Significant disturbances to the gut microbiome can be induced by numerous diet and lifestyle factors, as well as medications such as antibiotics. Imbalances in gut microbiome populations (dysbiosis) are associated with many diseases and poor health outcomes, including asthma, inflammatory bowel disease, autism, and obesity. A greater understanding of factors influencing gut microbiome resilience (the ability to resist and recover from change), and with it an expanded range of microbiome resilience biomarkers, is expected to lead to strategies to boost resilience and improve health outcomes. Clinical trials and in vivo studies have shown that gut microbiome populations often take 3-6 months to return back to the pre-antibiotic state, and longer lasting dysbiosis is possible and microbiome and interindividual dependent factors may influence the recovery time.
As an initial step we will use in vitro fermentation with human stool to understand the ability of dietary factors to impact the resilience of gut microbes that have been exposed to broad spectrum antibiotics. Multi-omics approaches then will be used to give insights into changes in microbiome community composition and function and help identify and measure biomarkers of microbiome resilience.
We will also test commercially available prebiotics and probiotics, as well as other foods or ingredients to benefit the gut microbiome and their possible impacts on the resilience of gut microbiome in the in vitro fermentation model. These findings will be used to assist in the development of a predictive model of microbiome resilience that can be tested and built upon through further in vitro and in vivo testing, and ultimately used to assist in clinical therapies or dietary strategies that improve health.