A thousand metagenome-assembled genomes of Akkermansia reveal new phylogroups and geographical and functional variations in human gut

Abstract

The present study revealed the genomic architecture of Akkermansia in human gut by analyzing 1,119 near-complete metagenome-assembled genomes, 84 public available genomes, and 1 newly sequenced A. glycaniphila strain. We found that 1) the genomes of Akkermansia formed 4 species (including 2 candidate species) with distinct interspecies similarity and differed genomic characteristics, and 2) the population of A. muciniphila was structured by 3 previously identified phylogroups (Amuc I, II, and III) referring to 1,132 genomes and 1 new phylogroup (defined as Amuc IV) that contained 62 genomes. Amuc III was presented in Chinese population and Amuc IV was mainly distributed in western populations. A large number of gene of functions, pathways, and carbohydrate active enzymes that specifically associated to phylogroups. Our findings based on over a thousand genomes strengthened the previous knowledge and provided new insights into the population structure and ecology of Akkermansia in human gut.