Ontology type: schema:ScholarlyArticle Open Access: True
2021-08-18
AUTHORSAndrey N. Shkoporov, Ekaterina V. Khokhlova, Niamh Stephens, Cara Hueston, Samuel Seymour, Andrew J. Hryckowian, Dimitri Scholz, R. Paul Ross, Colin Hill
ABSTRACTBackgroundThe crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of lysogeny, these viruses demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals.ResultsHere we show that rapid phase variation of alternate capsular polysaccharides in Bacteroides intestinalis cultures plays an important role in a dynamic equilibrium between phage sensitivity and resistance, allowing phage and bacteria to multiply in parallel. The data also suggests the role of a concomitant phage persistence mechanism associated with delayed lysis of infected cells, similar to carrier state infection. From an ecological and evolutionary standpoint, this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other “benign” forms of phage infection when the host is stably present at high abundance.ConclusionLong-term persistence of bacteriophage and host could result from mutually beneficial mechanisms driving bacterial strain-level diversity and phage survival in complex environments. More... »
PAGES163
http://scigraph.springernature.com/pub.10.1186/s12915-021-01084-3
DOIhttp://dx.doi.org/10.1186/s12915-021-01084-3
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1140504065
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/34407825
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"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Bacteria",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Bacteriophages",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Bacteroides",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Humans",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Phase Variation",
"type": "DefinedTerm"
},
{
"inDefinedTermSet": "https://www.nlm.nih.gov/mesh/",
"name": "Phylogeny",
"type": "DefinedTerm"
}
],
"author": [
{
"affiliation": {
"alternateName": "APC Microbiome Ireland, University College Cork, Cork, Ireland",
"id": "http://www.grid.ac/institutes/grid.7872.a",
"name": [
"School of Microbiology, University College Cork, Cork, Ireland",
"APC Microbiome Ireland, University College Cork, Cork, Ireland"
],
"type": "Organization"
},
"familyName": "Shkoporov",
"givenName": "Andrey N.",
"id": "sg:person.013632227706.97",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013632227706.97"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "APC Microbiome Ireland, University College Cork, Cork, Ireland",
"id": "http://www.grid.ac/institutes/grid.7872.a",
"name": [
"APC Microbiome Ireland, University College Cork, Cork, Ireland"
],
"type": "Organization"
},
"familyName": "Khokhlova",
"givenName": "Ekaterina V.",
"id": "sg:person.01212614703.32",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01212614703.32"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland",
"id": "http://www.grid.ac/institutes/grid.7886.1",
"name": [
"Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland"
],
"type": "Organization"
},
"familyName": "Stephens",
"givenName": "Niamh",
"id": "sg:person.01171306757.11",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01171306757.11"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "APC Microbiome Ireland, University College Cork, Cork, Ireland",
"id": "http://www.grid.ac/institutes/grid.7872.a",
"name": [
"APC Microbiome Ireland, University College Cork, Cork, Ireland"
],
"type": "Organization"
},
"familyName": "Hueston",
"givenName": "Cara",
"id": "sg:person.01273212110.97",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01273212110.97"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "APC Microbiome Ireland, University College Cork, Cork, Ireland",
"id": "http://www.grid.ac/institutes/grid.7872.a",
"name": [
"APC Microbiome Ireland, University College Cork, Cork, Ireland"
],
"type": "Organization"
},
"familyName": "Seymour",
"givenName": "Samuel",
"id": "sg:person.011433532475.66",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011433532475.66"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, USA",
"id": "http://www.grid.ac/institutes/grid.14003.36",
"name": [
"Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA",
"Department of Medical Microbiology & Immunology, University of Wisconsin School of Medicine and Public Health, Madison, USA"
],
"type": "Organization"
},
"familyName": "Hryckowian",
"givenName": "Andrew J.",
"id": "sg:person.0647750436.00",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0647750436.00"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland",
"id": "http://www.grid.ac/institutes/grid.7886.1",
"name": [
"Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland"
],
"type": "Organization"
},
"familyName": "Scholz",
"givenName": "Dimitri",
"id": "sg:person.013026473475.88",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.013026473475.88"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "APC Microbiome Ireland, University College Cork, Cork, Ireland",
"id": "http://www.grid.ac/institutes/grid.7872.a",
"name": [
"School of Microbiology, University College Cork, Cork, Ireland",
"APC Microbiome Ireland, University College Cork, Cork, Ireland"
],
"type": "Organization"
},
"familyName": "Ross",
"givenName": "R. Paul",
"id": "sg:person.014605670062.43",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014605670062.43"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "APC Microbiome Ireland, University College Cork, Cork, Ireland",
"id": "http://www.grid.ac/institutes/grid.7872.a",
"name": [
"School of Microbiology, University College Cork, Cork, Ireland",
"APC Microbiome Ireland, University College Cork, Cork, Ireland"
],
"type": "Organization"
},
"familyName": "Hill",
"givenName": "Colin",
"id": "sg:person.01202224511.99",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01202224511.99"
],
"type": "Person"
}
],
"citation": [
{
"id": "sg:pub.10.1038/s41564-019-0494-6",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1117827489",
"https://doi.org/10.1038/s41564-019-0494-6"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s40168-021-01036-7",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1137149789",
"https://doi.org/10.1186/s40168-021-01036-7"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature17193",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042855631",
"https://doi.org/10.1038/nature17193"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41564-020-0746-5",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1128827018",
"https://doi.org/10.1038/s41564-020-0746-5"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2334-14-22",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038103506",
"https://doi.org/10.1186/1471-2334-14-22"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/npjbiofilms.2016.10",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047129282",
"https://doi.org/10.1038/npjbiofilms.2016.10"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41467-018-07225-7",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1109832832",
"https://doi.org/10.1038/s41467-018-07225-7"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41467-019-14103-3",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1124097608",
"https://doi.org/10.1038/s41467-019-14103-3"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41564-017-0096-0",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1100351856",
"https://doi.org/10.1038/s41564-017-0096-0"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s00018-016-2242-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1027167248",
"https://doi.org/10.1007/s00018-016-2242-x"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature09944",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1026204536",
"https://doi.org/10.1038/nature09944"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41586-020-2921-5",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1132678305",
"https://doi.org/10.1038/s41586-020-2921-5"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nature09199",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031776599",
"https://doi.org/10.1038/nature09199"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s40168-018-0598-x",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1110518235",
"https://doi.org/10.1186/s40168-018-0598-x"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/ncomms5498",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1047569017",
"https://doi.org/10.1038/ncomms5498"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nmicrobiol.2017.26",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1085056999",
"https://doi.org/10.1038/nmicrobiol.2017.26"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41467-021-21350-w",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1135373185",
"https://doi.org/10.1038/s41467-021-21350-w"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/s41564-017-0053-y",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1092638712",
"https://doi.org/10.1038/s41564-017-0053-y"
],
"type": "CreativeWork"
}
],
"datePublished": "2021-08-18",
"datePublishedReg": "2021-08-18",
"description": "BackgroundThe crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of lysogeny, these viruses demonstrate long-term persistence in the human gut microbiome, dominating the virome in some individuals.ResultsHere we show that rapid phase variation of alternate capsular polysaccharides in Bacteroides intestinalis cultures plays an important role in a dynamic equilibrium between phage sensitivity and resistance, allowing phage and bacteria to multiply in parallel. The data also suggests the role of a concomitant phage persistence mechanism associated with delayed lysis of infected cells, similar to carrier state infection. From an ecological and evolutionary standpoint, this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other \u201cbenign\u201d forms of phage infection when the host is stably present at high abundance.ConclusionLong-term persistence of bacteriophage and host could result from mutually beneficial mechanisms driving bacterial strain-level diversity and phage survival in complex environments.",
"genre": "article",
"id": "sg:pub.10.1186/s12915-021-01084-3",
"inLanguage": "en",
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.3984108",
"type": "MonetaryGrant"
},
{
"id": "sg:grant.7670448",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1032884",
"issn": [
"1478-5854",
"1741-7007"
],
"name": "BMC Biology",
"publisher": "Springer Nature",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "19"
}
],
"keywords": [
"long-term persistence",
"strain-level diversity",
"phage-host interactions",
"human gut virome",
"crAss-like phages",
"human gut microbiome",
"abundant members",
"evolutionary standpoint",
"phage infection",
"order Bacteroidales",
"Bacteroides intestinalis",
"high abundance",
"gut virome",
"infected cells",
"persistence mechanisms",
"phage sensitivity",
"phage survival",
"carrier state infection",
"commensal bacteria",
"virome",
"phase variation",
"gut microbiome",
"phages",
"bacteria",
"host",
"capsular polysaccharide",
"important role",
"dynamic equilibrium",
"lysogeny",
"winner model",
"Bacteroidales",
"persistence",
"beneficial mechanisms",
"diversity",
"microbiome",
"abundance",
"bacteriophages",
"intestinalis",
"mechanism",
"role",
"cells",
"ResultsHere",
"polysaccharides",
"variation",
"members",
"lysis",
"virus",
"complex environments",
"survival",
"interaction",
"infection",
"culture",
"resistance",
"rapid phase variations",
"environment",
"preferences",
"individuals",
"types",
"form",
"parallel",
"sensitivity",
"data",
"piggyback",
"equilibrium",
"model",
"standpoint"
],
"name": "Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis",
"pagination": "163",
"productId": [
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1140504065"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1186/s12915-021-01084-3"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"34407825"
]
}
],
"sameAs": [
"https://doi.org/10.1186/s12915-021-01084-3",
"https://app.dimensions.ai/details/publication/pub.1140504065"
],
"sdDataset": "articles",
"sdDatePublished": "2022-05-10T10:32",
"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_893.jsonl",
"type": "ScholarlyArticle",
"url": "https://doi.org/10.1186/s12915-021-01084-3"
}
]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/s12915-021-01084-3'
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/s12915-021-01084-3'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/s12915-021-01084-3'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/s12915-021-01084-3'
This table displays all metadata directly associated to this object as RDF triples.
288 TRIPLES
22 PREDICATES
115 URIs
90 LITERALS
13 BLANK NODES