VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.
Identifieur interne : 000091 ( Main/Exploration ); précédent : 000090; suivant : 000092VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.
Auteurs : Hiroshi Mori [Japon] ; Takayuki Maruyama [Japon] ; Masahiro Yano [Japon] ; Takuji Yamada [Japon] ; Ken Kurokawa [Japon]Source :
- BMC systems biology [ 1752-0509 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ARN ribosomique 16S, Dosage génique.
- méthodes : Analyse de séquence d'ARN, Métagénomique.
- Infographie, Internet, Logiciel, Microbiologie, Phylogenèse.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Ribosomal, 16S.
- genetics : Gene Dosage.
- methods : Metagenomics, Sequence Analysis, RNA.
- Computer Graphics, Internet, Microbiology, Phylogeny, Software.
Abstract
BACKGROUND
The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary relationships among taxa are inferred by a phylogenetic tree. Thus, the combined representation of taxonomic composition and phylogenetic relationships among taxa is a powerful method for understanding microbial community structure; however, applying phylogenetic tree-based representation with information on the abundance of thousands or more taxa in each community is a difficult task. For this purpose, we previously developed the tool VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community), which is based on the genome-sequenced microbes' phylogenetic information. Here, we introduce VITCOMIC2, which incorporates substantive improvements over VITCOMIC that were necessary to address several issues associated with 16S rRNA gene-based analysis of microbial communities.
RESULTS
We developed VITCOMIC2 to provide (i) sequence identity searches against broad reference taxa including uncultured taxa; (ii) normalization of 16S rRNA gene copy number differences among taxa; (iii) rapid sequence identity searches by applying the graphics processing unit-based sequence identity search tool CLAST; (iv) accurate taxonomic composition inference and nearly full-length 16S rRNA gene sequence reconstructions for metagenomic shotgun sequencing; and (v) an interactive user interface for simultaneous representation of the taxonomic composition of microbial communities and phylogenetic relationships among taxa. We validated the accuracy of processes (ii) and (iv) by using metagenomic shotgun sequencing data from a mock microbial community.
CONCLUSIONS
The improvements incorporated into VITCOMIC2 enable users to acquire an intuitive understanding of microbial community composition based on the 16S rRNA gene sequence data obtained from both metagenomic shotgun and amplicon sequencing.
DOI: 10.1186/s12918-018-0545-2
PubMed: 29560821
PubMed Central: PMC5861490
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Maruyama</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550</wicri:regionArea><wicri:noRegion>152-8550</wicri:noRegion></affiliation></author><author><name sortKey="Yano, Masahiro" sort="Yano, Masahiro" uniqKey="Yano M" first="Masahiro" last="Yano">Masahiro Yano</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550</wicri:regionArea><wicri:noRegion>152-8550</wicri:noRegion></affiliation></author><author><name sortKey="Yamada, Takuji" sort="Yamada, Takuji" uniqKey="Yamada T" first="Takuji" last="Yamada">Takuji Yamada</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.</nlm:affiliation><country xml:lang="fr">Japon</country><wicri:regionArea>Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550</wicri:regionArea><wicri:noRegion>152-8550</wicri:noRegion></affiliation></author><author><name sortKey="Kurokawa, Ken" sort="Kurokawa, Ken" uniqKey="Kurokawa K" 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(genetics)</term><term>Sequence Analysis, RNA (methods)</term><term>Software (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN ribosomique 16S (génétique)</term><term>Analyse de séquence d'ARN (méthodes)</term><term>Dosage génique (génétique)</term><term>Infographie (MeSH)</term><term>Internet (MeSH)</term><term>Logiciel (MeSH)</term><term>Microbiologie (MeSH)</term><term>Métagénomique (méthodes)</term><term>Phylogenèse (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Ribosomal, 16S</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Gene Dosage</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN ribosomique 16S</term><term>Dosage génique</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term><term>Sequence Analysis, RNA</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Analyse de séquence d'ARN</term><term>Métagénomique</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Graphics</term><term>Internet</term><term>Microbiology</term><term>Phylogeny</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Infographie</term><term>Internet</term><term>Logiciel</term><term>Microbiologie</term><term>Phylogenèse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary relationships among taxa are inferred by a phylogenetic tree. Thus, the combined representation of taxonomic composition and phylogenetic relationships among taxa is a powerful method for understanding microbial community structure; however, applying phylogenetic tree-based representation with information on the abundance of thousands or more taxa in each community is a difficult task. For this purpose, we previously developed the tool VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community), which is based on the genome-sequenced microbes' phylogenetic information. Here, we introduce VITCOMIC2, which incorporates substantive improvements over VITCOMIC that were necessary to address several issues associated with 16S rRNA gene-based analysis of microbial communities.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>We developed VITCOMIC2 to provide (i) sequence identity searches against broad reference taxa including uncultured taxa; (ii) normalization of 16S rRNA gene copy number differences among taxa; (iii) rapid sequence identity searches by applying the graphics processing unit-based sequence identity search tool CLAST; (iv) accurate taxonomic composition inference and nearly full-length 16S rRNA gene sequence reconstructions for metagenomic shotgun sequencing; and (v) an interactive user interface for simultaneous representation of the taxonomic composition of microbial communities and phylogenetic relationships among taxa. We validated the accuracy of processes (ii) and (iv) by using metagenomic shotgun sequencing data from a mock microbial community.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The improvements incorporated into VITCOMIC2 enable users to acquire an intuitive understanding of microbial community composition based on the 16S rRNA gene sequence data obtained from both metagenomic shotgun and amplicon sequencing.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29560821</PMID><DateCompleted><Year>2019</Year><Month>05</Month><Day>29</Day></DateCompleted><DateRevised><Year>2019</Year><Month>05</Month><Day>29</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1752-0509</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>Suppl 2</Issue><PubDate><Year>2018</Year><Month>03</Month><Day>19</Day></PubDate></JournalIssue><Title>BMC systems biology</Title><ISOAbbreviation>BMC Syst Biol</ISOAbbreviation></Journal><ArticleTitle>VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing.</ArticleTitle><Pagination><MedlinePgn>30</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12918-018-0545-2</ELocationID><Abstract><AbstractText Label="BACKGROUND">The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary relationships among taxa are inferred by a phylogenetic tree. Thus, the combined representation of taxonomic composition and phylogenetic relationships among taxa is a powerful method for understanding microbial community structure; however, applying phylogenetic tree-based representation with information on the abundance of thousands or more taxa in each community is a difficult task. For this purpose, we previously developed the tool VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community), which is based on the genome-sequenced microbes' phylogenetic information. Here, we introduce VITCOMIC2, which incorporates substantive improvements over VITCOMIC that were necessary to address several issues associated with 16S rRNA gene-based analysis of microbial communities.</AbstractText><AbstractText Label="RESULTS">We developed VITCOMIC2 to provide (i) sequence identity searches against broad reference taxa including uncultured taxa; (ii) normalization of 16S rRNA gene copy number differences among taxa; (iii) rapid sequence identity searches by applying the graphics processing unit-based sequence identity search tool CLAST; (iv) accurate taxonomic composition inference and nearly full-length 16S rRNA gene sequence reconstructions for metagenomic shotgun sequencing; and (v) an interactive user interface for simultaneous representation of the taxonomic composition of microbial communities and phylogenetic relationships among taxa. We validated the accuracy of processes (ii) and (iv) by using metagenomic shotgun sequencing data from a mock microbial community.</AbstractText><AbstractText Label="CONCLUSIONS">The improvements incorporated into VITCOMIC2 enable users to acquire an intuitive understanding of microbial community composition based on the 16S rRNA gene sequence data obtained from both metagenomic shotgun and amplicon sequencing.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Mori</LastName><ForeName>Hiroshi</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Genome Evolution Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan. hmori@nig.ac.jp.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Maruyama</LastName><ForeName>Takayuki</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yano</LastName><ForeName>Masahiro</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yamada</LastName><ForeName>Takuji</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kurokawa</LastName><ForeName>Ken</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Genome Evolution Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan.</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>2018</Year><Month>03</Month><Day>19</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Syst Biol</MedlineTA><NlmUniqueID>101301827</NlmUniqueID><ISSNLinking>1752-0509</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012336">RNA, Ribosomal, 16S</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D003196" MajorTopicYN="N">Computer Graphics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018628" MajorTopicYN="N">Gene Dosage</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020407" MajorTopicYN="N">Internet</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D056186" MajorTopicYN="N">Metagenomics</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008829" MajorTopicYN="Y">Microbiology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="Y">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012336" MajorTopicYN="N">RNA, Ribosomal, 16S</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" 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IdType="pmc">PMC5861490</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Genome Res. 2009 Jul;19(7):1141-52</Citation><ArticleIdList><ArticleId IdType="pubmed">19383763</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2004 Feb 25;32(4):1363-71</Citation><ArticleIdList><ArticleId IdType="pubmed">14985472</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2016 Dec 22;17 (Suppl 19):508</Citation><ArticleIdList><ArticleId IdType="pubmed">28155666</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2017 Dec 1;33(23 ):3808-3810</Citation><ArticleIdList><ArticleId IdType="pubmed">28961926</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS Comput Biol. 2012;8(10):e1002743</Citation><ArticleIdList><ArticleId IdType="pubmed">23133348</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Microbiol. 2009 Sep 25;9:208</Citation><ArticleIdList><ArticleId IdType="pubmed">19781086</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Dec 15;28(24):3211-7</Citation><ArticleIdList><ArticleId IdType="pubmed">23071270</ArticleId></ArticleIdList></Reference><Reference><Citation>Indian J Microbiol. 2012 Dec;52(4):544-50</Citation><ArticleIdList><ArticleId IdType="pubmed">24293708</ArticleId></ArticleIdList></Reference><Reference><Citation>Clin Microbiol Rev. 2004 Oct;17(4):840-62, table of contents</Citation><ArticleIdList><ArticleId IdType="pubmed">15489351</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2014 Dec 11;15:406</Citation><ArticleIdList><ArticleId IdType="pubmed">25495907</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2011 Aug 15;27(16):2194-200</Citation><ArticleIdList><ArticleId IdType="pubmed">21700674</ArticleId></ArticleIdList></Reference><Reference><Citation>Microbiome. 2014 Apr 07;2:11</Citation><ArticleIdList><ArticleId IdType="pubmed">24708850</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2009 May;75(10):3263-70</Citation><ArticleIdList><ArticleId IdType="pubmed">19270149</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2011 Jul;39(13):e90</Citation><ArticleIdList><ArticleId IdType="pubmed">21576222</ArticleId></ArticleIdList></Reference><Reference><Citation>Methods Mol Biol. 2014;1079:131-46</Citation><ArticleIdList><ArticleId IdType="pubmed">24170399</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2004 May;186(9):2629-35</Citation><ArticleIdList><ArticleId IdType="pubmed">15090503</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2012;13 Suppl 7:S29</Citation><ArticleIdList><ArticleId IdType="pubmed">23282134</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2007 Aug;73(16):5261-7</Citation><ArticleIdList><ArticleId IdType="pubmed">17586664</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Microbiol. 2013 Apr 17;4:85</Citation><ArticleIdList><ArticleId IdType="pubmed">23626587</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 1997 Nov;63(11):4516-22</Citation><ArticleIdList><ArticleId IdType="pubmed">9361437</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2014 Jan;42(Database issue):D633-42</Citation><ArticleIdList><ArticleId IdType="pubmed">24288368</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 1997 May 2;276(5313):734-40</Citation><ArticleIdList><ArticleId IdType="pubmed">9115194</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Biol. 1990 Oct 5;215(3):403-10</Citation><ArticleIdList><ArticleId IdType="pubmed">2231712</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342-6</Citation><ArticleIdList><ArticleId IdType="pubmed">4598299</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2002;3:2</Citation><ArticleIdList><ArticleId IdType="pubmed">11869452</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2009 Oct 1;25(19):2455-65</Citation><ArticleIdList><ArticleId IdType="pubmed">19648142</ArticleId></ArticleIdList></Reference><Reference><Citation>J Mol Evol. 1980 Dec;16(2):111-20</Citation><ArticleIdList><ArticleId IdType="pubmed">7463489</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2007;35(9):3100-8</Citation><ArticleIdList><ArticleId IdType="pubmed">17452365</ArticleId></ArticleIdList></Reference><Reference><Citation>Sci Data. 2016 Sep 27;3:160081</Citation><ArticleIdList><ArticleId IdType="pubmed">27673566</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2015 Jan;43(Database issue):D6-17</Citation><ArticleIdList><ArticleId IdType="pubmed">25398906</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 2009 Jun;37(10):e76</Citation><ArticleIdList><ArticleId IdType="pubmed">19417062</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2011 Feb;28(2):1057-74</Citation><ArticleIdList><ArticleId IdType="pubmed">21059789</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2010 Oct 1;26(19):2460-1</Citation><ArticleIdList><ArticleId IdType="pubmed">20709691</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Methods. 2008 Mar;5(3):235-7</Citation><ArticleIdList><ArticleId IdType="pubmed">18264105</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2009 Dec 15;10:421</Citation><ArticleIdList><ArticleId IdType="pubmed">20003500</ArticleId></ArticleIdList></Reference><Reference><Citation>DNA Res. 2014;21(2):217-27</Citation><ArticleIdList><ArticleId IdType="pubmed">24277737</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2010 Jun 18;11:332</Citation><ArticleIdList><ArticleId IdType="pubmed">20565810</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2007 Jan 1;23(1):127-8</Citation><ArticleIdList><ArticleId IdType="pubmed">17050570</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2009 Jan 22;457(7228):480-4</Citation><ArticleIdList><ArticleId IdType="pubmed">19043404</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>Japon</li></country></list><tree><country name="Japon"><noRegion><name sortKey="Mori, Hiroshi" sort="Mori, Hiroshi" uniqKey="Mori H" first="Hiroshi" last="Mori">Hiroshi Mori</name></noRegion><name sortKey="Kurokawa, Ken" sort="Kurokawa, Ken" uniqKey="Kurokawa K" first="Ken" last="Kurokawa">Ken Kurokawa</name><name sortKey="Maruyama, Takayuki" sort="Maruyama, Takayuki" uniqKey="Maruyama T" first="Takayuki" last="Maruyama">Takayuki Maruyama</name><name sortKey="Yamada, Takuji" sort="Yamada, Takuji" uniqKey="Yamada T" first="Takuji" last="Yamada">Takuji Yamada</name><name sortKey="Yano, Masahiro" sort="Yano, Masahiro" uniqKey="Yano M" first="Masahiro" last="Yano">Masahiro Yano</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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