Bacteroides fragilis in vivo gene expression
Ontology highlight
ABSTRACT:
ORGANISM(S): Bacteroides fragilis 638R
PROVIDER: GSE53883 | GEO | 2014/08/07
SECONDARY ACCESSION(S): PRJNA233624
REPOSITORIES: GEO
Similar Datasets
Project description:Compare BF638R gene expression during growth in vivo in a rat tissue cage/artificial abscess model, to cells grown in vitro in minimal defined media with either glucose or mucin glycans as sole carbon/energy source 11 chip study with 8 technical replicates on each chip comparing gene expression in vivo in a rat tissue cage model over an 8 day period to in vitro cultures grown to mid-log phase in defined media
2014-08-07 | E-GEOD-53883 | biostudies-arrayexpress
Project description:Purpose: Examining the transcriptome of human gut bacteria (Bacteroides xylanisolvens/Bacteroides ovatus) that grow on mucin O-linked glycans as a sole carbon source Methods: Strains were grown on 10 mg/ml mucin O-linked glycans (MOG) or 5 mg/ml glucose as a sole carbon source in vitro. Fold change was calculated as MOG over glucose. Once cells reached an optical density corresponding to mid-log phase growth, 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.) Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and biological replicates with a normalized expression level >1% of the overall average RPKM expression level. Results: We identified genes activated in response to mucin O-linked glycans from Bacteroides xylanisolvens/Bacteroides ovatus strains
2020-12-01 | GSE155869 | GEO
Project description:The phylum Bacteroidetes is a major component of the human gut microbiota which has a broad impact on the development and physiology of its host, and a potential role in a wide range of disease syndromes1-3. The predominance of Bacteroidetes and the genus Bacteroides in the distal gut is due in large part to the expansion of paralogous gene clusters, termed Polysaccharide Utilization Loci (PULs), dedicated to the uptake and catabolism of host derived and dietary polysaccharides4,5. It is generally thought that the diversity of PULs is key to Bacteroides successful competition for nutrients in the gut environment6. The nutritive value of the available polysaccharides varies greatly and thus their utilization is hierarchical and strictly controlled. A typical PUL includes regulatory genes that control expression in response to the presence of specific glycan substrates. However the existence of additional regulatory mechanisms has been predicted to explain phenomena such as the hierarchical control, catabolite repression, and the fine tuning of gene expression to match catabolic activity7-9. Using Bacteroides fragilis as a model organism, this report describes a previously unknown layer of regulatory control in which cis-encoded antisense small RNAs (sRNA) act as repressors of the PULsâ catabolic genes. Nearly 30% of B. fragilis PULs are subject to this type of sRNA control and these PULs tend to be more closely linked to the utilization of host-derived glycans than dietary polysaccharides. The findings described here indicate the presence of a global control mechanism that underlies the known regulatory circuits which modulate PUL expression in response to substrate availability, and hence provide novel insight into regulation of the gut Bacteroidetes physiology. This is a 4 chip study with 8 technical replicates on each chip. This was an in vitro, exploratory study to determine if mutation or overexpression of a sRNA associated with the Don locus would affect gene expression. In vitro cultures were grown in defined media with mucin glycans as the sole carbon source. The two chips representing growth of the wild type strain (638R) on mucin glycans were also used in a related study GSE53883 (GSM1303101 and GSM1303102).
2016-07-22 | E-GEOD-73107 | biostudies-arrayexpress
Project description:Gene expression profiles of Bacteroides thetaiotaomicron in vitro during growth on host mucosal polysaccharides as sole carbon sources. All substrates in this series are derived from porcine gastric mucin and include mucin O-glycans and glycosaminoglycans.
2008-11-21 | GSE11944 | GEO
Project description:Gene expression profiles of Bacteroides thetaiotaomicron in vitro during growth on host mucosal polysaccharides as sole carbon sources. All substrates in this series are derived from porcine gastric mucin and include mucin O-glycans and glycosaminoglycans. Two different culture formats used: 800ml batch-culture bioreactors and 5ml tube cultures (format is indicated within each sample title). Each set of growths was referenced to a minimal medium glucose reference corressponding to the same culture format. Unfractionated porcine mucosal glycan (PMG) growths were compared to previously published in vivo datasets, which were referenced to the 800ml minimal medium glucose reference dataset.
2008-11-20 | E-GEOD-11944 | biostudies-arrayexpress
Project description:We previously observed in mice that Bacteroides thetaiotaomicron (B. theta) significantly increased in abundance in the gut microbiome of mice when mice were fed egg and yeast dietary protein sources. We also observed that B. theta was expressing proteins previously connected to growth on mucin glycans when mice were fed an egg-white diet. To confirm that the bacterium were actually responding to the protein sources, we grew it in vitro using a defined medium, where the sole carbon source was dietary protein, mucin, or glucose. Our controls were glucose and mucin, and our experimental protein sources were soy protein, egg-white protein, and Torula yeast protein. We grew four B. theta cultures per carbon source statically at 37°C in a Coy anaerobic chamber (2.5 % H2 /10 % CO2 /88.5 % N2) in minimal medium (100 mM KH2PO4, 8.5 mM [NH2]4SO4, 15 mM NaCl, 5.8 μM vitamin K3, 1.44 μM FeSO4⋅7H2O, 1 mM MgCl2, 1.9 μM hematin, 0.2 mM L-histidine, 3.69 nM vitamin B12, 208 μM L-cysteine, and 7.2 μM CaCl2⋅2H2O) with one of the above mentioned nutrients added at 0.5% (wt/v) concentration. In order to aid the solubilization of the dietary proteins, we pre-prepared the proteins in 200 mM NaOH at 37°C for four days, the glucose control was also dissolved in 200 mM NaOH. After 8 hours, we enumerated CFUs to confirm growth, and we pelleted cells by centrifuging at 4,000 g for 10 minutes. We then removed the supernatant and froze the pellets at -80°C within 30 minutes.
2024-12-18 | PXD050296 | Pride
Project description:Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques—a known mucin-degrader that remains poorly studied despite its implication in inflammatory bowel diseases (IBDs)— degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong fucosidase, sialidase and b1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron. This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which may contribute to its association with IBD.
2024-06-19 | GSE262875 | GEO
Project description:Gut-educated IgA-secreting plasma cells that disseminate beyond the mucosa and into systemic tissues can help prevent disease in several contexts. Here we show, the commensal bacteria Bacteroides fragilis (Bf), is an efficient inducer of systemic IgA responses. The generation of bone marrow IgA plasma cells and high levels of serum IgA specific to Bf requires robust intestinal colonization. Bf-specific IgA responses were severely diminished in mice lacking Peyer’s patches, but not mice lacking a cecal patch. Colonization resulted in few changes in the host transcriptional profile in the gut, suggesting a commensal relationship. High levels of Bf-specific serum IgA, but not IgG, provided protection from peritoneal abscess formation in a bowel perforation model of Bf dissemination. These findings demonstrate a critical role for bacterial colonization and Peyer’s patches in the induction of robust systemic IgA responses that confer protection from bacterial dissemination originating from the gut.
2024-07-25 | GSE272717 | GEO
Project description:The goal of this project was to sequence the transcriptome of wild type Bacteroides thetaiotaomicron VPI-5482 grown in minimal media with either glucose or bovine alpha 1 acid glycoprotein (AAGP) as the sole carbon source. Using these data we could then compare relative gene expression levels under each condition and identify genes specifically upregulated during growth on AAGP. Analysis of the spent media indicated that only the N-glycan component of the AAGP had been used by the cells to support growth.
2019-04-26 | GSE129572 | GEO
Project description:The large-scale application of genomic and metagenomic sequencing technologies has yielded a number of insights about the metabolic potential of symbiotic human gut microbes. Bacteria that colonize the mucosal layer that overlies the gut epithelium have access to highly-sulfated polysaccharides (i.e., mucin oligosaccharides and glycosaminoglycans), which they could potentially forage as nutrient sources. To be active, sulfatases must undergo a critical post-translational modification catalyzed in anaerobic bacteria by the AdoMet enzyme anSME (anaerobic Sulfatase-Maturating Enzyme). In the present study, we have tested the role of this pathway in the prominent gut symbiont Bacteroides thetaiotaomicron, which possesses more predicted sulfatases (28) than in the human genome and a single predicted anSME. In vitro studies revealed that deletion of its anSME (BT0238) results in loss of sulfatase activity and impaired ability to use sulfated polysaccharides as carbon sources. Co-colonization of germ-free animals with both isogenic strains, or invasion experiments involving the introduction of one then the other strain, established that anSME activity and the sulfatases that are activated via this pathway, are important fitness factors for B. thetaiotaomicron, especially when mice are fed a simple sugar diet that requires this saccharolytic bacterium to adaptively forage on host glycans as nutrients. Whole genome transcriptional profiling of wild-type and the anSME mutant in vivo revealed that loss of this enzyme alters expression of genes involved in mucin utilization and that this disrupted ability to access mucosal glycans likely underlies the observed dramatic colonization defect. Comparative genomic analysis reveals that 100% of 46 fully sequenced human gut Bacteroidetes contain homologs of BT0238 and genes encoding sulfatases, suggesting that this is an important and evolutionarily conserved feature.
2011-01-01 | GSE25415 | GEO