213 lines
22 KiB
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213 lines
22 KiB
XML
<document ID-DOI="10.1099/ijsem.0.004644" ID-GBIF-Dataset="6b321035-fd9c-4b25-a3b6-79a05a309793" ID-ISSN="1466-5034" ID-PMC="PMC8346765" ID-PubMed="33533708" ID-Zenodo-Dep="6048739" checkinTime="1644597549702" checkinUser="felipe" docAuthor="Li, Fuyong, Cheng, Christopher C., Zheng, Jinshui, Liu, Junhong, Quevedo, Rodrigo Margain, Li, Junjie, Roos, Stefan, Gänzle, Michael G. & Walter, Jens" docDate="2021" docId="CD6F3526FFC9252A477EFF6BFE3223A8" docLanguage="en" docName="IntJSystEvolMicrobiol.71.2.004644.pdf" docOrigin="International Journal of Systematic and Evolutionary Microbiology (004644) 71 (2)" docSource="http://dx.doi.org/10.1099/ijsem.0.004644" docStyle="DocumentStyle:C64F0A4F4C66F6FC2AD4ED89351C6242.1:IntJSystEvolMicrobiol.2017-.journal_article" docStyleId="C64F0A4F4C66F6FC2AD4ED89351C6242" docStyleName="IntJSystEvolMicrobiol.2017-.journal_article" docStyleVersion="1" docTitle="Limosilactobacillus reuteri SUBSP. MURIUM 2021, SUBSP. NOV." docType="treatment" docVersion="7" lastPageNumber="19" masterDocId="31564D5EFFDB25384707FFD3FFC62635" masterDocTitle="Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts" masterLastPageNumber="21" masterPageNumber="1" pageNumber="19" updateTime="1668130802247" updateUser="ExternalLinkService">
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<mods:mods xmlns:mods="http://www.loc.gov/mods/v3">
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<mods:titleInfo>
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<mods:title>Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts</mods:title>
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</mods:titleInfo>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Li, Fuyong</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Cheng, Christopher C.</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Zheng, Jinshui</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Liu, Junhong</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Quevedo, Rodrigo Margain</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Li, Junjie</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Roos, Stefan</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Gänzle, Michael G.</mods:namePart>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Walter, Jens</mods:namePart>
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</mods:name>
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<mods:typeOfResource>text</mods:typeOfResource>
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<mods:title>International Journal of Systematic and Evolutionary Microbiology</mods:title>
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</mods:titleInfo>
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<mods:part>
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<mods:date>2021</mods:date>
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<mods:detail type="series">
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<mods:title>004644</mods:title>
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<mods:detail type="pubDate">
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<mods:number>2021-02-01</mods:number>
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</mods:detail>
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<mods:detail type="volume">
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<mods:number>71</mods:number>
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</mods:detail>
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<mods:detail type="issue">
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<mods:number>2</mods:number>
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<mods:start>1</mods:start>
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<mods:end>21</mods:end>
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<mods:url>http://dx.doi.org/10.1099/ijsem.0.004644</mods:url>
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<mods:identifier type="DOI">10.1099/ijsem.0.004644</mods:identifier>
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<mods:identifier type="ISSN">1466-5034</mods:identifier>
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<mods:identifier type="PMC">PMC8346765</mods:identifier>
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<mods:identifier type="PubMed">33533708</mods:identifier>
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<treatment ID-DOI="http://doi.org/10.5281/zenodo.6310189" ID-GBIF-Taxon="193366150" ID-Zenodo-Dep="6310189" LSID="urn:lsid:plazi:treatment:CD6F3526FFC9252A477EFF6BFE3223A8" httpUri="http://treatment.plazi.org/id/CD6F3526FFC9252A477EFF6BFE3223A8" lastPageNumber="19" pageId="18" pageNumber="19">
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<subSubSection pageId="18" pageNumber="19" type="nomenclature">
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<paragraph blockId="18.[120,766,184,1437]" pageId="18" pageNumber="19">
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<heading allCaps="true" bold="true" fontSize="12" level="2" pageId="18" pageNumber="19" reason="3">
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<emphasis bold="true" pageId="18" pageNumber="19">
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DESCRIPTION OF
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<taxonomicName authority="SUBSP. MURIUM" authorityName="SUBSP. MURIUM" authorityYear="2021" class="Bacilli" family="Lactobacillaceae" genus="Limosilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="18" pageNumber="19" phylum="Firmicutes" rank="species" species="reuteri" status="SUBSP. NOV.">
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<emphasis bold="true" italics="true" pageId="18" pageNumber="19">LIMOSILACTOBACILLUS REUTERI</emphasis>
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SUBSP.
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<emphasis bold="true" box="[360,476,221,250]" italics="true" pageId="18" pageNumber="19">MURIUM</emphasis>
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</taxonomicName>
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<taxonomicNameLabel box="[485,661,221,250]" pageId="18" pageNumber="19" rank="subSpecies">SUBSP. NOV.</taxonomicNameLabel>
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</emphasis>
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</heading>
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</paragraph>
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</subSubSection>
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<subSubSection pageId="18" pageNumber="19" type="etymology">
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<paragraph blockId="18.[120,766,184,1437]" pageId="18" pageNumber="19">
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<taxonomicName authorityName="Li & Cheng & Zheng & Liu & Quevedo & Li & Roos & Gänzle & Walter" authorityYear="2021" box="[121,558,263,287]" class="Bacilli" family="Lactobacillaceae" genus="Limosilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="18" pageNumber="19" phylum="Firmicutes" rank="subSpecies" species="reuteri" subSpecies="murium">
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<emphasis box="[121,395,263,287]" italics="true" pageId="18" pageNumber="19">Limosilactobacillus reuteri</emphasis>
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subsp.
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<emphasis box="[472,558,264,287]" italics="true" pageId="18" pageNumber="19">murium</emphasis>
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</taxonomicName>
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(mu′ ri.um. L. plur. gen. n.
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<taxonomicName authority="Li & Cheng & Zheng & Liu & Quevedo & Li & Roos & Gänzle & Walter, 2021" authorityName="Li & Cheng & Zheng & Liu & Quevedo & Li & Roos & Gänzle & Walter" authorityYear="2021" box="[197,283,294,317]" pageId="18" pageNumber="19" rank="subSpecies" status="SUBSP. NOV." subSpecies="Murium">
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<emphasis box="[197,283,294,317]" italics="true" pageId="18" pageNumber="19">murium</emphasis>
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</taxonomicName>
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of mice, referring to the adaptation of strains of the subspecies to rodents including mice).
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</paragraph>
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</subSubSection>
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<subSubSection pageId="18" pageNumber="19" type="reference_group">
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<paragraph blockId="18.[120,766,184,1437]" pageId="18" pageNumber="19">
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<taxonomicName authorityName="SUBSP. MURIUM" authorityYear="2021" box="[121,224,371,394]" class="Bacilli" family="Lactobacillaceae" genus="Limosilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="18" pageNumber="19" phylum="Firmicutes" rank="species" species="reuteri">
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<emphasis box="[121,224,371,394]" italics="true" pageId="18" pageNumber="19">L. reuteri</emphasis>
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</taxonomicName>
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strains clustered in lineage I (
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<figureCitation box="[571,635,370,394]" captionStart="Fig" captionStartId="11.[185,216,1007,1026]" captionTargetBox="[227,1361,181,954]" captionTargetId="figure-462@11.[227,1361,181,954]" captionTargetPageId="11" captionText="Fig. 3. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among six L. reuteri subspecies.The tree was reconstructed using 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium) and L. balticus BG-AF3-AT was used as an outgroup. Further information on the involved genome sequences is listed in Table S1. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. The tree was drawn with iTOL [54]." figureDoi="http://doi.org/10.5281/zenodo.6048749" httpUri="https://zenodo.org/record/6048749/files/figure.png" pageId="18" pageNumber="19">Fig. 3</figureCitation>
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) belong to
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<taxonomicName authorityName="Li & Cheng & Zheng & Liu & Quevedo & Li & Roos & Gänzle & Walter" authorityYear="2021" box="[121,413,401,425]" class="Bacilli" family="Lactobacillaceae" genus="Limosilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="18" pageNumber="19" phylum="Firmicutes" rank="subSpecies" species="reuteri" subSpecies="murium">
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<emphasis box="[121,228,401,424]" italics="true" pageId="18" pageNumber="19">L. reuteri</emphasis>
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subsp.
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<emphasis box="[323,413,401,424]" italics="true" pageId="18" pageNumber="19">murium</emphasis>
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</taxonomicName>
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and they were isolated from rodents [
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<bibRefCitation author="Duar RM & Frese SA & Lin XB & Fernando SC & Burkey TE" box="[217,231,431,455]" pageId="18" pageNumber="19" refId="ref15514" refString="5. Duar RM, Frese SA, Lin XB, Fernando SC, Burkey TE et al. Experimental evaluation of host adaptation of Lactobacillus reuteri to different vertebrate species. Appl Environ Microbiol 2017; 83: e 00132 - 17." type="journal volume" year="2017">5</bibRefCitation>
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–
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<bibRefCitation author="Oh PL & Benson AK & Peterson DA & Patil PB & Moriyama EN" box="[249,264,431,455]" pageId="18" pageNumber="19" pagination="377 - 387" refId="ref15599" refString="7. Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN et al. Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. Isme J 2010; 4: 377 - 387." type="journal article" year="2010">7</bibRefCitation>
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]. Strains of this subspecies have ANI values of 96.8–99.1 % with each other and ANI values of 94.5–96.5% with other
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<taxonomicName authorityName="SUBSP. MURIUM" authorityYear="2021" box="[243,343,493,516]" class="Bacilli" family="Lactobacillaceae" genus="Limosilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="18" pageNumber="19" phylum="Firmicutes" rank="species" species="reuteri">
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<emphasis box="[243,343,493,516]" italics="true" pageId="18" pageNumber="19">L. reuteri</emphasis>
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</taxonomicName>
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strains belonging to different subspecies (
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<figureCitation box="[178,239,523,547]" captionStart="Fig" captionStartId="12.[121,152,788,807]" captionTargetBox="[121,760,181,735]" captionTargetId="figure-792@12.[121,760,181,735]" captionTargetPageId="12" captionText="Fig. 4. Pairwise average nucleotide identity values (ANI; %) of genome sequences belonging to the same or different L. reuteri subspecies. ANI values within the same subspecies and between different subspecies were calculated for 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp.murium, n=10for L. reuteri subsp.reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium). Further information on the involved genome sequences is listed in Table S1." figureDoi="http://doi.org/10.5281/zenodo.6048753" httpUri="https://zenodo.org/record/6048753/files/figure.png" pageId="18" pageNumber="19">Fig. 4</figureCitation>
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). Acid is produced from L-arabinose,D-ribose, D-galactose,D-glucose, maltose, lactose, melibiose, sucrose and raffinose; acid production from potassium gluconate is strain-specific; acid is not produced from D-xylose, D-fructose, D-mannose, methyl α- D-glucopyranoside, aesculin, glycerol, erythritol, D-arabinose, L-xylose, D-adonitol, methyl
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<emphasis box="[386,400,707,731]" italics="true" pageId="18" pageNumber="19">β</emphasis>
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-D-xylopyranoside, L-sorbose, L-rhamnose, dulcitol, inositol, D-mannitol, D-sorbitol, methyl α- D-mannopyranoside, N-acetylglucosamine, amygdalin, arbutin, salicin, cellobiose, trehalose, inulin, melezitose, starch, glycogen, xylitol, gentiobiose, turanose, D-lyxose,D-tagatose,D-fucose,L-fucose,D-arabitol, L-arabitol, potassium 2-ketogluconate or potassium 5-ketogluconate. Phylogenetic analyses based on the core genes identified in this study (
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<figureCitation box="[448,507,953,977]" captionStart="Fig" captionStartId="11.[185,216,1007,1026]" captionTargetBox="[227,1361,181,954]" captionTargetId="figure-462@11.[227,1361,181,954]" captionTargetPageId="11" captionText="Fig. 3. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among six L. reuteri subspecies.The tree was reconstructed using 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium) and L. balticus BG-AF3-AT was used as an outgroup. Further information on the involved genome sequences is listed in Table S1. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. The tree was drawn with iTOL [54]." figureDoi="http://doi.org/10.5281/zenodo.6048749" httpUri="https://zenodo.org/record/6048749/files/figure.png" pageId="18" pageNumber="19">Fig. 3</figureCitation>
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) and a previous studies [
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<bibRefCitation author="Duar RM & Frese SA & Lin XB & Fernando SC & Burkey TE" box="[128,144,983,1007]" pageId="18" pageNumber="19" refId="ref15514" refString="5. Duar RM, Frese SA, Lin XB, Fernando SC, Burkey TE et al. Experimental evaluation of host adaptation of Lactobacillus reuteri to different vertebrate species. Appl Environ Microbiol 2017; 83: e 00132 - 17." type="journal volume" year="2017">5</bibRefCitation>
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], AFLP and MLSA (using concatenated sequences of
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<emphasis box="[718,752,983,1007]" italics="true" pageId="18" pageNumber="19">ddl</emphasis>
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,
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<emphasis box="[121,155,1014,1038]" italics="true" pageId="18" pageNumber="19">pkt</emphasis>
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,
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<emphasis box="[167,212,1014,1038]" italics="true" pageId="18" pageNumber="19">leuS</emphasis>
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,
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<emphasis box="[225,275,1015,1038]" italics="true" pageId="18" pageNumber="19">gyrB</emphasis>
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,
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<emphasis box="[288,335,1014,1038]" italics="true" pageId="18" pageNumber="19">dltA</emphasis>
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,
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<emphasis box="[347,402,1014,1037]" italics="true" pageId="18" pageNumber="19">rpoA</emphasis>
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and
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<emphasis box="[454,503,1014,1037]" italics="true" pageId="18" pageNumber="19">recA</emphasis>
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genes) [
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<bibRefCitation author="Oh PL & Benson AK & Peterson DA & Patil PB & Moriyama EN" box="[593,609,1014,1037]" pageId="18" pageNumber="19" pagination="377 - 387" refId="ref15599" refString="7. Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN et al. Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. Isme J 2010; 4: 377 - 387." type="journal article" year="2010">7</bibRefCitation>
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] indicate that strains clustered in this lineage are rodent-specific. Strains of
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<taxonomicName authorityName="Li & Cheng & Zheng & Liu & Quevedo & Li & Roos & Gänzle & Walter" authorityYear="2021" box="[152,433,1075,1099]" class="Bacilli" family="Lactobacillaceae" genus="Limosilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="18" pageNumber="19" phylum="Firmicutes" rank="subSpecies" species="reuteri" subSpecies="murium">
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<emphasis box="[152,255,1076,1099]" italics="true" pageId="18" pageNumber="19">L. reuteri</emphasis>
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subsp.
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<emphasis box="[343,433,1076,1099]" italics="true" pageId="18" pageNumber="19">murium</emphasis>
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</taxonomicName>
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displayed elevated fitness in mice through the colonization and biofilm formation on the forestomach epithelium [
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||
<bibRefCitation author="Duar RM & Frese SA & Lin XB & Fernando SC & Burkey TE" box="[436,452,1136,1160]" pageId="18" pageNumber="19" refId="ref15514" refString="5. Duar RM, Frese SA, Lin XB, Fernando SC, Burkey TE et al. Experimental evaluation of host adaptation of Lactobacillus reuteri to different vertebrate species. Appl Environ Microbiol 2017; 83: e 00132 - 17." type="journal volume" year="2017">5</bibRefCitation>
|
||
,
|
||
<bibRefCitation author="Oh PL & Benson AK & Peterson DA & Patil PB & Moriyama EN" box="[463,478,1137,1160]" pageId="18" pageNumber="19" pagination="377 - 387" refId="ref15599" refString="7. Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN et al. Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. Isme J 2010; 4: 377 - 387." type="journal article" year="2010">7</bibRefCitation>
|
||
,
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<bibRefCitation author="Frese SA & Mackenzie DA & Peterson DA & Schmaltz R & Fangman T" box="[488,517,1137,1161]" pageId="18" pageNumber="19" pagination="1004057" refId="ref15768" refString="11. Frese SA, Mackenzie DA, Peterson DA, Schmaltz R, Fangman T et al. Molecular characterization of host-specific biofilm formation in a vertebrate gut symbiont. PLoS Genet 2013; 9: e 1004057." type="journal article" year="2013">11</bibRefCitation>
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], suggesting that their evolution with rodents was adaptive and led to host specificity. Large surface proteins (>750 aa) exist among strains belonging to this subspecies, which involve in epithelial adhesion and biofilm formation [
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<bibRefCitation author="Frese SA & Benson AK & Tannock GW & Loach DM & Kim J" box="[483,500,1259,1283]" pageId="18" pageNumber="19" pagination="1001314" refId="ref15558" refString="6. Frese SA, Benson AK, Tannock GW, Loach DM, Kim J et al. The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet 2011; 7: e 1001314." type="journal article" year="2011">6</bibRefCitation>
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]. Strains of this subspecies produce the enzyme urease for acid resistance and rarely produce the antimicrobial compound reuterin [
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<bibRefCitation author="Frese SA & Benson AK & Tannock GW & Loach DM & Kim J" box="[704,720,1321,1345]" pageId="18" pageNumber="19" pagination="1001314" refId="ref15558" refString="6. Frese SA, Benson AK, Tannock GW, Loach DM, Kim J et al. The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet 2011; 7: e 1001314." type="journal article" year="2011">6</bibRefCitation>
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,
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||
<bibRefCitation author="Walter J & Britton RA & Roos S." box="[731,747,1321,1345]" pageId="18" pageNumber="19" pagination="4645 - 4652" refId="ref15642" refString="8. Walter J, Britton RA, Roos S. Host-microbial symbiosis in the vertebrate gastrointestinal tract and the Lactobacillus reuteri paradigm. Proc Natl Acad Sci U S A 2011; 108 Suppl 1: 4645 - 4652." type="journal article" year="2011">8</bibRefCitation>
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].
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</paragraph>
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</subSubSection>
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||
<subSubSection pageId="18" pageNumber="19" type="reference_group">
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<paragraph blockId="18.[120,766,184,1437]" pageId="18" pageNumber="19">
|
||
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The
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strain, lpuph1
|
||
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(=DSM 110570
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|
||
=
|
||
<accessionNumber box="[598,733,1351,1375]" httpUri="http://www.ncbi.nlm.nih.gov/protein/LMG31634" pageId="18" pageNumber="19">LMG 31634</accessionNumber>
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<superScript attach="right" box="[734,744,1350,1364]" fontSize="6" pageId="18" pageNumber="19">T</superScript>
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), was isolated from mouse gastrointestinal tract [
|
||
<bibRefCitation author="Frese SA & Benson AK & Tannock GW & Loach DM & Kim J" box="[646,662,1382,1406]" pageId="18" pageNumber="19" pagination="1001314" refId="ref15558" refString="6. Frese SA, Benson AK, Tannock GW, Loach DM, Kim J et al. The evolution of host specialization in the vertebrate gut symbiont Lactobacillus reuteri. PLoS Genet 2011; 7: e 1001314." type="journal article" year="2011">6</bibRefCitation>
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,
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||
<bibRefCitation author="Oh PL & Benson AK & Peterson DA & Patil PB & Moriyama EN" box="[674,690,1382,1405]" pageId="18" pageNumber="19" pagination="377 - 387" refId="ref15599" refString="7. Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN et al. Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. Isme J 2010; 4: 377 - 387." type="journal article" year="2010">7</bibRefCitation>
|
||
], with a DNA G+C content of 38.4mol%.
|
||
</materialsCitation>
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |