Abstract
Akkermansia muciniphila
is a champion of mucin degradation in the human gastrointestinal tract. Here, we report the isolation of six novel strains from healthy human donors and their genomic, proteomic and physiological characterization in comparison to the type-strains
A. muciniphila
Muc
T
and
A. glycaniphila
Pyt
T
. Complete genome sequencing revealed that, despite their large genomic similarity (>97.6%), the novel isolates clustered into two distinct subspecies of
A. muciniphila
: Amuc1, which includes the type-strain Muc
T
, and AmucU, a cluster of unassigned strains that have not yet been well characterized. CRISPR analysis showed all strains to be unique and confirmed that single healthy subjects can carry more than one
A. muciniphila
strain. Mucin degradation pathways were strongly conserved amongst all isolates, illustrating the exemplary niche adaptation of
A. muciniphila
to the mucin interface. This was confirmed by analysis of the predicted glycoside hydrolase profiles and supported by comparing the proteomes of
A. muciniphila
strain H2, belonging to the AmucU cluster, to Muc
T
and
A. glycaniphila
Pyt
T
(including 610 and 727 proteins, respectively). While some intrinsic resistance was observed among the
A. muciniphila
straind, none of these seem to pose strain-specific risks in terms of their antibiotic resistance patterns nor a significant risk for the horizontal transfer of antibiotic resistance determinants, opening the way to apply the type-strain Muc
T
or these new
A. muciniphila
strains as next generation beneficial microbes.