The consequences of bifidobacteria diversity for ecosystem functioning

Cynthia Rodriguez, University of California, Irvine and Jennifer B.H. Martiny, Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA

Background/Question/Methods
Improving health through the regulation and manipulation of the gut microbiota is a strategy that has been proposed to treat disease and promote wellness in humans as the loss of bacterial richness in the gut has been correlated with obesity, insulin resistance, and inflammatory diseases. In addition, allergies that develop in childhood have been linked with low bacterial richness, particularly low abundance of bifidobacteria. Bifidobacteria are known to be abundant in neonates and to structure the human gut microbiome in the early stages of life. Moreover, this bacterial group is important for digestion and production of beneficial metabolites. Over their lifetime, humans harbor a diversity of bifidobacteria in their gut and the composition and abundance of this diversity varies. However, it remains unclear how the composition and richness of bifidobacteria affects gut functioning. To understand the relationship between biodiversity and ecosystem functioning (BEF), plant and animal ecologists often experimentally manipulate diversity and compare how functioning varies among these communities. In this study, we applied a similar approach to investigate how microbial diversity influences bifidobacteria’s ecosystem processes and coexistence. To this end, we isolated new strains of bifidobacteria from the feces of healthy humans, performed phylogenetic and pangenome analyses, and conducted BEF microcosm experiments.
Results/Conclusions
Based on the phylogenetic and comparative genomic analyses, we selected 16 diverse isolates for BEF experiments. The analyses revealed two functional groups distinguished by their CAZyme content and pangenome similarity, including strains from Bifidobacterium longum, B. adolescentis, B. pseudocatenulatum, B. breve, B. angulatum, and B. animalis species. Next, we conducted in vitro microcosm experiments varying bifidobacteria strain richness and the number of functional groups to test whether bifidobacteria follow a positive BEF relationship, where increasing bifidobacteria strain richness and/or functional groups increases ecosystem functioning. This was assessed by cell biomass and metabolite production. Current work aims to disentangle whether the observed BEF relationship is due to resource partitioning, cross-feeding interactions, or sampling effects. Ultimately, these results will begin to uncover the ecological mechanisms behind the observed correlations between gut bacterial diversity and human health. Furthermore, this could lead to the understanding of microbiome interventions such as the ingestion of probiotics, which in itself can be thought of as a coalescence event.