Ontology type: schema:ScholarlyArticle Open Access: True
2015-09-15
AUTHORSRan Blekhman, Julia K. Goodrich, Katherine Huang, Qi Sun, Robert Bukowski, Jordana T. Bell, Timothy D. Spector, Alon Keinan, Ruth E. Ley, Dirk Gevers, Andrew G. Clark
ABSTRACTBackgroundThe composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. This study is part of an expanding effort to comprehensively profile the interactions between human genetic variation and the composition of this microbial ecosystem on a genome- and microbiome-wide scale.ResultsHere, we jointly analyze the composition of the human microbiome and host genetic variation. By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, we gathered information on host genetic variation for 93 individuals for whom bacterial abundance data are also available. Using this dataset, we identify significant associations between host genetic variation and microbiome composition in 10 of the 15 body sites tested. These associations are driven by host genetic variation in immunity-related pathways, and are especially enriched in host genes that have been previously associated with microbiome-related complex diseases, such as inflammatory bowel disease and obesity-related disorders. Lastly, we show that host genomic regions associated with the microbiome have high levels of genetic differentiation among human populations, possibly indicating host genomic adaptation to environment-specific microbiomes.ConclusionsOur results highlight the role of host genetic variation in shaping the composition of the human microbiome, and provide a starting point toward understanding the complex interaction between human genetics and the microbiome in the context of human evolution and disease. More... »
PAGES191
http://scigraph.springernature.com/pub.10.1186/s13059-015-0759-1
DOIhttp://dx.doi.org/10.1186/s13059-015-0759-1
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1017080966
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/26374288
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"
},
{
"id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0605",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Microbiology",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Bacteria",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genetic Variation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Genome, Human",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Humans",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Metagenomics",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Microbiota",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "Department of Ecology, Evolution, and Behavior, University of Minnesota, 55108, St. Paul, MN, USA",
"id": "http://www.grid.ac/institutes/grid.17635.36",
"name": [
"Department of Genetics, Cell Biology, and Development, University of Minnesota, 55455, Minneapolis, MN, USA",
"Department of Ecology, Evolution, and Behavior, University of Minnesota, 55108, St. Paul, MN, USA"
],
"type": "Organization"
},
"familyName": "Blekhman",
"givenName": "Ran",
"id": "sg:person.01342212257.50",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01342212257.50"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Microbiology, Cornell University, 14853, Ithaca, NY, USA",
"id": "http://www.grid.ac/institutes/grid.5386.8",
"name": [
"Department of Molecular Biology and Genetics, Cornell University, 14853, Ithaca, NY, USA",
"Department of Microbiology, Cornell University, 14853, Ithaca, NY, USA"
],
"type": "Organization"
},
"familyName": "Goodrich",
"givenName": "Julia K.",
"id": "sg:person.0734677126.50",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0734677126.50"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA",
"id": "http://www.grid.ac/institutes/grid.66859.34",
"name": [
"Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA"
],
"type": "Organization"
},
"familyName": "Huang",
"givenName": "Katherine",
"id": "sg:person.01133240553.94",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01133240553.94"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, 14853, Ithaca, NY, USA",
"id": "http://www.grid.ac/institutes/grid.5386.8",
"name": [
"BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, 14853, Ithaca, NY, USA"
],
"type": "Organization"
},
"familyName": "Sun",
"givenName": "Qi",
"id": "sg:person.01343731362.79",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01343731362.79"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, 14853, Ithaca, NY, USA",
"id": "http://www.grid.ac/institutes/grid.5386.8",
"name": [
"BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, 14853, Ithaca, NY, USA"
],
"type": "Organization"
},
"familyName": "Bukowski",
"givenName": "Robert",
"id": "sg:person.0777421022.06",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0777421022.06"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Twin Research & Genetic Epidemiology, King\u2019s College, London, UK",
"id": "http://www.grid.ac/institutes/grid.13097.3c",
"name": [
"Department of Twin Research & Genetic Epidemiology, King\u2019s College, London, UK"
],
"type": "Organization"
},
"familyName": "Bell",
"givenName": "Jordana T.",
"id": "sg:person.012420471572.13",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012420471572.13"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Twin Research & Genetic Epidemiology, King\u2019s College, London, UK",
"id": "http://www.grid.ac/institutes/grid.13097.3c",
"name": [
"Department of Twin Research & Genetic Epidemiology, King\u2019s College, London, UK"
],
"type": "Organization"
},
"familyName": "Spector",
"givenName": "Timothy D.",
"id": "sg:person.015324146274.09",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015324146274.09"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Biological Statistics and Computational Biology, Cornell University, 14853, Ithaca, NY, USA",
"id": "http://www.grid.ac/institutes/grid.5386.8",
"name": [
"Department of Biological Statistics and Computational Biology, Cornell University, 14853, Ithaca, NY, USA"
],
"type": "Organization"
},
"familyName": "Keinan",
"givenName": "Alon",
"id": "sg:person.01066503340.60",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01066503340.60"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Microbiology, Cornell University, 14853, Ithaca, NY, USA",
"id": "http://www.grid.ac/institutes/grid.5386.8",
"name": [
"Department of Molecular Biology and Genetics, Cornell University, 14853, Ithaca, NY, USA",
"Department of Microbiology, Cornell University, 14853, Ithaca, NY, USA"
],
"type": "Organization"
},
"familyName": "Ley",
"givenName": "Ruth E.",
"id": "sg:person.0725775131.01",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0725775131.01"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Current address: Janssen Human Microbiome Institute, Janssen Research and Development, 02142, Cambridge, MA, USA",
"id": "http://www.grid.ac/institutes/None",
"name": [
"Broad Institute of MIT and Harvard, 02142, Cambridge, MA, USA",
"Current address: Janssen Human Microbiome Institute, Janssen Research and Development, 02142, Cambridge, MA, USA"
],
"type": "Organization"
},
"familyName": "Gevers",
"givenName": "Dirk",
"id": "sg:person.01123602703.16",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01123602703.16"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Molecular Biology and Genetics, Cornell University, 14853, Ithaca, NY, USA",
"id": "http://www.grid.ac/institutes/grid.5386.8",
"name": [
"Department of Molecular Biology and Genetics, Cornell University, 14853, Ithaca, NY, USA"
],
"type": "Organization"
},
"familyName": "Clark",
"givenName": "Andrew G.",
"id": "sg:person.01072105370.02",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01072105370.02"
],
"type": "Person"
}
],
"citation": [
{
"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/ng.806",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1010244476",
"https://doi.org/10.1038/ng.806"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature11632",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1000661742",
"https://doi.org/10.1038/nature11632"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature07336",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1020900000",
"https://doi.org/10.1038/nature07336"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ismej.2014.64",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1039762239",
"https://doi.org/10.1038/ismej.2014.64"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ni.1825",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022884317",
"https://doi.org/10.1038/ni.1825"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature10809",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1022220176",
"https://doi.org/10.1038/nature10809"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nri1350",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033571944",
"https://doi.org/10.1038/nri1350"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature11450",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004546178",
"https://doi.org/10.1038/nature11450"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature11053",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1052378845",
"https://doi.org/10.1038/nature11053"
],
"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/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.10.1038/ng1946",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1014224859",
"https://doi.org/10.1038/ng1946"
],
"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/nature07540",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1030170002",
"https://doi.org/10.1038/nature07540"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature10209",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011250403",
"https://doi.org/10.1038/nature10209"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature09534",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1010608717",
"https://doi.org/10.1038/nature09534"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nrmicro2540",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1045931365",
"https://doi.org/10.1038/nrmicro2540"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature12506",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003823032",
"https://doi.org/10.1038/nature12506"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng.2653",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1032444369",
"https://doi.org/10.1038/ng.2653"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmeth.f.303",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1009032055",
"https://doi.org/10.1038/nmeth.f.303"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature12820",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1013830289",
"https://doi.org/10.1038/nature12820"
],
"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/nature11209",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1027248000",
"https://doi.org/10.1038/nature11209"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gm228",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029672269",
"https://doi.org/10.1186/gm228"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature05414",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023893418",
"https://doi.org/10.1038/nature05414"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2012-13-9-r79",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1029450096",
"https://doi.org/10.1186/gb-2012-13-9-r79"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ng786",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041343500",
"https://doi.org/10.1038/ng786"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nri3421",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1018641520",
"https://doi.org/10.1038/nri3421"
],
"type": "CreativeWork"
}
],
"datePublished": "2015-09-15",
"datePublishedReg": "2015-09-15",
"description": "BackgroundThe composition of bacteria in and on the human body varies widely across human individuals, and has been associated with multiple health conditions. While microbial communities are influenced by environmental factors, some degree of genetic influence of the host on the microbiome is also expected. This study is part of an expanding effort to comprehensively profile the interactions between human genetic variation and the composition of this microbial ecosystem on a genome- and microbiome-wide scale.ResultsHere, we jointly analyze the composition of the human microbiome and host genetic variation. By mining the shotgun metagenomic data from the Human Microbiome Project for host DNA reads, we gathered information on host genetic variation for 93 individuals for whom bacterial abundance data are also available. Using this dataset, we identify significant associations between host genetic variation and microbiome composition in 10 of the 15 body sites tested. These associations are driven by host genetic variation in immunity-related pathways, and are especially enriched in host genes that have been previously associated with microbiome-related complex diseases, such as inflammatory bowel disease and obesity-related disorders. Lastly, we show that host genomic regions associated with the microbiome have high levels of genetic differentiation among human populations, possibly indicating host genomic adaptation to environment-specific microbiomes.ConclusionsOur results highlight the role of host genetic variation in shaping the composition of the human microbiome, and provide a starting point toward understanding the complex interaction between human genetics and the microbiome in the context of human evolution and disease.",
"genre": "article",
"id": "sg:pub.10.1186/s13059-015-0759-1",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.2683802",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2500517",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2529470",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.2699346",
"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": "16"
}
],
"keywords": [
"host genetic variation",
"genetic variation",
"bacterial abundance data",
"host genomic regions",
"human microbiome",
"human genetic variation",
"shotgun metagenomic data",
"composition of bacteria",
"microbiome composition",
"immunity-related pathways",
"Human Microbiome Project",
"human body sites",
"genetic differentiation",
"genomic adaptation",
"genomic regions",
"microbial communities",
"microbial ecosystem",
"host genes",
"metagenomic data",
"Microbiome Project",
"DNA reads",
"abundance data",
"human genetics",
"human evolution",
"complex diseases",
"microbiome",
"human population",
"environmental factors",
"genetic influences",
"complex interactions",
"genome",
"genes",
"human individuals",
"genetics",
"obesity-related disorders",
"ecosystems",
"ConclusionsOur results",
"reads",
"bacteria",
"sites",
"differentiation",
"pathway",
"variation",
"high levels",
"host",
"composition",
"body sites",
"interaction",
"ResultsHere",
"adaptation",
"evolution",
"role",
"disease",
"population",
"community",
"individuals",
"region",
"association",
"starting point",
"human body",
"levels",
"significant association",
"factors",
"body",
"data",
"inflammatory bowel disease",
"conditions",
"part",
"dataset",
"study",
"efforts",
"disorders",
"bowel disease",
"information",
"results",
"degree",
"context",
"scale",
"influence",
"point",
"multiple health conditions",
"project",
"health conditions"
],
"name": "Host genetic variation impacts microbiome composition across human body sites",
"pagination": "191",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1017080966"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/s13059-015-0759-1"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"26374288"
]
}
],
"sameAs": [
"https://doi.org/10.1186/s13059-015-0759-1",
"https://app.dimensions.ai/details/publication/pub.1017080966"
],
"sdDataset": "articles",
"sdDatePublished": "2022-08-04T17:04",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220804/entities/gbq_results/article/article_670.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1186/s13059-015-0759-1"
}
]
Download the RDF metadata as: json-ld nt turtle xml License info
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/s13059-015-0759-1'
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/s13059-015-0759-1'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-015-0759-1'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-015-0759-1'
This table displays all metadata directly associated to this object as RDF triples.
386 TRIPLES
21 PREDICATES
144 URIs
106 LITERALS
13 BLANK NODES