Gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA641528 | ENA |
REPOSITORIES: ENA
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Project description:The secretion of Extracellular Vesicles ((EVs) is a common process in both prokaryotic and eukaryotic cells for intercellular communication, survival, and pathogenesis. Previous studies have illustrated the presence of EVs in supernatants from pure cultures of bacteria, including Gram-positive and Gram-negative glycan-degrading gut commensals. However, the composition of vesicles formed in complex microbial communities has not been clearly defined. In a recent paper, we reported that wood-derived complex β-mannan, which shares structural similarity with conventional dietary fibers, can be used to modulate the porcine gut microbiota composition and activity. In this paper, we investigated the production, size, composition, and proteome of EVs secreted by the pig fecal microbiota after 24 h enrichment on complex β-mannan. Using transmission electron microscopy and nanoparticle tracking analysis, we identified EVs with an average size of 105 nm. We utilized mass spectrometry-based metaproteomic profiling of EV proteins against a database of 355 metagenome-assembled genomes (MAGs) from the porcine colon and thereby identified 303 proteins, of which 55% were only detected in the EVs isolated from the β-mannan culture. Most of the proteins extracted from the EVs isolated from the culture grown on β-mannan mapped to two MAGs, MAG53 and MAG272, belonging to the orders Clostridiales and Bacilli, respectively. Furthermore, the MAG with the third-most-detected proteins was MAG 343 belonging to the order Enterobacteriales. The most abundant proteins detected in the β-mannan proteome were involved in translation, energy production, amino acid and carbohydrate transport, as well as metabolism. Overall, our results demonstrate the release of EVs in a complex microbial community whereby the protein content of the EVs reflects the response of specific microbes to the available carbohydrate source.
2021-09-09 | PXD017420 | Pride
Project description:Analysis of breast cancer survivors' gut microbiota after lifestyle intervention, during the COVID-19 lockdown, by 16S sequencing of fecal samples.
2023-01-13 | E-MTAB-12486 | biostudies-arrayexpress
Project description:Metagenome assembled genomes (MAGs) from Gulf of Khambhat pelagic sediments
| PRJNA598413 | ENA
Project description:Metagenome assembled genomes (MAGs) from Gulf of Kutch pelagic sediments
| PRJNA598416 | ENA
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:Metagenome-assembled genomes from the chicken gut
| PRJNA792475 | ENA
Project description:<p>A variety of anthropogenic organohalide contaminants generated from industry are released into the environment, and thus cause serious pollution that endangers human health. In the present study, we investigated the microbial community composition of industrial saponification wastewater using 16S rRNA sequencing, providing genomic insights of potential organohalide dehalogenation bacteria (OHDBs) by whole-metagenome sequencing. We also explored yet-to-culture OHDBs involved in the microbial community. Microbial diversity analysis reveals that Proteobacteria and Patescibacteria phyla dominate microbiome abundance of the wastewater. In addition, a total of six bacterial groups (Rhizobiales, Rhodobacteraceae, Rhodospirillales, Flavobạcteriales, Micrococcales, and Saccharimonadales) were found as biomarkers in the key organohalide removal module. Ninety-four metagenome-assembled genomes (MAGs) were reconstructed from the microbial community, and 105 hydrolytic dehalogenase genes within 42 MAGs were identified, suggesting that the potential for hydrolytic organohalide dehalogenation is present in the microbial community. Subsequently, we characterized the organohalide dehalogenation of an isolated OHDB, Microbacterium sp. J1-1, which shows the dehalogenation activities of chloropropanol, dichloropropanol, and epichlorohydrin. This study provides a community-integrated multi-omics approach to gain functional OHDBs for industrial organohalide dehalogenation.</p>
2022-11-21 | MTBLS3916 | MetaboLights