The Role of Akkermansia Species and Subspecies in Human Health

Abstract

Akkermansia are mucin-degrading bacteria commonly found in the human gastrointestinal (GI) tract. The prevalence and abundance of these bacteria, notably Akkermansia muciniphila, are correlated with immunological and metabolic health in humans and have gained notoriety as a potential next-generation probiotic. Until recently, A. muciniphila was the only species of the phylum Verrucomicrobia identified in the human GI tract. However, it is increasingly clear that Akkermansia in the GI tract are diverse and that there are several human-associated Akkermansia species with significantly larger genomes than A. muciniphila. I hypothesize that this added genetic content may impact how various subgroups of Akkermansia modulate host immunological and metabolic health.To define the breadth of diversity within the genus Akkermansia, I conducted a pangenomic analysis of 234 Akkermansia genomes. My findings based on average nucleotide identity, full-length 16S rRNA gene identity, and conservation among core Akkermansia genes identified a novel group of Akkermansia and indicated that the genus Akkermansia should be split into several species. Further analysis of fatty acid composition and biochemical characterization of representative isolates supported this notion. Additionally, I found that A. muciniphila sensu stricto, the most prevalent Akkermansia species in humans, should be subdivided into two subspecies clades. Having defined species boundaries between strains that were previously all classified as one, I next sought to determine if these distinctions are relevant to the previously established correlations between Akkermansia and human health. To this end, I employed high-resolution species and clade assignments to reanalyze publicly available metagenomic datasets to determine if there are species or clade-specific relationships between Akkermansia and various disease outcomes. I observed species-specific correlations between Akkermansia abundance and obesity in a pediatric cohort. For a set of inflammatory bowel disease cohorts, I identified species-specific and clade-specific decreased abundance of Akkermansia in patients with Crohn’s disease or ulcerative colitis. In patients who had undergone hematopoietic cell transplantation, I found no correlation between Akkermansia species or phylogroups and graph-versus-host-disease development. In patients undergoing immune checkpoint inhibitor therapies for non-small cell lung cancer, I observed a significant association between one A. muciniphila clade and survival outcomes. Additionally, I showed that these species-predictive methods could be applied to additional species of Akkermansia and another mucophilic gastrointestinal bacterium, Ruminococcus gnavus. Finally, I described variability in biofilm production across isolates of the Akkermansia genus. I describe the generation of a library of transposon mutants in one biofilm-producing strain, Akk147, providing a possible link between mucin degradation and biofilm production in modulating the association between Akkermansia and the host. Finally, I tested whether biofilm production enhances the colonization ability of three A. muciniphila isolates of varying biofilm-production and determined that in vitro biofilm production does not enhance colonization of the murine GI tract. Overall, my findings suggest that the prevalence of specific Akkermansia species and clades may be crucial in evaluating their association with host health, and thus their usefulness in promoting health. As these associations differ between disease contexts, making these distinctions should be an important consideration when using Akkermansia as a probiotic or therapeutic supplement.