Project description:Host factors in the intestine, such as mucus secretion, play an important role in selecting for the colonization of bacteria that contribute to intestinal health. Here we characterized the capability of commensal species to cleave and transport mucin-associated monosaccharides and found that several members of the Clostridiales order can utilize intestinal mucins as an energy source. One such mucin utilizer, Peptostreptococcus russellii, reduces susceptibility to epithelial injury in mice. Several Peptostreptococcus species contain a gene cluster that enables the production of the tryptophan metabolite indoleacrylic acid (IA), which we show has a beneficial effect on intestinal epithelial barrier function and mitigates inflammatory responses. Furthermore, metagenomic analysis of human stool samples revealed that the genetic capability of microbes to utilize mucins and metabolize tryptophan was diminished in patients with inflammatory bowel disease. Our data suggest that stimulating the production of IA to promote anti-inflammatory responses could have therapeutic benefit.
2017-07-11 | GSE98884 | GEO
Project description:Metagenomic analysis of Ruminal Microbes
Project description:Engineering microbes with novel metabolic properties is a critical step for production of biofuels and biochemicals. Synthetic biology enables identification and engineering of metabolic pathways into microbes; however, knowledge of how to reroute cellular regulatory signals and metabolic flux remains lacking. Here we used network analysis of multi-omic data to dissect the mechanism of anaerobic xylose fermentation, a trait important for biochemical production from plant lignocellulose. We compared transcriptomic, proteomic, and phosphoproteomic differences across a series of strains evolved to ferment xylose under various conditions.
Project description:Engineering microbes with novel metabolic properties is a critical step for production of biofuels and biochemicals. Synthetic biology enables identification and engineering of metabolic pathways into microbes; however, knowledge of how to reroute cellular regulatory signals and metabolic flux remains lacking. Here we used network analysis of multi-omic data to dissect the mechanism of anaerobic xylose fermentation, a trait important for biochemical production from plant lignocellulose. We compared transcriptomic, proteomic, and phosphoproteomic differences across a series of strains evolved to ferment xylose under various conditions.
Project description:Our overarching goal is to understand how microbes along a glacier forefield chronosequence and productivity gradient interact with their environment, how this influences carbon and nitrogen cycling, and how the microbes respond to temperature increases. Specifically, using the novel approach of quantitative SIP paired with metagenomic sequencing, we will calculate growth rates for targeted functional genes and metagenome assembled genomes, quantifying their ecophysiology, in situ. And when paired with gene expression using metatranscriptomic libraries and metabolite production, we will gain a clearer understanding of how microbes grow, how they cycle carbon and nitrogen and how their metabolic activity changes in response to warming.
The work (proposal:https://doi.org/10.46936/10.25585/60008115) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231.
Project description:We analyzed the effects of antibiotics using a popular model of gut microbiota depletion in mice by a cocktail of antibiotics. We combined intestinal transcriptome together with metagenomic analysis of the gut microbiota to develop a new bioinformatics approach that probes the links between microbial components and host functions. We found that most antibiotic-induced alterations can be explained by three factors: depletion of the microbiota; direct effects of antibiotics on host tissues; and the effects of remaining antibiotic-resistant microbes. While microbe depletion led to down-regulation of immunity, the two other factors primarily inhibited mitochondrial gene expression and amounts of active mitochondria, and induced cell death. By reconstructing and analyzing a transkingdom network, we discovered that these toxic effects were mediated by virulence/quorum sensing in antibiotic-resistant bacteria. This SuperSeries is composed of the SubSeries listed below. Refer to individual Series