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Page 2 of 8 Kumar et al. Microbiome Res Rep 2024;3:37 https://dx.doi.org/10.20517/mrr.2024.28

a mucin-degrading strain from a healthy adult, which they named Akkermansia muciniphila and is
[1]
represented by the type strain MucT (= ATCC BAA-835) . Since then, two more validly published species
under The International Code of Nomenclature of Prokaryotes (ICNP) of the genus Akkermansia have been
[2]
identified: A. glycaniphila isolated from reticulated python feces (PytT) and A. biwaensis (type strain
WON2089T) .
[3]
In addition, several new Akkermansia species have been proposed, such as Candidatus A. intestinavium
isolated from the gut of birds , Candidatus A. intestinigallinarum isolated from the gut of hens , and the
[4]
[4]
human gut isolates A. massiliensis sp. nov. with strain Marseille-P6666T (= CSUR P6666 = CECT 30548) as
the type strain and Candidatus A. timonensis with Akk0196 as the type strain . Figure 1 shows the
[5]
[5]
genomic phylogenetic tree and corresponding proteome of the current and proposed Akkermansia species
generated using the BV-BRC server . Interestingly, the recently named A. biwaensis and the proposed
[6]
Candidatus A. timonensis type strains are 99.5% similar based on genome-wide average nucleotide identity
(gANI); hence, they represent the same species. A. biwaensis is on the notification list for taxonomic
validation . A recent phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-
[7]
[8]
assembled genomes suggested the existence of at least 25 Akkermansia species at the genomic level .
Based on extensive metagenomic assembly, Akkermansia strains in the human gut were grouped into five
candidate species including A. muciniphila based upon species-level genome bins (SGBs), with significant
genomic diversity despite similar 16S rRNA gene sequences . Karcher et al. highlighted that this
[9]
surprisingly high similarity based on 16S rRNA (at least 98%) is likely the reason for the wrong taxonomic
assignment of several cultivated strains to the A. muciniphila species and leading to an underestimated
diversity of the genus Akkermansia and less researched and characterized Akkermansia species beyond
[9]
A. muciniphila . The publication also highlighted that the corrin ring biosynthesis operon genes are
consistently present only in two candidate species, namely SGB9227 and SGB9228, but not A. muciniphila.
A comparison of the public genome of cultured isolates from NCBI within SGB9228 to the proposed type
strain for A. massiliensis sp. nov. Marseille-P6666T shows that SGB9228 corresponds to the proposed
A. massiliensis species (> 95% gANI similarity), and SGB9224 similarly corresponds to A. biwaensis.

AKKERMANSIA MASSILIENSIS SP. NOV. - A RE-EXAMINATION OF ITS PRESENCE IN
THE GUT MICROBIOME
In the survey published by Karcher et al. , they reported the prevalence of A. muciniphila in gut
[9]
metagenomes from adults (n = 7,995) as 34%, A. massiliensis sp. nov. (SGB9228) as 8%, and A. biwaensis
(SGB9224) as 2%. While it is true that the high similarity of the 16S rRNA genes among these species and
the lack of reference sequences in taxonomic databases contributed to their historical under-classification in
microbiome datasets, these species can be distinguished using newer high-resolution clustering algorithms
such as DADA2 that defines amplicon sequence variants (ASVs) based on single base pair differences . If
[10]
utilizing the commonly sequenced V4 region of the 16S rRNA gene (515f/806r primer pair), there are four
base pair differences between each A. muciniphila (GenBank Accession: AY271254) and A. massiliensis sp.
nov. (GenBank Accession: ON014381) and likewise between A. muciniphila and A. biwaensis (GenBank
Accession: LC711105), which provides sufficient resolution to distinguish ASVs from the species within
Akkermansia. Thus, we examined the prevalence and abundance of these species in three studies where fecal
16S rRNA V4 amplicon data were collected: (1) The American Gut Project (n = 5,000), which involved a
[11]
crowd-sourced sampling of adults; (2) IsoMic clinical study (ClinicalTrials.gov identifier NCT05150184),
which was comprised of healthy adults [Body mass index (BMI) 18.5-25 kg/m ] from 5 ethnicities residing
2
in the United States; and (3) Next Generation Probiotics for Metabolic Health (NGPs for MH) clinical study
(ClinicalTrials.gov identifier NCT04229082), which included lean (BMI 18-25 kg/m ) and obese (BMI 27.5-
2