Ontology type: schema:ScholarlyArticle Open Access: True
2019-06-25
AUTHORSMichelle Wille, Mang Shi, Marcel Klaassen, Aeron C. Hurt, Edward C. Holmes
ABSTRACTModels of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae and Reoviridae), single-stranded RNA viruses (Astroviridae, Caliciviridae, Picornaviridae), a retro-transcribing DNA virus (Hepadnaviridae), and a single-stranded DNA virus (Parvoviridae). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity (host sharing) and heterogeneity (host specificity). Virome connectivity was apparent in two well described multi-host virus species -avian coronavirus and influenza A virus- and a novel Rotavirus species that were shared among some Anseriform species, while virome heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes, as well as differences in viral abundance and alpha diversity among species. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations. More... »
PAGES2603-2616
http://scigraph.springernature.com/pub.10.1038/s41396-019-0458-0
DOIhttp://dx.doi.org/10.1038/s41396-019-0458-0
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1117494070
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/31239538
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/2008/05",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Environmental Sciences",
"type": "DefinedTerm"
},
{
"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/2008/10",
"inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/",
"name": "Technology",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Animals",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Animals, Wild",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Anseriformes",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Biodiversity",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Charadriiformes",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Phylogeny",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Viruses",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia",
"id": "http://www.grid.ac/institutes/grid.483778.7",
"name": [
"WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia"
],
"type": "Organization"
},
"familyName": "Wille",
"givenName": "Michelle",
"id": "sg:person.01307112017.28",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01307112017.28"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia",
"id": "http://www.grid.ac/institutes/grid.1013.3",
"name": [
"Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia"
],
"type": "Organization"
},
"familyName": "Shi",
"givenName": "Mang",
"id": "sg:person.0636064674.00",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0636064674.00"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Centre for Integrative Ecology, Deakin University, Geelong, Australia",
"id": "http://www.grid.ac/institutes/grid.1021.2",
"name": [
"Centre for Integrative Ecology, Deakin University, Geelong, Australia"
],
"type": "Organization"
},
"familyName": "Klaassen",
"givenName": "Marcel",
"id": "sg:person.01050036006.44",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050036006.44"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia",
"id": "http://www.grid.ac/institutes/grid.483778.7",
"name": [
"WHO Collaborating Centre for Reference and Research on Influenza, at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia"
],
"type": "Organization"
},
"familyName": "Hurt",
"givenName": "Aeron C.",
"id": "sg:person.0603570064.56",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0603570064.56"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia",
"id": "http://www.grid.ac/institutes/grid.1013.3",
"name": [
"Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, Australia"
],
"type": "Organization"
},
"familyName": "Holmes",
"givenName": "Edward C.",
"id": "sg:person.012501436222.04",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012501436222.04"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1007/bf00038690",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044980959",
"https://doi.org/10.1007/bf00038690"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/srep36839",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1025847778",
"https://doi.org/10.1038/srep36839"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13567-016-0308-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1026589054",
"https://doi.org/10.1186/s13567-016-0308-2"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13059-014-0550-8",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1015222646",
"https://doi.org/10.1186/s13059-014-0550-8"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature20167",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024156938",
"https://doi.org/10.1038/nature20167"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s10393-017-1305-2",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1103682987",
"https://doi.org/10.1007/s10393-017-1305-2"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41586-018-0012-7",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1101862110",
"https://doi.org/10.1038/s41586-018-0012-7"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41598-018-24407-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1103249578",
"https://doi.org/10.1038/s41598-018-24407-x"
],
"type": "CreativeWork"
}
],
"datePublished": "2019-06-25",
"datePublishedReg": "2019-06-25",
"description": "Models of host-microbe dynamics typically assume a single-host population infected by a single pathogen. In reality, many hosts form multi-species aggregations and may be infected with an assemblage of pathogens. We used a meta-transcriptomic approach to characterize the viromes of nine avian species in the Anseriformes (ducks) and Charadriiformes (shorebirds). This revealed the presence of 27 viral species, of which 24 were novel, including double-stranded RNA viruses (Picobirnaviridae and Reoviridae), single-stranded RNA viruses (Astroviridae, Caliciviridae, Picornaviridae), a retro-transcribing DNA virus (Hepadnaviridae), and a single-stranded DNA virus (Parvoviridae). These viruses comprise multi-host generalist viruses and those that are host-specific, indicative of both virome connectivity (host sharing) and heterogeneity (host specificity). Virome connectivity was apparent in two well described multi-host virus species -avian coronavirus and influenza A virus- and a novel Rotavirus species that were shared among some Anseriform species, while virome heterogeneity was reflected in the absence of viruses shared between Anseriformes and Charadriiformes, as well as differences in viral abundance and alpha diversity among species. Overall, we demonstrate complex virome structures across host species that co-exist in multi-species aggregations.",
"genre": "article",
"id": "sg:pub.10.1038/s41396-019-0458-0",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.6809668",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.3565107",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.5128927",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1038436",
"issn": [
"1751-7362",
"1751-7370"
],
"name": "The ISME Journal: Multidisciplinary Journal of Microbial Ecology",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "10",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "13"
}
],
"keywords": [
"multi-species aggregations",
"DNA viruses",
"RNA viruses",
"host-microbe dynamics",
"meta-transcriptomic approach",
"double-stranded RNA virus",
"single host population",
"generalist viruses",
"virome structure",
"host species",
"anseriform species",
"shorebird communities",
"viral abundance",
"alpha diversity",
"avian species",
"viral species",
"rotavirus species",
"species",
"Charadriiformes",
"Anseriformes",
"absence of virus",
"pathogens",
"virus",
"virome",
"single pathogen",
"diversity",
"abundance",
"aggregation",
"assemblages",
"host",
"heterogeneity",
"population",
"community",
"connectivity",
"absence",
"dynamics",
"presence",
"structure",
"coronavirus",
"influenza",
"differences",
"approach",
"model",
"reality"
],
"name": "Virome heterogeneity and connectivity in waterfowl and shorebird communities",
"pagination": "2603-2616",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1117494070"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/s41396-019-0458-0"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"31239538"
]
}
],
"sameAs": [
"https://doi.org/10.1038/s41396-019-0458-0",
"https://app.dimensions.ai/details/publication/pub.1117494070"
],
"sdDataset": "articles",
"sdDatePublished": "2022-08-04T17:09",
"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_829.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1038/s41396-019-0458-0"
}
]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.10.1038/s41396-019-0458-0'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41396-019-0458-0'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41396-019-0458-0'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41396-019-0458-0'
This table displays all metadata directly associated to this object as RDF triples.
209 TRIPLES
21 PREDICATES
85 URIs
68 LITERALS
14 BLANK NODES