João Carlos Gomes Neto, PhD will present as part of the Food for Health Seminar Series.

Talk Title: How can bacterial population genomics be used under the concept of “food for health”?

Talk Summary:
The recent advances in whole-genome sequencing (WGS) and increasing volume of freely available genome sequences has dramatically changed how molecular epidemiology is done worldwide. For instance, WGS has dramatically enhanced the resolution to assess the population structure across divergent bacterial species which has improved diagnostics and surveillance of pathogens, and allowed for putatively causative loci underlying ecological phenotypes to be mapped in different contexts. However, due to the large volume of data, there remains multiple computational challenge on how to optimize algorithms and statistical approaches to 1) map and track genotypes at different levels of resolution in real-time; 2) predict lineages or genotypes of interest in either an epidemiological or ecological context; and 3) identify the causative genetic variants (i.e., SNPs or loci) that are determinants of fitness variation across hosts/environments. Given those challenges, we have developed ProkEvo – an automated, freely available, and portable pipeline that allows for hierarchical population structure analysis and pan-genomic mapping. While our work has been centered around zoonotic foodborne pathogens such as Salmonella enterica, the framework can be deployed to beneficial microbes that would impact health positively both in livestock and humans. Therefore, the goal of this talk is 1) to demonstrate how ProkEvo can facilitate population genomic analyses to guide the identification of pathogenic or beneficial bacterial lineages to be studied in the context of gastrointestinal (GI) health; 2) to discuss how genotypic and functional prediction can be done with the accessory genome considering the population structure; and 3) to discuss strategies that are yet to be tested with such an approach. “Food for health” is a concept that applies both to livestock and humans alike. Since, part of the biological mechanism underlying changes in host health through food will come from modulation of the GI microbiome, it is only pertinent to ask whether the phenotypes sought (e.g., colonization resistance to pathogens or metabolic changes in the host) can be fine-tunned by specific strains of a given species. Population genomics can probe those features and guide the design of future animal and human studies in this area in conjunction with other disciplines.

An in-person reception will be hosted at 11:30am, outside FIC 277 auditorium on Innovation Campus.
Seminar: Noon - 1pm CT
This seminar will be in-person & streamed via Zoom.

Email Allie Eaton for Zoom connection information.