series of in-vitro and in-vivo assays, we reveal that FopS sRNAs repress the translation of SusC-like glycan transporters when substrates are limited—an effect antagonized by RbpB. Ablation of RbpB in Bacteroides thetaiotaomicron compromises colonization in the mouse gut in a diet-dependent manner. Together, this study adds to our understanding of RNA-coordinated metabolic control as an important factor contributing to the in-vivo fitness of predominant microbiota species in dynamic nutrient landscapes.

2024-12-05 | GSE244816 | GEO

Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

Project description:Role of OxyR and iron in gene regulation in Bacteroides thetaiotaomicron

2023-03-30 | GSE169260 | GEO

In vitro transcriptional profiling of Bacteroides thetaiotaomicron in lactose, galactose and human milk oligosaccharides

Project description:Investigation of the overall in vitro response of Bacteroides thetaiotaomicron to human milk oligosaccharides. Comparison with response to MM-lactose and MM-galactose (Analysis performed using as a baseline datasets GSM301635 and GSM301637 corresponding to Bacteroides thetaiotaomicron response in MM-Glucose)

2013-01-01 | GSE26772 | GEO

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