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.
Project description:Tidal marsh and estuarine marine microbial sediment metagenomes from the Great Bay Estuary of New Hampshire were sequenced and found to be dominated by Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Both types of sediment contained many unclassified bacterial sequences, including the mollusk pathogen Perkinsus marinus, and detectable xenobiotic degradation and nitrogen transformation genes.
Project description:We use multi-omics (ATAC-seq, single cell RNA-seq and differential bulk RNA-seq) to increase resolution of the sea urchin posterior gut GRN for the cells expressing the ParaHox gene Sp-Pdx1.
