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RNA-seq analysis of intestinal epithelia of Ruminococcus torques treated mice

ABSTRACT: RNA-seq analysis of intestinal epithelia of Ruminococcus torques treated mice

PROVIDER: PRJNA1104543 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28809500_1.fastq.gz	Fastqsanger.gz
	SRR28809500_2.fastq.gz	Fastqsanger.gz
	SRR28809501_1.fastq.gz	Fastqsanger.gz
	SRR28809501_2.fastq.gz	Fastqsanger.gz
	SRR28809496_1.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of intestinal epithelia of Ruminococcus torques treated mice

Project description:Purpose: To explore the influence of Ruminococcus torques treatment in mice intestinal epithelia. Method: Mice were pretreated with antibiotics for 3 days, then mice were fed with a high-fat diet and gavaged with PBS or R. torques (108 CFU/mouse) every 3 days for 2 weeks. mRNA profiles were generated by deep sequencing.Results: Several signaling pathways were changed after R. torques treatment, including response to hypoxia pathway. R. torques treatment significantly inhibits Epas1-mediated transcription effect.

2024-06-04 | GSE265852 | GEO

[Ruminococcus] torques

Project description:Genome announcements of the Ruminococcus torques

| PRJDB15994 | ENA

Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron

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

[Ruminococcus] torques CAG:61

Project description:Ruminococcus torques CAG:61 overview

| PRJNA207254 | ENA

Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron

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 1,4-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 | PXD051107 | Pride

[Ruminococcus] torques L2-14

Project description:Ruminococcus torques L2-14 genome sequencing project

| PRJNA39169 | ENA

[Ruminococcus] torques strain:VIII-239

Project description:[Ruminococcus] torques strain:VIII-239 Genome sequencing

| PRJNA1082318 | ENA

[Ruminococcus] torques strain:CIP112193 | isolate:MC-3-4

Project description:[Ruminococcus] torques strain:CIP112193 | isolate:MC-3-4 Genome sequencing

| PRJNA1179941 | ENA

Ruminococcus torques TSDC19.2-1.1

Project description:Strain Ruminococcus torques TSDC19.2-1.1 (species Ruminococcus torques) was isolated from the fecal microbiota of a USA female at time point zero (bacterial isolates were sequenced from this donor on day 0 and 47). The species name was assigned by genome clustering.

| PRJEB3858 | ENA

Ruminococcus torques TS7.1-1.3

Project description:Strain Ruminococcus torques TS7.1-1.3 (species Ruminococcus torques) was isolated from the fecal microbiota of a USA female at time point zero (bacterial isolates were sequenced from this donor on day 0, 364, 399, and 484). The species name was assigned by genome clustering.

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