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Research Areas


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Gut microbiome dysbiosis and Clostridium diffiicile infection

Our primary research focus is to understand how gut microbiota prevent colonization of the gut by eneteric pathogens such as C. difficile. Primary trigger of C. difficile infection is the dysbiosis of the gut microbiota following antibiotic treatment. Severe cases of C. difficile infection is treated by fecal ransplantation from healthy donors. We are interested in developing defined bacterial mixes for treating C. difficile infection. We have developed a healthy gut microbiome culture library and we are testing the efficacy of select bacterial species in supressing the growth of C. difficile using a gnotobiotic pig model. 

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Bacterial culturomics to develop probiotics

Mammalian gut contain hundreds of species. Many of them are beneficial and critical in maintaining gut health. We are using "culturomics" methods to mine gut microbiota to identify beneficial bacteria. Our lab has developed a new method where hundreds of isolates can be retrieved from gut microbiota using highthroughput anaerobic culturing and MALDI-TOF. Beneficial strains from this screen is then identified using phylogenomics and co-culture assays. 

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Understanding mechanisms of bacterial community interactions

Another focus of our lab is to understand the inter-species interactions between commensals and pathogens in the gut. We use bioreactor based assays of synthetic communities to study competition between commensal bacteria and pathogens such as Salmonella enterica. Pictured on the left is bioreactor arrays we use for competition experiments. These mini-bioreactor arrays were originally developed by Rob Britton's lab at the Baylor College of Medicine. We obtained the design through a collaboration with Britton lab.

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Genomic epidemiology

Our lab is a member of the GenomeTrakr project funded by the Food and Drug Administration. We are sequencing the genomes of hundreds of foodborne pathogens with a focus on Salmonella enterica. We are using this oppertunity to develop genomic epidemiology methods for studying Salmonella transmission and evolution. Raw genome sequence data for the isolates we sequenced are available for download at this link at NCBI SRA