Why do some gut bacteria stick to one host species, while others seem to hop around freely between them? What changes in their genomes when they move between hosts? And how can we begin to develop the data and tools we need to study these questions across the vast diversity of animal life? My work is centered on the idea that a comparative phylogenetic perspective can help us to navigate the incredible diversity and complexity of animal gut bacteria—and that recent advances in software and hardware automation give us the tools we need to tackle the problem in the non-model animal systems most useful for answering these fundamental questions. At CIHMID, I am focusing on implementing high-throughput microbial cultivation and sequencing, combined with long-read metagenomics, to reconstruct the genomic evolutionary history of gut bacteria in the deer mice, genus Peromyscus. By efficiently retrieving high-quality complete genomic information from thousands of bacteria across many host species, while simultaneously maintaining a living reference catalogue of these same bacteria, I hope to use phylogenomic analyses to identify and in vitro and in vivo assays to test hypotheses about the genomic basis of host specificity in the mammalian gut microbiome.
Title: CIHMID Postdoctoral Fellow
Roles: CIHMID Postdoc