Strain variation up close at the functional genomic level OR What metagenomics and metatranscriptomics can’t tell you
Roderick I. Mackie, Ph.D.
Professor of Microbiology
Department of Animal Sciences & Division of Nutritional Sciences,
Carl R. Woese Institute for Genomic Biology, University of Illinois
Research in our laboratory has focused on using comparative whole genome sequence transcriptional profiling to examine and understand how two closely related strains of Ruminococcus albus, strain 7 and 8, function at the genomic level. Phenotypically the two strains appear and behave differently, although both strains have a similar genomic size and CAZyme repertoire. A series of experiments on a range of polysaccharides show that their strategies and preferences for these substrates are markedly different. Overall our data shows that strain 7 preferentially utilizes cellulose, while strain 8 prefers to utilize hemicellulose contained in the plant cell wall. Based on differential phenotypes between the two strains for substrate attachment during growth, we examined global regulators known to be involved in biofilm formation of bacteria: the bacterial second messenger, cyclic-di-GMP, regulatory system and the Agr quorum sensing system. Marked differential responses were measured when the two strains were grown in co-culture. In addition, growth studies demonstrated that R. albus 7 is a folate prototroph while R. albus 8 is a folate auxotroph. These findings support the concept that each strain of Ruminococcus performs a different ecological role in ruminal fiber and folate metabolism and are interdependent for these metabolic functions.
We conclude that these two closely related strains of R. albus that are lumped into the same OTU by metagenomic and metatranscriptomic analyses are actually functionally different and therefore non-redundant. Our research shows that both R. albus 7 and 8 co-exist in a complementary manner on complex substrates and support a strong case for bacterial specialization and niche differentiation. We propose that these findings with R. albus are a common feature of the gut microbiome in humans and animals.
Wednesday, April 1, 2020 at 12:00 PM
2506 Veterinary Medicine Basic Sciences Building
2001 South Lincoln Avenue, Urbana
For more information contact the Department of Pathobiology at 217-333-2449, email klp68@illinois.edu.
