Human Gut Microbiome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA792991 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To investigate the TVA diet's effect on mouse gut microbiome, we fed C57/BL6 mice with TVA diet or CON diet for 18 days We then collected feces of the mice and performed 16S ribosomal RNA (rRNA) sequencing.
2023-09-21 | GSE202266 | GEO
Project description:Opioid analgesics are frequently prescribed in the United States and worldwide. However, serious side effects such as addiction, immunosuppression and gastrointestinal symptoms limit long term use. In the current study using a chronic morphine-murine model a longitudinal approach was undertaken to investigate the role of morphine modulation of gut microbiome as a mechanism contributing to the negative consequences associated with opioids use. The results revealed a significant shift in the gut microbiome and metabolome within 24 hours following morphine treatment when compared to placebo. Morphine induced gut microbial dysbiosis exhibited distinct characteristic signatures profiles including significant increase in communities associated with pathogenic function, decrease in communities associated with stress tolerance. Collectively, these results reveal opioids-induced distinct alteration of gut microbiome, may contribute to opioids-induced pathogenesis. Therapeutics directed at these targets may prolong the efficacy long term opioid use with fewer side effects.
2018-04-16 | E-MTAB-5550 | biostudies-arrayexpress
Project description:Aging is associated with declining immunity and inflammation as well as alterations in the gut microbiome with a decrease of beneficial microbes and increase in pathogenic ones. The aim of this study was to investigate aging associated gut microbiome in relation to immunologic and metabolic profile in a non-human primate (NHP) model. 12 old (age>18 years) and 4 young (age 3-6 years) Rhesus macaques were included in this study. Immune cell subsets were characterized in PBMC by flow cytometry and plasma cytokines levels were determined by bead based multiplex cytokine analysis. Stool samples were collected by ileal loop and investigated for microbiome analysis by shotgun metagenomics. Serum, gut microbial lysate and microbe-free fecal extract were subjected to metabolomic analysis by mass-spectrometry. Our results showed that the old animals exhibited higher inflammatory biomarkers in plasma and lower CD4 T cells with altered distribution of naïve and memory T cell maturation subsets. The gut microbiome in old animals had higher abundance of Archaeal and Proteobacterial species and lower Firmicutes than the young. Significant enrichment of metabolites that contribute to inflammatory and cytotoxic pathways was observed in serum and feces of old animals compared to the young. We conclude that aging NHP undergo immunosenescence and age associated alterations in the gut microbiome that has a distinct metabolic profile.
2022-02-01 | E-MTAB-10160 | biostudies-arrayexpress
Project description:Obesity is a risk factor for Osteoarthritis (OA), the greatest cause of disability in the US. The impact of obesity on OA is driven by systemic inflammation, now understood to be caused by an altered gut microbiome. Oligofructose, a non-digestible prebiotic fiber, can correct the obese gut microbiome, suggesting a novel approach to treat the OA of obesity. Here we report that in the obese murine gut, beneficial Bifidobacteria are lost while key proinflammatory species gain in abundance. A downstream systemic inflammatory signature culminates with accelerated knee OA. Oligofructose supplementation corrects the obese gut microbiome in part by supporting key commensal microflora, particularly Bifidobacterium pseudolongum. This leads to reduced inflammation in the colon, circulation and knee, and protection from OA. This novel recognition of a gut microbiome-OA connection sets the stage for discovery of new OA therapeutics targeting specific microbes inhabiting the intestinal space to inhibit disease pathology.
2018-06-22 | GSE98287 | GEO
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: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.
2013-12-05 | E-GEOD-46761 | biostudies-arrayexpress
Project description:Environmental perturbations impact gene transcription. A subset of these transcriptional changes can be passed on to the next generation even in the absence of the initial stimulus. This phenomenon is known as transgenerational inheritance of environmental exposures (TIEE). Previous studies have mainly focused on what is transferred through the germ-line, i.e. DNA methylation, histone modifications, non-coding RNAs, etc. Nevertheless, the germ cells are not the only cells that are passed on from one generation to the next. The microbiota is also transmitted together with the host cells. In this study, we investigated the role of the gut microbiome in TIEE using Drosophila melanogaster as a model organism. We have reared flies in cold and control temperatures, 18 and 25 °C respectively, and looked at the transcriptional pattern in their offspring -grown in control condition- using RNA sequencing. To study the effect of the microbiome, we have carefully exchanged the parental feces introduced to the offspring. We observed genes responsive to thermal alteration, which have preserved their transcriptional status transgenerationally. A subset of these genes, mainly genes expressed in gut, were transcriptionally dependent on which microbiome they acquired. These findings show that the microbiota plays a previously unknown role in TIEE. Our study unveiled a new route for transmittance of environmental memories and thus represents an uncharted area to explore for researchers addressing non-genetic transgenerational inheritance.
2018-10-10 | GSE111116 | GEO
Project description:Environmental perturbations impact gene transcription. A subset of these transcriptional changes can be passed on to the next generation even in the absence of the initial stimulus. This phenomenon is known as transgenerational inheritance of environmental exposures (TIEE). Previous studies have mainly focused on what is transferred through the germ-line, i.e. DNA methylation, histone modifications, non-coding RNAs, etc. Nevertheless, the germ cells are not the only cells that are passed on from one generation to the next. The microbiota is also transmitted together with the host cells. In this study, we investigated the role of the gut microbiome in TIEE using Drosophila melanogaster as a model organism. We have reared flies in cold and control temperatures, 18 and 25 °C respectively, and looked at the transcriptional pattern in their offspring -grown in control condition- using RNA sequencing. To study the effect of the microbiome, we have carefully exchanged the parental feces introduced to the offspring. We observed genes responsive to thermal alteration, which have preserved their transcriptional status transgenerationally. A subset of these genes, mainly genes expressed in gut, were transcriptionally dependent on which microbiome they acquired. These findings show that the microbiota plays a previously unknown role in TIEE. Our study unveiled a new route for transmittance of environmental memories and thus represents an uncharted area to explore for researchers addressing non-genetic transgenerational inheritance.
2018-10-10 | GSE111048 | GEO
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
2016-08-01 | E-GEOD-76590 | 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