Host genetic variation and its microbiome interactions within the Human Microbiome Project View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2018-01-29

AUTHORS

Raivo Kolde, Eric A. Franzosa, Gholamali Rahnavard, Andrew Brantley Hall, Hera Vlamakis, Christine Stevens, Mark J. Daly, Ramnik J. Xavier, Curtis Huttenhower

ABSTRACT

BackgroundDespite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and microbiome characterization have been performed.MethodsWe performed whole-genome sequencing of 298 donors from the Human Microbiome Project (HMP) healthy cohort study to accompany existing deep characterization of their microbiomes at various body sites. This analysis yielded an average sequencing depth of 32x, with which we identified 27 million (M) single nucleotide variants and 2.3 M insertions-deletions.ResultsTaxonomic composition and functional potential of the microbiome covaried significantly with genetic principal components in the gastrointestinal tract and oral communities, but not in the nares or vaginal microbiota. Example associations included validation of known associations between FUT2 secretor status, as well as a variant conferring hypolactasia near the LCT gene, with Bifidobacterium longum abundance in stool. The associations of microbial features with both high-level genetic attributes and single variants were specific to particular body sites, highlighting the opportunity to find unique genetic mechanisms controlling microbiome properties in the microbial communities from multiple body sites.ConclusionsThis study adds deep sequencing of host genomes to the body-wide microbiome sequences already extant from the HMP healthy cohort, creating a unique, versatile, and well-controlled reference for future studies seeking to identify host genetic modulators of the microbiome. More... »

PAGES

6

References to SciGraph publications

  • 2014-06-29. Whole-genome sequence variation, population structure and demographic history of the Dutch population in NATURE GENETICS
  • 2012-06-13. Structure, function and diversity of the healthy human microbiome in NATURE
  • 2013-01-06. Genome-wide association analysis identifies new susceptibility loci for Behçet's disease and epistasis between HLA-B*51 and ERAP1 in NATURE GENETICS
  • 2016-10-03. The effect of host genetics on the gut microbiome in NATURE GENETICS
  • 2015-09-29. MetaPhlAn2 for enhanced metagenomic taxonomic profiling in NATURE METHODS
  • 2016-07-13. Mobile genes in the human microbiome are structured from global to individual scales in NATURE
  • 2002-01-14. Identification of a variant associated with adult-type hypolactasia in NATURE GENETICS
  • 2014-12-17. Host genetics and diet, but not immunoglobulin A expression, converge to shape compositional features of the gut microbiome in an advanced intercross population of mice in GENOME BIOLOGY
  • 2016-10-03. Association of host genome with intestinal microbial composition in a large healthy cohort in NATURE GENETICS
  • 2015-09-30. A global reference for human genetic variation in NATURE
  • 2010-10-17. A genome-wide association study identifies new psoriasis susceptibility loci and an interaction between HLA-C and ERAP1 in NATURE GENETICS
  • 2011-07-10. Interaction between ERAP1 and HLA-B27 in ankylosing spondylitis implicates peptide handling in the mechanism for HLA-B27 in disease susceptibility in NATURE GENETICS
  • 2014-02-23. Pathogens and host immunity in the ancient human oral cavity in NATURE GENETICS
  • 2014-07-25. Host lifestyle affects human microbiota on daily timescales in GENOME BIOLOGY
  • 2015-08-24. Meta-analysis of shared genetic architecture across ten pediatric autoimmune diseases in NATURE MEDICINE
  • 2012-06-13. A framework for human microbiome research in NATURE
  • 2015-07-27. The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment in NATURE MEDICINE
  • 2014-04-16. Dynamics and associations of microbial community types across the human body in NATURE
  • 2014-12-02. Complex host genetics influence the microbiome in inflammatory bowel disease in GENOME MEDICINE
  • 2012-10-31. Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease in NATURE
  • 2014-04-03. mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities in BMC GENOMICS
  • 2017-09-20. Strains, functions and dynamics in the expanded Human Microbiome Project in NATURE
  • 2014-10-01. Biogeography and individuality shape function in the human skin metagenome in NATURE
  • 2015-09-15. Host genetic variation impacts microbiome composition across human body sites in GENOME BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1186/s13073-018-0515-8

    DOI

    http://dx.doi.org/10.1186/s13073-018-0515-8

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1100690062

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/29378630


    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": "Genetic Variation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genotype", 
            "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": "Microbiota", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Principal Component Analysis", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sequence Analysis, DNA", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Tissue Donors", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge St, 02114, Boston, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.32224.35", 
              "name": [
                "Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge St, 02114, Boston, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Kolde", 
            "givenName": "Raivo", 
            "id": "sg:person.0654747534.44", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0654747534.44"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.66859.34", 
              "name": [
                "Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, 02115, Boston, MA, USA", 
                "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Franzosa", 
            "givenName": "Eric A.", 
            "id": "sg:person.0772302366.11", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772302366.11"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.66859.34", 
              "name": [
                "Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, 02115, Boston, MA, USA", 
                "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Rahnavard", 
            "givenName": "Gholamali", 
            "id": "sg:person.01325533721.33", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01325533721.33"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.66859.34", 
              "name": [
                "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Hall", 
            "givenName": "Andrew Brantley", 
            "id": "sg:person.01024545742.89", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024545742.89"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.66859.34", 
              "name": [
                "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Vlamakis", 
            "givenName": "Hera", 
            "id": "sg:person.0773476547.34", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773476547.34"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.66859.34", 
              "name": [
                "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Stevens", 
            "givenName": "Christine", 
            "id": "sg:person.01146571421.48", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01146571421.48"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge St, 02114, Boston, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.32224.35", 
              "name": [
                "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA", 
                "Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge St, 02114, Boston, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Daly", 
            "givenName": "Mark J.", 
            "id": "sg:person.011517303117.07", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011517303117.07"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Center for Microbiome Informatics & Therapeutics, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.116068.8", 
              "name": [
                "Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge St, 02114, Boston, MA, USA", 
                "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA", 
                "Center for Microbiome Informatics & Therapeutics, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Xavier", 
            "givenName": "Ramnik J.", 
            "id": "sg:person.0717130066.82", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717130066.82"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA", 
              "id": "http://www.grid.ac/institutes/grid.66859.34", 
              "name": [
                "Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, 02115, Boston, MA, USA", 
                "The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Huttenhower", 
            "givenName": "Curtis", 
            "id": "sg:person.01214462502.85", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01214462502.85"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1038/ng.873", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1041967517", 
              "https://doi.org/10.1038/ng.873"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature15393", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021812064", 
              "https://doi.org/10.1038/nature15393"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nm.3933", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037606023", 
              "https://doi.org/10.1038/nm.3933"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3693", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002138629", 
              "https://doi.org/10.1038/ng.3693"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13073-014-0107-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006350078", 
              "https://doi.org/10.1186/s13073-014-0107-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-15-257", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002664833", 
              "https://doi.org/10.1186/1471-2164-15-257"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature23889", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1091863851", 
              "https://doi.org/10.1038/nature23889"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.694", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023718631", 
              "https://doi.org/10.1038/ng.694"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-014-0552-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024893270", 
              "https://doi.org/10.1186/s13059-014-0552-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/s13059-015-0759-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1017080966", 
              "https://doi.org/10.1186/s13059-015-0759-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2014-15-7-r89", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022685985", 
              "https://doi.org/10.1186/gb-2014-15-7-r89"
            ], 
            "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/nature11582", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046541188", 
              "https://doi.org/10.1038/nature11582"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nm.3914", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1009083133", 
              "https://doi.org/10.1038/nm.3914"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.3021", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1030784697", 
              "https://doi.org/10.1038/ng.3021"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature18927", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026832225", 
              "https://doi.org/10.1038/nature18927"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.2520", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008881446", 
              "https://doi.org/10.1038/ng.2520"
            ], 
            "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/ng.3663", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018819579", 
              "https://doi.org/10.1038/ng.3663"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature13786", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022632622", 
              "https://doi.org/10.1038/nature13786"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature13178", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1022430209", 
              "https://doi.org/10.1038/nature13178"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11209", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027248000", 
              "https://doi.org/10.1038/nature11209"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng826", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051591016", 
              "https://doi.org/10.1038/ng826"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.2906", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1004737256", 
              "https://doi.org/10.1038/ng.2906"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2018-01-29", 
        "datePublishedReg": "2018-01-29", 
        "description": "BackgroundDespite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and microbiome characterization have been performed.MethodsWe performed whole-genome sequencing of 298 donors from the Human Microbiome Project (HMP) healthy cohort study to accompany existing deep characterization of their microbiomes at various body sites. This analysis yielded an average sequencing depth of 32x, with which we identified 27 million (M) single nucleotide variants and 2.3\u00a0M insertions-deletions.ResultsTaxonomic composition and functional potential of the microbiome covaried significantly with genetic principal components in the gastrointestinal tract and oral communities, but not in the nares or vaginal microbiota. Example associations included validation of known associations between FUT2 secretor status, as well as a variant conferring hypolactasia near the LCT gene, with Bifidobacterium longum abundance in stool. The associations of microbial features with both high-level genetic attributes and single variants were specific to particular body sites, highlighting the opportunity to find unique genetic mechanisms controlling microbiome properties in the microbial communities from multiple body sites.ConclusionsThis study adds deep sequencing of host genomes to the body-wide microbiome sequences already extant from the HMP healthy cohort, creating a unique, versatile, and well-controlled reference for future studies seeking to identify host genetic modulators of the microbiome.", 
        "genre": "article", 
        "id": "sg:pub.10.1186/s13073-018-0515-8", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isFundedItemOf": [
          {
            "id": "sg:grant.2699180", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2699326", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.3806830", 
            "type": "MonetaryGrant"
          }, 
          {
            "id": "sg:grant.2439002", 
            "type": "MonetaryGrant"
          }
        ], 
        "isPartOf": [
          {
            "id": "sg:journal.1040124", 
            "issn": [
              "1756-994X"
            ], 
            "name": "Genome Medicine", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "1", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "10"
          }
        ], 
        "keywords": [
          "microbial communities", 
          "average sequencing depth", 
          "unique genetic mechanism", 
          "host genetic variation", 
          "Human Microbiome Project", 
          "single nucleotide variants", 
          "whole-genome sequencing", 
          "body sites", 
          "genetic variation", 
          "genetic mechanisms", 
          "host genome", 
          "microbiome properties", 
          "deep sequencing", 
          "genetic attributes", 
          "microbiome interactions", 
          "FUT2 secretor status", 
          "Microbiome Project", 
          "sequencing depth", 
          "nucleotide variants", 
          "LCT gene", 
          "functional potential", 
          "large population-based cohort", 
          "genetic modulators", 
          "genetic principal components", 
          "microbiome characterization", 
          "oral community", 
          "population-based cohort", 
          "microbiome sequences", 
          "host genetic factors", 
          "microbial features", 
          "multiple body sites", 
          "molecular interactions", 
          "single variant", 
          "microbiome", 
          "cohort study", 
          "sequencing", 
          "deep characterization", 
          "healthy cohort", 
          "particular body site", 
          "gastrointestinal tract", 
          "vaginal microbiota", 
          "secretor status", 
          "genetic factors", 
          "ConclusionsThis study", 
          "genome", 
          "incomplete understanding", 
          "cohort", 
          "genes", 
          "sites", 
          "variants", 
          "association", 
          "future studies", 
          "abundance", 
          "community", 
          "interaction", 
          "sequence", 
          "microbiota", 
          "characterization", 
          "stool", 
          "principal components", 
          "BackgroundDespite", 
          "MethodsWe", 
          "composition", 
          "tract", 
          "hypolactasia", 
          "nares", 
          "study", 
          "modulator", 
          "human body", 
          "factors", 
          "mechanism", 
          "health", 
          "role", 
          "status", 
          "variation", 
          "donors", 
          "understanding", 
          "components", 
          "potential", 
          "body", 
          "analysis", 
          "recognition", 
          "validation", 
          "features", 
          "attributes", 
          "opportunities", 
          "requirements", 
          "reference", 
          "depth", 
          "properties", 
          "project"
        ], 
        "name": "Host genetic variation and its microbiome interactions within the Human Microbiome Project", 
        "pagination": "6", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1100690062"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1186/s13073-018-0515-8"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "29378630"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1186/s13073-018-0515-8", 
          "https://app.dimensions.ai/details/publication/pub.1100690062"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-06-01T22:19", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220601/entities/gbq_results/article/article_768.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1186/s13073-018-0515-8"
      }
    ]
     

    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/s13073-018-0515-8'

    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/s13073-018-0515-8'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13073-018-0515-8'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13073-018-0515-8'


     

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

    356 TRIPLES      22 PREDICATES      149 URIs      117 LITERALS      15 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1186/s13073-018-0515-8 schema:about N55a91fa0b9874068819502a8c68acce1
    2 N72c20fcfa20540ee864535546f75c966
    3 N8ae91923ec1740b984c1a077f391e5f5
    4 Na0b02ac85054465b8a90d4c705ee8579
    5 Nb881f8bd4b9b4ea7a985a6a67a5082f4
    6 Nd0bf4a2f5ad541be8f5614c82235267c
    7 Ndc2db4d762c24797b1292dfb1c75a3df
    8 Ndead0f62689c404a95bf86fd838fe963
    9 anzsrc-for:06
    10 anzsrc-for:0604
    11 schema:author N176a60a65d724fc59606bea600b8c1f3
    12 schema:citation sg:pub.10.1038/nature11209
    13 sg:pub.10.1038/nature11234
    14 sg:pub.10.1038/nature11582
    15 sg:pub.10.1038/nature13178
    16 sg:pub.10.1038/nature13786
    17 sg:pub.10.1038/nature15393
    18 sg:pub.10.1038/nature18927
    19 sg:pub.10.1038/nature23889
    20 sg:pub.10.1038/ng.2520
    21 sg:pub.10.1038/ng.2906
    22 sg:pub.10.1038/ng.3021
    23 sg:pub.10.1038/ng.3663
    24 sg:pub.10.1038/ng.3693
    25 sg:pub.10.1038/ng.694
    26 sg:pub.10.1038/ng.873
    27 sg:pub.10.1038/ng826
    28 sg:pub.10.1038/nm.3914
    29 sg:pub.10.1038/nm.3933
    30 sg:pub.10.1038/nmeth.3589
    31 sg:pub.10.1186/1471-2164-15-257
    32 sg:pub.10.1186/gb-2014-15-7-r89
    33 sg:pub.10.1186/s13059-014-0552-6
    34 sg:pub.10.1186/s13059-015-0759-1
    35 sg:pub.10.1186/s13073-014-0107-1
    36 schema:datePublished 2018-01-29
    37 schema:datePublishedReg 2018-01-29
    38 schema:description BackgroundDespite the increasing recognition that microbial communities within the human body are linked to health, we have an incomplete understanding of the environmental and molecular interactions that shape the composition of these communities. Although host genetic factors play a role in these interactions, these factors have remained relatively unexplored given the requirement for large population-based cohorts in which both genotyping and microbiome characterization have been performed.MethodsWe performed whole-genome sequencing of 298 donors from the Human Microbiome Project (HMP) healthy cohort study to accompany existing deep characterization of their microbiomes at various body sites. This analysis yielded an average sequencing depth of 32x, with which we identified 27 million (M) single nucleotide variants and 2.3 M insertions-deletions.ResultsTaxonomic composition and functional potential of the microbiome covaried significantly with genetic principal components in the gastrointestinal tract and oral communities, but not in the nares or vaginal microbiota. Example associations included validation of known associations between FUT2 secretor status, as well as a variant conferring hypolactasia near the LCT gene, with Bifidobacterium longum abundance in stool. The associations of microbial features with both high-level genetic attributes and single variants were specific to particular body sites, highlighting the opportunity to find unique genetic mechanisms controlling microbiome properties in the microbial communities from multiple body sites.ConclusionsThis study adds deep sequencing of host genomes to the body-wide microbiome sequences already extant from the HMP healthy cohort, creating a unique, versatile, and well-controlled reference for future studies seeking to identify host genetic modulators of the microbiome.
    39 schema:genre article
    40 schema:inLanguage en
    41 schema:isAccessibleForFree true
    42 schema:isPartOf N2835bb8acd4f473eae0fbf5f09796536
    43 N87f8ad370cd9406a8707d11fb1c9baaa
    44 sg:journal.1040124
    45 schema:keywords BackgroundDespite
    46 ConclusionsThis study
    47 FUT2 secretor status
    48 Human Microbiome Project
    49 LCT gene
    50 MethodsWe
    51 Microbiome Project
    52 abundance
    53 analysis
    54 association
    55 attributes
    56 average sequencing depth
    57 body
    58 body sites
    59 characterization
    60 cohort
    61 cohort study
    62 community
    63 components
    64 composition
    65 deep characterization
    66 deep sequencing
    67 depth
    68 donors
    69 factors
    70 features
    71 functional potential
    72 future studies
    73 gastrointestinal tract
    74 genes
    75 genetic attributes
    76 genetic factors
    77 genetic mechanisms
    78 genetic modulators
    79 genetic principal components
    80 genetic variation
    81 genome
    82 health
    83 healthy cohort
    84 host genetic factors
    85 host genetic variation
    86 host genome
    87 human body
    88 hypolactasia
    89 incomplete understanding
    90 interaction
    91 large population-based cohort
    92 mechanism
    93 microbial communities
    94 microbial features
    95 microbiome
    96 microbiome characterization
    97 microbiome interactions
    98 microbiome properties
    99 microbiome sequences
    100 microbiota
    101 modulator
    102 molecular interactions
    103 multiple body sites
    104 nares
    105 nucleotide variants
    106 opportunities
    107 oral community
    108 particular body site
    109 population-based cohort
    110 potential
    111 principal components
    112 project
    113 properties
    114 recognition
    115 reference
    116 requirements
    117 role
    118 secretor status
    119 sequence
    120 sequencing
    121 sequencing depth
    122 single nucleotide variants
    123 single variant
    124 sites
    125 status
    126 stool
    127 study
    128 tract
    129 understanding
    130 unique genetic mechanism
    131 vaginal microbiota
    132 validation
    133 variants
    134 variation
    135 whole-genome sequencing
    136 schema:name Host genetic variation and its microbiome interactions within the Human Microbiome Project
    137 schema:pagination 6
    138 schema:productId N3f38eac623324ced9dc4c4285dd91088
    139 N51977b56ed5245778d885a611fbfd847
    140 N6f73262c39f1409a8c69ecbc138854c4
    141 schema:sameAs https://app.dimensions.ai/details/publication/pub.1100690062
    142 https://doi.org/10.1186/s13073-018-0515-8
    143 schema:sdDatePublished 2022-06-01T22:19
    144 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    145 schema:sdPublisher N10759a68cea5428487d7f039b74f5f1d
    146 schema:url https://doi.org/10.1186/s13073-018-0515-8
    147 sgo:license sg:explorer/license/
    148 sgo:sdDataset articles
    149 rdf:type schema:ScholarlyArticle
    150 N10759a68cea5428487d7f039b74f5f1d schema:name Springer Nature - SN SciGraph project
    151 rdf:type schema:Organization
    152 N11bfb95677894cc6841c2892cf6df2a7 rdf:first sg:person.01214462502.85
    153 rdf:rest rdf:nil
    154 N176a60a65d724fc59606bea600b8c1f3 rdf:first sg:person.0654747534.44
    155 rdf:rest N92d1f26379dd4693ac2831596af896be
    156 N1ac0068c537c493483f111b84fb45876 rdf:first sg:person.011517303117.07
    157 rdf:rest N7f885213bc6747fa9d4e9ed80f027f53
    158 N2835bb8acd4f473eae0fbf5f09796536 schema:volumeNumber 10
    159 rdf:type schema:PublicationVolume
    160 N3f38eac623324ced9dc4c4285dd91088 schema:name doi
    161 schema:value 10.1186/s13073-018-0515-8
    162 rdf:type schema:PropertyValue
    163 N49eb5f450b2d4391a4ecc1c4a2ac1740 rdf:first sg:person.01325533721.33
    164 rdf:rest Ncefb4b9d7ff34c70b090cd8cc1ad9982
    165 N51977b56ed5245778d885a611fbfd847 schema:name dimensions_id
    166 schema:value pub.1100690062
    167 rdf:type schema:PropertyValue
    168 N55a91fa0b9874068819502a8c68acce1 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    169 schema:name Principal Component Analysis
    170 rdf:type schema:DefinedTerm
    171 N6c31a0ebd0bc4f90b64e3453476ebbca rdf:first sg:person.0773476547.34
    172 rdf:rest Ne9e816ee4eba4650a2c4728b66c24e68
    173 N6f73262c39f1409a8c69ecbc138854c4 schema:name pubmed_id
    174 schema:value 29378630
    175 rdf:type schema:PropertyValue
    176 N72c20fcfa20540ee864535546f75c966 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    177 schema:name Microbiota
    178 rdf:type schema:DefinedTerm
    179 N7f885213bc6747fa9d4e9ed80f027f53 rdf:first sg:person.0717130066.82
    180 rdf:rest N11bfb95677894cc6841c2892cf6df2a7
    181 N87f8ad370cd9406a8707d11fb1c9baaa schema:issueNumber 1
    182 rdf:type schema:PublicationIssue
    183 N8ae91923ec1740b984c1a077f391e5f5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    184 schema:name Humans
    185 rdf:type schema:DefinedTerm
    186 N92d1f26379dd4693ac2831596af896be rdf:first sg:person.0772302366.11
    187 rdf:rest N49eb5f450b2d4391a4ecc1c4a2ac1740
    188 Na0b02ac85054465b8a90d4c705ee8579 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    189 schema:name Genotype
    190 rdf:type schema:DefinedTerm
    191 Nb881f8bd4b9b4ea7a985a6a67a5082f4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    192 schema:name Metagenome
    193 rdf:type schema:DefinedTerm
    194 Ncefb4b9d7ff34c70b090cd8cc1ad9982 rdf:first sg:person.01024545742.89
    195 rdf:rest N6c31a0ebd0bc4f90b64e3453476ebbca
    196 Nd0bf4a2f5ad541be8f5614c82235267c schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    197 schema:name Tissue Donors
    198 rdf:type schema:DefinedTerm
    199 Ndc2db4d762c24797b1292dfb1c75a3df schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    200 schema:name Genetic Variation
    201 rdf:type schema:DefinedTerm
    202 Ndead0f62689c404a95bf86fd838fe963 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    203 schema:name Sequence Analysis, DNA
    204 rdf:type schema:DefinedTerm
    205 Ne9e816ee4eba4650a2c4728b66c24e68 rdf:first sg:person.01146571421.48
    206 rdf:rest N1ac0068c537c493483f111b84fb45876
    207 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    208 schema:name Biological Sciences
    209 rdf:type schema:DefinedTerm
    210 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    211 schema:name Genetics
    212 rdf:type schema:DefinedTerm
    213 sg:grant.2439002 http://pending.schema.org/fundedItem sg:pub.10.1186/s13073-018-0515-8
    214 rdf:type schema:MonetaryGrant
    215 sg:grant.2699180 http://pending.schema.org/fundedItem sg:pub.10.1186/s13073-018-0515-8
    216 rdf:type schema:MonetaryGrant
    217 sg:grant.2699326 http://pending.schema.org/fundedItem sg:pub.10.1186/s13073-018-0515-8
    218 rdf:type schema:MonetaryGrant
    219 sg:grant.3806830 http://pending.schema.org/fundedItem sg:pub.10.1186/s13073-018-0515-8
    220 rdf:type schema:MonetaryGrant
    221 sg:journal.1040124 schema:issn 1756-994X
    222 schema:name Genome Medicine
    223 schema:publisher Springer Nature
    224 rdf:type schema:Periodical
    225 sg:person.01024545742.89 schema:affiliation grid-institutes:grid.66859.34
    226 schema:familyName Hall
    227 schema:givenName Andrew Brantley
    228 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01024545742.89
    229 rdf:type schema:Person
    230 sg:person.01146571421.48 schema:affiliation grid-institutes:grid.66859.34
    231 schema:familyName Stevens
    232 schema:givenName Christine
    233 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01146571421.48
    234 rdf:type schema:Person
    235 sg:person.011517303117.07 schema:affiliation grid-institutes:grid.32224.35
    236 schema:familyName Daly
    237 schema:givenName Mark J.
    238 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011517303117.07
    239 rdf:type schema:Person
    240 sg:person.01214462502.85 schema:affiliation grid-institutes:grid.66859.34
    241 schema:familyName Huttenhower
    242 schema:givenName Curtis
    243 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01214462502.85
    244 rdf:type schema:Person
    245 sg:person.01325533721.33 schema:affiliation grid-institutes:grid.66859.34
    246 schema:familyName Rahnavard
    247 schema:givenName Gholamali
    248 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01325533721.33
    249 rdf:type schema:Person
    250 sg:person.0654747534.44 schema:affiliation grid-institutes:grid.32224.35
    251 schema:familyName Kolde
    252 schema:givenName Raivo
    253 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0654747534.44
    254 rdf:type schema:Person
    255 sg:person.0717130066.82 schema:affiliation grid-institutes:grid.116068.8
    256 schema:familyName Xavier
    257 schema:givenName Ramnik J.
    258 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0717130066.82
    259 rdf:type schema:Person
    260 sg:person.0772302366.11 schema:affiliation grid-institutes:grid.66859.34
    261 schema:familyName Franzosa
    262 schema:givenName Eric A.
    263 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0772302366.11
    264 rdf:type schema:Person
    265 sg:person.0773476547.34 schema:affiliation grid-institutes:grid.66859.34
    266 schema:familyName Vlamakis
    267 schema:givenName Hera
    268 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0773476547.34
    269 rdf:type schema:Person
    270 sg:pub.10.1038/nature11209 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027248000
    271 https://doi.org/10.1038/nature11209
    272 rdf:type schema:CreativeWork
    273 sg:pub.10.1038/nature11234 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007740093
    274 https://doi.org/10.1038/nature11234
    275 rdf:type schema:CreativeWork
    276 sg:pub.10.1038/nature11582 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046541188
    277 https://doi.org/10.1038/nature11582
    278 rdf:type schema:CreativeWork
    279 sg:pub.10.1038/nature13178 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022430209
    280 https://doi.org/10.1038/nature13178
    281 rdf:type schema:CreativeWork
    282 sg:pub.10.1038/nature13786 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022632622
    283 https://doi.org/10.1038/nature13786
    284 rdf:type schema:CreativeWork
    285 sg:pub.10.1038/nature15393 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021812064
    286 https://doi.org/10.1038/nature15393
    287 rdf:type schema:CreativeWork
    288 sg:pub.10.1038/nature18927 schema:sameAs https://app.dimensions.ai/details/publication/pub.1026832225
    289 https://doi.org/10.1038/nature18927
    290 rdf:type schema:CreativeWork
    291 sg:pub.10.1038/nature23889 schema:sameAs https://app.dimensions.ai/details/publication/pub.1091863851
    292 https://doi.org/10.1038/nature23889
    293 rdf:type schema:CreativeWork
    294 sg:pub.10.1038/ng.2520 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008881446
    295 https://doi.org/10.1038/ng.2520
    296 rdf:type schema:CreativeWork
    297 sg:pub.10.1038/ng.2906 schema:sameAs https://app.dimensions.ai/details/publication/pub.1004737256
    298 https://doi.org/10.1038/ng.2906
    299 rdf:type schema:CreativeWork
    300 sg:pub.10.1038/ng.3021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030784697
    301 https://doi.org/10.1038/ng.3021
    302 rdf:type schema:CreativeWork
    303 sg:pub.10.1038/ng.3663 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018819579
    304 https://doi.org/10.1038/ng.3663
    305 rdf:type schema:CreativeWork
    306 sg:pub.10.1038/ng.3693 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002138629
    307 https://doi.org/10.1038/ng.3693
    308 rdf:type schema:CreativeWork
    309 sg:pub.10.1038/ng.694 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023718631
    310 https://doi.org/10.1038/ng.694
    311 rdf:type schema:CreativeWork
    312 sg:pub.10.1038/ng.873 schema:sameAs https://app.dimensions.ai/details/publication/pub.1041967517
    313 https://doi.org/10.1038/ng.873
    314 rdf:type schema:CreativeWork
    315 sg:pub.10.1038/ng826 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051591016
    316 https://doi.org/10.1038/ng826
    317 rdf:type schema:CreativeWork
    318 sg:pub.10.1038/nm.3914 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009083133
    319 https://doi.org/10.1038/nm.3914
    320 rdf:type schema:CreativeWork
    321 sg:pub.10.1038/nm.3933 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037606023
    322 https://doi.org/10.1038/nm.3933
    323 rdf:type schema:CreativeWork
    324 sg:pub.10.1038/nmeth.3589 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028162909
    325 https://doi.org/10.1038/nmeth.3589
    326 rdf:type schema:CreativeWork
    327 sg:pub.10.1186/1471-2164-15-257 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002664833
    328 https://doi.org/10.1186/1471-2164-15-257
    329 rdf:type schema:CreativeWork
    330 sg:pub.10.1186/gb-2014-15-7-r89 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022685985
    331 https://doi.org/10.1186/gb-2014-15-7-r89
    332 rdf:type schema:CreativeWork
    333 sg:pub.10.1186/s13059-014-0552-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024893270
    334 https://doi.org/10.1186/s13059-014-0552-6
    335 rdf:type schema:CreativeWork
    336 sg:pub.10.1186/s13059-015-0759-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017080966
    337 https://doi.org/10.1186/s13059-015-0759-1
    338 rdf:type schema:CreativeWork
    339 sg:pub.10.1186/s13073-014-0107-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006350078
    340 https://doi.org/10.1186/s13073-014-0107-1
    341 rdf:type schema:CreativeWork
    342 grid-institutes:grid.116068.8 schema:alternateName Center for Microbiome Informatics & Therapeutics, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA
    343 schema:name Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge St, 02114, Boston, MA, USA
    344 Center for Microbiome Informatics & Therapeutics, Massachusetts Institute of Technology, 02139, Cambridge, MA, USA
    345 The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA
    346 rdf:type schema:Organization
    347 grid-institutes:grid.32224.35 schema:alternateName Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge St, 02114, Boston, MA, USA
    348 Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge St, 02114, Boston, MA, USA
    349 schema:name Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge St, 02114, Boston, MA, USA
    350 Center for Human Genetic Research, Massachusetts General Hospital, 185 Cambridge St, 02114, Boston, MA, USA
    351 The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA
    352 rdf:type schema:Organization
    353 grid-institutes:grid.66859.34 schema:alternateName The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA
    354 schema:name Department of Biostatistics, Harvard T. H. Chan School of Public Health, 655 Huntington Ave, 02115, Boston, MA, USA
    355 The Broad Institute of MIT and Harvard, 415 Main St, 02142, Cambridge, MA, USA
    356 rdf:type schema:Organization
     




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


    ...