Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly

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dc.contributor.author Karcher, Nicolai
dc.contributor.author Nigro, Eleonora
dc.contributor.author Puncochar, Michal
dc.contributor.author Blanco-Miguez, Aitor
dc.contributor.author Ciciani, Matteo
dc.contributor.author Manghi, Paolo
dc.contributor.author Zolfo, Moreno
dc.contributor.author Cumbo, Fabio
dc.contributor.author Manara, Serena
dc.contributor.author Golzato, Davide
dc.contributor.author Cereseto, Anna
dc.contributor.author Arumugam, Manimozhiyan
dc.contributor.author Bui, Thi Phuong Nam
dc.contributor.author Tytgat, Hanne L. P.
dc.contributor.author Valles-Colomer, Mireia
dc.contributor.author de Vos, Willem M.
dc.contributor.author Segata, Nicola
dc.date.accessioned 2021-09-21T06:33:03Z
dc.date.available 2021-09-21T06:33:03Z
dc.date.issued 2021-07-14
dc.identifier.citation Karcher , N , Nigro , E , Puncochar , M , Blanco-Miguez , A , Ciciani , M , Manghi , P , Zolfo , M , Cumbo , F , Manara , S , Golzato , D , Cereseto , A , Arumugam , M , Bui , T P N , Tytgat , H L P , Valles-Colomer , M , de Vos , W M & Segata , N 2021 , ' Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly ' , Genome Biology , vol. 22 , no. 1 , 209 . https://doi.org/10.1186/s13059-021-02427-7
dc.identifier.other PURE: 168637356
dc.identifier.other PURE UUID: 1f8512d1-bec4-482a-821a-fe94751dfca5
dc.identifier.other WOS: 000673579200001
dc.identifier.uri http://hdl.handle.net/10138/334474
dc.description.abstract Background Akkermansia muciniphila is a human gut microbe with a key role in the physiology of the intestinal mucus layer and reported associations with decreased body mass and increased gut barrier function and health. Despite its biomedical relevance, the genomic diversity of A. muciniphila remains understudied and that of closely related species, except for A. glycaniphila, unexplored. Results We present a large-scale population genomics analysis of the Akkermansia genus using 188 isolate genomes and 2226 genomes assembled from 18,600 metagenomes from humans and other animals. While we do not detect A. glycaniphila, the Akkermansia strains in the human gut can be grouped into five distinct candidate species, including A. muciniphila, that show remarkable whole-genome divergence despite surprisingly similar 16S rRNA gene sequences. These candidate species are likely human-specific, as they are detected in mice and non-human primates almost exclusively when kept in captivity. In humans, Akkermansia candidate species display ecological co-exclusion, diversified functional capabilities, and distinct patterns of associations with host body mass. Analysis of CRISPR-Cas loci reveals new variants and spacers targeting newly discovered putative bacteriophages. Remarkably, we observe an increased relative abundance of Akkermansia when cognate predicted bacteriophages are present, suggesting ecological interactions. A. muciniphila further exhibits subspecies-level genetic stratification with associated functional differences such as a putative exo/lipopolysaccharide operon. Conclusions We uncover a large phylogenetic and functional diversity of the Akkermansia genus in humans. This variability should be considered in the ongoing experimental and metagenomic efforts to characterize the health-associated properties of A. muciniphila and related bacteria. en
dc.format.extent 24
dc.language.iso eng
dc.relation.ispartof Genome Biology
dc.rights cc_by
dc.rights.uri info:eu-repo/semantics/openAccess
dc.subject CRISPR-CAS SYSTEMS
dc.subject ANTIBIOTIC-RESISTANCE
dc.subject GEN. NOV.
dc.subject MUCINIPHILA
dc.subject ALIGNMENT
dc.subject BACTERIUM
dc.subject DRIVEN
dc.subject VIROME
dc.subject TOOL
dc.subject 1182 Biochemistry, cell and molecular biology
dc.title Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly en
dc.type Article
dc.contributor.organization Department of Bacteriology and Immunology
dc.contributor.organization Willem Meindert Vos de / Principal Investigator
dc.contributor.organization de Vos & Salonen group
dc.contributor.organization Research Programs Unit
dc.contributor.organization HUMI - Human Microbiome Research
dc.contributor.organization Faculty of Medicine
dc.description.reviewstatus Peer reviewed
dc.relation.doi https://doi.org/10.1186/s13059-021-02427-7
dc.relation.issn 1474-760X
dc.rights.accesslevel openAccess
dc.type.version publishedVersion

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