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Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Park, Sein | - |
dc.contributor.author | Steinegger, Martin | - |
dc.contributor.author | Cho, Ho-Seong | - |
dc.contributor.author | Chun, Jongsik | - |
dc.date.accessioned | 2022-04-20T11:51:43Z | - |
dc.date.available | 2022-04-20T11:51:43Z | - |
dc.date.created | 2020-12-30 | - |
dc.date.created | 2020-12-30 | - |
dc.date.created | 2020-12-30 | - |
dc.date.created | 2020-12-30 | - |
dc.date.issued | 2020-11 | - |
dc.identifier.citation | Frontiers in Microbiology, Vol.11, p. 585622 | - |
dc.identifier.issn | 1664-302X | - |
dc.identifier.other | 120022 | - |
dc.identifier.uri | https://hdl.handle.net/10371/179143 | - |
dc.description.abstract | Limosilactobacillus 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.language | 영어 | - |
dc.publisher | Frontiers Media S.A. | - |
dc.title | Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation | - |
dc.type | Article | - |
dc.contributor.AlternativeAuthor | 천종식 | - |
dc.identifier.doi | 10.3389/fmicb.2020.585622 | - |
dc.citation.journaltitle | Frontiers in Microbiology | - |
dc.identifier.wosid | 000593929000001 | - |
dc.identifier.scopusid | 2-s2.0-85096898914 | - |
dc.citation.startpage | 585622 | - |
dc.citation.volume | 11 | - |
dc.identifier.sci | 000593929000001 | - |
dc.description.isOpenAccess | Y | - |
dc.contributor.affiliatedAuthor | Steinegger, Martin | - |
dc.contributor.affiliatedAuthor | Chun, Jongsik | - |
dc.type.docType | Article | - |
dc.description.journalClass | 1 | - |
dc.subject.keywordPlus | LACTOBACILLUS-REUTERI | - |
dc.subject.keywordPlus | DATABASE | - |
dc.subject.keywordPlus | TOOL | - |
dc.subject.keywordAuthor | Limosilactobacillus reuteri | - |
dc.subject.keywordAuthor | metagenome | - |
dc.subject.keywordAuthor | pan-genome | - |
dc.subject.keywordAuthor | host-specificity | - |
dc.subject.keywordAuthor | host-symbiont interaction | - |
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