The human gut is colonized by a diversity of microorganisms that perform a number of functions essential for normal human physiology. For example, many gut bacteria are able to degrade dietary polysaccharides, or glycans, that are otherwise indigestible by humans. In doing so, these bacteria produce fermentation products including short chain fatty acids that supply energy to gut epithelial cells. A subset of these gut bacteria can also degrade host-derived glycans like mucin that form the mucus layers that line and protect gut epithelial cells. Since maintenance of the gut mucus layer is essential for host health, the ability to degrade host mucin was generally regarded as a pathogenicity factor in bacteria. However, it is now known that many mutualistic bacteria of the gut microbiome can use mucin as a carbon and energy source. One such bacterium is Akkermansia muciniphila. A. muciniphila is a mucin-degrading specialist 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, compared to other gut mucin degraders, A. muciniphila is vastly understudied as only one species has been formally described and a mechanistic understanding of its mucin-degrading capabilities is lacking. The overall objective of this study is to fill this void by providing specific details about the genomic content, metabolic mechanisms, and cultivable diversity of this mucin-degrading specialist through complementary genomic- and cultivation-based approaches. Specifically, we will:
(Aim 1) Determine the pan-genomic content of Akkermansia using shotgun metagenomic sequencing of fecal samples to investigate genomic potential within this lineage;
(Aim 2) Determine whole-genome transcriptional profile of A. muciniphila MucT grown in vitro on mucin as the sole carbon source using RNAseq;
and (Aim 3) Isolate mucolytic Akkermansia spp. from human fecal samples on selective mucin medium and determine carbon substrate utilization abilities of representative isolates. These objectives will help address the overarching hypothesis that Akkermansia are beneficial members of the gut microbiome that can be used as a biomarker of a healthy gut. 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.
The current paradigm that Akkermansia muciniphila is a beneficial member of the gut microbiome is based on an incomplete understanding of the genomic potential, metabolic mechanisms, and cultivable diversity within this lineage. This proposed study would fill this void and help to support or refute this hypothesis by providing specific details about the diversity and mechanistic activity of this human- associated bacterial lineage.
