Environmental metagenome classification for constructing a microbiome fingerprint.
Identifieur interne : 002398 ( Ncbi/Merge ); précédent : 002397; suivant : 002399Environmental metagenome classification for constructing a microbiome fingerprint.
Auteurs : Jolanta Kawulok [Pologne] ; Michal Kawulok [Pologne] ; Sebastian Deorowicz [Pologne]Source :
- Biology direct [ 1745-6150 ] ; 2019.
Abstract
Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Contrary to the existing methods for environmental classification that are based on taxonomic or functional classification, we rely on the similarity between a sample and the reference database computed at a reads level.
DOI: 10.1186/s13062-019-0251-z
PubMed: 31722729
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000366
- to stream PubMed, to step Curation: 000366
- to stream PubMed, to step Checkpoint: 000581
Links to Exploration step
pubmed:31722729Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Environmental metagenome classification for constructing a microbiome fingerprint.</title><author><name sortKey="Kawulok, Jolanta" sort="Kawulok, Jolanta" uniqKey="Kawulok J" first="Jolanta" last="Kawulok">Jolanta Kawulok</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland. jolanta.kawulok@polsl.pl.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea><wicri:noRegion>Gliwice</wicri:noRegion></affiliation></author><author><name sortKey="Kawulok, Michal" sort="Kawulok, Michal" uniqKey="Kawulok M" first="Michal" last="Kawulok">Michal Kawulok</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea><wicri:noRegion>Gliwice</wicri:noRegion></affiliation></author><author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea><wicri:noRegion>Gliwice</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:31722729</idno><idno type="pmid">31722729</idno><idno type="doi">10.1186/s13062-019-0251-z</idno><idno type="wicri:Area/PubMed/Corpus">000366</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000366</idno><idno type="wicri:Area/PubMed/Curation">000366</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000366</idno><idno type="wicri:Area/PubMed/Checkpoint">000581</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000581</idno><idno type="wicri:Area/Ncbi/Merge">002398</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Environmental metagenome classification for constructing a microbiome fingerprint.</title><author><name sortKey="Kawulok, Jolanta" sort="Kawulok, Jolanta" uniqKey="Kawulok J" first="Jolanta" last="Kawulok">Jolanta Kawulok</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland. jolanta.kawulok@polsl.pl.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea><wicri:noRegion>Gliwice</wicri:noRegion></affiliation></author><author><name sortKey="Kawulok, Michal" sort="Kawulok, Michal" uniqKey="Kawulok M" first="Michal" last="Kawulok">Michal Kawulok</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea><wicri:noRegion>Gliwice</wicri:noRegion></affiliation></author><author><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland.</nlm:affiliation><country xml:lang="fr">Pologne</country><wicri:regionArea>Institute of Informatics, Silesian University of Technology, Gliwice</wicri:regionArea><wicri:noRegion>Gliwice</wicri:noRegion></affiliation></author></analytic><series><title level="j">Biology direct</title><idno type="eISSN">1745-6150</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Contrary to the existing methods for environmental classification that are based on taxonomic or functional classification, we rely on the similarity between a sample and the reference database computed at a reads level.</div></front></TEI><pubmed><MedlineCitation Status="In-Process" Owner="NLM"><PMID Version="1">31722729</PMID><DateRevised><Year>2020</Year><Month>02</Month><Day>05</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1745-6150</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><Issue>1</Issue><PubDate><Year>2019</Year><Month>11</Month><Day>13</Day></PubDate></JournalIssue><Title>Biology direct</Title><ISOAbbreviation>Biol. Direct</ISOAbbreviation></Journal><ArticleTitle>Environmental metagenome classification for constructing a microbiome fingerprint.</ArticleTitle><Pagination><MedlinePgn>20</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s13062-019-0251-z</ELocationID><Abstract><AbstractText Label="BACKGROUND">Nowadays, not only are single genomes commonly analyzed, but also metagenomes, which are sets of, DNA fragments (reads) derived from microbes living in a given environment. Metagenome analysis is aimed at extracting crucial information on the organisms that have left their traces in an investigated environmental sample.In this study we focus on the MetaSUB Forensics Challenge (organized within the CAMDA 2018 conference) which consists in predicting the geographical origin of metagenomic samples. Contrary to the existing methods for environmental classification that are based on taxonomic or functional classification, we rely on the similarity between a sample and the reference database computed at a reads level.</AbstractText><AbstractText Label="RESULTS">We report the results of our extensive experimental study to investigate the behavior of our method and its sensitivity to different parameters. In our tests, we have followed the protocol of the MetaSUB Challenge, which allowed us to compare the obtained results with the solutions based on taxonomic and functional classification.</AbstractText><AbstractText Label="CONCLUSIONS">The results reported in the paper indicate that our method is competitive with those based on taxonomic classification. Importantly, by measuring the similarity at the reads level, we avoid the necessity of using large databases with annotated gene sequences. Hence our main finding is that environmental classification of metagenomic data can be proceeded without using large databases required for taxonomic or functional classification.</AbstractText><AbstractText Label="REVIEWERS">This article was reviewed by Eran Elhaik, Alexandra Bettina Graf, Chengsheng Zhu, and Andre Kahles.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kawulok</LastName><ForeName>Jolanta</ForeName><Initials>J</Initials><Identifier Source="ORCID">0000-0002-8321-7760</Identifier><AffiliationInfo><Affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland. jolanta.kawulok@polsl.pl.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kawulok</LastName><ForeName>Michal</ForeName><Initials>M</Initials><Identifier Source="ORCID">0000-0002-3669-5110</Identifier><AffiliationInfo><Affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Deorowicz</LastName><ForeName>Sebastian</ForeName><Initials>S</Initials><Identifier Source="ORCID">0000-0002-9496-733X</Identifier><AffiliationInfo><Affiliation>Institute of Informatics, Silesian University of Technology, Gliwice, Poland.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2019</Year><Month>11</Month><Day>13</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Biol Direct</MedlineTA><NlmUniqueID>101258412</NlmUniqueID><ISSNLinking>1745-6150</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">CAMDA challenge</Keyword><Keyword MajorTopicYN="Y">Environmental classification</Keyword><Keyword MajorTopicYN="Y">K-mers</Keyword><Keyword MajorTopicYN="Y">MetaSUB</Keyword><Keyword MajorTopicYN="Y">Metagenome</Keyword><Keyword MajorTopicYN="Y">Sequence classification</Keyword><Keyword MajorTopicYN="Y">Urban microbiome</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>10</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>10</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>11</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>11</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>11</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31722729</ArticleId><ArticleId IdType="doi">10.1186/s13062-019-0251-z</ArticleId><ArticleId IdType="pii">10.1186/s13062-019-0251-z</ArticleId><ArticleId IdType="pmc">PMC6854650</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>PLoS One. 2015 Apr 17;10(4):e0121453</Citation><ArticleIdList><ArticleId IdType="pubmed">25884504</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Biol Direct. 2018 Oct 12;13(1):22</Citation><ArticleIdList><ArticleId IdType="pubmed">30621760</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Biol Direct. 2018 Aug 22;13(1):15</Citation><ArticleIdList><ArticleId IdType="pubmed">30134953</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Biol Direct. 2018 May 22;13(1):10</Citation><ArticleIdList><ArticleId IdType="pubmed">29789016</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Biol Direct. 2018 Apr 20;13(1):6</Citation><ArticleIdList><ArticleId IdType="pubmed">29678199</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Biol Direct. 2019 Aug 1;14(1):12</Citation><ArticleIdList><ArticleId IdType="pubmed">31370905</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>PLoS One. 2012;7(11):e48558</Citation><ArticleIdList><ArticleId IdType="pubmed">23139793</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Bioinformatics. 2016 Feb 15;32(4):605-7</Citation><ArticleIdList><ArticleId IdType="pubmed">26515820</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Bioinformatics. 2015 Nov 15;31(22):3584-92</Citation><ArticleIdList><ArticleId IdType="pubmed">26209798</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Bioinformatics. 2017 Mar 15;33(6):791-798</Citation><ArticleIdList><ArticleId IdType="pubmed">27256312</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Nat Methods. 2014 Nov;11(11):1144-6</Citation><ArticleIdList><ArticleId IdType="pubmed">25218180</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>PLoS Comput Biol. 2016 Jul 11;12(7):e1004977</Citation><ArticleIdList><ArticleId IdType="pubmed">27400279</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Biol Direct. 2018 May 9;13(1):9</Citation><ArticleIdList><ArticleId IdType="pubmed">29743119</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Bioinformatics. 2017 Sep 1;33(17):2759-2761</Citation><ArticleIdList><ArticleId IdType="pubmed">28472236</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Nature. 2017 Oct 5;550(7674):61-66</Citation><ArticleIdList><ArticleId IdType="pubmed">28953883</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Biochem Biophys Res Commun. 2016 Jan 22;469(4):967-77</Citation><ArticleIdList><ArticleId IdType="pubmed">26718401</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Nat Methods. 2016 May;13(5):435-8</Citation><ArticleIdList><ArticleId IdType="pubmed">26999001</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Bioinformatics. 2015 May 15;31(10):1569-76</Citation><ArticleIdList><ArticleId IdType="pubmed">25609798</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Nucleic Acids Res. 2017 Jan 25;45(2):e7</Citation><ArticleIdList><ArticleId IdType="pubmed">27651451</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Biol Direct. 2019 Jul 24;14(1):11</Citation><ArticleIdList><ArticleId IdType="pubmed">31340852</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Nat Biotechnol. 2017 Sep 12;35(9):833-844</Citation><ArticleIdList><ArticleId IdType="pubmed">28898207</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Nat Commun. 2017 Dec 22;8(1):2260</Citation><ArticleIdList><ArticleId IdType="pubmed">29273717</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Genome Res. 2017 Apr;27(4):626-638</Citation><ArticleIdList><ArticleId IdType="pubmed">28167665</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>BMC Bioinformatics. 2012 May 10;13:92</Citation><ArticleIdList><ArticleId IdType="pubmed">22574964</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Curr Protoc Microbiol. 2012 Nov;Chapter 1:Unit 1E.5.</Citation><ArticleIdList><ArticleId IdType="pubmed">23184592</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Genome Biol. 2019 Nov 5;20(1):232</Citation><ArticleIdList><ArticleId IdType="pubmed">31690338</ArticleId></ArticleIdList></Reference></ReferenceList><ReferenceList><Reference><Citation>Nat Commun. 2017 Oct 10;8(1):845</Citation><ArticleIdList><ArticleId IdType="pubmed">29018189</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Pologne</li></country></list><tree><country name="Pologne"><noRegion><name sortKey="Kawulok, Jolanta" sort="Kawulok, Jolanta" uniqKey="Kawulok J" first="Jolanta" last="Kawulok">Jolanta Kawulok</name></noRegion><name sortKey="Deorowicz, Sebastian" sort="Deorowicz, Sebastian" uniqKey="Deorowicz S" first="Sebastian" last="Deorowicz">Sebastian Deorowicz</name><name sortKey="Kawulok, Michal" sort="Kawulok, Michal" uniqKey="Kawulok M" first="Michal" last="Kawulok">Michal Kawulok</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002398 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 002398 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Ncbi
|étape= Merge
|type= RBID
|clé= pubmed:31722729
|texte= Environmental metagenome classification for constructing a microbiome fingerprint.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:31722729" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |