Mouse gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA616059 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11445100_1.fastq.gz | Fastqsanger.gz | |||
| SRR11445100_2.fastq.gz | Fastqsanger.gz | |||
| SRR11445101_1.fastq.gz | Fastqsanger.gz | |||
| SRR11445101_2.fastq.gz | Fastqsanger.gz | |||
| SRR11445102_1.fastq.gz | Fastqsanger.gz |
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Project description:The gut microbiota promotes immune system development in early life, but the interactions between the gut metabolome and immune cells in the neonatal gut remains largely undefined. Here, we demonstrate that the neonatal gut is uniquely enriched with neurotransmitters, including serotonin; specific gut bacteria produce serotonin directly while downregulating monoamine oxidase A to limit serotonin breakdown. Serotonin directly signals to T cells to increase intracellular indole-3-acetaldehdye to inhibit mTOR activation and thereby promotes the differentiation of regulatory T cells, both ex vivo and in vivo in the neonatal intestine. Oral gavage of serotonin into neonatal mice leads to long-term T cell-mediated antigen-specific immune tolerance towards both dietary antigens and commensal bacteria. Together, our study has uncovered an important role for unique gut bacteria to increase serotonin availability in the neonatal gut and a novel function of gut serotonin to shape T cell response to dietary antigens and commensal bacteria to promote immune tolerance in early life.
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Project description:Triclosan (TCS), an antimicrobial agent in thousands of consumer products, is a risk factor for colitis and colitis-associated colorectal cancer. While the intestinal toxicities of TCS require the presence of gut microbiota, the molecular mechanisms involved have not been defined. Here we show that intestinal commensal microbes mediate metabolic activation of TCS in the colon and drive its gut toxicology. Using a range of in vitro, ex vivo, and in vivo approaches, we identify specific microbial β-glucuronidase (GUS) enzymes involved and pinpoint molecular motifs required to metabolically activate TCS in the gut. Finally, we show that targeted inhibition of bacterial GUS enzymes abolishes the colitis-promoting effects of TCS, supporting the essential roles of specific microbial proteins in TCS toxicity. Our results define a mechanism by which intestinal microbes cause the gut toxicity of environmental chemicals and suggest a therapeutic approach to alleviate colitis and associated diseases.
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Project description:Long-term dietary intake influences the structure and activity of the trillions of microorganisms residing in the human gut, but it remains unclear how rapidly and reproducibly the human gut microbiome responds to short-term macronutrient change. Here we show that the short-term consumption of diets composed entirely of animal or plant products alters microbial community structure and overwhelms inter-individual differences in microbial gene expression. The animal-based diet increased the abundance of bile-tolerant microorganisms (Alistipes, Bilophila and Bacteroides) and decreased the levels of Firmicutes that metabolize dietary plant polysaccharides (Roseburia, Eubacterium rectale and Ruminococcus bromii). Microbial activity mirrored differences between herbivorous and carnivorous mammals, reflecting trade-offs between carbohydrate and protein fermentation. Foodborne microbes from both diets transiently colonized the gut, including bacteria, fungi and even viruses. Finally, increases in the abundance and activity of Bilophila wadsworthia on the animal-based diet support a link between dietary fat, bile acids and the outgrowth of microorganisms capable of triggering inflammatory bowel disease. In concert, these results demonstrate that the gut microbiome can rapidly respond to altered diet, potentially facilitating the diversity of human dietary lifestyles. RNA-Seq analysis of the human gut microbiome during consumption of a plant- or animal-based diet.
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Project description:Objective Western Diet (WD) appears to be an important factor associated with inflammatory bowel diseases (IBD). Refined sugars represent up to 40% of caloric intake in industrialized countries. Unlike fats, the impact of dietary sugar on healthy and inflamed intestine remains poorly described. Design We investigated the effects of a high sucrose diet (HSD) on dextran sulfate sodium (DSS)-induced colitis and on healthy intestine in mice. Several techniques ranging from macroscopic to molecular were used in vivo and direct effect of sugars was examined in cellulo on Caco-2 cell distinguishing differential effect of fructose and glucose. Results During established colitis in mice, HSD aggravated inflammation by increasing gut permeability, raising immune cells in spleen and impairing autophagy process in colonic mucosa. On healthy intestine, HSD caused spontaneous endoscopic lesions, systemic broad immunosuppression and dysregulation of stress-related genes, associated with gut microbiota dysbiosis. Global reprogramming of colonic transcriptome was detected in HSD-fed mice and amazingly, functional annotations demonstrated association with IBD and “colitis” without DSS-treatment. In vitro, low dose of fructose as well as high dose of glucose induced alteration of junctions confirming the deleterious effects of sugar on intestine. These effects seem to be partially reversible on microbiome and transcriptome of mice after switching back to normal diet. Conclusions Our results demonstrated for the first time that under pathological conditions mimicking pre-diabetes (mild hyperglycemia-associated with overweight), a pre-IBD state is established and depending on host sensitivity, in colitis conditions, this exacerbates the inflammation severity by disturbing cell-cell junction organization and autophagy process.
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