Gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA357304 | ENA |
REPOSITORIES: ENA
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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:Maternal inheritence of the koala gut microbiome
| PRJNA749124 | ENA
Project description:Bifidobacteria dominate the composition of the neonatal gut microbiota in the first number of weeks following birth. A number of species in particular are found with a significantly higher frequency in the microbiome of breastfed infants, owing to their ability to rely on Human Milk Oligosacchraides (HMOs) as their sole carbohydrate substrate; namely B. bifidum, B. longum spp. infantis and B. breve. Bifidobacterium kashiwanohense is a species that has been isolated previously only from the faeces of infants, but extremely infrequently at that. Relatively little is currently known about the species itself, let alone the metabolic pathways that allow it to successfully establish a population in the infant gut. We have isolated a novel strain of B. kashiwanohense from the faeces of a breastfed infant on the basis of its ability to utilise the HMO component fucosyllactose as its sole carbohydrate source. In this study, we read and annotate the full genome sequence of this novel strain, and use the data obtained to direct our further experimental analysis of fucosyllactose metabolism in B. kashiwanohense. Using transcriptomic and growth analysis results, we identify the genes responsible for B. kashiwanohense to utilise fucosyllactose, and employ a combination of cloning, in vitro hydrolysis assays, and further, recombinant transcriptomic and growth assays to elucidate the pathway for fucosyllactose metabolism in B. kashiwanohense, as well as revealing insight into fucosyllactose and fucose metabolism in Bifidobacteria as whole.
2019-11-12 | GSE107439 | GEO
Project description:Australia’s most iconic animal, the koala (Phascolarctos cinereus), faces significant population decline from habitat loss, disease, and environmental pressures. Conservation has focused on assisted breeding technology and reproductive pathologies, yet koala reproductive biology remains poorly understood, particularly the accessory sex glands. The koala prostate has an important role both in the production of seminal plasma and in facilitating successful reproduction. Furthermore, prostatitis regularly occurs as a consequence of chlamydiosis, a substantial factor in the ongoing decline of koalas. This study presents the first proteomic profile of the koala prostate, offering insights into its histological segmentation and its broader functional significance. Prostate tissue from six mature male koalas was collected during breeding season, sampling the anterior and posterior segments. Proteins were digested using filter-aided sample preparation and analysed via LC-MS/MS with Zeno-SWATH acquisition. Peptide spectra were processed using DIA-NN and evaluated in RStudio™ to identify differentially expressed proteins and compare the koala prostate proteome with those of other species. Functional annotation and pathway analysis were performed using DAVID and Ingenuity Pathway Analysis, while secretory protein predictions were conducted using UniProt and SignalP. Segment-specific proteomic profiles revealed proteomic differentiation with secretory proteins contributing to segment-specific functions. Cross-species comparisons highlight strong homology between the koala and human prostate proteomes. This proteome provides a foundation for future investigations into prostate-related pathologies in koalas. Furthermore, Understanding the koala prostate at a molecular level helps advance wildlife conservation through a better comprehension of its role in male fertility and offers broader evolutionary insights into marsupial reproduction.
2026-01-23 | PXD067256 | Pride