Relating human gut metagenome and metaproteome
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PXD004039
PROVIDER: PRJEB19090 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.
2017-07-19 | PXD005780 | Pride
Project description:This study demonstrates the usefulness of the API by generating a baseline gut microbiota profile of a healthy population and estimating reference intervals for the functional abundance of manually selected KEGG pathways. API facilitates microbiome research by providing dynamic and customizable tools for estimating reference intervals for gut microbiota functional abundances. Through the API, researchers can rapidly generate gut microbiota functional profiles of healthy populations to use as a baseline for comparison. The API also allows users to manually select specific KEGG pathways and estimate reference intervals for the functional abundance of those pathways. By generating these customized reference intervals, researchers can better understand the expected range of gut microbiota functions in healthy individuals. API enables microbiome studies to go beyond simple taxonomic profiling and delve deeper into the functional potential of gut microbiome communities. In summary, API represents a valuable tool for microbiome researchers that enhances the ability to elucidate connections between gut microbial functions and human health.
2023-10-20 | GSE228552 | GEO
Project description:Increasing evidence indicates that gut microbiota plays an important role in cancer progression. We have employed RNA-seq or microarray for genome including mRNA, microRNA or circRNA profiling in an gut microbiota -dependent manner, as a discovery platform to identify target genes with the potential to involve in tumor regulation. The deep sequencing analysis reveals regulatory functions of microbiota-mediated circular RNA (circRNA)/microRNA networks that may contribute to cancer progression.
2020-10-13 | GSE140886 | GEO
Project description:Increasing evidence indicates that gut microbiota plays an important role in cancer progression. We have employed RNA-seq or microarray for genome including mRNA, microRNA or circRNA profiling in an gut microbiota -dependent manner, as a discovery platform to identify target genes with the potential to involve in tumor regulation. The deep sequencing analysis reveals regulatory functions of microbiota-mediated circular RNA (circRNA)/microRNA networks that may contribute to cancer progression.
2020-10-13 | GSE140885 | GEO
Project description:Increasing evidence indicates that gut microbiota plays an important role in cancer progression. We have employed RNA-seq or microarray for genome including mRNA, microRNA or circRNA profiling in an gut microbiota -dependent manner, as a discovery platform to identify target genes with the potential to involve in tumor regulation. The deep sequencing analysis reveals regulatory functions of microbiota-mediated circular RNA (circRNA)/microRNA networks that may contribute to cancer progression.
2020-10-13 | GSE140339 | GEO
Project description:Increasing evidence indicates that gut microbiota plays an important role in cancer progression. We have employed RNA-seq or microarray for genome including mRNA, microRNA or circRNA profiling in an gut microbiota -dependent manner, as a discovery platform to identify target genes with the potential to involve in tumor regulation. The deep sequencing analysis reveals regulatory functions of microbiota-mediated circular RNA (circRNA)/microRNA networks that may contribute to cancer progression.
2020-10-13 | GSE140338 | GEO
Project description:To compare the similarities and differences in species diversity of the gut microbiota between the patients with melasma and healthy subjects. The feces were collected for 16S rRNA sequencing analysis of the gut microbiota.
2022-10-25 | GSE214430 | GEO
Project description:Gut microbiota participates in diverse metabolic and homeostatic functions related to health and well-being. Individual variation in its composition depends on many factors including dietary factors. We profiled enzymatic activity of fecal microbiota in 63 healthy adult individuals using metaproteomics, and identified Bacteroides and Prevotella –derived microbial CAZy (carbohydrate-active) enzymes involved in glycan foraging. One particular profile with many Bacteroides-derived CAZy was identified in one-third of subjects (n=20), and it associated with high abundancy of Bacteroides in most subjects. In other subjects (n=8) with dietary parameters similar to former, microbiota showed intense expression of Prevotella-derived CAZy including exo−beta−(1,4)−xylanase, xylan-1,4−beta−xylosidase, alpha−L−arabinofuranosidase and several other CAZy belonging to glycosyl hydrolase families involved in digestion of complex plant-derived polysaccharides. This associated invariably with robust representation of Prevotella in gut microbiota, while subjects with intermediate representation of Prevotella showed no CAZy profile. Identification of Bacteroides- and Prevotella-derived CAZy in microbiota proteome and their association with robust differences in microbiota composition, the latter with exceptionally high Prevotella abundancy in the gut, are in evidence of individual variation in metabolic adaptation of gut microbiota with an impact on colonizing competence.
2021-06-30 | PXD017059 | Pride
Project description:We analyzed the effects of antibiotics using a popular model of gut microbiota depletion in mice by a cocktail of antibiotics. We combined intestinal transcriptome together with metagenomic analysis of the gut microbiota to develop a new bioinformatics approach that probes the links between microbial components and host functions. We found that most antibiotic-induced alterations can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues; and the effects of remaining antibiotic-resistant microbes. While microbe depletion led to down-regulation of immunity, the two other factors primarily inhibited mitochondrial gene expression and amounts of active mitochondria, and induced cell death. By reconstructing and analyzing a transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2015-01-26 | E-GEOD-60568 | biostudies-arrayexpress
Project description:Gut microbiota plays an important role during early development via bidirectional gut- brain signaling. We aimed to explore the potential link between gut microbiota/gut derived metabolites and sympathoadrenal stress responsivity
2018-11-25 | GSE122754 | GEO