Functional Characterization of Microbial Symbiotic Associations by Metaproteomics

Rarely are microbes found in isolation in the environment, but rather form symbiotic associations with other microbes or eukaryotic hosts. The advent of the systems biology era has allowed global characterization of these symbiotic associations at levels not previously possible. However, while metagenomic studies have revealed microbial membership and potential genomic information among members taking part in the symbiosis, there is still a significant lag in the functional characterization within these symbiotic associations. Thus, in this dissertation, we utilized a metaproteomic approach to study microbial symbiotic associations. We have developed and applied this robust platform to investigate various symbiotic associations ranging in complexity. Beginning with perhaps one of the simplest symbiotic systems, we investigated the proteomic response of infection of S. thermophilus with bacteriophage 2972, to reveal insights into the anti-viral CRISPR/Cas response. Then, transitioning to a more complex but tractable symbiotic interaction, we evaluated co-occurring proteobacterial endosymbionts of the marine worm Olavius algarvensis and uncovered novel pathways for carbon and energy use, in addition to unraveling abundant transposase protein expression. Finally, we progressed to a complex microbial community and its commensalistic association with its human host in the infant gut microbiome. Simultaneous measurements of microbial and human proteins over a time course during early infant development revealed functional adaptation of the host in response to the changing microbiome, resulting in a dynamic interplay between the host and its resident microbes. In each of these symbiotic systems, we found that a proteomics/metaproteomics approach was very powerful for the characterization of the functional signatures of all members of the symbiotic interaction, and yielded biological insights into each system that would have been unattainable by any other platform.