209 lines
21 KiB
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209 lines
21 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="CD6F3526FFC9252A477EFA0FFBEE25A4" 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. SUIS 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: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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<treatment ID-DOI="http://doi.org/10.5281/zenodo.6310191" ID-GBIF-Taxon="193366151" ID-Zenodo-Dep="6310191" LSID="urn:lsid:plazi:treatment:CD6F3526FFC9252A477EFA0FFBEE25A4" httpUri="http://treatment.plazi.org/id/CD6F3526FFC9252A477EFA0FFBEE25A4" lastPageNumber="19" pageId="18" pageNumber="19">
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<subSubSection pageId="18" pageNumber="19" type="nomenclature">
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<paragraph blockId="18.[121,766,1500,1956]" 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. SUIS" authorityName="SUBSP. SUIS" 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 SUBSP. SUIS</emphasis>
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</taxonomicName>
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<taxonomicNameLabel box="[430,606,1538,1567]" 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.[121,766,1500,1956]" pageId="18" pageNumber="19">
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<taxonomicName authorityName="Li & Cheng & Zheng & Liu & Quevedo & Li & Roos & Gänzle & Walter" authorityYear="2021" box="[121,512,1580,1604]" class="Bacilli" family="Lactobacillaceae" genus="Limosilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="18" pageNumber="19" phylum="Firmicutes" rank="subSpecies" species="reuteri" subSpecies="suis">
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<emphasis box="[121,395,1580,1604]" italics="true" pageId="18" pageNumber="19">Limosilactobacillus reuteri</emphasis>
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subsp.
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<emphasis box="[473,512,1580,1603]" italics="true" pageId="18" pageNumber="19">suis</emphasis>
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</taxonomicName>
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(su′ is. L. gen. n.
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<emphasis box="[688,727,1580,1603]" italics="true" pageId="18" pageNumber="19">suis</emphasis>
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, of swine, reflecting the host origin of most strains of this subspecies being the swine intestinal tract).
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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.[121,766,1500,1956]" lastBlockId="18.[827,1473,184,913]" pageId="18" pageNumber="19">
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<taxonomicName authorityName="SUBSP. SUIS" authorityYear="2021" box="[121,225,1687,1710]" 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="[121,225,1687,1710]" italics="true" pageId="18" pageNumber="19">L. reuteri</emphasis>
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</taxonomicName>
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strains clustered in lineage IV (
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<figureCitation box="[600,665,1687,1711]" 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="[153,440,1717,1741]" class="Bacilli" family="Lactobacillaceae" genus="Limosilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="18" pageNumber="19" phylum="Firmicutes" rank="subSpecies" species="reuteri" subSpecies="porcinus">
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<emphasis box="[153,257,1718,1741]" italics="true" pageId="18" pageNumber="19">L. reuteri</emphasis>
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subsp.
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<emphasis box="[347,440,1718,1741]" italics="true" pageId="18" pageNumber="19">porcinus</emphasis>
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</taxonomicName>
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and were isolated from pig [
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<bibRefCitation author="Duar RM & Frese SA & Lin XB & Fernando SC & Burkey TE" box="[129,145,1748,1772]" 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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||
<bibRefCitation author="Oh PL & Benson AK & Peterson DA & Patil PB & Moriyama EN" box="[164,181,1749,1772]" 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 belonging to this subspecies have ANI values of 98.7–99.5% with each other and ANI values of 94.6–96.3% with other
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<taxonomicName authorityName="SUBSP. SUIS" authorityYear="2021" box="[438,546,1810,1833]" 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="[438,546,1810,1833]" italics="true" pageId="18" pageNumber="19">L. reuteri</emphasis>
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</taxonomicName>
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strains belonging to different subspecies (
|
||
<figureCitation box="[400,466,1840,1864]" 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-xylose, D-galactose, D-glucose, maltose, lactose, melibiose, sucrose and raffinose; acid is not produced from D-fructose, D-mannose, methyl α- D-glucopyranoside, aesculin, potassium gluconate, glycerol, erythritol, D-arabinose, L-xylose, D-adonitol, methyl
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||
<emphasis box="[931,945,245,269]" 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- Dmannopyranoside,
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<emphasis box="[1069,1088,307,330]" italics="true" pageId="18" pageNumber="19">N</emphasis>
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-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 (
|
||
<figureCitation box="[947,1006,491,515]" 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 previous studies [
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<bibRefCitation author="Duar RM & Frese SA & Lin XB & Fernando SC & Burkey TE" box="[1255,1270,490,514]" 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="Yu J & Zhao J & Song Y & Zhang J & Yu Z" box="[1281,1309,491,515]" pageId="18" pageNumber="19" pagination="1151" refId="ref17050" refString="43. Yu J, Zhao J, Song Y, Zhang J, Yu Z et al. Comparative genomics of the herbivore gut symbiont Lactobacillus reuteri reveals genetic diversity and lifestyle adaptation. Front Microbiol 2018; 9: 1151." type="journal article" year="2018">43</bibRefCitation>
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,
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<bibRefCitation author="Wegmann U & MacKenzie DA & Zheng J & Goesmann A & Roos S" box="[1318,1346,491,515]" pageId="18" pageNumber="19" pagination="1023" refId="ref17183" refString="46. Wegmann U, MacKenzie DA, Zheng J, Goesmann A, Roos S et al. The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. BMC Genomics 2015; 16: 1023." type="journal article" year="2015">46</bibRefCitation>
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,
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<bibRefCitation author="Lee JY & Han GG & Choi J & Jin GD & Kang SK" box="[1356,1386,491,515]" pageId="18" pageNumber="19" pagination="709 - 721" refId="ref17223" refString="47. Lee JY, Han GG, Choi J, Jin GD, Kang SK et al. Pan-genomic approaches in Lactobacillus reuteri as a porcine probiotic: investigation of host adaptation and antipathogenic activity. Microb Ecol 2017; 74: 709 - 721." type="journal article" year="2017">47</bibRefCitation>
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], AFLP and MLSA (using concatenated sequences of
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<emphasis box="[1320,1354,521,545]" italics="true" pageId="18" pageNumber="19">ddl</emphasis>
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||
,
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||
<emphasis box="[1368,1402,521,545]" italics="true" pageId="18" pageNumber="19">pkt</emphasis>
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||
,
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<emphasis box="[1415,1460,521,545]" italics="true" pageId="18" pageNumber="19">leuS</emphasis>
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||
,
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||
<emphasis box="[828,878,553,576]" italics="true" pageId="18" pageNumber="19">gyrB</emphasis>
|
||
,
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||
<emphasis box="[893,940,552,576]" italics="true" pageId="18" pageNumber="19">dltA</emphasis>
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||
,
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||
<emphasis box="[955,1010,552,575]" italics="true" pageId="18" pageNumber="19">rpoA</emphasis>
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||
and
|
||
<emphasis box="[1068,1117,552,575]" italics="true" pageId="18" pageNumber="19">recA</emphasis>
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||
genes) [
|
||
<bibRefCitation author="Oh PL & Benson AK & Peterson DA & Patil PB & Moriyama EN" box="[1213,1229,552,575]" 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 pig-specific. A mucus-binding protein (Mub) that could bind mucus and/or IgA [
|
||
<bibRefCitation author="Walter J & Britton RA & Roos S." box="[1368,1383,613,637]" 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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||
,
|
||
<bibRefCitation author="Roos S & Jonsson H." box="[1394,1422,613,637]" pageId="18" pageNumber="19" pagination="433 - 442" refId="ref16980" refString="41. Roos S, Jonsson H. A high-molecular-mass cell-surface protein from Lactobacillus reuteri 1063 adheres to mucus components. Microbiology 2002; 148: 433 - 442." type="journal article" year="2002">41</bibRefCitation>
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||
,
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||
<bibRefCitation author="MacKenzie DA & Tailford LE & Hemmings AM & Juge N." box="[1431,1460,613,637]" pageId="18" pageNumber="19" pagination="32444 - 32453" refId="ref17010" refString="42. MacKenzie DA, Tailford LE, Hemmings AM, Juge N. Crystal structure of a mucus-binding protein repeat reveals an unexpected functional immunoglobulin binding activity. J Biol Chem 2009; 284: 32444 - 32453." type="journal article" year="2009">42</bibRefCitation>
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] exists within this subspecies and it specifically supports the colonization of this subspecies to the porcine gastrointestinal tract. Strains within this subspecies have been applied as probiotics to improve porcine intestinal health, enhance production, prevent diarrhoea, release stress and immune modulation [
|
||
<bibRefCitation author="Hou C & Zeng X & Yang F & Liu H & Qiao S." box="[976,1009,797,821]" pageId="18" pageNumber="19" pagination="14" refId="ref17270" refString="48. Hou C, Zeng X, Yang F, Liu H, Qiao S. Study and use of the probiotic Lactobacillus reuteri in pigs: a review. J Anim Sci Biotechnol 2015; 6: 14." type="journal article" year="2015">48</bibRefCitation>
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].
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||
</paragraph>
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||
</subSubSection>
|
||
<subSubSection pageId="18" pageNumber="19" type="reference_group">
|
||
<paragraph blockId="18.[827,1473,184,913]" pageId="18" pageNumber="19">
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||
<materialsCitation ID-GBIF-Occurrence="3465844311" pageId="18" pageNumber="19" typeStatus="holotype">
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The
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<typeStatus box="[1080,1128,798,822]" pageId="18" pageNumber="19">type</typeStatus>
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||
strain, ATCC 53608
|
||
<superScript attach="left" box="[1363,1373,796,810]" fontSize="6" pageId="18" pageNumber="19">T</superScript>
|
||
(=
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||
<accessionNumber httpUri="http://www.ncbi.nlm.nih.gov/protein/LMG31752" pageId="18" pageNumber="19">LMG 31752</accessionNumber>
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=1063
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[original designation]), was isolated from porcine gastrointestinal tract [
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,
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<bibRefCitation author="MacKenzie DA & Jeffers F & Parker ML & Vibert-Vallet A & Bongaerts RJ" box="[1188,1216,859,883]" pageId="18" pageNumber="19" pagination="3368 - 3378" refId="ref17311" refString="49. MacKenzie DA, Jeffers F, Parker ML, Vibert-Vallet A, Bongaerts RJ et al. Strain-specific diversity of mucus-binding proteins in the adhesion and aggregation properties of Lactobacillus reuteri. Microbiology 2010; 156: 3368 - 3378." type="journal article" year="2010">49</bibRefCitation>
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,
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<bibRefCitation author="Axelsson L & Lindgren S." box="[1227,1258,858,882]" pageId="18" pageNumber="19" pagination="433 - 440" refId="ref17354" refString="50. Axelsson L, Lindgren S. Characterization and DNA homology of Lactobacillus strains isolated from pig intestine. J Appl Bacteriol 1987; 62: 433 - 440." type="journal article" year="1987">50</bibRefCitation>
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], with a DNA G+C content of 39.0mol%.
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</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |