Human gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA598446 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11047625_1.fastq.gz | Fastqsanger.gz | |||
| SRR11047625_2.fastq.gz | Fastqsanger.gz | |||
| SRR11047626_1.fastq.gz | Fastqsanger.gz | |||
| SRR11047626_2.fastq.gz | Fastqsanger.gz | |||
| SRR11047627_1.fastq.gz | Fastqsanger.gz |
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Project description:Opioids such as morphine have many beneficial properties as analgesics, however, opioids may induce multiple adverse gastrointestinal symptoms. We have recently demonstrated that morphine treatment results in significant disruption in gut barrier function leading to increased translocation of gut commensal bacteria. However, it is unclear how opioids modulate the gut homeostasis. By using a mouse model of morphine treatment, we studied effects of morphine treatment on gut microbiome. We characterized phylogenetic profiles of gut microbes, and found a significant shift in the gut microbiome and increase of pathogenic bacteria following morphine treatment when compared to placebo. In the present study, wild type mice (C57BL/6J) were implanted with placebo, morphine pellets subcutaneously. Fecal matter were taken for bacterial 16s rDNA sequencing analysis at day 3 post treatment. A scatter plot based on an unweighted UniFrac distance matrics obtained from the sequences at OTU level with 97% similarity showed a distinct clustering of the community composition between the morphine and placebo treated groups. By using the chao1 index to evaluate alpha diversity (that is diversity within a group) and using unweighted UniFrac distance to evaluate beta diversity (that is diversity between groups, comparing microbial community based on compositional structures), we found that morphine treatment results in a significant decrease in alpha diversity and shift in fecal microbiome at day 3 post treatment compared to placebo treatment. Taxonomical analysis showed that morphine treatment results in a significant increase of potential pathogenic bacteria. Our study shed light on effects of morphine on the gut microbiome, and its role in the gut homeostasis.
2018-04-16 | E-MTAB-5546 | biostudies-arrayexpress
Project description:The human gut is colonized by trillions of microorganisms that influence human health and disease through the metabolism of xenobiotics, including therapeutic drugs and antibiotics. The diversity and metabolic potential of the human gut microbiome have been extensively characterized, but it remains unclear which microorganisms are active and which perturbations can influence this activity. Here, we use flow cytometry, 16S rRNA gene sequencing, and metatranscriptomics to demonstrate that the human gut contains distinctive subsets of active and damaged microorganisms, primarily composed of Firmicutes, which display marked temporal variation. Short-term exposure to a panel of xenobiotics resulted in significant changes in the physiology and gene expression of this active microbiome. Xenobiotic-responsive genes were found across multiple bacterial phyla, encoding novel candidate proteins for antibiotic resistance, drug metabolism, and stress response. These results demonstrate the power of moving beyond DNA-based measurements of microbial communities to better understand their physiology and metabolism. RNA-Seq analysis of the human gut microbiome during exposure to antibiotics and therapeutic drugs.
2012-10-30 | E-GEOD-38151 | biostudies-arrayexpress
Project description:Bazedoxifene and conjugated estrogens (CE+BZA) combination has been shown to prevent visceral adiposity and weight gain after menopause. However, its interaction with the microbiota has yet to be examined. In the present study, we use several –omics technologies to characterize the effects of various estrogens on the health of gut-liver axis. As reported in previous studies, CE+BZA combination is very effective at preventing ovariectomy-induced weight gain in mice fed a high-fat diet. Additionally, CE+BZA induces unique liver transcriptomic and blood metabolite profiles compared to estradiol, conjugated estrogens alone, and bazedoxifene alone. Several pathways and metabolites influenced are associated with lower rates of inflammation and overall benefits to gut and liver health. Finally, microbiome analysis shows that several bacterial species that potentially metabolize estrogens and affect their half-life in the body were significantly changed in CE+BZA treated mice. Our findings indicate a possible link between certain estrogens and gut microbiome and suggest a metabolic benefit of estrogens through manipulation of the gut-liver axis.
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Project description:Bazedoxifene and conjugated estrogens (CE+BZA) combination has been shown to prevent visceral adiposity and weight gain after menopause. However, its interaction with the microbiota has yet to be examined. In the present study, we use several –omics technologies to characterize the effects of various estrogens on the health of gut-liver axis. As reported in previous studies, CE+BZA combination is very effective at preventing ovariectomy-induced weight gain in mice fed a high-fat diet. Additionally, CE+BZA induces unique liver transcriptomic and blood metabolite profiles compared to estradiol, conjugated estrogens alone, and bazedoxifene alone. Several pathways and metabolites influenced are associated with lower rates of inflammation and overall benefits to gut and liver health. Finally, microbiome analysis shows that several bacterial species that potentially metabolize estrogens and affect their half-life in the body were significantly changed in CE+BZA treated mice. Our findings indicate a possible link between certain estrogens and gut microbiome and suggest a metabolic benefit of estrogens through manipulation of the gut-liver axis.
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Project description:Hundreds of microbial species were found to be transcriptionally active in the human gut microbiome based on the expression profiling of ca. 680.000 microbial genes As a part of the MetaHIT cohort 233 human stool samples were transcriptionally profiled using a custom made microarray that included probes for most prevalent microbial genes in the cohort as established by whole-genome sequencing of the same samples
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Project description:Comparison study of gut microbiome and health status
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Project description:Hundreds of microbial species were found to be transcriptionally active in the human gut microbiome based on the expression profiling of ca. 680.000 microbial genes
2016-08-01 | GSE76590 | GEO
Project description:Morphine and its pharmacological derivatives are the most prescribed analgesics for moderate to severe pain management. However, chronic use of morphine reduces pathogen clearance and induces bacterial translocation across the gut barrier. The enteric microbiome has been shown to play a critical role in the preservation of the mucosal barrier function and metabolic homeostasis. Here, we show for the first time, using bacterial 16s rDNA sequencing, that chronic morphine treatment significantly alters the gut microbial composition and induces preferential expansion of the gram-positive pathogenic and reduction of bile-deconjugating bacterial strains. A significant reduction in both primary and secondary bile acid levels was seen in the gut, but not in the liver with morphine treatment. Morphine induced microbial dysbiosis and gut barrier disruption was rescued by transplanting placebo-treated microbiota into morphine-treated animals, indicating that microbiome modulation could be exploited as a therapeutic strategy for patients using morphine for pain management. In this study, we establish a link between the two phenomena, namely gut barrier compromise and dysregulated bile acid metabolism. We show for the first time that morphine fosters significant gut microbial dysbiosis and disrupts cholesterol/bile acid metabolism. Changes in the gut microbial composition is strongly correlated to disruption in host inflammatory homeostasis13,14 and in many diseases (e.g. cancer/HIV infection), persistent inflammation is known to aid and promote the progression of the primary morbidity. We show here that chronic morphine, gut microbial dysbiosis, disruption of cholesterol/bile acid metabolism and gut inflammation; have a linear correlation. This opens up the prospect of devising minimally invasive adjunct treatment strategies involving microbiome and bile acid modulation and thus bringing down morphine-mediated inflammation in the host.
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