Project description:The aim of the current study was to characterize the differential cellular and exosomal miRNAs during inflammation or high fat diet-induced obesity in mice. Mesenteric adipose tissue (MAT) and abdominal aorta (AA) from mice fed a normal chow diet (NCD) or a high fat diet (HFD) were harvested for miRNA profiling. MAT-derived adipocytes (MAT-Ad) challenged with either lipopolysaccharide (LPS, 1 µg/ml) or PBS were harvested for miRNA profiling. Meanwhile, miRNAs encapsulated in MAT-Ad-derived exosomes (MAT-Ad-EX) were also analyzed. Hierarchical clustering analysis performed on most significantly regulated miRNAs (HFD vs NCD in tissues; LPS challenge vs PBS in the cells) showed a set of miRNAs that are differentially expressed in obese versus lean MAT or AA tissues, and in LPS-challenged versus PBS-treated MAT-Ads. The dysregulated of miRNAs in MAT-Ad-EX was also generated and hierarchically clustered, induced by prolonged exposure to microbial product.
Project description:Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme’s response (R2, 0.51–0.80, p < 0.01 in all cases). Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide (latitude 62.2°S–16°N, MAT –1.4ºC–29.5ºC) validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility, confirm the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response
Project description:Hundreds of microbial species were found to be transcriptionally active in the human gut microbiome based on the expression profiling of ca. 680.000 microbial genes
Project description:The gut microbiome is significantly altered in inflammatory bowel diseases, but the basis of these changes is not well understood. We have combined metagenomic and metatranscriptomic profiling of the gut microbiome to assess changes to both bacterial community structure and transcriptional activity in a mouse model of colitis. Gene families involved in microbial resistance to oxidative stress, including Dps/ferritin, Fe-dependent peroxidase and glutathione S-transferase, were transcriptionally up-regulated in colitis, implicating a role for increased oxygen tension in gut microbiota modulation. Transcriptional profiling of the host gut tissue and host RNA in the gut lumen revealed a marked increase in the transcription of genes with an activated macrophage and granulocyte signature, suggesting the involvement of these cell types in influencing microbial gene expression. Down-regulation of host glycosylation genes further supports a role for inflammation-driven changes to the gut niche that may impact the microbiome. We propose that members of the bacterial community react to inflammation-associated increased oxygen tension by inducing genes involved in oxidative stress resistance. Furthermore, correlated transcriptional responses between host glycosylation and bacterial glycan utilisation support a role for altered usage of host-derived carbohydrates in colitis. Complementary transcription profiling data from the mouse hosts have also been deposited at ArrayExpress under accession number E-MTAB-3590 ( http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3590/ ).