254 lines
24 KiB
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254 lines
24 KiB
XML
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<mods:title id="5596843A5CB967EDDE485046C7D30844">A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae</mods:title>
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<mods:namePart id="704D491ACDC7A1CC87E001C1C5A66BFC">Zheng, Jinshui</mods:namePart>
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<mods:namePart id="8E52BD952F34AA2B6951384A7F5AA459">Wittouck, Stijn</mods:namePart>
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<mods:namePart id="ECAD098C1E0596D045791F7F14E32B71">Watanabe, Koichi</mods:namePart>
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<mods:namePart id="B05E6B3897F9D16DD5DCE8DDA53CF19C">Wuyts, Sander</mods:namePart>
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<mods:namePart id="B3766CA75D8140CABACEC7338F07DD8C">Felis, Giovanna E.</mods:namePart>
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<mods:namePart id="2CA15EA64B97426EC6B0E70BD6F63CF6">Gänzle, Michael G.</mods:namePart>
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<mods:namePart id="12242629530803E3A12F6B7A72277D99">Lebeer, Sarah</mods:namePart>
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<mods:title id="76636BA67DC472A229E9F91E0E9CF1CC">International Journal of Systematic and Evolutionary Microbiology</mods:title>
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<mods:part id="EEB5515BDBE44C0C6785EB5C1F6C1769">
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<mods:date id="86D91BE93DADF2AAADE8B5852732E332">2020</mods:date>
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<treatment id="0389878AFFA52158DA0BFB0AFDCB63A4" ID-DOI="http://doi.org/10.5281/zenodo.6309847" ID-Zenodo-Dep="6309847" LSID="urn:lsid:plazi:treatment:0389878AFFA52158DA0BFB0AFDCB63A4" httpUri="http://treatment.plazi.org/id/0389878AFFA52158DA0BFB0AFDCB63A4" lastPageId="41" lastPageNumber="2823" pageId="40" pageNumber="2822">
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<subSubSection id="C33A6517FFA52159DA0BFB0AFB2E66B9" pageId="40" pageNumber="2822" type="nomenclature">
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<paragraph id="8B9F369CFFA52159DA0BFB0AFB2E66B9" blockId="40.[826,1468,1180,1955]" pageId="40" pageNumber="2822">
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<heading id="D0D781F0FFA52159DA0BFB0AFB2E66B9" allCaps="true" bold="true" fontSize="12" level="2" pageId="40" pageNumber="2822" reason="3">
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<emphasis id="B954EA8EFFA52159DA0BFB0AFB2E66B9" bold="true" pageId="40" pageNumber="2822">
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DESCRIPTION OF
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<taxonomicName id="4C204D1FFFA52159DD02FB0AFBAA66B9" authority="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer, 2020" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" class="Bacilli" family="Lactobacillaceae" genus="Ligilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="40" pageNumber="2822" phylum="Firmicutes" rank="species" species="araffinosus" status="sp. nov.">
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<emphasis id="B954EA8EFFA52159DD02FB0AFBAA66B9" bold="true" italics="true" pageId="40" pageNumber="2822">LIGILACTOBACILLUS ARAFFINOSUS</emphasis>
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</taxonomicName>
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<taxonomicNameLabel id="A26757F5FFA52159DD3AFB57FB2E66B9" box="[1037,1153,1217,1246]" pageId="40" pageNumber="2822" rank="species">SP. NOV.</taxonomicNameLabel>
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</emphasis>
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</heading>
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</paragraph>
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<subSubSection id="C33A6517FFA52159DA0BFB7AFBE06725" pageId="40" pageNumber="2822" type="etymology">
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<paragraph id="8B9F369CFFA52159DA0BFB7AFBE06725" blockId="40.[826,1468,1180,1955]" pageId="40" pageNumber="2822">
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<taxonomicName id="4C204D1FFFA52159DA0BFB7AFBF96763" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" box="[828,1110,1260,1284]" class="Bacilli" family="Lactobacillaceae" genus="Ligilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="40" pageNumber="2822" phylum="Firmicutes" rank="species" species="araffinosus">
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<emphasis id="B954EA8EFFA52159DA0BFB7AFBF96763" box="[828,1110,1260,1284]" italics="true" pageId="40" pageNumber="2822">Ligilactobacillus araffinosus</emphasis>
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</taxonomicName>
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(a.raf.fi.no’sus. Gr. pref.
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<emphasis id="B954EA8EFFA52159DC7AFB7BFAF56763" box="[1357,1370,1261,1284]" italics="true" pageId="40" pageNumber="2822">a</emphasis>
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not; N.L. masc. adj.
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<emphasis id="B954EA8EFFA52159DA9BFA9DFBBE6744" box="[940,1041,1291,1315]" italics="true" pageId="40" pageNumber="2822">raffinosus</emphasis>
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of raffinose; N.L. masc. adj.
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<taxonomicName id="4C204D1FFFA52159DC75FA9DFA1B6744" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" box="[1346,1460,1291,1315]" class="Bacilli" family="Lactobacillaceae" genus="Ligilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="40" pageNumber="2822" phylum="Firmicutes" rank="species" species="araffinosus">
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<emphasis id="B954EA8EFFA52159DC75FA9DFA1B6744" box="[1346,1460,1291,1315]" italics="true" pageId="40" pageNumber="2822">araffinosus</emphasis>
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</taxonomicName>
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, not fermenting raffinose).
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</paragraph>
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<subSubSection id="C33A6517FFA52158DA0BFACFFDCD637C" lastPageId="41" lastPageNumber="2823" pageId="40" pageNumber="2822" type="description">
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<paragraph id="8B9F369CFFA52159DA0BFACFFBFD67C8" blockId="40.[826,1468,1180,1955]" pageId="40" pageNumber="2822">
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Basonym:
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<taxonomicName id="4C204D1FFFA52159DA9AFACFFC0767F7" authority="Fujisawa et al. 1985" authorityName="Fujisawa" authorityYear="1985" class="Bacilli" family="Lactobacillaceae" genus="Lactobacillus" kingdom="Bacteria" order="Lactobacillales" pageId="40" pageNumber="2822" phylum="Firmicutes" rank="subSpecies" species="aviarius" subSpecies="araffinosus">
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<emphasis id="B954EA8EFFA52159DA9AFACFFB3D6717" box="[941,1170,1369,1393]" italics="true" pageId="40" pageNumber="2822">Lactobacillus aviarius</emphasis>
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subsp.
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<emphasis id="B954EA8EFFA52159DDD3FACFFAF96716" box="[1252,1366,1369,1393]" italics="true" pageId="40" pageNumber="2822">araffinosus</emphasis>
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Fujisawa
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<emphasis id="B954EA8EFFA52159DA0BFAEFFCC867F7" box="[828,871,1400,1424]" italics="true" pageId="40" pageNumber="2822">et al</emphasis>
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. 1985
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</taxonomicName>
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, 223
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<superScript id="7C559BD4FFA52159DAEEFAE1FC4267E2" attach="right" box="[985,1005,1399,1413]" fontSize="6" pageId="40" pageNumber="2822">VP</superScript>
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; Fujisawa
|
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<emphasis id="B954EA8EFFA52159DD6DFAEFFB2967F7" box="[1114,1158,1400,1424]" italics="true" pageId="40" pageNumber="2822">et al</emphasis>
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. 1986, (Effective publication: Fujisawa
|
||
<emphasis id="B954EA8EFFA52159DAA9FA0EFC6567C8" box="[926,970,1431,1455]" italics="true" pageId="40" pageNumber="2822">et al</emphasis>
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., 1984, 419).
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</paragraph>
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<paragraph id="8B9F369CFFA52159DA0BFA50FB7D6570" blockId="40.[826,1468,1180,1955]" pageId="40" pageNumber="2822">
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||
Placement of
|
||
<taxonomicName id="4C204D1FFFA52159DAFCFA50FBF767B9" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" box="[971,1112,1478,1502]" class="Bacilli" family="Lactobacillaceae" genus="Ligilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="40" pageNumber="2822" phylum="Firmicutes" rank="species" species="araffinosus">
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<emphasis id="B954EA8EFFA52159DAFCFA50FBF767B9" box="[971,1112,1478,1502]" italics="true" pageId="40" pageNumber="2822">L. araffinosus</emphasis>
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</taxonomicName>
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in a separate species is supported by ANI values and digital DNA–DNA hybridization [
|
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<bibRefCitation id="EFB14B6DFFA52159DC53FA73FA2C679A" author="Wittouck S & Wuyts S & Meehan CJ & van Noort V & Lebeer S." box="[1380,1411,1509,1533]" pageId="40" pageNumber="2822" refId="ref60115" refString="10. Wittouck S, Wuyts S, Meehan CJ, van Noort V, Lebeer S. A genome-based species taxonomy of the Lactobacillus Genus Complex. mSystems 2019; 4: e 00264 - 19." type="journal volume" year="2019">10</bibRefCitation>
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]. The availability of the genome sequences of the
|
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<typeStatus id="549B883EFFA52159DC2BF993FAE4647A" box="[1308,1355,1541,1565]" pageId="40" pageNumber="2822">type</typeStatus>
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strains of both subspecies revealed that they are only distantly related with an ANI value of 88.98%, substantially below the 95–96 % threshold recognised for the species level. Furthermore, their core nucleotide identity (CNI) [
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<bibRefCitation id="EFB14B6DFFA52159DDECF914FB5664FD" author="Wittouck S & Wuyts S & Meehan CJ & van Noort V & Lebeer S." box="[1243,1273,1666,1690]" pageId="40" pageNumber="2822" refId="ref60115" refString="10. Wittouck S, Wuyts S, Meehan CJ, van Noort V, Lebeer S. A genome-based species taxonomy of the Lactobacillus Genus Complex. mSystems 2019; 4: e 00264 - 19." type="journal volume" year="2019">10</bibRefCitation>
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] is 91.1, which is below the 94 % threshold at which two strains are allocated to the same species. Finally, their
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<emphasis id="B954EA8EFFA52159DDA0F957FB4A64BF" box="[1175,1253,1728,1752]" italics="true" pageId="40" pageNumber="2822">in silico</emphasis>
|
||
DDH value is 37.80, which additionally supports that these two subspecies should be recognised as different species [
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||
<bibRefCitation id="EFB14B6DFFA52159DD9FF969FB686570" author="Wittouck S & Wuyts S & Meehan CJ & van Noort V & Lebeer S." box="[1192,1223,1791,1815]" pageId="40" pageNumber="2822" refId="ref60115" refString="10. Wittouck S, Wuyts S, Meehan CJ, van Noort V, Lebeer S. A genome-based species taxonomy of the Lactobacillus Genus Complex. mSystems 2019; 4: e 00264 - 19." type="journal volume" year="2019">10</bibRefCitation>
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||
].
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||
</paragraph>
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<paragraph id="8B9F369CFFA52158DA0BF8BBFDF1628A" blockId="40.[826,1468,1180,1955]" lastBlockId="41.[121,760,182,452]" lastPageId="41" lastPageNumber="2823" pageId="40" pageNumber="2822">
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||
Cells are Gram- positive, non-motile, non-spore-forming rods with rounded ends, usually occurring singly or in short chains.
|
||
<taxonomicName id="4C204D1FFFA52159DABDF8FAFBBB65E3" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" box="[906,1044,1900,1924]" class="Bacilli" family="Lactobacillaceae" genus="Ligilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="40" pageNumber="2822" phylum="Firmicutes" rank="species" species="araffinosus">
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||
<emphasis id="B954EA8EFFA52159DABDF8FAFBBB65E3" box="[906,1044,1900,1924]" italics="true" pageId="40" pageNumber="2822">L. araffinosus</emphasis>
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||
</taxonomicName>
|
||
strains ferment trehalose and cellobiose, they do not produce acid from galactose, lactose, melibiose and raffinose [
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||
<bibRefCitation id="EFB14B6DFFA42158D826FF20FE9F62A9" author="Fujisawa T & Shirasaka S & Watabe J & Mitsuoka T." box="[273,304,182,206]" pageId="41" pageNumber="2823" pagination="414 - 420" refId="ref61679" refString="51. Fujisawa T, Shirasaka S, Watabe J, Mitsuoka T. Lactobacillus aviarius sp. nov.: a new species isolated from the intestine of chickens. Syst Appl Microbiol 1984; 5: 414 - 420." type="journal article" year="1984">51</bibRefCitation>
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||
]. The genome size of the
|
||
<typeStatus id="549B883EFFA42158DB0BFF21FDC562A8" box="[572,618,183,207]" pageId="41" pageNumber="2823">type</typeStatus>
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||
strain is 1.48 Mbp. The mol% G+C content of DNA is 38.1.
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||
</paragraph>
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<paragraph id="8B9F369CFFA42158D94EFE95FDCD637C" blockId="41.[121,760,182,452]" box="[121,610,259,283]" pageId="41" pageNumber="2823">Isolated from the intestine and faeces of birds.</paragraph>
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||
</subSubSection>
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<subSubSection id="C33A6517FFA42158D94EFEA7FD95633B" pageId="41" pageNumber="2823" type="materials_examined">
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<paragraph id="8B9F369CFFA42158D94EFEA7FD95633B" blockId="41.[121,760,182,452]" pageId="41" pageNumber="2823">
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<materialsCitation id="3B483CC1FFA42158D94EFEA7FD95633B" accessionNumber="DSM 20653" collectionCode="T, DSM" pageId="41" pageNumber="2823" specimenCode="ML2, ATCC 43235, CCUG 32231, CIP 103145, JCM 5667" specimenCount="1" typeStatus="holotype">
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||
The
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||
<typeStatus id="549B883EFFA42158D99DFEA7FF76632E" box="[170,217,305,329]" pageId="41" pageNumber="2823">type</typeStatus>
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||
strain is
|
||
<specimenCode id="DB869EE7FFA42158D875FEA7FED9632E" box="[322,374,305,329]" collectionCode="ML" country="France" name="Musee de Lectoure" pageId="41" pageNumber="2823">ML2</specimenCode>
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</superScript>
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=
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<specimenCode id="DB869EE7FFA42158D896FEA7FD9F632E" box="[417,560,305,329]" collectionCode="ATCC" country="USA" httpUri="http://grbio.org/cool/b0k1-wg01" name="American Type Culture Collection" pageId="41" pageNumber="2823">ATCC 43235</specimenCode>
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</superScript>
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=
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||
<collectionCode id="ED31AE59FFA42158DB64FEA7FD23632E" box="[595,652,305,329]" country="Germany" httpUri="http://grbio.org/cool/4644-42cg" name="Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" pageId="41" pageNumber="2823">DSM</collectionCode>
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20653
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<collectionCode id="ED31AE59FFA42158DBE1FEA6FD4F6359" box="[726,736,304,318]" name="Tavera, Department of Geology and Geophysics" pageId="41" pageNumber="2823">T</collectionCode>
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</superScript>
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=
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||
<specimenCode id="DB869EE7FFA42158D94EFEC6FEA6630F" box="[121,265,336,360]" collectionCode="CCUG" country="Sweden" httpUri="http://grbio.org/cool/td22-j49f" name="Culture Collection, University of Goteborg, Department of Clinical Bacteriology" pageId="41" pageNumber="2823">CCUG 32231</specimenCode>
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</superScript>
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=
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||
<specimenCode id="DB869EE7FFA42158D816FEC6FE306300" box="[289,415,335,360]" collectionCode="CIP" country="Colombia" httpUri="http://grbio.org/cool/kny8-abms" name="Centro de Investigaciones Pesqueras" pageId="41" pageNumber="2823">CIP 103145</specimenCode>
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=
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<specimenCode id="DB869EE7FFA42158D8F3FEC6FD806300" box="[452,559,335,360]" collectionCode="JCM" country="Japan" httpUri="http://grbio.org/cool/iyky-md37" name="Japan Collection of Microorganisms" pageId="41" pageNumber="2823">JCM 5667</specimenCode>
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</materialsCitation>
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</paragraph>
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</subSubSection>
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<subSubSection id="C33A6517FFA42158D94EFEEBFD1163F2" box="[121,702,381,405]" pageId="41" pageNumber="2823" type="description">
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<paragraph id="8B9F369CFFA42158D94EFEEBFD1163F2" blockId="41.[121,760,182,452]" box="[121,702,381,405]" pageId="41" pageNumber="2823">Genome sequence accession number: AYYZ00000000.</paragraph>
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||
</subSubSection>
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||
<subSubSection id="C33A6517FFA42158D94EFE3DFDCB63A4" box="[121,612,427,452]" pageId="41" pageNumber="2823" type="materials_examined">
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<paragraph id="8B9F369CFFA42158D94EFE3DFDCB63A4" blockId="41.[121,760,182,452]" box="[121,612,427,452]" pageId="41" pageNumber="2823">
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||
16S rRNA gene accession number:
|
||
<accessionNumber id="9473AB7FFFA42158D8D9FE3DFDCF63A4" box="[494,608,427,451]" httpUri="https://www.ebi.ac.uk/ena/browser/api/embl/AB289043" pageId="41" pageNumber="2823">AB289043</accessionNumber>
|
||
.
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |