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


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2021-07-14

AUTHORS

Nicolai Karcher, Eleonora Nigro, Michal Punčochář, Aitor Blanco-Míguez, Matteo Ciciani, Paolo Manghi, Moreno Zolfo, Fabio Cumbo, Serena Manara, Davide Golzato, Anna Cereseto, Manimozhiyan Arumugam, Thi Phuong Nam Bui, Hanne L. P. Tytgat, Mireia Valles-Colomer, Willem M. de Vos, Nicola Segata

ABSTRACT

BackgroundAkkermansia 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.ResultsWe 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.ConclusionsWe 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. More... »

PAGES

209

References to SciGraph publications

  • 2021-01-14. Sex- and age-related trajectories of the adult human gut microbiota shared across populations of different ethnicities in NATURE AGING
  • 2017-11-28. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients in GENOME MEDICINE
  • 2019-10-04. Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing in NATURE COMMUNICATIONS
  • 2012. Carbohydrate-Active Enzymes Database, Metagenomic Expert Resource in ENCYCLOPEDIA OF METAGENOMICS
  • 2013-08-23. MAFFT: Iterative Refinement and Additional Methods in MULTIPLE SEQUENCE ALIGNMENT METHODS
  • 2014-11-17. Fast and sensitive protein alignment using DIAMOND in NATURE METHODS
  • 2017-10-18. Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas in BMC GENOMICS
  • 2019-07-01. Supplementation with Akkermansia muciniphila in overweight and obese human volunteers: a proof-of-concept exploratory study in NATURE MEDICINE
  • 2019-02-11. A new genomic blueprint of the human gut microbiota in NATURE
  • 2012-06-13. Structure, function and diversity of the healthy human microbiome in NATURE
  • 2017-10-31. Accessible, curated metagenomic data through ExperimentHub in NATURE METHODS
  • 2018-07-31. Whole genome sequencing and function prediction of 133 gut anaerobes isolated from chicken caecum in pure cultures in BMC GENOMICS
  • 2015-09-29. MetaPhlAn2 for enhanced metagenomic taxonomic profiling in NATURE METHODS
  • 2016-03-21. Strain-level microbial epidemiology and population genomics from shotgun metagenomics in NATURE METHODS
  • 2018-03-19. Extensive impact of non-antibiotic drugs on human gut bacteria in NATURE
  • 2019-12-28. Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species in GENOME BIOLOGY
  • 2020-01-07. The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria in NATURE COMMUNICATIONS
  • 2017-10-16. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets in NATURE BIOTECHNOLOGY
  • 2019-03-13. New insights from uncultivated genomes of the global human gut microbiome in NATURE
  • 2020-06-04. Diversity within species: interpreting strains in microbiomes in NATURE REVIEWS MICROBIOLOGY
  • 2017-09-21. DESMAN: a new tool for de novo extraction of strains from metagenomes in GENOME BIOLOGY
  • 2009-12-15. BLAST+: architecture and applications in BMC BIOINFORMATICS
  • 2019-09-02. A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research in NATURE MEDICINE
  • 2012-06-10. Metagenomic microbial community profiling using unique clade-specific marker genes in NATURE METHODS
  • 2020-05-19. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0 in NATURE COMMUNICATIONS
  • 2015-09-22. The outer mucus layer hosts a distinct intestinal microbial niche in NATURE COMMUNICATIONS
  • 2013-08-14. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes in NATURE COMMUNICATIONS
  • 2019-12-19. Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants in NATURE REVIEWS MICROBIOLOGY
  • 2010-03. A human gut microbial gene catalogue established by metagenomic sequencing in NATURE
  • 2019-12-02. Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea in NATURE COMMUNICATIONS
  • 2020-07-20. A unified catalog of 204,938 reference genomes from the human gut microbiome in NATURE BIOTECHNOLOGY
  • 2018-11-30. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries in NATURE COMMUNICATIONS
  • 2012-12-05. Genomic variation landscape of the human gut microbiome in NATURE
  • 2016-12-02. Transmission of viruses via our microbiomes in MICROBIOME
  • 2020-06-08. Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations in GENOME BIOLOGY
  • 2016-06-20. Mash: fast genome and metagenome distance estimation using MinHash in GENOME BIOLOGY
  • 2015-09-07. ConStrains identifies microbial strains in metagenomic datasets in NATURE BIOTECHNOLOGY
  • 2018-11-14. Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2019-04-01. Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer in NATURE MEDICINE
  • 2019-11-20. Detecting contamination in viromes using ViromeQC in NATURE BIOTECHNOLOGY
  • 2012-03-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
  • 2019-08-09. Comparative genomic and functional analysis of Akkermansia muciniphila and closely related species in GENES & GENOMICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13059-021-02427-7

    DOI

    http://dx.doi.org/10.1186/s13059-021-02427-7

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1139684002

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/34261503


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Akkermansia", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Animals", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Bacteriophages", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Clustered Regularly Interspaced Short Palindromic Repeats", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gastrointestinal Microbiome", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genetic Variation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome, Bacterial", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Humans", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Metagenome", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Mice", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Operon", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phylogeny", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "RNA, Ribosomal, 16S", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Karcher", 
            "givenName": "Nicolai", 
            "id": "sg:person.012354262313.62", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012354262313.62"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark", 
              "id": "http://www.grid.ac/institutes/grid.5254.6", 
              "name": [
                "Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Nigro", 
            "givenName": "Eleonora", 
            "id": "sg:person.013262116247.61", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013262116247.61"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Pun\u010doch\u00e1\u0159", 
            "givenName": "Michal", 
            "id": "sg:person.012560426435.20", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012560426435.20"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Blanco-M\u00edguez", 
            "givenName": "Aitor", 
            "id": "sg:person.0700710637.71", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700710637.71"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ciciani", 
            "givenName": "Matteo", 
            "id": "sg:person.016220046237.06", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016220046237.06"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Manghi", 
            "givenName": "Paolo", 
            "id": "sg:person.016267051257.23", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016267051257.23"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Zolfo", 
            "givenName": "Moreno", 
            "id": "sg:person.01330203271.52", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01330203271.52"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Cumbo", 
            "givenName": "Fabio", 
            "id": "sg:person.0652034035.75", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0652034035.75"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Manara", 
            "givenName": "Serena", 
            "id": "sg:person.016525324253.98", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016525324253.98"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Golzato", 
            "givenName": "Davide", 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Cereseto", 
            "givenName": "Anna", 
            "id": "sg:person.0711517664.17", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0711517664.17"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark", 
              "id": "http://www.grid.ac/institutes/grid.5254.6", 
              "name": [
                "Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Arumugam", 
            "givenName": "Manimozhiyan", 
            "id": "sg:person.01235472333.35", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01235472333.35"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands", 
              "id": "http://www.grid.ac/institutes/grid.4818.5", 
              "name": [
                "Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Bui", 
            "givenName": "Thi Phuong Nam", 
            "id": "sg:person.01344663707.83", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01344663707.83"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Current address: Nestl\u00e9 Institute of Health Sciences, Nestl\u00e9 Research, Soci\u00e9t\u00e9 des Produits Nestl\u00e9 S.A., Lausanne, Switzerland", 
              "id": "http://www.grid.ac/institutes/grid.419905.0", 
              "name": [
                "Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands", 
                "Current address: Nestl\u00e9 Institute of Health Sciences, Nestl\u00e9 Research, Soci\u00e9t\u00e9 des Produits Nestl\u00e9 S.A., Lausanne, Switzerland"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Tytgat", 
            "givenName": "Hanne L. P.", 
            "id": "sg:person.0670767463.71", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0670767463.71"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Department CIBIO, University of Trento, Trento, Italy", 
              "id": "http://www.grid.ac/institutes/grid.11696.39", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Valles-Colomer", 
            "givenName": "Mireia", 
            "id": "sg:person.0701060711.59", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0701060711.59"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland", 
              "id": "http://www.grid.ac/institutes/grid.7737.4", 
              "name": [
                "Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands", 
                "Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland"
              ], 
              "type": "Organization"
            }, 
            "familyName": "de Vos", 
            "givenName": "Willem M.", 
            "id": "sg:person.01114225554.30", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01114225554.30"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "IEO, European Institute of Oncology IRCCS, Milan, Italy", 
              "id": "http://www.grid.ac/institutes/grid.15667.33", 
              "name": [
                "Department CIBIO, University of Trento, Trento, Italy", 
                "IEO, European Institute of Oncology IRCCS, Milan, Italy"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Segata", 
            "givenName": "Nicola", 
            "id": "sg:person.0736227144.03", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0736227144.03"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/nature08821", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050498034", 
              "https://doi.org/10.1038/nature08821"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41591-019-0495-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1117655252", 
              "https://doi.org/10.1038/s41591-019-0495-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11711", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004024856", 
              "https://doi.org/10.1038/nature11711"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13073-017-0490-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1093054943", 
              "https://doi.org/10.1186/s13073-017-0490-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3988", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092237583", 
              "https://doi.org/10.1038/nbt.3988"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2105-10-421", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050579230", 
              "https://doi.org/10.1186/1471-2105-10-421"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-019-13836-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1123920393", 
              "https://doi.org/10.1038/s41467-019-13836-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms9292", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1013796702", 
              "https://doi.org/10.1038/ncomms9292"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.4468", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092462741", 
              "https://doi.org/10.1038/nmeth.4468"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-016-0997-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050687712", 
              "https://doi.org/10.1186/s13059-016-0997-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-019-1923-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1123710056", 
              "https://doi.org/10.1186/s13059-019-1923-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41587-019-0334-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1122746602", 
              "https://doi.org/10.1038/s41587-019-0334-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12864-018-4959-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1105932478", 
              "https://doi.org/10.1186/s12864-018-4959-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-020-02042-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1128301041", 
              "https://doi.org/10.1186/s13059-020-02042-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.2066", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010611135", 
              "https://doi.org/10.1038/nmeth.2066"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1923", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006541515", 
              "https://doi.org/10.1038/nmeth.1923"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-019-13443-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1123048808", 
              "https://doi.org/10.1038/s41467-019-13443-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s13258-019-00855-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1120249270", 
              "https://doi.org/10.1007/s13258-019-00855-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-1-62703-646-7_8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016522201", 
              "https://doi.org/10.1007/978-1-62703-646-7_8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.3589", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028162909", 
              "https://doi.org/10.1038/nmeth.3589"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41591-019-0406-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1113160869", 
              "https://doi.org/10.1038/s41591-019-0406-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41586-019-0965-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1112059155", 
              "https://doi.org/10.1038/s41586-019-0965-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-018-07641-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1110204842", 
              "https://doi.org/10.1038/s41467-018-07641-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ncomms3304", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040093094", 
              "https://doi.org/10.1038/ncomms3304"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s43587-020-00014-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1134587622", 
              "https://doi.org/10.1038/s43587-020-00014-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.3176", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023901695", 
              "https://doi.org/10.1038/nmeth.3176"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature25979", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1101559358", 
              "https://doi.org/10.1038/nature25979"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41586-019-1058-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1112734629", 
              "https://doi.org/10.1038/s41586-019-1058-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41591-019-0559-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1120764379", 
              "https://doi.org/10.1038/s41591-019-0559-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-017-1309-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091875781", 
              "https://doi.org/10.1186/s13059-017-1309-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-020-16366-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1127705453", 
              "https://doi.org/10.1038/s41467-020-16366-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41396-018-0304-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1109906726", 
              "https://doi.org/10.1038/s41396-018-0304-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41579-019-0299-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1123532950", 
              "https://doi.org/10.1038/s41579-019-0299-x"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41467-019-12448-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1121473139", 
              "https://doi.org/10.1038/s41467-019-12448-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41579-020-0368-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1128189490", 
              "https://doi.org/10.1038/s41579-020-0368-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s12864-017-4195-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1092272577", 
              "https://doi.org/10.1186/s12864-017-4195-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nbt.3319", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019116134", 
              "https://doi.org/10.1038/nbt.3319"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-1-4614-6418-1_25-10", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1084859685", 
              "https://doi.org/10.1007/978-1-4614-6418-1_25-10"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11234", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007740093", 
              "https://doi.org/10.1038/nature11234"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.3802", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044732511", 
              "https://doi.org/10.1038/nmeth.3802"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/s41587-020-0603-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1129483269", 
              "https://doi.org/10.1038/s41587-020-0603-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s40168-016-0212-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040135732", 
              "https://doi.org/10.1186/s40168-016-0212-z"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2021-07-14", 
        "datePublishedReg": "2021-07-14", 
        "description": "BackgroundAkkermansia 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.ResultsWe 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.ConclusionsWe 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.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/s13059-021-02427-7", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.7834110", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.7926400", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.8556217", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.6623271", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1023439", 
            "issn": [
              "1474-760X", 
              "1465-6906"
            ], 
            "name": "Genome Biology", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "22"
          }
        ], 
        "keywords": [
          "candidate species", 
          "genomic diversity", 
          "whole-genome divergence", 
          "population genomic analyses", 
          "rRNA gene sequences", 
          "host body mass", 
          "CRISPR-Cas loci", 
          "human gut microbes", 
          "ecological interactions", 
          "putative bacteriophages", 
          "functional diversity", 
          "genomic analysis", 
          "gene sequences", 
          "isolate genomes", 
          "related bacteria", 
          "A. muciniphila", 
          "metagenomic assembly", 
          "Akkermansia genus", 
          "relative abundance", 
          "body mass", 
          "biomedical relevance", 
          "gut microbes", 
          "human gut", 
          "species", 
          "functional differences", 
          "genome", 
          "Akkermansia species", 
          "diversity", 
          "genus", 
          "genetic stratification", 
          "gut barrier function", 
          "gut microbiome", 
          "exo/", 
          "bacteriophages", 
          "intestinal mucus layer", 
          "non-human primates", 
          "key role", 
          "distinct patterns", 
          "metagenomes", 
          "operon", 
          "muciniphila", 
          "barrier function", 
          "mucus layer", 
          "ecology", 
          "microbes", 
          "loci", 
          "humans", 
          "captivity", 
          "abundance", 
          "microbiome", 
          "Akkermansia", 
          "divergence", 
          "bacteria", 
          "functional capabilities", 
          "physiology", 
          "sequence", 
          "assembly", 
          "gut", 
          "cognates", 
          "association", 
          "new variant", 
          "primates", 
          "variants", 
          "animals", 
          "spacer", 
          "mice", 
          "role", 
          "ResultsWe", 
          "interaction", 
          "health", 
          "ConclusionsWe", 
          "function", 
          "analysis", 
          "patterns", 
          "mass", 
          "variability", 
          "stratification", 
          "differences", 
          "relevance", 
          "Further", 
          "efforts", 
          "properties", 
          "capability", 
          "layer"
        ], 
        "name": "Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly", 
        "pagination": "209", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1139684002"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s13059-021-02427-7"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "34261503"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s13059-021-02427-7", 
          "https://app.dimensions.ai/details/publication/pub.1139684002"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-12-01T06:43", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20221201/entities/gbq_results/article/article_902.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/s13059-021-02427-7"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/s13059-021-02427-7'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/s13059-021-02427-7'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-021-02427-7'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-021-02427-7'


     

    This table displays all metadata directly associated to this object as RDF triples.

    502 TRIPLES      21 PREDICATES      164 URIs      114 LITERALS      20 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s13059-021-02427-7 schema:about N1976cfc719c345c294af1b0eb7711bde
    2 N1df8e07968e94693ae13f31571337dd6
    3 N2c999e2b5b6a4de396379ff415390e12
    4 N341bc1444f4946958707af5516169dd3
    5 N55e2bd7f203840ae94b6e14d23d1a5c9
    6 N5e35e2f2a185453ca882a67ff3f1fe65
    7 N66c1d3a1e6c14cd89e15eb8720b4bbdc
    8 N6ecb36c84e1e4fe3874741c564e03e03
    9 Nb592a5bab75c414e9ba2df4106f7e143
    10 Nb9a3dfeaf6204adbb5e8cce46eb68e17
    11 Ncebf1b61ff3a452dafb3f682a9273971
    12 Nd29419c0acb5416ea6748159de218bf1
    13 Ne64d5bff3c1c48eab1ff3c6600fdb312
    14 anzsrc-for:06
    15 anzsrc-for:0604
    16 schema:author Nf8180c7e0d9547e29ec843b301783989
    17 schema:citation sg:pub.10.1007/978-1-4614-6418-1_25-10
    18 sg:pub.10.1007/978-1-62703-646-7_8
    19 sg:pub.10.1007/s13258-019-00855-1
    20 sg:pub.10.1038/nature08821
    21 sg:pub.10.1038/nature11234
    22 sg:pub.10.1038/nature11711
    23 sg:pub.10.1038/nature25979
    24 sg:pub.10.1038/nbt.3319
    25 sg:pub.10.1038/nbt.3988
    26 sg:pub.10.1038/ncomms3304
    27 sg:pub.10.1038/ncomms9292
    28 sg:pub.10.1038/nmeth.1923
    29 sg:pub.10.1038/nmeth.2066
    30 sg:pub.10.1038/nmeth.3176
    31 sg:pub.10.1038/nmeth.3589
    32 sg:pub.10.1038/nmeth.3802
    33 sg:pub.10.1038/nmeth.4468
    34 sg:pub.10.1038/s41396-018-0304-9
    35 sg:pub.10.1038/s41467-018-07641-9
    36 sg:pub.10.1038/s41467-019-12448-3
    37 sg:pub.10.1038/s41467-019-13443-4
    38 sg:pub.10.1038/s41467-019-13836-5
    39 sg:pub.10.1038/s41467-020-16366-7
    40 sg:pub.10.1038/s41579-019-0299-x
    41 sg:pub.10.1038/s41579-020-0368-1
    42 sg:pub.10.1038/s41586-019-0965-1
    43 sg:pub.10.1038/s41586-019-1058-x
    44 sg:pub.10.1038/s41587-019-0334-5
    45 sg:pub.10.1038/s41587-020-0603-3
    46 sg:pub.10.1038/s41591-019-0406-6
    47 sg:pub.10.1038/s41591-019-0495-2
    48 sg:pub.10.1038/s41591-019-0559-3
    49 sg:pub.10.1038/s43587-020-00014-2
    50 sg:pub.10.1186/1471-2105-10-421
    51 sg:pub.10.1186/s12864-017-4195-3
    52 sg:pub.10.1186/s12864-018-4959-4
    53 sg:pub.10.1186/s13059-016-0997-x
    54 sg:pub.10.1186/s13059-017-1309-9
    55 sg:pub.10.1186/s13059-019-1923-9
    56 sg:pub.10.1186/s13059-020-02042-y
    57 sg:pub.10.1186/s13073-017-0490-5
    58 sg:pub.10.1186/s40168-016-0212-z
    59 schema:datePublished 2021-07-14
    60 schema:datePublishedReg 2021-07-14
    61 schema:description BackgroundAkkermansia 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.ResultsWe 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.ConclusionsWe 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.
    62 schema:genre article
    63 schema:isAccessibleForFree true
    64 schema:isPartOf N2a99393638e3434fa2fd0c8767baca17
    65 N98dcb0797fed42a7943e665cdc2f8cd4
    66 sg:journal.1023439
    67 schema:keywords A. muciniphila
    68 Akkermansia
    69 Akkermansia genus
    70 Akkermansia species
    71 CRISPR-Cas loci
    72 ConclusionsWe
    73 Further
    74 ResultsWe
    75 abundance
    76 analysis
    77 animals
    78 assembly
    79 association
    80 bacteria
    81 bacteriophages
    82 barrier function
    83 biomedical relevance
    84 body mass
    85 candidate species
    86 capability
    87 captivity
    88 cognates
    89 differences
    90 distinct patterns
    91 divergence
    92 diversity
    93 ecological interactions
    94 ecology
    95 efforts
    96 exo/
    97 function
    98 functional capabilities
    99 functional differences
    100 functional diversity
    101 gene sequences
    102 genetic stratification
    103 genome
    104 genomic analysis
    105 genomic diversity
    106 genus
    107 gut
    108 gut barrier function
    109 gut microbes
    110 gut microbiome
    111 health
    112 host body mass
    113 human gut
    114 human gut microbes
    115 humans
    116 interaction
    117 intestinal mucus layer
    118 isolate genomes
    119 key role
    120 layer
    121 loci
    122 mass
    123 metagenomes
    124 metagenomic assembly
    125 mice
    126 microbes
    127 microbiome
    128 muciniphila
    129 mucus layer
    130 new variant
    131 non-human primates
    132 operon
    133 patterns
    134 physiology
    135 population genomic analyses
    136 primates
    137 properties
    138 putative bacteriophages
    139 rRNA gene sequences
    140 related bacteria
    141 relative abundance
    142 relevance
    143 role
    144 sequence
    145 spacer
    146 species
    147 stratification
    148 variability
    149 variants
    150 whole-genome divergence
    151 schema:name Genomic diversity and ecology of human-associated Akkermansia species in the gut microbiome revealed by extensive metagenomic assembly
    152 schema:pagination 209
    153 schema:productId N69f0d943d51a40db977d562144e5d271
    154 Nbdef096cef374955a7cc096d8afcbe5f
    155 Nd882a26ca46b4502891984469ca8cb5b
    156 schema:sameAs https://app.dimensions.ai/details/publication/pub.1139684002
    157 https://doi.org/10.1186/s13059-021-02427-7
    158 schema:sdDatePublished 2022-12-01T06:43
    159 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    160 schema:sdPublisher Nba21a47ce9bb4ca3a699cc3797b6ae03
    161 schema:url https://doi.org/10.1186/s13059-021-02427-7
    162 sgo:license sg:explorer/license/
    163 sgo:sdDataset articles
    164 rdf:type schema:ScholarlyArticle
    165 N0351ae7296ca46ab8dfdfc1f37d1c966 rdf:first sg:person.0711517664.17
    166 rdf:rest N87f30e71262d4f6a863a42c56eb825f0
    167 N0711d631eb804a6cb179b5d1a094b2ed rdf:first Ned95a335a8394ed781a212d57744a83b
    168 rdf:rest N0351ae7296ca46ab8dfdfc1f37d1c966
    169 N1177656b1379447cbb2aafd22b2f4b1b rdf:first sg:person.013262116247.61
    170 rdf:rest Nea5c490fdb974531b244b6b96ab69517
    171 N1976cfc719c345c294af1b0eb7711bde schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    172 schema:name Genome, Bacterial
    173 rdf:type schema:DefinedTerm
    174 N1b084654d5004812ba74863687ca9b48 rdf:first sg:person.0701060711.59
    175 rdf:rest Neba46a71fa6d4e6a8ad29eeaff3df6b1
    176 N1df8e07968e94693ae13f31571337dd6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    177 schema:name Operon
    178 rdf:type schema:DefinedTerm
    179 N2a99393638e3434fa2fd0c8767baca17 schema:issueNumber 1
    180 rdf:type schema:PublicationIssue
    181 N2c999e2b5b6a4de396379ff415390e12 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    182 schema:name Humans
    183 rdf:type schema:DefinedTerm
    184 N341bc1444f4946958707af5516169dd3 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    185 schema:name Clustered Regularly Interspaced Short Palindromic Repeats
    186 rdf:type schema:DefinedTerm
    187 N34965e41ff634608905e5b2f8e339634 rdf:first sg:person.016220046237.06
    188 rdf:rest Naffe780da7ae420db4cb9ed796f649e8
    189 N36932225f69c40ffa518ae555a1424d1 rdf:first sg:person.016525324253.98
    190 rdf:rest N0711d631eb804a6cb179b5d1a094b2ed
    191 N55e2bd7f203840ae94b6e14d23d1a5c9 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    192 schema:name Animals
    193 rdf:type schema:DefinedTerm
    194 N5e35e2f2a185453ca882a67ff3f1fe65 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    195 schema:name Genetic Variation
    196 rdf:type schema:DefinedTerm
    197 N6469b4bc4c0042de99da4618d51e78ba rdf:first sg:person.01344663707.83
    198 rdf:rest Nf7f1bf42de8d4c96ae96e79a2dfad72f
    199 N66c1d3a1e6c14cd89e15eb8720b4bbdc schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    200 schema:name Phylogeny
    201 rdf:type schema:DefinedTerm
    202 N69f0d943d51a40db977d562144e5d271 schema:name pubmed_id
    203 schema:value 34261503
    204 rdf:type schema:PropertyValue
    205 N6ecb36c84e1e4fe3874741c564e03e03 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    206 schema:name Akkermansia
    207 rdf:type schema:DefinedTerm
    208 N87f30e71262d4f6a863a42c56eb825f0 rdf:first sg:person.01235472333.35
    209 rdf:rest N6469b4bc4c0042de99da4618d51e78ba
    210 N98dcb0797fed42a7943e665cdc2f8cd4 schema:volumeNumber 22
    211 rdf:type schema:PublicationVolume
    212 Naffe780da7ae420db4cb9ed796f649e8 rdf:first sg:person.016267051257.23
    213 rdf:rest Nd2d10493533142b9a518abc36b87c207
    214 Nb592a5bab75c414e9ba2df4106f7e143 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    215 schema:name RNA, Ribosomal, 16S
    216 rdf:type schema:DefinedTerm
    217 Nb9a3dfeaf6204adbb5e8cce46eb68e17 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    218 schema:name Gastrointestinal Microbiome
    219 rdf:type schema:DefinedTerm
    220 Nba21a47ce9bb4ca3a699cc3797b6ae03 schema:name Springer Nature - SN SciGraph project
    221 rdf:type schema:Organization
    222 Nbdef096cef374955a7cc096d8afcbe5f schema:name doi
    223 schema:value 10.1186/s13059-021-02427-7
    224 rdf:type schema:PropertyValue
    225 Ncebf1b61ff3a452dafb3f682a9273971 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    226 schema:name Metagenome
    227 rdf:type schema:DefinedTerm
    228 Nd23cbfc772d54838bf0d7c2b7c893dfc rdf:first sg:person.0700710637.71
    229 rdf:rest N34965e41ff634608905e5b2f8e339634
    230 Nd29419c0acb5416ea6748159de218bf1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    231 schema:name Mice
    232 rdf:type schema:DefinedTerm
    233 Nd2d10493533142b9a518abc36b87c207 rdf:first sg:person.01330203271.52
    234 rdf:rest Ndb2d10adf45e4abdbca2ec121649cb50
    235 Nd882a26ca46b4502891984469ca8cb5b schema:name dimensions_id
    236 schema:value pub.1139684002
    237 rdf:type schema:PropertyValue
    238 Ndb2d10adf45e4abdbca2ec121649cb50 rdf:first sg:person.0652034035.75
    239 rdf:rest N36932225f69c40ffa518ae555a1424d1
    240 Ne64d5bff3c1c48eab1ff3c6600fdb312 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    241 schema:name Bacteriophages
    242 rdf:type schema:DefinedTerm
    243 Nea5c490fdb974531b244b6b96ab69517 rdf:first sg:person.012560426435.20
    244 rdf:rest Nd23cbfc772d54838bf0d7c2b7c893dfc
    245 Neba46a71fa6d4e6a8ad29eeaff3df6b1 rdf:first sg:person.01114225554.30
    246 rdf:rest Nf963b453edaf47f7a476b97e0fc88007
    247 Ned95a335a8394ed781a212d57744a83b schema:affiliation grid-institutes:grid.11696.39
    248 schema:familyName Golzato
    249 schema:givenName Davide
    250 rdf:type schema:Person
    251 Nf7f1bf42de8d4c96ae96e79a2dfad72f rdf:first sg:person.0670767463.71
    252 rdf:rest N1b084654d5004812ba74863687ca9b48
    253 Nf8180c7e0d9547e29ec843b301783989 rdf:first sg:person.012354262313.62
    254 rdf:rest N1177656b1379447cbb2aafd22b2f4b1b
    255 Nf963b453edaf47f7a476b97e0fc88007 rdf:first sg:person.0736227144.03
    256 rdf:rest rdf:nil
    257 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    258 schema:name Biological Sciences
    259 rdf:type schema:DefinedTerm
    260 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    261 schema:name Genetics
    262 rdf:type schema:DefinedTerm
    263 sg:grant.6623271 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-021-02427-7
    264 rdf:type schema:MonetaryGrant
    265 sg:grant.7834110 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-021-02427-7
    266 rdf:type schema:MonetaryGrant
    267 sg:grant.7926400 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-021-02427-7
    268 rdf:type schema:MonetaryGrant
    269 sg:grant.8556217 http://pending.schema.org/fundedItem sg:pub.10.1186/s13059-021-02427-7
    270 rdf:type schema:MonetaryGrant
    271 sg:journal.1023439 schema:issn 1465-6906
    272 1474-760X
    273 schema:name Genome Biology
    274 schema:publisher Springer Nature
    275 rdf:type schema:Periodical
    276 sg:person.01114225554.30 schema:affiliation grid-institutes:grid.7737.4
    277 schema:familyName de Vos
    278 schema:givenName Willem M.
    279 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01114225554.30
    280 rdf:type schema:Person
    281 sg:person.012354262313.62 schema:affiliation grid-institutes:grid.11696.39
    282 schema:familyName Karcher
    283 schema:givenName Nicolai
    284 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012354262313.62
    285 rdf:type schema:Person
    286 sg:person.01235472333.35 schema:affiliation grid-institutes:grid.5254.6
    287 schema:familyName Arumugam
    288 schema:givenName Manimozhiyan
    289 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01235472333.35
    290 rdf:type schema:Person
    291 sg:person.012560426435.20 schema:affiliation grid-institutes:grid.11696.39
    292 schema:familyName Punčochář
    293 schema:givenName Michal
    294 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012560426435.20
    295 rdf:type schema:Person
    296 sg:person.013262116247.61 schema:affiliation grid-institutes:grid.5254.6
    297 schema:familyName Nigro
    298 schema:givenName Eleonora
    299 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013262116247.61
    300 rdf:type schema:Person
    301 sg:person.01330203271.52 schema:affiliation grid-institutes:grid.11696.39
    302 schema:familyName Zolfo
    303 schema:givenName Moreno
    304 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01330203271.52
    305 rdf:type schema:Person
    306 sg:person.01344663707.83 schema:affiliation grid-institutes:grid.4818.5
    307 schema:familyName Bui
    308 schema:givenName Thi Phuong Nam
    309 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01344663707.83
    310 rdf:type schema:Person
    311 sg:person.016220046237.06 schema:affiliation grid-institutes:grid.11696.39
    312 schema:familyName Ciciani
    313 schema:givenName Matteo
    314 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016220046237.06
    315 rdf:type schema:Person
    316 sg:person.016267051257.23 schema:affiliation grid-institutes:grid.11696.39
    317 schema:familyName Manghi
    318 schema:givenName Paolo
    319 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016267051257.23
    320 rdf:type schema:Person
    321 sg:person.016525324253.98 schema:affiliation grid-institutes:grid.11696.39
    322 schema:familyName Manara
    323 schema:givenName Serena
    324 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016525324253.98
    325 rdf:type schema:Person
    326 sg:person.0652034035.75 schema:affiliation grid-institutes:grid.11696.39
    327 schema:familyName Cumbo
    328 schema:givenName Fabio
    329 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0652034035.75
    330 rdf:type schema:Person
    331 sg:person.0670767463.71 schema:affiliation grid-institutes:grid.419905.0
    332 schema:familyName Tytgat
    333 schema:givenName Hanne L. P.
    334 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0670767463.71
    335 rdf:type schema:Person
    336 sg:person.0700710637.71 schema:affiliation grid-institutes:grid.11696.39
    337 schema:familyName Blanco-Míguez
    338 schema:givenName Aitor
    339 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0700710637.71
    340 rdf:type schema:Person
    341 sg:person.0701060711.59 schema:affiliation grid-institutes:grid.11696.39
    342 schema:familyName Valles-Colomer
    343 schema:givenName Mireia
    344 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0701060711.59
    345 rdf:type schema:Person
    346 sg:person.0711517664.17 schema:affiliation grid-institutes:grid.11696.39
    347 schema:familyName Cereseto
    348 schema:givenName Anna
    349 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0711517664.17
    350 rdf:type schema:Person
    351 sg:person.0736227144.03 schema:affiliation grid-institutes:grid.15667.33
    352 schema:familyName Segata
    353 schema:givenName Nicola
    354 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0736227144.03
    355 rdf:type schema:Person
    356 sg:pub.10.1007/978-1-4614-6418-1_25-10 schema:sameAs https://app.dimensions.ai/details/publication/pub.1084859685
    357 https://doi.org/10.1007/978-1-4614-6418-1_25-10
    358 rdf:type schema:CreativeWork
    359 sg:pub.10.1007/978-1-62703-646-7_8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016522201
    360 https://doi.org/10.1007/978-1-62703-646-7_8
    361 rdf:type schema:CreativeWork
    362 sg:pub.10.1007/s13258-019-00855-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1120249270
    363 https://doi.org/10.1007/s13258-019-00855-1
    364 rdf:type schema:CreativeWork
    365 sg:pub.10.1038/nature08821 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050498034
    366 https://doi.org/10.1038/nature08821
    367 rdf:type schema:CreativeWork
    368 sg:pub.10.1038/nature11234 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007740093
    369 https://doi.org/10.1038/nature11234
    370 rdf:type schema:CreativeWork
    371 sg:pub.10.1038/nature11711 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004024856
    372 https://doi.org/10.1038/nature11711
    373 rdf:type schema:CreativeWork
    374 sg:pub.10.1038/nature25979 schema:sameAs https://app.dimensions.ai/details/publication/pub.1101559358
    375 https://doi.org/10.1038/nature25979
    376 rdf:type schema:CreativeWork
    377 sg:pub.10.1038/nbt.3319 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019116134
    378 https://doi.org/10.1038/nbt.3319
    379 rdf:type schema:CreativeWork
    380 sg:pub.10.1038/nbt.3988 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092237583
    381 https://doi.org/10.1038/nbt.3988
    382 rdf:type schema:CreativeWork
    383 sg:pub.10.1038/ncomms3304 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040093094
    384 https://doi.org/10.1038/ncomms3304
    385 rdf:type schema:CreativeWork
    386 sg:pub.10.1038/ncomms9292 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013796702
    387 https://doi.org/10.1038/ncomms9292
    388 rdf:type schema:CreativeWork
    389 sg:pub.10.1038/nmeth.1923 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006541515
    390 https://doi.org/10.1038/nmeth.1923
    391 rdf:type schema:CreativeWork
    392 sg:pub.10.1038/nmeth.2066 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010611135
    393 https://doi.org/10.1038/nmeth.2066
    394 rdf:type schema:CreativeWork
    395 sg:pub.10.1038/nmeth.3176 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023901695
    396 https://doi.org/10.1038/nmeth.3176
    397 rdf:type schema:CreativeWork
    398 sg:pub.10.1038/nmeth.3589 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028162909
    399 https://doi.org/10.1038/nmeth.3589
    400 rdf:type schema:CreativeWork
    401 sg:pub.10.1038/nmeth.3802 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044732511
    402 https://doi.org/10.1038/nmeth.3802
    403 rdf:type schema:CreativeWork
    404 sg:pub.10.1038/nmeth.4468 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092462741
    405 https://doi.org/10.1038/nmeth.4468
    406 rdf:type schema:CreativeWork
    407 sg:pub.10.1038/s41396-018-0304-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1109906726
    408 https://doi.org/10.1038/s41396-018-0304-9
    409 rdf:type schema:CreativeWork
    410 sg:pub.10.1038/s41467-018-07641-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1110204842
    411 https://doi.org/10.1038/s41467-018-07641-9
    412 rdf:type schema:CreativeWork
    413 sg:pub.10.1038/s41467-019-12448-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1121473139
    414 https://doi.org/10.1038/s41467-019-12448-3
    415 rdf:type schema:CreativeWork
    416 sg:pub.10.1038/s41467-019-13443-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1123048808
    417 https://doi.org/10.1038/s41467-019-13443-4
    418 rdf:type schema:CreativeWork
    419 sg:pub.10.1038/s41467-019-13836-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1123920393
    420 https://doi.org/10.1038/s41467-019-13836-5
    421 rdf:type schema:CreativeWork
    422 sg:pub.10.1038/s41467-020-16366-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1127705453
    423 https://doi.org/10.1038/s41467-020-16366-7
    424 rdf:type schema:CreativeWork
    425 sg:pub.10.1038/s41579-019-0299-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1123532950
    426 https://doi.org/10.1038/s41579-019-0299-x
    427 rdf:type schema:CreativeWork
    428 sg:pub.10.1038/s41579-020-0368-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1128189490
    429 https://doi.org/10.1038/s41579-020-0368-1
    430 rdf:type schema:CreativeWork
    431 sg:pub.10.1038/s41586-019-0965-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1112059155
    432 https://doi.org/10.1038/s41586-019-0965-1
    433 rdf:type schema:CreativeWork
    434 sg:pub.10.1038/s41586-019-1058-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1112734629
    435 https://doi.org/10.1038/s41586-019-1058-x
    436 rdf:type schema:CreativeWork
    437 sg:pub.10.1038/s41587-019-0334-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1122746602
    438 https://doi.org/10.1038/s41587-019-0334-5
    439 rdf:type schema:CreativeWork
    440 sg:pub.10.1038/s41587-020-0603-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1129483269
    441 https://doi.org/10.1038/s41587-020-0603-3
    442 rdf:type schema:CreativeWork
    443 sg:pub.10.1038/s41591-019-0406-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1113160869
    444 https://doi.org/10.1038/s41591-019-0406-6
    445 rdf:type schema:CreativeWork
    446 sg:pub.10.1038/s41591-019-0495-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1117655252
    447 https://doi.org/10.1038/s41591-019-0495-2
    448 rdf:type schema:CreativeWork
    449 sg:pub.10.1038/s41591-019-0559-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1120764379
    450 https://doi.org/10.1038/s41591-019-0559-3
    451 rdf:type schema:CreativeWork
    452 sg:pub.10.1038/s43587-020-00014-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1134587622
    453 https://doi.org/10.1038/s43587-020-00014-2
    454 rdf:type schema:CreativeWork
    455 sg:pub.10.1186/1471-2105-10-421 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050579230
    456 https://doi.org/10.1186/1471-2105-10-421
    457 rdf:type schema:CreativeWork
    458 sg:pub.10.1186/s12864-017-4195-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1092272577
    459 https://doi.org/10.1186/s12864-017-4195-3
    460 rdf:type schema:CreativeWork
    461 sg:pub.10.1186/s12864-018-4959-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1105932478
    462 https://doi.org/10.1186/s12864-018-4959-4
    463 rdf:type schema:CreativeWork
    464 sg:pub.10.1186/s13059-016-0997-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1050687712
    465 https://doi.org/10.1186/s13059-016-0997-x
    466 rdf:type schema:CreativeWork
    467 sg:pub.10.1186/s13059-017-1309-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091875781
    468 https://doi.org/10.1186/s13059-017-1309-9
    469 rdf:type schema:CreativeWork
    470 sg:pub.10.1186/s13059-019-1923-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1123710056
    471 https://doi.org/10.1186/s13059-019-1923-9
    472 rdf:type schema:CreativeWork
    473 sg:pub.10.1186/s13059-020-02042-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1128301041
    474 https://doi.org/10.1186/s13059-020-02042-y
    475 rdf:type schema:CreativeWork
    476 sg:pub.10.1186/s13073-017-0490-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1093054943
    477 https://doi.org/10.1186/s13073-017-0490-5
    478 rdf:type schema:CreativeWork
    479 sg:pub.10.1186/s40168-016-0212-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1040135732
    480 https://doi.org/10.1186/s40168-016-0212-z
    481 rdf:type schema:CreativeWork
    482 grid-institutes:grid.11696.39 schema:alternateName Department CIBIO, University of Trento, Trento, Italy
    483 schema:name Department CIBIO, University of Trento, Trento, Italy
    484 rdf:type schema:Organization
    485 grid-institutes:grid.15667.33 schema:alternateName IEO, European Institute of Oncology IRCCS, Milan, Italy
    486 schema:name Department CIBIO, University of Trento, Trento, Italy
    487 IEO, European Institute of Oncology IRCCS, Milan, Italy
    488 rdf:type schema:Organization
    489 grid-institutes:grid.419905.0 schema:alternateName Current address: Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
    490 schema:name Current address: Nestlé Institute of Health Sciences, Nestlé Research, Société des Produits Nestlé S.A., Lausanne, Switzerland
    491 Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    492 rdf:type schema:Organization
    493 grid-institutes:grid.4818.5 schema:alternateName Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    494 schema:name Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    495 rdf:type schema:Organization
    496 grid-institutes:grid.5254.6 schema:alternateName Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
    497 schema:name Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
    498 rdf:type schema:Organization
    499 grid-institutes:grid.7737.4 schema:alternateName Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
    500 schema:name Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
    501 Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
    502 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...