319 lines
32 KiB
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319 lines
32 KiB
XML
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<mods:title id="4ED6DC80A129D3DC78616D8494EC629B">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="FCAF10C1A774D5A5818C6B2ACA64CF06">Zheng, Jinshui</mods:namePart>
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<mods:namePart id="7D4C54D7A2A68146080A63BE772865E6">Wuyts, Sander</mods:namePart>
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<mods:namePart id="9D109414F44A02E46FEE2B1F04EE5AB0">Gänzle, Michael G.</mods:namePart>
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<mods:namePart id="A6C5A866A8FB8224BC4253D970AF920D">Lebeer, Sarah</mods:namePart>
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<mods:title id="78C5F7CE8EB497CDFA2881ECFCF9516D">International Journal of Systematic and Evolutionary Microbiology</mods:title>
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<mods:date id="81CD5062D9C957141AEFF3C7B3A9697F">2020</mods:date>
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<treatment id="0389878AFF90216CD94EF99DFA8A60F4" ID-DOI="http://doi.org/10.5281/zenodo.6309694" ID-Zenodo-Dep="6309694" LSID="urn:lsid:plazi:treatment:0389878AFF90216CD94EF99DFA8A60F4" httpUri="http://treatment.plazi.org/id/0389878AFF90216CD94EF99DFA8A60F4" lastPageNumber="2811" pageId="29" pageNumber="2811">
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<emphasis id="B954EA8EFF90216CD94EF99DFED6642A" bold="true" pageId="29" pageNumber="2811">
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DESCRIPTION OF
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<taxonomicName id="4C204D1FFF90216CD845F99DFF63642A" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" baseAuthorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" baseAuthorityYear="2020" class="Bacilli" family="Lactobacillaceae" genus="Lacticaseibacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="casei" status="comb. nov.">
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<emphasis id="B954EA8EFF90216CD845F99DFF63642A" bold="true" italics="true" pageId="29" pageNumber="2811">LACTICASEIBACILLUS CASEI</emphasis>
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<taxonomicNameLabel id="A26757F5FF90216CD9E3F9A6FED6642A" box="[212,377,1584,1613]" pageId="29" pageNumber="2811" rank="species">COMB. NOV.</taxonomicNameLabel>
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</emphasis>
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<subSubSection id="C33A6517FF90216CD94EF9CCFD626415" box="[121,717,1626,1650]" pageId="29" pageNumber="2811" type="etymology">
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<paragraph id="8B9F369CFF90216CD94EF9CCFD626415" blockId="29.[120,762,1547,1956]" box="[121,717,1626,1650]" pageId="29" pageNumber="2811">
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<taxonomicName id="4C204D1FFF90216CD94EF9CCFEC96416" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" baseAuthorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" baseAuthorityYear="2020" box="[121,358,1626,1650]" class="Bacilli" family="Lactobacillaceae" genus="Lacticaseibacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="casei">
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<emphasis id="B954EA8EFF90216CD94EF9CCFEC96416" box="[121,358,1626,1650]" italics="true" pageId="29" pageNumber="2811">Lacticaseibacillus casei</emphasis>
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(ca’se.i. L. gen. n.
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<taxonomicName id="4C204D1FFF90216CDB13F9CCFDF96416" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" baseAuthorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" baseAuthorityYear="2020" box="[548,598,1626,1649]" class="Bacilli" family="Lactobacillaceae" genus="Lacticaseibacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="casei">
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<emphasis id="B954EA8EFF90216CDB13F9CCFDF96416" box="[548,598,1626,1649]" italics="true" pageId="29" pageNumber="2811">casei</emphasis>
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of cheese).
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</paragraph>
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<paragraph id="8B9F369CFF90216CD94EF91EFE9664BA" blockId="29.[120,762,1547,1956]" pageId="29" pageNumber="2811">
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Basonym:
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<taxonomicName id="4C204D1FFF90216CD9DFF91EFE0764F8" authorityName="Hansen & Lessel" authorityYear="1971" baseAuthorityName="Orla-Jensen" baseAuthorityYear="1916" box="[232,424,1672,1696]" class="Bacilli" family="Lactobacillaceae" genus="Lactobacillus" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="casei">
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<emphasis id="B954EA8EFF90216CD9DFF91EFE0764F8" box="[232,424,1672,1696]" italics="true" pageId="29" pageNumber="2811">Lactobacillus casei</emphasis>
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</taxonomicName>
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(
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<collectingRegion id="49E4F87EFF90216CD881F91EFE4764C7" box="[438,488,1672,1696]" country="Russia" name="Orel" pageId="29" pageNumber="2811">Orla</collectingRegion>
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Jensen 1916, Hansen and Lessel 1971, 71 (Approved Lists) (
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<taxonomicName id="4C204D1FFF90216CD8E3F930FD1564D9" box="[468,698,1702,1726]" class="Bacilli" family="Lactobacillaceae" genus="Streptobacterium" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="casei">
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<emphasis id="B954EA8EFF90216CD8E3F930FD1564D9" box="[468,698,1702,1726]" italics="true" pageId="29" pageNumber="2811">Streptobacterium casei</emphasis>
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Orla-Jensen 1919, 166).
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</paragraph>
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<paragraph id="8B9F369CFF90216CD94EF965FEB265C3" blockId="29.[120,762,1547,1956]" pageId="29" pageNumber="2811">
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The species includes strains previously classified as
|
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<taxonomicName id="4C204D1FFF90216CDBACF965FF4A654E" authorityName="Dicks et al." authorityYear="1996" baseAuthorityName="ex Kuznetsov" baseAuthorityYear="1959" class="Bacilli" family="Lactobacillaceae" genus="Lactobacillus" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="zeae">
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<emphasis id="B954EA8EFF90216CDBACF965FF4A654E" italics="true" pageId="29" pageNumber="2811">Lactobacillus zeae</emphasis>
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</taxonomicName>
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[
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<bibRefCitation id="EFB14B6DFF90216CD9C2F887FE8D654E" author="Tindall B." box="[245,290,1809,1833]" pageId="29" pageNumber="2811" pagination="1764 - 1765" refId="ref66444" refString="155. Tindall B. The type strain of Lactobacillus casei is ATCC 393, ATCC 334 cannot serve as the type because it represents a different taxon, the name Lactobacillus paracasei and its subspecies names are not rejected and the revival of the name " Lactobacillus zeae " contravenes Rules 51 b (1) and (2) of the International Code of Nomenclature of Bacteria. Opinion 82. Int J Syst Evol Microbiol 2008; 58: 1764 - 1765." type="journal article" year="2008">155</bibRefCitation>
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]. Original characteristics of
|
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<taxonomicName id="4C204D1FFF90216CDB6FF884FD07654E" box="[600,680,1810,1833]" class="Bacilli" family="Lactobacillaceae" genus="Streptobacterium" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="casei">
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<emphasis id="B954EA8EFF90216CDB6FF884FD07654E" box="[600,680,1810,1833]" italics="true" pageId="29" pageNumber="2811">L. casei</emphasis>
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</taxonomicName>
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strains are provided by [
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<bibRefCitation id="EFB14B6DFF90216CD804F8A6FEEC652F" author="Orla-Jensen S." box="[307,323,1840,1864]" pageId="29" pageNumber="2811" refId="ref59849" refString="2. Orla-Jensen S. The lactic acid bacteria. Copenhagen: Andr Fred HOst and Son; 1919." type="book" year="1919">2</bibRefCitation>
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,
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<bibRefCitation id="EFB14B6DFF90216CD878F8A6FED8652F" author="Orla-Jensen S." box="[335,375,1840,1864]" pageId="29" pageNumber="2811" refId="ref66530" refString="156. Orla-Jensen S. Maelkeri-Bakteriologi 1916." type="book" year="1916">156</bibRefCitation>
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,
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<bibRefCitation id="EFB14B6DFF90216CD8B4F8A6FE01652F" author="Hansen PA & Lessel EF" box="[387,430,1840,1864]" pageId="29" pageNumber="2811" pagination="69 - 71" refId="ref66538" refString="157. Hansen PA, Lessel EF. Lactobacillus casei (Orla-Jensen) comb. nov. Int J Syst Bacteriol 1971; 21: 69 - 71." type="journal article" year="1971">157</bibRefCitation>
|
||
].
|
||
<taxonomicName id="4C204D1FFF90216CD8F7F8A7FDA0652F" box="[448,527,1841,1864]" class="Bacilli" family="Lactobacillaceae" genus="Streptobacterium" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="casei">
|
||
<emphasis id="B954EA8EFF90216CD8F7F8A7FDA0652F" box="[448,527,1841,1864]" italics="true" pageId="29" pageNumber="2811">L. casei</emphasis>
|
||
</taxonomicName>
|
||
is differentiated from most other lactobacilli by catalase activity [
|
||
<bibRefCitation id="EFB14B6DFF90216CDB73F8D9FDCB6500" author="Wuyts S & Wittouck S & De Boeck I & Allonsius CN & Pasolli E" box="[580,612,1871,1895]" pageId="29" pageNumber="2811" refId="ref61525" refString="47. Wuyts S, Wittouck S, De Boeck I, Allonsius CN, Pasolli E et al. Large-scale phylogenomics of the Lactobacillus casei group highlights taxonomic inconsistencies and reveals novel cladeassociated features. mSystems 2017; 2: e 00061 - 17." type="journal volume" year="2017">47</bibRefCitation>
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||
]. The genome size of the
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<typeStatus id="549B883EFF90216CD9D8F8F8FEB265E1" box="[239,285,1902,1926]" pageId="29" pageNumber="2811">type</typeStatus>
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||
strain is 2.83 Mbp. The mol% G+C content of DNA is 46.5.
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||
</paragraph>
|
||
<paragraph id="8B9F369CFF90216CDA0BFF21FB6C63EC" blockId="29.[826,1468,183,660]" pageId="29" pageNumber="2811">
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Isolates were obtained from diverse sources including chinese traditional pickle, infant faeces, corn liquor, oat silage, commercial dietary supplements, sputum, nasopharynx [
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<bibRefCitation id="EFB14B6DFF90216CDA74FE83FCCC634A" author="Wuyts S & Wittouck S & De Boeck I & Allonsius CN & Pasolli E" box="[835,867,277,301]" pageId="29" pageNumber="2811" refId="ref61525" refString="47. Wuyts S, Wittouck S, De Boeck I, Allonsius CN, Pasolli E et al. Large-scale phylogenomics of the Lactobacillus casei group highlights taxonomic inconsistencies and reveals novel cladeassociated features. mSystems 2017; 2: e 00061 - 17." type="journal volume" year="2017">47</bibRefCitation>
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]. Information on the lifestyle of
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||
<taxonomicName id="4C204D1FFF90216CDDFDFE83FAB5634B" box="[1226,1306,277,300]" class="Bacilli" family="Lactobacillaceae" genus="Streptobacterium" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="casei">
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<emphasis id="B954EA8EFF90216CDDFDFE83FAB5634B" box="[1226,1306,277,300]" italics="true" pageId="29" pageNumber="2811">L. casei</emphasis>
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</taxonomicName>
|
||
is counded by the unclear taxonomy over the past decades; most genomes of designated as
|
||
<taxonomicName id="4C204D1FFF90216CDADFFEC2FB9C630C" box="[1000,1075,340,363]" class="Bacilli" family="Lactobacillaceae" genus="Streptobacterium" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="casei">
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<emphasis id="B954EA8EFF90216CDADFFEC2FB9C630C" box="[1000,1075,340,363]" italics="true" pageId="29" pageNumber="2811">L. casei</emphasis>
|
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</taxonomicName>
|
||
in the NCBI database should be classified as
|
||
<taxonomicName id="4C204D1FFF90216CDAA1FEE5FBBC63ED" box="[918,1043,371,394]" class="Bacilli" family="Lactobacillaceae" genus="Lactobacillus" kingdom="Bacteria" order="Lactobacillales" pageId="29" pageNumber="2811" phylum="Firmicutes" rank="species" species="paracasei">
|
||
<emphasis id="B954EA8EFF90216CDAA1FEE5FBBC63ED" box="[918,1043,371,394]" italics="true" pageId="29" pageNumber="2811">L. paracasei</emphasis>
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</taxonomicName>
|
||
instead [
|
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<bibRefCitation id="EFB14B6DFF90216CDD45FEE5FB2063EC" author="Wittouck S & Wuyts S & Meehan CJ & van Noort V & Lebeer S." box="[1138,1167,371,395]" pageId="29" pageNumber="2811" 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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<bibRefCitation id="EFB14B6DFF90216CDDADFEE5FB1763EC" author="Wuyts S & Wittouck S & De Boeck I & Allonsius CN & Pasolli E" box="[1178,1208,371,395]" pageId="29" pageNumber="2811" refId="ref61525" refString="47. Wuyts S, Wittouck S, De Boeck I, Allonsius CN, Pasolli E et al. Large-scale phylogenomics of the Lactobacillus casei group highlights taxonomic inconsistencies and reveals novel cladeassociated features. mSystems 2017; 2: e 00061 - 17." type="journal volume" year="2017">47</bibRefCitation>
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].
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</paragraph>
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</subSubSection>
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<paragraph id="8B9F369CFF90216CDA0BFE37FB416051" blockId="29.[826,1468,183,660]" pageId="29" pageNumber="2811">
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<materialsCitation id="3B483CC1FF90216CDA0BFE37FB416051" accessionNumber="IAM 12473, DSM 20011" collectionCode="IAM, R, T, DSM, NRRL" collectorName="Orland & P. Tittsler" pageId="29" pageNumber="2811" specimenCode="ATCC 393, BCRC 10697, CCUG 21451, CECT 475, CIP 103137, NBRC 15883, JCM 1134, KCTC 3109, LMG 6904, NCIMB 11970" specimenCount="1" typeStatus="holotype">
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The
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<typeStatus id="549B883EFF90216CDA5DFE34FC3763DD" box="[874,920,418,442]" pageId="29" pageNumber="2811">type</typeStatus>
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strain is 03 [7,
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<collectionCode id="ED31AE59FF90216CDD0DFE37FBC363DE" box="[1082,1132,417,441]" country="Spain" httpUri="http://grbio.org/cool/ahcp-gp9g" name="Instituto Arguelogico Municipal" pageId="29" pageNumber="2811">IAM</collectionCode>
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12473,
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<collectorName id="26D5534AFF90216CDD88FE37FAA363DE" box="[1215,1292,417,441]" pageId="29" pageNumber="2811">Orland</collectorName>
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L-323,
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<collectionCode id="ED31AE59FF90216CDC6BFE34FAC063DE" box="[1372,1391,418,441]" country="Chile" name="Departamento de Geologia, Universidad de Chile" pageId="29" pageNumber="2811">R</collectionCode>
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.
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<collectorName id="26D5534AFF90216CDC45FE34FCCE63BF" pageId="29" pageNumber="2811">P. Tittsler</collectorName>
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303]
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=
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<specimenCode id="DB869EE7FF90216CDA9CFE57FBB463BE" box="[939,1051,449,473]" collectionCode="ATCC" country="USA" httpUri="http://grbio.org/cool/b0k1-wg01" name="American Type Culture Collection" pageId="29" pageNumber="2811">ATCC 393</specimenCode>
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=
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<specimenCode id="DB869EE7FF90216CDD05FE57FB1563BF" box="[1074,1210,448,473]" collectionCode="BCRC" country="Taiwan" httpUri="http://grbio.org/cool/cv7g-ikqh" name="Bioresource Collection and Research Center" pageId="29" pageNumber="2811">BCRC 10697</specimenCode>
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<collectionCode id="ED31AE59FF90216CDD8DFE29FB6C63AA" box="[1210,1219,447,461]" name="Tavera, Department of Geology and Geophysics" pageId="29" pageNumber="2811">T</collectionCode>
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=
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<specimenCode id="DB869EE7FF90216CDDE6FE57FACF63BF" box="[1233,1376,448,473]" collectionCode="CCUG" country="Sweden" httpUri="http://grbio.org/cool/td22-j49f" name="Culture Collection, University of Goteborg, Department of Clinical Bacteriology" pageId="29" pageNumber="2811">CCUG 21451</specimenCode>
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=
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<specimenCode id="DB869EE7FF90216CDC40FE57FCCC639F" collectionCode="CECT" country="Spain" httpUri="http://grbio.org/cool/n6ez-ekac" name="Coleccion Espanola de Cultivos Tipo" pageId="29" pageNumber="2811">CECT 475</specimenCode>
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=
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<specimenCode id="DB869EE7FF90216CDA4CFE76FBA4639F" box="[891,1035,480,504]" collectionCode="CIP" country="Colombia" httpUri="http://grbio.org/cool/kny8-abms" name="Centro de Investigaciones Pesqueras" pageId="29" pageNumber="2811">CIP 103137</specimenCode>
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=
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<collectionCode id="ED31AE59FF90216CDD13FE76FBF1639F" box="[1060,1118,480,504]" country="Germany" httpUri="http://grbio.org/cool/4644-42cg" name="Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH" pageId="29" pageNumber="2811">DSM</collectionCode>
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20011
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</superScript>
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=
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<collectionCode id="ED31AE59FF90216CDDF9FE76FAAC639F" box="[1230,1283,480,504]" country="Spain" httpUri="http://grbio.org/cool/ahcp-gp9g" name="Instituto Arguelogico Municipal" pageId="29" pageNumber="2811">IAM</collectionCode>
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12473
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</superScript>
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=
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<specimenCode id="DB869EE7FF90216CDC45FE76FCD26070" collectionCode="NBRC" country="Japan" httpUri="http://grbio.org/cool/sq2m-rc8c" name="NITE Biological Resource Center" pageId="29" pageNumber="2811">NBRC 15883</specimenCode>
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=
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<specimenCode id="DB869EE7FF90216CDAA2FE69FBA16070" box="[917,1038,511,535]" collectionCode="JCM" country="Japan" httpUri="http://grbio.org/cool/iyky-md37" name="Japan Collection of Microorganisms" pageId="29" pageNumber="2811">JCM 1134</specimenCode>
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</superScript>
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=
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<specimenCode id="DB869EE7FF90216CDD11FE69FB1E6070" box="[1062,1201,511,535]" collectionCode="KCTC" country="South Korea" httpUri="http://grbio.org/cool/2inw-p49s" name="Korean Collection for Type Cultures" pageId="29" pageNumber="2811">KCTC 3109</specimenCode>
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=
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<specimenCode id="DB869EE7FF90216CDDFEFE69FAE66070" box="[1225,1353,511,535]" collectionCode="LMG" country="Belgium" httpUri="http://grbio.org/cool/0fkg-rcci" name="Belgian Coordinated Collections of Microorganisms/ LMG Bacteria Collection" pageId="29" pageNumber="2811">LMG 6904</specimenCode>
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</superScript>
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=
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||
<specimenCode id="DB869EE7FF90216CDC56FE69FCD36050" collectionCode="NCIMB" country="United Kingdom" httpUri="http://grbio.org/cool/v838-riag" name="National Collections of Industrial Food and Marine Bacteria (incorporating the NCFB)" pageId="29" pageNumber="2811">NCIMB 11970</specimenCode>
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</superScript>
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=
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<specimenCode id="DB869EE7FF90216CDAA4FD89FB9E6050" box="[915,1073,543,567]" collectionCode="NCIMB" country="United Kingdom" httpUri="http://grbio.org/cool/v838-riag" name="National Collections of Industrial Food and Marine Bacteria (incorporating the NCFB)" pageId="29" pageNumber="2811">NCIMB 11970</specimenCode>
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<collectionCode id="ED31AE59FF90216CDD06FD8BFB94604C" box="[1073,1083,541,555]" name="Tavera, Department of Geology and Geophysics" pageId="29" pageNumber="2811">T</collectionCode>
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=
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<collectionCode id="ED31AE59FF90216CDD7FFD89FB226051" box="[1096,1165,543,566]" pageId="29" pageNumber="2811">NRRL</collectionCode>
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B-1922
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</superScript>
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.
|
||
</materialsCitation>
|
||
</paragraph>
|
||
</subSubSection>
|
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<subSubSection id="C33A6517FF90216CDA0BFDDBFAD56002" box="[828,1402,589,613]" pageId="29" pageNumber="2811" type="description">
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<paragraph id="8B9F369CFF90216CDA0BFDDBFAD56002" blockId="29.[826,1468,183,660]" box="[828,1402,589,613]" pageId="29" pageNumber="2811">Genome sequence accession number: BALS00000000.</paragraph>
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</subSubSection>
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<subSubSection id="C33A6517FF90216CDA0BFDEDFA8A60F4" box="[828,1317,635,660]" pageId="29" pageNumber="2811" type="materials_examined">
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<paragraph id="8B9F369CFF90216CDA0BFDEDFA8A60F4" blockId="29.[826,1468,183,660]" box="[828,1317,635,660]" pageId="29" pageNumber="2811">
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||
16S rRNA gene accession number:
|
||
<accessionNumber id="9473AB7FFF90216CDD86FDEDFA8E60F4" box="[1201,1313,635,659]" httpUri="https://www.ebi.ac.uk/ena/browser/api/embl/AF469172" pageId="29" pageNumber="2811">AF469172</accessionNumber>
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||
.
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||
</paragraph>
|
||
</subSubSection>
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||
</treatment>
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||
</document> |