Ontology type: schema:ScholarlyArticle Open Access: True
2019-10-08
AUTHORSKatherine R. Amato, Elizabeth K. Mallott, Daniel McDonald, Nathaniel J. Dominy, Tony Goldberg, Joanna E. Lambert, Larissa Swedell, Jessica L. Metcalf, Andres Gomez, Gillian A. O. Britton, Rebecca M. Stumpf, Steven R. Leigh, Rob Knight
ABSTRACTBackgroundComparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, non-human primates.ResultsContrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates.ConclusionsGiven similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health. More... »
PAGES201
http://scigraph.springernature.com/pub.10.1186/s13059-019-1807-z
DOIhttp://dx.doi.org/10.1186/s13059-019-1807-z
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1121557479
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/31590679
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/2008/0602",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Ecology",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Animals",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Cercopithecidae",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Diet",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Ecosystem",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Gastrointestinal Microbiome",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Hominidae",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Humans",
"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 of Anthropology, Northwestern University, 1810 Hinman Ave, 60208, Evanston, IL, USA",
"id": "http://www.grid.ac/institutes/grid.16753.36",
"name": [
"Department of Anthropology, Northwestern University, 1810 Hinman Ave, 60208, Evanston, IL, USA"
],
"type": "Organization"
},
"familyName": "Amato",
"givenName": "Katherine R.",
"id": "sg:person.0723021112.57",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0723021112.57"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Anthropology, Northwestern University, 1810 Hinman Ave, 60208, Evanston, IL, USA",
"id": "http://www.grid.ac/institutes/grid.16753.36",
"name": [
"Department of Anthropology, Northwestern University, 1810 Hinman Ave, 60208, Evanston, IL, USA"
],
"type": "Organization"
},
"familyName": "Mallott",
"givenName": "Elizabeth K.",
"id": "sg:person.0747535432.57",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0747535432.57"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Center for Microbiome Innovation, University of California San Diego, 92093, San Diego, USA",
"id": "http://www.grid.ac/institutes/grid.266100.3",
"name": [
"Department of Pediatrics, University of California San Diego, 92093, San Diego, USA",
"Center for Microbiome Innovation, University of California San Diego, 92093, San Diego, USA"
],
"type": "Organization"
},
"familyName": "McDonald",
"givenName": "Daniel",
"id": "sg:person.01324411177.44",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01324411177.44"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Anthropology, Dartmouth College, 03755, Hanover, USA",
"id": "http://www.grid.ac/institutes/grid.254880.3",
"name": [
"Department of Anthropology, Dartmouth College, 03755, Hanover, USA"
],
"type": "Organization"
},
"familyName": "Dominy",
"givenName": "Nathaniel J.",
"id": "sg:person.01012617262.86",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01012617262.86"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Pathobiological Sciences, University of Wisconsin-Madison, 53706, Madison, USA",
"id": "http://www.grid.ac/institutes/grid.14003.36",
"name": [
"Department of Pathobiological Sciences, University of Wisconsin-Madison, 53706, Madison, USA"
],
"type": "Organization"
},
"familyName": "Goldberg",
"givenName": "Tony",
"id": "sg:person.0604015544.19",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0604015544.19"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 80302, Boulder, USA",
"id": "http://www.grid.ac/institutes/grid.266190.a",
"name": [
"Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 80302, Boulder, USA"
],
"type": "Organization"
},
"familyName": "Lambert",
"givenName": "Joanna E.",
"id": "sg:person.0575677024.57",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0575677024.57"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Anthropology, City University of New York - Queens College, 11367, New York, USA",
"id": "http://www.grid.ac/institutes/grid.262273.0",
"name": [
"Department of Anthropology, City University of New York - Queens College, 11367, New York, USA"
],
"type": "Organization"
},
"familyName": "Swedell",
"givenName": "Larissa",
"id": "sg:person.01131120547.21",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01131120547.21"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Animal Sciences, Colorado State University, 80521, Fort Collins, USA",
"id": "http://www.grid.ac/institutes/grid.47894.36",
"name": [
"Department of Animal Sciences, Colorado State University, 80521, Fort Collins, USA"
],
"type": "Organization"
},
"familyName": "Metcalf",
"givenName": "Jessica L.",
"id": "sg:person.01233467326.58",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01233467326.58"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Animal Sciences, University of Minnesota, 55108, Minneapolis, USA",
"id": "http://www.grid.ac/institutes/grid.17635.36",
"name": [
"Department of Animal Sciences, University of Minnesota, 55108, Minneapolis, USA"
],
"type": "Organization"
},
"familyName": "Gomez",
"givenName": "Andres",
"id": "sg:person.01140437057.17",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01140437057.17"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Anthropology, Dartmouth College, 03755, Hanover, USA",
"id": "http://www.grid.ac/institutes/grid.254880.3",
"name": [
"Department of Anthropology, Dartmouth College, 03755, Hanover, USA"
],
"type": "Organization"
},
"familyName": "Britton",
"givenName": "Gillian A. O.",
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Anthropology, University of Illinois at Urbana-Champaign, 61801, Urbana, USA",
"id": "http://www.grid.ac/institutes/grid.35403.31",
"name": [
"Department of Anthropology, University of Illinois at Urbana-Champaign, 61801, Urbana, USA"
],
"type": "Organization"
},
"familyName": "Stumpf",
"givenName": "Rebecca M.",
"id": "sg:person.0725555417.03",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0725555417.03"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Anthropology, University of Colorado Boulder, 80302, Boulder, USA",
"id": "http://www.grid.ac/institutes/grid.266190.a",
"name": [
"Department of Anthropology, University of Colorado Boulder, 80302, Boulder, USA"
],
"type": "Organization"
},
"familyName": "Leigh",
"givenName": "Steven R.",
"id": "sg:person.01363372516.76",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01363372516.76"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Bioengineering, University of California San Diego, 92093, San Diego, USA",
"id": "http://www.grid.ac/institutes/grid.266100.3",
"name": [
"Department of Pediatrics, University of California San Diego, 92093, San Diego, USA",
"Center for Microbiome Innovation, University of California San Diego, 92093, San Diego, USA",
"Department of Computer Science and Engineering, University of California San Diego, 92093, San Diego, USA",
"Department of Bioengineering, University of California San Diego, 92093, San Diego, USA"
],
"type": "Organization"
},
"familyName": "Knight",
"givenName": "Rob",
"id": "sg:person.016311745377.96",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.016311745377.96"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1038/s41592-018-0141-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1107129414",
"https://doi.org/10.1038/s41592-018-0141-9"
],
"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.10.1007/s10764-008-9261-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1033573260",
"https://doi.org/10.1007/s10764-008-9261-x"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncomms2159",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001016378",
"https://doi.org/10.1038/ncomms2159"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ismej.2011.139",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051863807",
"https://doi.org/10.1038/ismej.2011.139"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s10764-012-9600-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1039476873",
"https://doi.org/10.1007/s10764-012-9600-9"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncomms14319",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1083860051",
"https://doi.org/10.1038/ncomms14319"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41597-019-0059-9",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1114144844",
"https://doi.org/10.1038/s41597-019-0059-9"
],
"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.10.1038/s41396-018-0175-0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1105492274",
"https://doi.org/10.1038/s41396-018-0175-0"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/bf02381415",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1010678178",
"https://doi.org/10.1007/bf02381415"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/scientificamerican0661-62",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1056556217",
"https://doi.org/10.1038/scientificamerican0661-62"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41467-019-09884-6",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1114225754",
"https://doi.org/10.1038/s41467-019-09884-6"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/bf02739365",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049651817",
"https://doi.org/10.1007/bf02739365"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/gb-2011-12-6-r60",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1000243423",
"https://doi.org/10.1186/gb-2011-12-6-r60"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature17654",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049400456",
"https://doi.org/10.1038/nature17654"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1016/j.mambio.2007.05.005",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1034330807",
"https://doi.org/10.1016/j.mambio.2007.05.005"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncomms4654",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1000325507",
"https://doi.org/10.1038/ncomms4654"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s12915-017-0454-7",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1100078029",
"https://doi.org/10.1186/s12915-017-0454-7"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1023/a:1021166502098",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1000494561",
"https://doi.org/10.1023/a:1021166502098"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncomms7505",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1046556597",
"https://doi.org/10.1038/ncomms7505"
],
"type": "CreativeWork"
}
],
"datePublished": "2019-10-08",
"datePublishedReg": "2019-10-08",
"description": "BackgroundComparative data from non-human primates provide insight into the processes that shaped the evolution of the human gut microbiome and highlight microbiome traits that differentiate humans from other primates. Here, in an effort to improve our understanding of the human microbiome, we compare gut microbiome composition and functional potential in 14 populations of humans from ten nations and 18 species of wild, non-human primates.ResultsContrary to expectations from host phylogenetics, we find that human gut microbiome composition and functional potential are more similar to those of cercopithecines, a subfamily of Old World monkey, particularly baboons, than to those of African apes. Additionally, our data reveal more inter-individual variation in gut microbiome functional potential within the human species than across other primate species, suggesting that the human gut microbiome may exhibit more plasticity in response to environmental variation compared to that of other primates.ConclusionsGiven similarities of ancestral human habitats and dietary strategies to those of baboons, these findings suggest that convergent ecologies shaped the gut microbiomes of both humans and cercopithecines, perhaps through environmental exposure to microbes, diet, and/or associated physiological adaptations. Increased inter-individual variation in the human microbiome may be associated with human dietary diversity or the ability of humans to inhabit novel environments. Overall, these findings show that diet, ecology, and physiological adaptations are more important than host-microbe co-diversification in shaping the human microbiome, providing a key foundation for comparative analyses of the role of the microbiome in human biology and health.",
"genre": "article",
"id": "sg:pub.10.1186/s13059-019-1807-z",
"inLanguage": "en",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.6540456",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.3106413",
"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": "20"
}
],
"keywords": [
"human gut microbiome",
"functional potential",
"human microbiome",
"physiological adaptations",
"gut microbiome",
"microbiome composition",
"inter-individual variation",
"gut microbiome composition",
"Old World monkeys",
"human gut microbiome composition",
"environmental variation",
"microbiome traits",
"populations of humans",
"more plasticity",
"human biology",
"primate species",
"ecology",
"World monkeys",
"microbiome",
"species",
"African apes",
"novel environment",
"non-human primates",
"cercopithecines",
"human species",
"human habitats",
"primates",
"phylogenetics",
"phylogeny",
"habitats",
"subfamilies",
"humans",
"adaptation",
"microbes",
"biology",
"traits",
"human ecology",
"diversity",
"comparative analysis",
"convergence of human",
"plasticity",
"variation",
"apes",
"dietary strategies",
"environmental exposures",
"composition",
"dietary diversity",
"similarity",
"baboons",
"diet",
"ResultsContrary",
"evolution",
"insights",
"potential",
"role",
"population",
"understanding",
"response",
"key foundation",
"ability",
"findings",
"importance",
"environment",
"exposure",
"data",
"analysis",
"monkeys",
"process",
"strategies",
"ability of humans",
"efforts",
"health",
"foundation",
"expectations",
"convergence",
"nations"
],
"name": "Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny",
"pagination": "201",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1121557479"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/s13059-019-1807-z"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"31590679"
]
}
],
"sameAs": [
"https://doi.org/10.1186/s13059-019-1807-z",
"https://app.dimensions.ai/details/publication/pub.1121557479"
],
"sdDataset": "articles",
"sdDatePublished": "2022-05-10T10:22",
"sdLicense": "https://scigraph.springernature.com/explorer/license/",
"sdPublisher": {
"name": "Springer Nature - SN SciGraph project",
"type": "Organization"
},
"sdSource": "s3://com-springernature-scigraph/baseset/20220509/entities/gbq_results/article/article_829.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1186/s13059-019-1807-z"
}
]
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/s13059-019-1807-z'
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/s13059-019-1807-z'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s13059-019-1807-z'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s13059-019-1807-z'
This table displays all metadata directly associated to this object as RDF triples.
375 TRIPLES
22 PREDICATES
132 URIs
103 LITERALS
16 BLANK NODES