The Impact of Host Variables and Tumor Necrosis Factor on the Gut Microbiome in a Mouse Model of Crohn\u27s Disease

Crohn’s Disease (CD) and Ulcerative Colitis (UC) are chronic, inflammatory conditions of the digestive tract that are collectively known as Inflammatory Bowel Disease (IBD). Currently, IBD has no cure and the exact mechanisms of disease development and progression are unknown. The gut microbiome is the collection of microbes that reside in the digestive tracts of humans and animals, and it has been shown to be associated with a variety of diseases, including IBD. Mouse models of colitis are often used to investigate the role of the gut microbiome in IBD. In this work, I investigated the role of tumor necrosis factor (TNF) on the gut microbiome in a mouse model of CD. Tumor necrosis factor is an inflammatory cytokine that plays a critical role in the inflammatory response. A common IBD treatment strategy is the use of TNF inhibitors. However, a subset of patients only responds to anti-TNF treatment for a limited time, while others do not respond at all. It is not fully understood how TNF, or TNF blockade, impacts the microbiome. Therefore, my overall objective was to determine how TNF and host variables impact the mouse gut microbiome during colitis. My hypotheses were that 1) Age, sex, and TNF affect the fecal microbiome of mice, and impact the severity of acute 2,4,6 trinitrobenzenesulfonic acid (TNBS) colitis. 2) TNF, sex and disease severity impact the microbiome in chronic TNBS colitis and the composition of the fecal microbiome will closely correlate with colitis severity. 3) Different mouse strains have a distinct fecal microbiome. To test my hypotheses, I induced acute and chronic TNBS colitis in WT mice and Tnf-/-mice. 16S rRNA gene sequencing, microbiome analysis, and multivariate analyses were used to determine the relationship of host factors to the gut microbiome. I found that TNF, age, and sex impact the gut microbiome in mice before and after colitis. Additionally, I identified specific microbes that are differentially abundant depending on TNF expression, GI site, as well as the mouse age, sex, strain, and vendor. This work highlights the importance of considering host factors in microbiome studies and provides important data to the literature concerning the role of the gut microbiome in IBD pathogenesis

A survey-based analysis of the academic job market

Many postdoctoral researchers apply for faculty positions knowing relatively little about the hiring process or what is needed to secure a job offer. To address this lack of knowledge about the hiring process we conducted a survey of applicants for faculty positions: the survey ran between May 2018 and May 2019, and received 317 responses. We analyzed the responses to explore the interplay between various scholarly metrics and hiring outcomes. We concluded that, above a certain threshold, the benchmarks traditionally used to measure research success - including funding, number of publications or journals published in - were unable to completely differentiate applicants with and without job offers. Respondents also reported that the hiring process was unnecessarily stressful, time-consuming, and lacking in feedback, irrespective of outcome. Our findings suggest that there is considerable scope to improve the transparency of the hiring process

The Impact of Host Variables and Tumor Necrosis Factor on the Gut Microbiome in a Mouse Model of Crohn’S Disease

Crohn’s Disease (CD) and Ulcerative Colitis (UC) are chronic, inflammatory conditions of the digestive tract that are collectively known as Inflammatory Bowel Disease (IBD). Currently, IBD has no cure and the exact mechanisms of disease development and progression are unknown. The gut microbiome is the collection of microbes that reside in the digestive tracts of humans and animals, and it has been shown to be associated with a variety of diseases, including IBD. Mouse models of colitis are often used to investigate the role of the gut microbiome in IBD. In this work, I investigated the role of tumor necrosis factor (TNF) on the gut microbiome in a mouse model of CD. Tumor necrosis factor is an inflammatory cytokine that plays a critical role in the inflammatory response. A common IBD treatment strategy is the use of TNF inhibitors. However, a subset of patients only responds to anti-TNF treatment for a limited time, while others do not respond at all. It is not fully understood how TNF, or TNF blockade, impacts the microbiome. Therefore, my overall objective was to determine how TNF and host variables impact the mouse gut microbiome during colitis. My hypotheses were that 1) Age, sex, and TNF affect the fecal microbiome of mice, and impact the severity of acute 2,4,6 trinitrobenzenesulfonic acid (TNBS) colitis. 2) TNF, sex and disease severity impact the microbiome in chronic TNBS colitis and the composition of the fecal microbiome will closely correlate with colitis severity. 3) Different mouse strains have a distinct fecal microbiome. To test my hypotheses, I induced acute and chronic TNBS colitis in WT mice and Tnf-/- mice. 16S rRNA gene sequencing, microbiome analysis, and multivariate analyses were used to determine the relationship of host factors to the gut microbiome. I found that TNF, age, and sex impact the gut microbiome in mice before and after colitis. Additionally, I identified specific microbes that are differentially abundant depending on TNF expression, GI site, as well as the mouse age, sex, strain, and vendor. This work highlights the importance of considering host factors in microbiome studies and provides important data to the literature concerning the role of the gut microbiome in IBD pathogenesis

Comparison of the fecal, cecal, and mucus microbiome in male and female mice after TNBS-induced colitis.

Crohn's Disease and Ulcerative Colitis are chronic, inflammatory conditions of the digestive tract, collectively known as Inflammatory Bowel Disease (IBD). The combined influence of lifestyle factors, genetics, and the gut microbiome contribute to IBD pathogenesis. Studies of the gut microbiome have shown significant differences in its composition between healthy individuals and those with IBD. Due to the high inter-individual microbiome variation seen in humans, mouse models of IBD are often used to investigate potential IBD mechanisms and their interplay between host, microbial, and environmental factors. While fecal samples are the predominant material used for microbial community analysis, they may not be the ideal sample to use for analysis of the microbiome of mice with experimental colitis, such as that induced by 2, 4, 6 trinitrobenzesulfonic acid (TNBS). As TNBS is administered intrarectally to induce colitis and inflammation is confined to the colon in this model, we hypothesized that the microbiome of the colonic mucus would most closely correlate with TNBS colitis severity. Based on our previous research, we also hypothesized that sex would be associated with both disease severity and microbial differences in mice with chronic TNBS colitis. We examined and compared the fecal, cecal content, and colonic mucus microbiota of 8-week old male and female C57BL/6J wild-type mice prior to and after the induction of TNBS colitis via 16S rRNA gene sequencing. We found that the colonic mucus microbiome was more closely correlated with disease severity than were alterations in the fecal and cecal microbiomes. We also found that the microbiomes of the feces, cecum, and mucus were distinct, but found no significant differences that were associated with sex in either compartment. Our findings highlight the importance of sampling colonic mucus in TNBS-induced colitis. Moreover, consideration of the differential impact of sex on the microbiome across mouse strains may be critical for the appropriate application of TNBS colitis models and robust comparisons across studies in the future

Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species

Roseburia species are important denizens of the human gut microbiome that ferment complex polysaccharides to butyrate as a terminal fermentation product, which influences human physiology and serves as an energy source for colonocytes. Previous comparative genomics analyses of the genus Roseburia have examined polysaccharide degradation genes. Here, we characterize the core and pangenomes of the genus Roseburia with respect to central carbon and energy metabolism, as well as biosynthesis of amino acids and B vitamins using orthology-based methods, uncovering significant differences among species in their biosynthetic capacities. Variation in gene content among Roseburia species and strains was most significant for cofactor biosynthesis. Unlike all other species of Roseburia that we analysed, Roseburia inulinivorans strains lacked biosynthetic genes for riboflavin or pantothenate but possessed folate biosynthesis genes. Differences in gene content for B vitamin synthesis were matched with differences in putative salvage and synthesis strategies among species. For example, we observed extended biotin salvage capabilities in R. intestinalis strains, which further suggest that B vitamin acquisition strategies may impact fitness in the gut ecosystem. As differences in the functional potential to synthesize components of biomass (e.g. amino acids, vitamins) can drive interspecies interactions, variation in auxotrophies of the Roseburia spp. genomes may influence in vivo gut ecology. This study serves to advance our understanding of the potential metabolic interactions that influence the ecology of Roseburia spp. and, ultimately, may provide a basis for rational strategies to manipulate the abundances of these species