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Mueller et al. Microbiome Res Rep 2024;3:33 Microbiome Research
DOI: 10.20517/mrr.2024.09
Reports

Original Article Open Access

Pangenomic analysis identifies correlations between
Akkermansia species and subspecies and human

health outcomes

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1,2
2,4
1,2
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Katherine D. Mueller , M. Emilia Panzetta , Lauren Davey , Jessica R. McCann , John F. Rawls , Gilberto
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E. Flores , Raphael H. Valdivia 1,2
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Department of Integrative Immunobiology, Duke University, Durham, NC 27710, USA.
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Duke Microbiome Center, Duke University School of Medicine, Durham, NC 27710, USA.
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Department of Biochemistry and Microbiology, University of Victoria, Victoria V8P 5C2, British Columbia, Canada.
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Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27710, USA.
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Department of Biology, California State University, Northridge, CA 91330, USA.
Correspondence to: Dr. Raphael H. Valdivia, Department of Integrative Immunobiology, Duke University, 3110 MSRB3, 3
Genome Court, Durham, NC 27710, USA. E-mail: raphael.valdivia@duke.edu
How to cite this article: Mueller KD, Panzetta ME, Davey L, McCann JR, Rawls JF, Flores GE, Valdivia RH. Pangenomic analysis
identifies correlations between Akkermansia species and subspecies and human health outcomes. Microbiome Res Rep 2024;3:33.
https://dx.doi.org/10.20517/mrr.2024.09
Received: 31 Jan 2024 First Decision: 29 Mar 2024 Revised: 28 May 2024 Accepted: 4 Jun 2024 Published: 11 Jun 2024
Academic Editors: Marco Ventura, Anneleen Segers Copy Editor: Dong-Li Li Production Editor: Dong-Li Li

Abstract
Aim: Akkermansia are common members of the human gastrointestinal microbiota. The prevalence of these
mucophilic bacteria, especially Akkermansia muciniphila (A. muciniphila), correlates with immunological and
metabolic health. The genus Akkermansia in humans includes species with significantly larger genomes than
A. muciniphila, leading us to postulate that this added genetic content may influence how they impact human
metabolic and immunological health.

Methods: We conducted a pangenomic analysis of 234 Akkermansia complete or near-complete genomes. We also
used high-resolution species and subspecies assignments to reanalyze publicly available metagenomic datasets to
determine if there are relationships between Akkermansia species and A. muciniphila clades with various disease
outcomes.

Results: Analysis of genome-wide average nucleotide identity, 16S rRNA gene identity, conservation of core
Akkermansia genes, and analysis of the fatty acid composition of representative isolates support the partitioning of

© The Author(s) 2024. Open Access This article is licensed under a Creative Commons Attribution 4.0
International License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, sharing,
adaptation, distribution and reproduction in any medium or format, for any purpose, even commercially, as
long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and
indicate if changes were made.

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