Integrated studies into the genomic, metabolic, and cultivable diversity of the human gut symbiont Akkermansia muciniphila

Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most healthy humans, typically at 1 to 4% relative abundance. A number of studies in humans and model organisms have found positive associations between the abundance of this organism and intestinal health, suggesting that Akkermansia may be a beneficial member of the gut microbiome and could be used as a biomarker of a healthy gut. However, A. muciniphila MucT represents the sole described species of the Verrucomicrobial phylum associated with humans despite a diversity of phylotypes being observed in several studies. The paucity of biochemical data and cultured representatives within this enigmatic lineage makes broad-scale conclusions about its health benefits tenuous and impedes an overall mechanistic understanding of microbial interactions in the human gut. The overall objective of this study is to broaden our understanding of the genomic potential, metabolic mechanisms, and cultivable diversity of symbiotic Akkermansia spp. through complementary genomic- and cultivation-based approaches. Specific Aim 1: Determine the ?pangenomic? content of Akkermansia using shotgun metagenomic sequencing of fecal samples to investigate genomic potential within this lineage. Hypothesis 1: In addition to genes predicted to be involved in mucin degradation, Akkermansia spp. will possess an assortment of glycoside hydrolases predicted to act upon a diversity of other glycan substrates. Specific Aim 2: Determine whole-genome transcriptional profile of Akkermansia muciniphila MucT grown in vitro on mucin as the sole carbon source using RNAseq. Hypothesis 2: Genes coding for sialidases, sulfatases, and glycoside hydrolases in the genome of A. muciniphila MucT will be significantly upregulated when grown on mucin as the sole carbon source. Specific Aim 3: Isolate mucolytic Akkermansia spp. from human fecal samples on selective mucin medium and determine carbon substrate utilization abilities of representative isolates. Hypothesis 3: Although specialized on mucin, other polysaccharides will support growth in Akkermansia but utilization patterns will be strain specific. The current paradigm that Akkermansia muciniphila is a beneficial microbe is based on an incomplete understanding of the physiology and diversity within this lineage. This proposed study would help to support or refute this hypothesis by providing a more comprehensive understanding of the physiological diversity and mechanistic activity of human-associated Akkermansia spp. Future studies will utilize the strains and sequence data obtained from this project to investigate interactions between Akkermansia and other glycan-degraders of the human microbiome. This work will provide a new line of inquiry for a junior faculty member at a Hispanic and Asian American/Native American-Pacific Islander serving institution who actively engages underrepresented students in research.