Dietary fiber to mitigate antibiotic-induced microbiome dysbiosis: a multi-omics approach

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To enhance the use of currently available antibiotics, we need to understand how they impact both pathogenic and beneficial bacteria within the host. Identifying methodologies that reduce the impacts of antibiotics on the core microbiome may help to reduce multiple microbiome-related diseases, such as Clostridium difficile- associated diarrhea and inflammatory bowel disease. Microbial metabolism is known to be a key modulator of antibiotic susceptibility and we propose that changing the metabolic environment in the microbiome via dietary innervation may reduce the antibiotic susceptibility of beneficial taxa. Our preliminary data indicate that a diet high in plant-derived fiber provides significant protection to the structure of the murine microbiome during antibiotic insult compared to a typical Western low fiber diet. We hypothesize that specific forms of plant-derived polysaccharides can impact bacterial metabolism and thereby modulate antibiotic susceptibility in commensal bacteria. In turn, this modulation may provide protection to microbiome diversity during antibiotic therapy. At this time, however, there is insufficient knowledge to predict how these common dietary components and supplements will impact the structure, function, and response of the microbiome. To overcome this limitation, we will take a multi-omic approach combining metagenomics, metatranscriptomics and metabolomics to profile the impacts of plant-derived polysaccharides on the structure, function, and metabolic state of the microbiome and to relate those factors to antibiotic-induced microbiome disruption and resilience. We will conduct this work in the following two aims: Aim 1. Profile the impacts of a fiber-rich diet on the function, structure, and metabolic response of the murine microbiome during antibiotic therapy. Aim 2. Systematically determine the impacts of short-term and long-term purified fiber supplementation on murine microbiome homeostasis and its metabolic response during antibiotic therapy. Understanding the impacts of fiber on antibiotic disruption of the microbiome could have significant translational potential by identifying prebiotic adjuvants that reduce antibiotic-induced dysbiosis. On a basic science level, our metatranscriptomic and metabolomic analysis will allow us to profile how changes in microbiome metabolism can impact antibiotic action. This knowledge can direct future development of targeted therapies that further reduce the off-target impacts of antibiotic treatment.