2023 Theses Doctoral

Prediction of Human Gut Bacterial Secreted Proteins and their Interactions with Human Colonic Proteins

Velez-Cortes, Florencia

The gut microbiome is known to interact with the human host and deviations from a healthy gut microbiome can have serious repercussions for host health, but our knowledge of bacterial mediators of these interactions lags behind our ability to identify correlations with the gut microbiome. In this work I utilize computational pipelines to analyze publicly available gut microbiome data to identify potential mediators of gut interactions, first between bacteria, and later with host colonic cells.

Using previously published metagenomic data from sites along the gastrointestinal tract, I charted the biogeography of bacterial secreted proteins predicted from the human gut microbiome and identify functions that are enriched along the digestive tract and in the gut mucosa and lumen. These studies provide a dataset of gut bacterial secreted proteins that can serve as a resource for studies of potential interbacterial and host-bacterial interactions, and represent the largest-scale effort to date of annotation of potential human sequence homologs in gut commensal bacteria.