Comparative Genomics and Physiology of Akkermansia muciniphila Isolates from Human Intestine Reveal Specialized Mucosal Adaptation
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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 MucT and A. glycaniphila PytT. 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 MucT, 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 MucT and A. glycaniphila PytT (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 MucT or these new A. muciniphila strains as next generation beneficial microbes.
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In this review, Akkermansia was characterized by several host-interaction and persistence-related features, including epithelial adherence, aggregation, pili, autotransporters, sulfatases, mucin-associated enzymes, oxygen tolerance, Amuc-related proteins, and genes associated with B12/corrin-related biosynthesis.
“In this review, Akkermansia was characterized by several host-interaction and persistence-related features, including epithelial adherence, aggregation, pili, autotransporters, sulfatases, mucin-associated enzymes, oxygen tolerance, Amuc-related proteins, and genes associated with B12/corrin-related biosynthesis. 12,14,21,24,31”
From Comparative Genomic Insights into Pangenome Diversity and Functional Adaptation of Akkermansia and Faecalibacterium as Gut-Associated Next-Generation Probiotics: A Systematic Review (2026) · cites this paper as [24]
The Results (§§3.1, 3.7–3.8; page unavailable) report aggregation, mucin-degrading enzymes, and Amuc-related proteins; the Discussion (§4; page unavailable) reports PilQ, a protein involved in type IV pilus production. The passages do not establish epithelial adherence, autotransporters, sulfatases, or oxygen tolerance. The Discussion also says none of the six isolated A. muciniphila strains could synthesize vitamin B12, rather than identifying B12/corrin-biosynthesis genes in those isolates. (LLM, conf=0.86)
Experimental — accuracy not yet measuredIn Akkermansia, adhesion to the mucus layer is relevant because access to mucins supports its ecological role.
“In Akkermansia , adhesion to the mucus layer is relevant because access to mucins supports its ecological role. 24,35”
From Comparative Genomic Insights into Pangenome Diversity and Functional Adaptation of Akkermansia and Faecalibacterium as Gut-Associated Next-Generation Probiotics: A Systematic Review (2026) · cites this paper as [24]
The Introduction describes A. muciniphila as a mucosal species that uses mucin for growth, and the Discussion links conserved mucin-degrading genes to adaptation to the mucus layer. The copy does not establish that adhesion to the mucus layer enables mucin access, so that part of the claim is unsupported. (LLM, conf=0.84)
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Uma, A., Sudarsanan, G. B., Karuppannan, A. K., & Palaniappan, S. (2023) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-023-10165-4 · Cited by 4 · see citing works
Probiotic Engraftment of Akkermansia muciniphila in an In Vitro Synthetic Microbial Community
Berkhout, M. D., de Ram, C., Boeren, S. A., Plugge, C. M., & Belzer, C. (2025) · Microbial Ecology · doi:10.1007/s00248-025-02605-1 · Cited by 1 · see citing works
Self-citationMechanism and application of Akkermansia muciniphila in inflammatory diseases
Xie, L., Lu, J., Han, H., Liu, Z., Dong, C., Wu, H., & Qiao, J. (2026) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2026.1819005 · Cited by 1 · see citing works
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Functional adaptive genomic characteristics of gut Akkermansia in obese populations
Ji, B., Huang, P., Zhang, C., Zhang, C., Wang, G., Cui, S., Lu, W., Yang, B., Wu, J., Lyu, X., et al. (2026) · Food Science and Human Wellness · doi:10.26599/fshw.2025.9250907
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- Authors
- Ouwerkerk, J. P., Tytgat, H. L. P., Elzinga, J., Koehorst, J., Van den Abbeele, P., Henrissat, B., Gueimonde, M., Cani, P. D., Van de Wiele, T., Belzer, C., & de Vos, W. M.
- Affiliations
- Wageningen University & Research (NL)
- Center for Microbial Ecology and Technology (CMET), Ghent University, 9000 Ghent, Belgium
- King Abdulaziz University (SA)
- Consejo Superior de Investigaciones Científicas (ES)
- Walloon Excellence in Lifesciences and Biotechnology (BE)
- Laboratory of Microbiology, Wageningen University, 6708 WE Wageningen, The Netherlands
- ORCID
- Venue
- Microorganisms
- Publisher
- MDPI AG
- Published
- 2022-08-09
- Volume
- 10
- Issue
- 8
- Pages
- 1605
- ISSN
- 2076-2607 (ISSN-L)
- PMC
- PMC9415379
- OpenAlex
- W4293514126
- Cited by
- 23
- References
- 67
- Citations by year
- 2026: 8 · 2025: 6 · 2024: 4 · 2023: 4 · 2022: 1
- FWCI
- 1.22
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Microorganisms (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Socio-Environmental Systems Modeling (acceptedVersion, cc-by)
- Ghent University Academic Bibliography (Ghent University) (submittedVersion, cc-by)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, cc-by)
- Digital Access to Libraries (submittedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Työväentutkimus Vuosikirja (submittedVersion)
- Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, cc-by)
- Data Archiving and Networked Services (DANS) (submittedVersion, cc-by)
- Funders
- UGent (BOF12-GOA-008, 250172, 024.002.002, WELBIO-CR-2022A-02)
- ERC Advanced Grand (BOF12-GOA-008, 250172, 024.002.002, WELBIO-CR-2022A-02)
- A-mansia Biotech SA (BOF12-GOA-008, 250172, 024.002.002, WELBIO-CR-2022A-02)
- Spinoza Award (BOF12-GOA-008, 250172, 024.002.002, WELBIO-CR-2022A-02)
- Netherlands Organization for Scientific Research (NWO) of WMdV (BOF12-GOA-008, 250172, 024.002.002, WELBIO-CR-2022A-02)
- FNRS (BOF12-GOA-008, 250172, 024.002.002, WELBIO-CR-2022A-02)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Agricultural and Biological Sciences › Food Science › Probiotics and Fermented Foods
- Health Sciences › Nursing › Nutrition and Dietetics › Infant Nutrition and Health
- Keywords
- Akkermansia muciniphila, mucin degradation, human gut microbiome, strain isolation, CRISPR typing, glycoside hydrolases, proteome, antibiotic resistance, mucosal adaptation, probiotics
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