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Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation

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dc.contributor.authorPark, Sein-
dc.contributor.authorSteinegger, Martin-
dc.contributor.authorCho, Ho-Seong-
dc.contributor.authorChun, Jongsik-
dc.date.accessioned2022-04-20T11:51:43Z-
dc.date.available2022-04-20T11:51:43Z-
dc.date.created2020-12-30-
dc.date.created2020-12-30-
dc.date.created2020-12-30-
dc.date.created2020-12-30-
dc.date.issued2020-11-
dc.identifier.citationFrontiers in Microbiology, Vol.11, p. 585622-
dc.identifier.issn1664-302X-
dc.identifier.other120022-
dc.identifier.urihttps://hdl.handle.net/10371/179143-
dc.description.abstractLimosilactobacillus reuteri is a model symbiont that colonizes the guts of vertebrates in studies on host adaptation of the gut symbiont. Previous studies have investigated host-specific phylogenetic and functional properties by isolating the genomic sequence. This dependency on genome isolation is a significant bottleneck. Here, we propose a method to study the association between L. reuteri and its hosts directly from metagenomic reads without strain isolation using pan-genomes. We characterized the host-specificity of L. reuteri in metagenomic samples, not only in previously studied organisms (mice and pigs) but also in dogs. For each sample, two types of profiles were generated: (1) genome-based strain type abundance profiles and (2) gene composition profiles. Our profiles showed host-association of L. reuteri in both phylogenetic and functional aspects without depending on host-specific genome isolation. We observed not only the presence of host-specific lineages, but also the dominant lineages associated with the different hosts. Furthermore, we showed that metagenome-assembled genomes provide detailed insights into the host-specificity of L. reuteri. We inferred evolutionary trajectories of host-associative L. reuteri strains in the metagenomic samples by placing the metagenome-assembled genomes into a phylogenetic tree and identified novel host-specific genes that were unannotated in existing pan-genome databases. Our pan-genomic approach reduces the need for time-consuming and expensive host-specific genome isolation, while producing consistent results with previous host-association findings in mice and pigs. Additionally, we predicted associations that have not yet been studied in dogs.-
dc.language영어-
dc.publisherFrontiers Media S.A.-
dc.titleMetagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation-
dc.typeArticle-
dc.contributor.AlternativeAuthor천종식-
dc.identifier.doi10.3389/fmicb.2020.585622-
dc.citation.journaltitleFrontiers in Microbiology-
dc.identifier.wosid000593929000001-
dc.identifier.scopusid2-s2.0-85096898914-
dc.citation.startpage585622-
dc.citation.volume11-
dc.identifier.sci000593929000001-
dc.description.isOpenAccessY-
dc.contributor.affiliatedAuthorSteinegger, Martin-
dc.contributor.affiliatedAuthorChun, Jongsik-
dc.type.docTypeArticle-
dc.description.journalClass1-
dc.subject.keywordPlusLACTOBACILLUS-REUTERI-
dc.subject.keywordPlusDATABASE-
dc.subject.keywordPlusTOOL-
dc.subject.keywordAuthorLimosilactobacillus reuteri-
dc.subject.keywordAuthormetagenome-
dc.subject.keywordAuthorpan-genome-
dc.subject.keywordAuthorhost-specificity-
dc.subject.keywordAuthorhost-symbiont interaction-
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Related Researcher

  • College of Natural Sciences
  • School of Biological Sciences
Research Area Development of algorithms to search, cluster and assemble sequence data, Metagenomic analysis, Pathogen detection in sequencing data

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