A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization

Akkermansia muciniphila, a prominent member of the gut microbiota, has been considered a next-generation probiotic because it can protect against metabolic disorders. It uses mucins as a sole carbon and nitrogen source; however, it is genetically intractable and thus the molecular mechanisms underlying mucin metabolism, gut colonization, and its impact on host physiology are not well understood. Here, we developed and applied transposon (Tn) mutagenesis to identify genetic determinants important for intestinal colonization and the use of mucin. We observed that mucin degradation products accumulate in internal compartments within A. muciniphila cells through a process that requires genes encoding pili and a periplasmic protein complex, that we term mucin utilization loci (MUL). Tn mutants grown with gastric mucin in vitro revealed that de novo biosynthesis of amino acids was required for growth on mucin, but most glycoside hydrolases were not needed. Insertion sequencing (INSeq) of mice colonized with an A. muciniphila Tn mutant pool also revealed a requirement for amino acids biosynthesis genes and MUL genes for gut colonization. In germ-free mice, mucin use by A. muciniphila repressed the expression of host genes required for mevalonate and cholesterol biosynthesis in the colon. Our genetic system for A. muciniphila provides an important tool to uncover molecular links between the metabolism of mucins, regulation of lipid homeostasis and potential probiotic activities.