219 lines
24 KiB
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219 lines
24 KiB
XML
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<mods:title id="0979AF5E22E3B5245E2F1AD6EE7DCBC6">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="E1C9219F35AE8A3CF891EC89E2CB4B77">Zheng, Jinshui</mods:namePart>
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<mods:namePart id="BC900F41557BC18A4C22D4C9E4174D71">Wittouck, Stijn</mods:namePart>
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<mods:namePart id="CD980F336BEB66546C8E629EBE8CC8CA">O’Toole, Paul W.</mods:namePart>
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<mods:namePart id="8894CCABD7384C2E8B0A7AB9285168F1">Pot, Bruno</mods:namePart>
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<mods:namePart id="3C389E7E6DE1E38D94CA0A9F96A47758">Walter, Jens</mods:namePart>
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<mods:namePart id="3F944769FF784B52D2D249871BE52249">Watanabe, Koichi</mods:namePart>
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<mods:namePart id="D5683234B57E3C3A91EFC8DCFC67F071">Wuyts, Sander</mods:namePart>
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<mods:namePart id="58934DC7C7659960D1344857C832AFD8">Felis, Giovanna E.</mods:namePart>
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<mods:namePart id="B60698C19E565CCB9A93A170BCE0CA25">Gänzle, Michael G.</mods:namePart>
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<mods:namePart id="E9D35ABA8248A77E068912C3EA5D03D0">Lebeer, Sarah</mods:namePart>
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<mods:title id="C9322684DC22428E5CC4E4703C99BC56">International Journal of Systematic and Evolutionary Microbiology</mods:title>
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<mods:date id="27A25303017EEF5442F055A5A0038BDB">2020</mods:date>
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<mods:number id="998E25718CCB112FD1D2E57FEA4A2F69">2020-04-15</mods:number>
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<mods:number id="E8B4397084C5367DB8FFE5C018D0375B">70</mods:number>
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<mods:identifier id="791D14EC6BE99C0E47E033B304040F3A" type="DOI">10.1099/ijsem.0.004107</mods:identifier>
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<treatment id="03A8D903D231027FFFD0FF4C503F368E" ID-DOI="http://doi.org/10.5281/zenodo.4728885" ID-GBIF-Taxon="181761591" ID-Zenodo-Dep="4728885" LSID="urn:lsid:plazi:treatment:03A8D903D231027FFFD0FF4C503F368E" httpUri="http://treatment.plazi.org/id/03A8D903D231027FFFD0FF4C503F368E" lastPageNumber="2844" pageId="62" pageNumber="2844">
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<subSubSection id="C31B3B9ED231027FFFD0FF4C51B833E4" pageId="62" pageNumber="2844" type="nomenclature">
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<paragraph id="8BBE6815D231027FFFD0FF4C51B833E4" blockId="62.[121,761,184,412]" pageId="62" pageNumber="2844">
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<heading id="D0F6DF79D231027FFFD0FF4C51B833E4" allCaps="true" bold="true" fontSize="12" level="3" pageId="62" pageNumber="2844" reason="0">
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<emphasis id="B975B407D231027FFFD0FF4C51B833E4" bold="true" pageId="62" pageNumber="2844">
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DESCRIPTIONOF
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<taxonomicName id="4C011396D231027FFEDBFF4C53A433CB" 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" box="[370,678,184,213]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="genus" status="gen. nov.">
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<emphasis id="B975B407D231027FFEDBFF4C53A433CB" bold="true" box="[370,678,184,213]" italics="true" pageId="62" pageNumber="2844">LENTILACTOBACILLUS</emphasis>
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</taxonomicName>
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<taxonomicNameLabel id="A246097CD231027FFD06FF4C51B833E4" pageId="62" pageNumber="2844" rank="genus">GEN. NOV.</taxonomicNameLabel>
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</emphasis>
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<subSubSection id="C31B3B9ED231027FFFD0FEF3530737A8" pageId="62" pageNumber="2844" type="discussion">
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<paragraph id="8BBE6815D231027FFFD0FEF353803282" blockId="62.[121,761,184,412]" pageId="62" pageNumber="2844">
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<taxonomicName id="4C011396D231027FFFD0FEF350323201" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" box="[121,304,263,287]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="genus">
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<emphasis id="B975B407D231027FFFD0FEF350323201" box="[121,304,263,287]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus</emphasis>
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</taxonomicName>
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(Len.ti.lac.to.ba.cil’lus. L. masc. adj.
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<emphasis id="B975B407D231027FFD13FEF353FA3201" box="[698,760,263,287]" italics="true" pageId="62" pageNumber="2844">lentus</emphasis>
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slow, sluggish, referring to the slow growth of species in the genus with lactate or propanediol as carbon course; N.L. masc. n.
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<taxonomicName id="4C011396D231027FFF71FE9150633263" authorityName="Beijerinck" authorityYear="1901" box="[216,353,357,381]" class="Bacilli" family="Lactobacillaceae" genus="Lactobacillus" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="genus">
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<emphasis id="B975B407D231027FFF71FE9150633263" box="[216,353,357,381]" italics="true" pageId="62" pageNumber="2844">Lactobacillus</emphasis>
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</taxonomicName>
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a bacterial genus name; N.L. masc. n.
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<taxonomicName id="4C011396D231027FFFD0FE7050323282" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" box="[121,304,388,412]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="genus">
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<emphasis id="B975B407D231027FFFD0FE7050323282" box="[121,304,388,412]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus</emphasis>
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</taxonomicName>
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a slow [growing] lactobacillus).
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</paragraph>
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<paragraph id="8BBE6815D231027FFFD0FE46530737A8" blockId="62.[120,760,434,1206]" pageId="62" pageNumber="2844">
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Gram-positive, rod-shaped, catalase negative, heterofermentative. Most strains grow at 15 °C and some also grow at 45 °C, the pH range of growth is highly variable but optimal growth is typically observed below pH 6.0. The genome size ranges from 1.57 Mbp for
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<taxonomicName id="4C011396D231027FFE72FDDB53F53159" box="[475,759,559,583]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="species" species="senioris">
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<emphasis id="B975B407D231027FFE72FDDB53F53159" box="[475,759,559,583]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus senioris</emphasis>
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</taxonomicName>
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to 4.91 Mbp for
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<taxonomicName id="4C011396D231027FFEE9FDBA53753178" box="[320,631,590,614]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="species" species="parakefiri">
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<emphasis id="B975B407D231027FFEE9FDBA53753178" box="[320,631,590,614]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus parakefiri</emphasis>
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</taxonomicName>
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, the mol% G+C content of DNA ranges from 39.1–45.2 %. Strains in thegenus were isolatedfrom silage, fermented vegetables, particularly as secondary fermentation or spoilage microbiota, (spoiled) wine and cereal mashes. Generally, strains in the species lead a free-living lifestyle; individual species of the genus, particularly
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<taxonomicName id="4C011396D231027FFE32FCFE5309303F" box="[411,523,778,801]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="species" species="senioris">
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<emphasis id="B975B407D231027FFE32FCFE5309303F" box="[411,523,778,801]" italics="true" pageId="62" pageNumber="2844">L. senioris</emphasis>
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</taxonomicName>
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, appear to transition to a specialized, host adapted lifestyle.
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<taxonomicName id="4C011396D231027FFD9EFCDC51C4307E" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="species" species="undetermined">
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<emphasis id="B975B407D231027FFD9EFCDC53FA305E" box="[567,760,808,832]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus</emphasis>
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species
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</taxonomicName>
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generally metabolize a broad spectrum of pentoses, hexoses, and disaccharides. Most species metabolize lactate to 1,2-propanediol and / or 1,2-propanediol to propanol and propionate; these pathways are virtually exclusive to heterofermentative lactobacilli and, among these, most common and most frequent in
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<taxonomicName id="4C011396D231027FFE45FC1753AF30E5" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" box="[492,685,995,1019]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="genus">
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<emphasis id="B975B407D231027FFE45FC1753AF30E5" box="[492,685,995,1019]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus</emphasis>
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</taxonomicName>
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. Most
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<taxonomicName id="4C011396D231027FFFD0FBF750883705" box="[121,394,1027,1051]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="species" species="undetermined">
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<emphasis id="B975B407D231027FFFD0FBF750343705" box="[121,310,1027,1051]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus</emphasis>
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species
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</taxonomicName>
|
||
also convert agmatine, a product of bacterial decarboxylation of arginine, via the agmatine deiminase pathway [
|
||
<bibRefCitation id="EF9015E4D231027FFEF5FBB550783747" author="Zheng J & Ruan L & Sun M & Ganzle M." box="[348,378,1089,1113]" journalOrPublisher="Appl Environ Microbiol" pageId="62" pageNumber="2844" pagination="7233 - 7243" part="81" refId="ref60098" refString="14. Zheng J, Ruan L, Sun M, Ganzle M. A genomic view of lactobacilli and pediococci demonstrates that phylogeny matches ecology and physiology. Appl Environ Microbiol 2015; 81: 7233 - 7243." title="A genomic view of lactobacilli and pediococci demonstrates that phylogeny matches ecology and physiology" type="journal article" year="2015">14</bibRefCitation>
|
||
,
|
||
<bibRefCitation id="EF9015E4D231027FFE2EFBB550B13747" author="Arena ME & Landete JM & Manca de Nadra MC & Pardo I & Ferrer S." box="[391,435,1089,1113]" pageId="62" pageNumber="2844" pagination="158 - 165" refId="ref73904" refString="326. Arena ME, Landete JM, Manca de Nadra MC, Pardo I, Ferrer S. Factors affecting the production of putrescine from agmatine by Lactobacillus hilgardii xB isolated from wine. J Appl Microbiol 2008; 105: 158 - 165." type="journal article" year="2008">326</bibRefCitation>
|
||
]; in lactobacilli, this pathway is associated with a free-living lifestyle.
|
||
<taxonomicName id="4C011396D231027FFD93FB9451C43789" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="species" species="undetermined">
|
||
<emphasis id="B975B407D231027FFD93FB9453FA3766" box="[570,760,1120,1144]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus</emphasis>
|
||
species
|
||
</taxonomicName>
|
||
are used commercially as silage starter cultures, and in few dairy and cereal applications.
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection id="C31B3B9ED231027FFFD0FB39503F368E" pageId="62" pageNumber="2844" type="description">
|
||
<paragraph id="8BBE6815D231027FFFD0FB3951A4363D" blockId="62.[121,760,1229,1315]" pageId="62" pageNumber="2844">
|
||
Aphylogenetic tree on the basis of 16S rRNA genes of all species in the genus
|
||
<taxonomicName id="4C011396D231027FFEF0FB185312361A" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" box="[345,528,1260,1284]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="genus">
|
||
<emphasis id="B975B407D231027FFEF0FB185312361A" box="[345,528,1260,1284]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus</emphasis>
|
||
</taxonomicName>
|
||
is provided in
|
||
<figureCitation id="133A7490D231027FFD1AFB1851A0363D" captionStart="Fig" captionStartId="7.[185,216,1617,1636]" captionTargetBox="[264,1323,181,1565]" captionTargetId="figure-17@7.[264,1323,181,1565]" captionTargetPageId="7" captionText="Fig. 6. Gene family presence/absence patterns in Lactobacillaceae and Leuconostocaceae. Each column represents a gene family presence/absence pattern in species of Lactobacillaceae and Leuconostoaceae, where presence is indicated with a dot. The absolute number of gene families that conform to each pattern is visualized in the marginal bar plot at the top. Separations between phylogroups are indicated with horizontal black lines. We defined genes that were present in all genomes of a clade and in none of the genomes outside of that clade as ‘signature genes’ (dark blue); other genes are shown in light blue. Only presence/absence patterns followed by four or more gene families are shown. Patterns of presence in a single species or all species are not shown. Unassigned species are clusters of closely related genomes which could not be assigned to a known species due to low whole-genome similarity to a type strain and/or low 16S rRNA similarity to a type strain." figureDoi="http://doi.org/10.5281/zenodo.4730552" httpUri="https://zenodo.org/record/4730552/files/figure.png" pageId="62" pageNumber="2844">Figure S6S</figureCitation>
|
||
.
|
||
</paragraph>
|
||
<paragraph id="8BBE6815D231027FFFD0FACD503F368E" blockId="62.[121,760,1337,1424]" pageId="62" pageNumber="2844">
|
||
The type speciesof the genus is
|
||
<taxonomicName id="4C011396D231027FFE73FACD53FA364F" 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="[474,760,1337,1361]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="species" species="buchneri" status="comb. nov.">
|
||
<emphasis id="B975B407D231027FFE73FACD53FA364F" box="[474,760,1337,1361]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus buchneri</emphasis>
|
||
</taxonomicName>
|
||
<taxonomicNameLabel id="A246097CD231027FFFD0FAAD51F0366E" box="[121,242,1369,1393]" pageId="62" pageNumber="2844" rank="species">comb. nov.</taxonomicNameLabel>
|
||
;
|
||
<taxonomicName id="4C011396D231027FFF57FAAD50B5366F" authorityName="Zheng & Wittouck & Salvetti & Franz & Harris & Mattarelli & O’Toole & Pot & Vandamme & Walter & Watanabe & Wuyts & Felis & Gänzle & Lebeer" authorityYear="2020" box="[254,439,1369,1393]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="genus">
|
||
<emphasis id="B975B407D231027FFF57FAAD50B5366F" box="[254,439,1369,1393]" italics="true" pageId="62" pageNumber="2844">Lentilactobacillus</emphasis>
|
||
</taxonomicName>
|
||
was previously referred to as
|
||
<taxonomicName id="4C011396D231027FFFD2FA8C51F3368E" 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="[123,241,1400,1424]" class="Bacilli" family="Lactobacillaceae" genus="Lentilactobacillus" higherTaxonomySource="GBIF" kingdom="Bacteria" order="Lactobacillales" pageId="62" pageNumber="2844" phylum="Firmicutes" rank="species" species="buchneri">
|
||
<emphasis id="B975B407D231027FFFD2FA8C51F3368E" box="[123,241,1400,1424]" italics="true" pageId="62" pageNumber="2844">L. buchneri</emphasis>
|
||
</taxonomicName>
|
||
group.
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |