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

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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

Titel: Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
Författare: Karcher, Nicolai; Nigro, Eleonora; Puncochar, Michal; Blanco-Miguez, Aitor; Ciciani, Matteo; Manghi, Paolo; Zolfo, Moreno; Cumbo, Fabio; Manara, Serena; Golzato, Davide; Cereseto, Anna; Arumugam, Manimozhiyan; Bui, Thi Phuong Nam; Tytgat, Hanne L. P.; Valles-Colomer, Mireia; de Vos, Willem M.; Segata, Nicola
Upphovmannens organisation: Department of Bacteriology and Immunology
Willem Meindert Vos de / Principal Investigator
de Vos & Salonen group
Research Programs Unit
HUMI - Human Microbiome Research
Faculty of Medicine
Datum: 2021-07-14
Språk: eng
Sidantal: 24
Tillhör serie: Genome Biology
ISSN: 1474-760X
DOI: https://doi.org/10.1186/s13059-021-02427-7
Permanenta länken (URI): http://hdl.handle.net/10138/334474
Abstrakt: 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.
Subject: CRISPR-CAS SYSTEMS
ANTIBIOTIC-RESISTANCE
GEN. NOV.
MUCINIPHILA
ALIGNMENT
BACTERIUM
DRIVEN
VIROME
TOOL
1182 Biochemistry, cell and molecular biology
Referentgranskad: Ja
Licens: cc_by
Användningsbegränsning: openAccess
Parallelpublicerad version: publishedVersion


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