Human gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA286718 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gut microbiota in CRC tissues and surrounding non CRC tissues raw sequence reads
| PRJNA286719 | ENA
Project description:Alterations in gut microbiota have been implicated in the pathogenesis of Colorectal Cancer (CRC). Here we collected fecal samples from 14 CRC patients and 14 healthy volunteer cohorts, and characterized their microbiota using label-free quantitative metaproteomics method. We have quantified 30,062 gut microbial protein groups, 91，902 peptides, and 195 genera of microbes, among which 341 proteins were found significantly different in abundance between the CRC patients and healthy volunteers. Our study demonstrates that gut bacteria involve in CRC pathogenesis not only via taxonomy abundance variations but also functional activity changes.
2020-02-23 | PXD013386 |
Project description:Dysbiotic configurations of the human gut microbiota have been linked with colorectal cancer (CRC). Human small non-coding RNAs are also implicated in CRC and recent findings suggest that their release in the gut lumen contributes to shape the gut microbiota. Bacterial small RNAs (bsRNAs) may also play a role in carcinogenesis but their role is less explored. Here, we performed small RNA and shotgun sequencing on 80 stool specimens of patients with CRC, or adenomas, and healthy subjects collected in a cross-sectional study to evaluate their combined use as a predictive tool for disease detection. We reported a considerable overlap and correlation between metagenomic and bsRNA quantitative taxonomic profiles obtained from the two approaches. Furthermore, we identified a combined predictive signature composed by 32 features from human and microbial small RNAs and DNA-based microbiome able to accurately classify CRC from healthy and adenoma samples (AUC= 0.87). In summary we reported evidence that host-microbiome dysbiosis in CRC can be observed also by altered small RNA stool profiles. Integrated analyses of the microbiome and small RNAs in the human stool may provide insights for designing more accurate tools for diagnostic purposes.
2019-08-30 | GSE132236 | GEO
Project description:Gut microbiota dysbiosis characterizes systemic metabolic alteration, yet its causality is debated. To address this issue, we transplanted antibiotic-free conventional wild-type mice with either dysbiotic (“obese”) or eubiotic (“lean”) gut microbiota and fed them either a NC or a 72%HFD. We report that, on NC, obese gut microbiota transplantation reduces hepatic gluconeogenesis with decreased hepatic PEPCK activity, compared to non-transplanted mice. Of note, this phenotype is blunted in conventional NOD2KO mice. By contrast, lean microbiota transplantation did not affect hepatic gluconeogenesis. In addition, obese microbiota transplantation changed both gut microbiota and microbiome of recipient mice. Interestingly, hepatic gluconeogenesis, PEPCK and G6Pase activity were reduced even once mice transplanted with the obese gut microbiota were fed a 72%HFD, together with reduced fed glycaemia and adiposity compared to non-transplanted mice. Notably, changes in gut microbiota and microbiome induced by the transplantation were still detectable on 72%HFD. Finally, we report that obese gut microbiota transplantation may impact on hepatic metabolism and even prevent HFD-increased hepatic gluconeogenesis. Our findings may provide a new vision of gut microbiota dysbiosis, useful for a better understanding of the aetiology of metabolic diseases. all livers are from NC-fed mice only.
2017-03-16 | GSE81318 | GEO
Project description:The ERC “MINERVA” project (GA 724734) aims at developing a multi-organ-on-a-chip engineered platform to recapitulate in vitro the main players involved in the MGBA crosstalk: the microbiota, the gut epithelium, the immune system, the blood-brain barrier and the brain. In this context, the gut epithelium represents a physiological barrier that separates the intestinal lumen from the systemic circulation, and in several pathological circumstances, seems that its permeability might significantly increase and allow the passage of biologically active molecules into the blood vessels surrounding the intestinal mucosa. In the present work, we present our MINERVA 2.0 device and our innovative gut-on-a-chip device obtained by culturing in MINERVA 2.0 and a human gut epithelial CaCo2 cell based model. In particular, we have cultured the cells under perfusion and have assessed cell behavior by addressing cellular viability, tight junction imaging, apparent permeability by FITC-Dextran and transepithelial electrical resistance evaluation. Transcriptomic profile was used to further elucidate the effects of dynamic perfusion on Caco-2 cells.
2022-10-31 | E-MTAB-11949 | biostudies-arrayexpress
Project description:The gut microbiota exerts a profound influence on host physiology, but its systemic impact on gene expression across diverse tissues remains poorly characterized. This study investigated the transcriptional effects of gut microbiota depletion and restoration in mice across six tissues (colon, jejunum, liver, heart, lung, and kidney) using whole-transcriptome sequencing. We found that the presence of gut microbiota significantly altered the transcriptome, with the most pronounced effects in the colon. Using a linear mixed-effects model, we identified 7,365 effector genes. Tissue-specific analysis revealed that these genes were associated with distinct functional pathways, such as immunity in the gut and lung, and metabolism in the liver. Further refinement with LASSO regression pinpointed gut microbiota-mediated key effector genes, whose expression levels were significantly associated with patient survival in corresponding human cancers (e.g., LIHC, LUAD, KIRC). Furthermore, we observed a widespread remodeling of competing endogenous RNA (ceRNA) networks by the gut microbiota. Single-cell data analysis highlighted a potential gut-liver axis interaction, primarily mediated by colonic enterocytes and hepatic cholangiocytes, meanwhile gut microbiota repressed the transcription initiation of Noct in colonic enterocytes, whose expression level was significantly negatively correlated to gut-liver axis interaction. Our findings provide a comprehensive map of the multi-tissue transcriptional landscape shaped by the gut microbiota, revealing tissue-specific regulatory mechanisms and identifying key genes with potential clinical relevance in cancer.
2026-03-27 | GSE322803 | GEO
Project description:Metaproteomic portrait of the healthy human gut microbiota. Re-analysis of existing datasets, selected based on the following inclusion criteria: human cohort including at least 5 healthy (clearly not labeled as diseased) adult (>18 years old) individuals; data derived from LC-MS/MS DDA label-free analysis of fecal samples (with neither subcellular fractionation of microbial cells nor offline fractionation of peptides); availability of raw MS data on public repositories.
2024-05-16 | PXD046818 | Pride