Biology subjects

Richie, T. G.

Publications and source records attributed to Richie, T. G..

4 recordsLinked to original sources

bioRxiv2025

Source of dietary protein alters the abundance of proteases, intestinal epithelial and immune proteins both directly and via interactions with the gut microbiota

Dietary protein source differentially impacts long-term health outcomes, yet the specific host responses underlying these health effects remain unclear, including which are direct effects of protein source and which are microbiota-mediated. Using metagenome-informed metaproteomics, we determined that protein source altered the abundance of host proteins related to proteolysis, immunity, and the gut barrier as well as microbial function in mice. These stool host responses further reflected site-specific responses throughout the intestinal tract. Additionally, while some host responses were microbiota-dependent, others were microbiota-independent. These effects of dietary protein source on the host and microbiota translated to humans. Notably, microbial enzymes related to mucin degradation increased consistently in response to egg white protein in both mice and humans. Our results show that protein source impacts multiple aspects of host physiology through microbiota-dependent and independent routes, providing essential insights into mechanisms underpinning protein source-driven differences in health outcomes.

microbiology↗

bioRxiv2024

Dietary protein from different sources escapes host digestion and is differentially modified by the microbiota

Protein is an essential macronutrient and variations in its source and quantity have been shown to impact long-term health outcomes. Differential health impacts of dietary proteins from various sources are likely driven by differences in their digestibility by the host and subsequent availability to the intestinal microbiota. However, our current understanding regarding the fate of dietary proteins from different sources in the gut, specifically how component proteins within these sources interact with the host and the gut microbiota, is limited. To determine which dietary proteins are efficiently digested by the host, and which proteins escape host digestion and are used by the gut microbiota, we used high-resolution mass spectrometry to quantify proteins that constitute different dietary protein sources before and after digestion in germ-free and conventionally raised mice. We detected proteins from all sources in fecal samples of both germ-free and conventional mice suggesting that even protein sources with high digestive efficiency make it to the colon where they can serve as metabolic substrate for gut microbiota. Additionally, we found that specific component proteins of dietary protein sources were degraded to a greater extent in the presence of the microbiota. We found that specific proteins with functions that could potentially impact host health and physiology were differentially enriched in germ-free or conventionally raised mice. These findings reveal large differences in the fate of dietary protein from various sources in the gut which could explain some of their differential health impacts.

microbiology↗

bioRxiv2024

Eubacterium rectale detoxification mechanism increases resilience of the gut environment

Lachnospiraceae members were highly detected in dysbiotic IL-10 KO mice that displayed similar physiological outcomes as control mice. Lachnospiraceae is a highly diverse family of microbes that have been shown to display both commensal and pathogenic characteristics in the colon environment. We investigated the impact of genetic variation in five Lachnospiraceae strains on lowering cellular inflammation and ROS levels. Cell free spent media (CFSM) from Eubacterium rectale resulted in lowered ROS, and nitric oxide levels in stressed colon cells. We demonstrated through an array of multi omics and molecular techniques that glutathione (GSH) biosynthesized by E. rectale was able to alleviate host ROS damage. We further showed downregulation of cell stress and immune response genes by host RNA sequencing, which is evidence that E. rectale microbial products promote recovery and alleviate ROS stress. HighlightsO_LILachnospiraceae detection correlated with lower host inflammation in vertically transmitted dysbiotic mice C_LIO_LICell free spent media from E. rectale lowered ROS and nitric oxide levels when introduced to stressed Caco-2 cells more effectively than 4 other strains of Lachnospiraceae C_LIO_LIEubacterium rectale spent media products include high levels of glutathione (GSH), carbohydrates, and amino acids C_LIO_LIEubacterium rectale potential gene function for glutathione biosynthesis and metabolism found in the genome C_LIO_LILower expression of repair and stress genes of intestinal cells treated with hydrogen peroxide was observed with E. rectale CFSM as well as treatment with 15 mM GSH C_LI

microbiology↗

bioRxiv2022

Limitation of sulfur-containing amino acid availability by specific bacterial populations during enhanced colitis in IBD mouse model

Members of the Enterobacteriaceae family including Escherichia coli are associated with persistent gut inflammation during disorders like inflammatory bowel disease. This is due to rapid microbial colonization during dysbiosis combined with pathogenic tendencies. We characterized the dysbiotic gut community, defined potential functional pathways, and investigated crosstalk between host gene expression and microbial detections in an intestinal inflammation murine model. Members of Enterobacteriaceae family and the Enterococcus genus were highly detected in dysbiotic mice. These metagenome assembled genomes (MAGs) contained several virulence factors and metabolic pathways necessary to drive perpetual inflammation. Two Enterobacteriaceae MAGs with L-cysteine and L-taurine dioxygenases were strongly correlated with upregulation of the host gene CSAD, responsible for cysteine metabolism. Suggesting these bacteria compete with the host to utilize essential amino acids. We observed that bacterial isolates from dysbiotic mice displayed increased growth rates supplemented with L-cysteine, confirming that these microbes can utilize host nutrients to sustain inflammation. In BriefInflammatory bowel disease is associated with an increase in Enterobacteriaceae and Enterococcus species, however the mechanisms are unclear. Richie et al. show that these bacterial populations use sulfur metabolism and tolerate host-derived immune-response, to drive host inflammation and fuel growth in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize these essential host nutrients. HighlightsO_LIMice receiving native microbial FMT showed lower colon inflammation scores, higher microbial diversity, detections and gene expression similar to control mice. C_LIO_LIDysbiotic mice displayed increased colon inflammation, higher detection of potential pathogenic MAGs, and upregulation of cysteine dioxygenase and other inflammation response genes C_LIO_LIMAGs assigned to Enterococcus and Enterobacteriaceae species were more frequently detected in dysbiotic mice, while almost absent in mice receiving FMT or control mice, they also contain several virulence factors and antibiotic resistance genes. C_LIO_LIThese MAGs also display potential functions of utilizing host products and nutrients including nitrate, cysteine, and taurine to further fuel their growth and metabolism, which results in persistent host intestinal inflammation. C_LIO_LIIsolates in the Enterobacteriaceae family from dysbiotic mice utilize L-cysteine for growth, whereas isolates from FMT and control mice show no significant difference, indicating these bacteria can utilize the host derived cysteine. C_LI

genomics↗