Metaproteomic Profiling of Functional Changes Driven by Gut Fungal Colonization

Gut microbiome modulates the host immune development, yet the functional contribution of gut fungi remains elusive. We previously showed that mice colonized only with fungi displayed allergic features and fecal metabolite profiles similar to germ-free mice. To gain insights into the functional changes attributed to fungal colonization, we performed proteomic analyses of feces and small intestine of gnotobiotic mice colonized with either bacteria, fungi, or both. Comparison of fecal metaproteomic profiles between mouse groups yielded broad changes in the relative levels of bacterial, fungal and mouse proteins. Many of the detected fungal proteins have been previously reported as a part of extracellular vesicles and having immunomodulating properties. Changes in the levels of mouse proteins derived from the small intestine impacted essential cellular pathways, including lipid metabolism and apoptosis. The results show how fungal colonization impacts the host proteome and suggest an influence on the host final cellular phenotype.