Project description:Metagenome data from soil samples were collected at 0 to 10cm deep from 2 avocado orchards in Channybearup, Western Australia, in 2024. Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters.
Project description:D-galactose orally intake ameliorate DNCB-induced atopic dermatitis by modulating microbiota composition and quorum sensing. The increased abundance of bacteroidetes and decreased abundance of firmicutes was confirmed. By D-galactose treatment, Bacteroides population was increased and prevotella, ruminococcus was decreased which is related to atopic dermatitis.
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:Macrophages are the main effector cells of inflammatory response and play an important role in the initiation and regression of inflammation. Macrophages are derived from monocytes which are differentiated into M1 macrophages (classically activated macrophages) or M2 macrophages (selectively activated macrophages) in response to different external stimuli, distinguished by the differential expression of cytokines, cell surface markers, and chemokines. In vitro macrophages are crucial models for understanding the regulatory mechanism of immune response and the establishment of infection models, ultimately, for the diagnosis or treatment of a variety of diseases. Porcine is the most important agricultural animal and one of the most valuable animal models for preclinical studies, but no unified method for porcine macrophage isolation and differentiation at present, neither a systematic study compared the porcine macrophage obtained by different methods. In this study, we used two strategies to induce porcine BMDM into M1 and two strategies to induce porcine BMDM into M2 macrophages. Subsequently, we compared the transcriptomic profile of BMDM treated with different induction methods by RNA-seq. The DEG analysis showed that porcine M1 macrophage and porcine M2 macrophage obtained have consistent gene signatures as mouse and human macrophages, respectively. We also observed differences in transcriptional levels in macrophages induced by different methods. We obtained the transcriptome sequencing data of macrophages infected by different pathogens from GEO and analyzed them quantitatively. We performed GSEA analysis on macrophages infected with different pathogens and porcine bone marrow-derived macrophages (BMDM). We found that the enrichment pathways of macrophages obtained by different induction methods and macrophages infected by different pathogens were different. Our study provided a framework to guide the interrogation of macrophage phenotypes in the context of health and disease. The approach described here could be used to propose new biomarkers for diagnosis in diverse clinical settings including porcine reproductive and respiratory syndrome virus (PRRSV), African swine fever virus (ASFV), and Toxoplasma gondii.