Antrihabitans stalagmiti sp. nov., isolated from a larva cave and a proposal to transfer Rhodococcus cavernicola Lee et al. 2020 to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov. comb. nov
An actinobacterial strain, designated YC3-6 T , was isolated from a larva cave in Jeju, Republic of Korea. The novel isolate was found to grow at 10–30 °C, pH 5.0–10.0 and 0–4% (w/v) NaCl. The 16S rRNA gene phylogeny showed that the novel isolate formed a distinct subline within the family Nocardiac...
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| Veröffentlicht in: | Antonie van Leeuwenhoek 2022-04, Vol.115 (4), p.521-532 |
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| creator | Kim, Sung-Min Lee, Soon Dong Koh, Young Sang Kim, In Seop |
| description | An actinobacterial strain, designated YC3-6
T
, was isolated from a larva cave in Jeju, Republic of Korea. The novel isolate was found to grow at 10–30 °C, pH 5.0–10.0 and 0–4% (w/v) NaCl. The 16S rRNA gene phylogeny showed that the novel isolate formed a distinct subline within the family
Nocardiaceae
. Levels of 16S rRNA gene similarity indicated that the close relatives are
Rhodococcus cavernicola
(98.4% sequence similarity) and “
Rhodococcus psychrotolerans
” (98.2%) followed by
Antrihabitans stalactiti
(96.8%). However, the core gene-based phylogeny revealed that the novel isolate formed a tight cluster with
A. stalactiti
and was separated from
R. cavernicola
and other members of the family
Nocardiaceae.
The morphological and chemotaxonomic characteristics of strain YC3-6
T
are in line with those of the genus
Antrihabitans
. Strain YC3-6
T
showed an average nucleotide identity of 75.5% and a digital DDH of 20.3% with
A. stalactiti.
In addition, the core gene analysis showed that
R. cavernicola
formed a distinct subline between an
Antrihabitans
cluster and
Aldersonia kunmingensis
, and well separated from members of the genus
Rhodococcus
. The average amino acid identity values of
R. cavernicola
to closely related neighbours were 69.3–69.4% with members of the genus
Antrihabitans
and 67.3% with
Ald. kunmingensis
, while the POCP values ranged from 56.9 to 63.6%. On the basis of results obtained here, strain YC3-6
T
is concluded to represent a novel species of the genus
Antrihabitans
, for which the name
Antrihabitans stalagmiti
sp. nov. (type strain, YC3-6
T
= KACC 19963
T
= DSM 107561
T
) is proposed. Based on overall genome relatedness and chemotaxonomic differences, it is also proposed that
R. cavernicola
Lee et al. 2020 be transferred to a new genus
Spelaeibacter
as
Spelaeibacter cavernicola
gen. nov., comb. nov. |
| doi_str_mv | 10.1007/s10482-022-01718-8 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2630930425</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2630930425</sourcerecordid><originalsourceid>FETCH-LOGICAL-c305t-c889707d4108580ff2f729d9e5f2cde573e062d8b1437507b0392c45a73599533</originalsourceid><addsrcrecordid>eNp9kc1u1DAUhSMEokPhBVggS2xYNMO1Hcf2sqqgII2ExM86cpybaarEDrYzFS_JM-GZlB91wcKy7_V3jq91iuIlhS0FkG8jhUqxElheVFJVqkfFhgrJSl1r_bjYAAAva5DsrHgW420uda3k0-KMCyp1LatN8fPSpTDcmHZIxkUSkxnNfhrSQOK8Jc4fthdkiH40CTvSBz8RQ0YTDoZYc0BiXJcbc_Czj2YkyZMUsk-PgXy-8Z233tolntjgBpt9yA6RYCJm3BIGDI4aQxzekT26jH6ZcTQ4tMambGIeNv51yoJ1RGL91J6Oz4snvRkjvrjfz4tv7999vfpQ7j5df7y63JWWg0ilVUpLkF1FQQkFfc96yXSnUfTMdigkR6hZp1pacSlAtsA1s5UwkgutBefnxZvVN3_9-4IxNdMQLY6jceiX2LCag-ZQMZHR1w_QW78El6fLVAWi5qJWmWIrZYOPMWDfzGGYTPjRUGiOaTdr2k1Ouzml3RxFr-6tl3bC7o_kd7wZ4CsQ85XbY_j79n9sfwG1wLU9</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2640563568</pqid></control><display><type>article</type><title>Antrihabitans stalagmiti sp. nov., isolated from a larva cave and a proposal to transfer Rhodococcus cavernicola Lee et al. 2020 to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov. comb. nov</title><source>SpringerLink Journals - AutoHoldings</source><creator>Kim, Sung-Min ; Lee, Soon Dong ; Koh, Young Sang ; Kim, In Seop</creator><creatorcontrib>Kim, Sung-Min ; Lee, Soon Dong ; Koh, Young Sang ; Kim, In Seop</creatorcontrib><description>An actinobacterial strain, designated YC3-6
T
, was isolated from a larva cave in Jeju, Republic of Korea. The novel isolate was found to grow at 10–30 °C, pH 5.0–10.0 and 0–4% (w/v) NaCl. The 16S rRNA gene phylogeny showed that the novel isolate formed a distinct subline within the family
Nocardiaceae
. Levels of 16S rRNA gene similarity indicated that the close relatives are
Rhodococcus cavernicola
(98.4% sequence similarity) and “
Rhodococcus psychrotolerans
” (98.2%) followed by
Antrihabitans stalactiti
(96.8%). However, the core gene-based phylogeny revealed that the novel isolate formed a tight cluster with
A. stalactiti
and was separated from
R. cavernicola
and other members of the family
Nocardiaceae.
The morphological and chemotaxonomic characteristics of strain YC3-6
T
are in line with those of the genus
Antrihabitans
. Strain YC3-6
T
showed an average nucleotide identity of 75.5% and a digital DDH of 20.3% with
A. stalactiti.
In addition, the core gene analysis showed that
R. cavernicola
formed a distinct subline between an
Antrihabitans
cluster and
Aldersonia kunmingensis
, and well separated from members of the genus
Rhodococcus
. The average amino acid identity values of
R. cavernicola
to closely related neighbours were 69.3–69.4% with members of the genus
Antrihabitans
and 67.3% with
Ald. kunmingensis
, while the POCP values ranged from 56.9 to 63.6%. On the basis of results obtained here, strain YC3-6
T
is concluded to represent a novel species of the genus
Antrihabitans
, for which the name
Antrihabitans stalagmiti
sp. nov. (type strain, YC3-6
T
= KACC 19963
T
= DSM 107561
T
) is proposed. Based on overall genome relatedness and chemotaxonomic differences, it is also proposed that
R. cavernicola
Lee et al. 2020 be transferred to a new genus
Spelaeibacter
as
Spelaeibacter cavernicola
gen. nov., comb. nov.</description><identifier>ISSN: 0003-6072</identifier><identifier>EISSN: 1572-9699</identifier><identifier>DOI: 10.1007/s10482-022-01718-8</identifier><identifier>PMID: 35179674</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Amino acids ; Biomedical and Life Sciences ; Clusters ; Genomes ; Life Sciences ; Medical Microbiology ; Microbiology ; Morphology ; New genera ; New species ; Nucleotides ; Original Paper ; Phylogeny ; Physical characteristics ; Plant Sciences ; Rhodococcus ; Roncocreagris cavernicola ; rRNA 16S ; Similarity ; Sodium chloride ; Soil Science & Conservation ; Taxonomic revision</subject><ispartof>Antonie van Leeuwenhoek, 2022-04, Vol.115 (4), p.521-532</ispartof><rights>The Author(s), under exclusive licence to Springer Nature Switzerland AG 2022</rights><rights>2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.</rights><rights>The Author(s), under exclusive licence to Springer Nature Switzerland AG 2022.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c305t-c889707d4108580ff2f729d9e5f2cde573e062d8b1437507b0392c45a73599533</citedby><cites>FETCH-LOGICAL-c305t-c889707d4108580ff2f729d9e5f2cde573e062d8b1437507b0392c45a73599533</cites><orcidid>0000-0002-8043-9544</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s10482-022-01718-8$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10482-022-01718-8$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35179674$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kim, Sung-Min</creatorcontrib><creatorcontrib>Lee, Soon Dong</creatorcontrib><creatorcontrib>Koh, Young Sang</creatorcontrib><creatorcontrib>Kim, In Seop</creatorcontrib><title>Antrihabitans stalagmiti sp. nov., isolated from a larva cave and a proposal to transfer Rhodococcus cavernicola Lee et al. 2020 to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov. comb. nov</title><title>Antonie van Leeuwenhoek</title><addtitle>Antonie van Leeuwenhoek</addtitle><addtitle>Antonie Van Leeuwenhoek</addtitle><description>An actinobacterial strain, designated YC3-6
T
, was isolated from a larva cave in Jeju, Republic of Korea. The novel isolate was found to grow at 10–30 °C, pH 5.0–10.0 and 0–4% (w/v) NaCl. The 16S rRNA gene phylogeny showed that the novel isolate formed a distinct subline within the family
Nocardiaceae
. Levels of 16S rRNA gene similarity indicated that the close relatives are
Rhodococcus cavernicola
(98.4% sequence similarity) and “
Rhodococcus psychrotolerans
” (98.2%) followed by
Antrihabitans stalactiti
(96.8%). However, the core gene-based phylogeny revealed that the novel isolate formed a tight cluster with
A. stalactiti
and was separated from
R. cavernicola
and other members of the family
Nocardiaceae.
The morphological and chemotaxonomic characteristics of strain YC3-6
T
are in line with those of the genus
Antrihabitans
. Strain YC3-6
T
showed an average nucleotide identity of 75.5% and a digital DDH of 20.3% with
A. stalactiti.
In addition, the core gene analysis showed that
R. cavernicola
formed a distinct subline between an
Antrihabitans
cluster and
Aldersonia kunmingensis
, and well separated from members of the genus
Rhodococcus
. The average amino acid identity values of
R. cavernicola
to closely related neighbours were 69.3–69.4% with members of the genus
Antrihabitans
and 67.3% with
Ald. kunmingensis
, while the POCP values ranged from 56.9 to 63.6%. On the basis of results obtained here, strain YC3-6
T
is concluded to represent a novel species of the genus
Antrihabitans
, for which the name
Antrihabitans stalagmiti
sp. nov. (type strain, YC3-6
T
= KACC 19963
T
= DSM 107561
T
) is proposed. Based on overall genome relatedness and chemotaxonomic differences, it is also proposed that
R. cavernicola
Lee et al. 2020 be transferred to a new genus
Spelaeibacter
as
Spelaeibacter cavernicola
gen. nov., comb. nov.</description><subject>Amino acids</subject><subject>Biomedical and Life Sciences</subject><subject>Clusters</subject><subject>Genomes</subject><subject>Life Sciences</subject><subject>Medical Microbiology</subject><subject>Microbiology</subject><subject>Morphology</subject><subject>New genera</subject><subject>New species</subject><subject>Nucleotides</subject><subject>Original Paper</subject><subject>Phylogeny</subject><subject>Physical characteristics</subject><subject>Plant Sciences</subject><subject>Rhodococcus</subject><subject>Roncocreagris cavernicola</subject><subject>rRNA 16S</subject><subject>Similarity</subject><subject>Sodium chloride</subject><subject>Soil Science & Conservation</subject><subject>Taxonomic revision</subject><issn>0003-6072</issn><issn>1572-9699</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNp9kc1u1DAUhSMEokPhBVggS2xYNMO1Hcf2sqqgII2ExM86cpybaarEDrYzFS_JM-GZlB91wcKy7_V3jq91iuIlhS0FkG8jhUqxElheVFJVqkfFhgrJSl1r_bjYAAAva5DsrHgW420uda3k0-KMCyp1LatN8fPSpTDcmHZIxkUSkxnNfhrSQOK8Jc4fthdkiH40CTvSBz8RQ0YTDoZYc0BiXJcbc_Czj2YkyZMUsk-PgXy-8Z233tolntjgBpt9yA6RYCJm3BIGDI4aQxzekT26jH6ZcTQ4tMambGIeNv51yoJ1RGL91J6Oz4snvRkjvrjfz4tv7999vfpQ7j5df7y63JWWg0ilVUpLkF1FQQkFfc96yXSnUfTMdigkR6hZp1pacSlAtsA1s5UwkgutBefnxZvVN3_9-4IxNdMQLY6jceiX2LCag-ZQMZHR1w_QW78El6fLVAWi5qJWmWIrZYOPMWDfzGGYTPjRUGiOaTdr2k1Ouzml3RxFr-6tl3bC7o_kd7wZ4CsQ85XbY_j79n9sfwG1wLU9</recordid><startdate>20220401</startdate><enddate>20220401</enddate><creator>Kim, Sung-Min</creator><creator>Lee, Soon Dong</creator><creator>Koh, Young Sang</creator><creator>Kim, In Seop</creator><general>Springer International Publishing</general><general>Springer Nature B.V</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QL</scope><scope>7T7</scope><scope>7U9</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-8043-9544</orcidid></search><sort><creationdate>20220401</creationdate><title>Antrihabitans stalagmiti sp. nov., isolated from a larva cave and a proposal to transfer Rhodococcus cavernicola Lee et al. 2020 to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov. comb. nov</title><author>Kim, Sung-Min ; Lee, Soon Dong ; Koh, Young Sang ; Kim, In Seop</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c305t-c889707d4108580ff2f729d9e5f2cde573e062d8b1437507b0392c45a73599533</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Amino acids</topic><topic>Biomedical and Life Sciences</topic><topic>Clusters</topic><topic>Genomes</topic><topic>Life Sciences</topic><topic>Medical Microbiology</topic><topic>Microbiology</topic><topic>Morphology</topic><topic>New genera</topic><topic>New species</topic><topic>Nucleotides</topic><topic>Original Paper</topic><topic>Phylogeny</topic><topic>Physical characteristics</topic><topic>Plant Sciences</topic><topic>Rhodococcus</topic><topic>Roncocreagris cavernicola</topic><topic>rRNA 16S</topic><topic>Similarity</topic><topic>Sodium chloride</topic><topic>Soil Science & Conservation</topic><topic>Taxonomic revision</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kim, Sung-Min</creatorcontrib><creatorcontrib>Lee, Soon Dong</creatorcontrib><creatorcontrib>Koh, Young Sang</creatorcontrib><creatorcontrib>Kim, In Seop</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Virology and AIDS Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><jtitle>Antonie van Leeuwenhoek</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kim, Sung-Min</au><au>Lee, Soon Dong</au><au>Koh, Young Sang</au><au>Kim, In Seop</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Antrihabitans stalagmiti sp. nov., isolated from a larva cave and a proposal to transfer Rhodococcus cavernicola Lee et al. 2020 to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov. comb. nov</atitle><jtitle>Antonie van Leeuwenhoek</jtitle><stitle>Antonie van Leeuwenhoek</stitle><addtitle>Antonie Van Leeuwenhoek</addtitle><date>2022-04-01</date><risdate>2022</risdate><volume>115</volume><issue>4</issue><spage>521</spage><epage>532</epage><pages>521-532</pages><issn>0003-6072</issn><eissn>1572-9699</eissn><abstract>An actinobacterial strain, designated YC3-6
T
, was isolated from a larva cave in Jeju, Republic of Korea. The novel isolate was found to grow at 10–30 °C, pH 5.0–10.0 and 0–4% (w/v) NaCl. The 16S rRNA gene phylogeny showed that the novel isolate formed a distinct subline within the family
Nocardiaceae
. Levels of 16S rRNA gene similarity indicated that the close relatives are
Rhodococcus cavernicola
(98.4% sequence similarity) and “
Rhodococcus psychrotolerans
” (98.2%) followed by
Antrihabitans stalactiti
(96.8%). However, the core gene-based phylogeny revealed that the novel isolate formed a tight cluster with
A. stalactiti
and was separated from
R. cavernicola
and other members of the family
Nocardiaceae.
The morphological and chemotaxonomic characteristics of strain YC3-6
T
are in line with those of the genus
Antrihabitans
. Strain YC3-6
T
showed an average nucleotide identity of 75.5% and a digital DDH of 20.3% with
A. stalactiti.
In addition, the core gene analysis showed that
R. cavernicola
formed a distinct subline between an
Antrihabitans
cluster and
Aldersonia kunmingensis
, and well separated from members of the genus
Rhodococcus
. The average amino acid identity values of
R. cavernicola
to closely related neighbours were 69.3–69.4% with members of the genus
Antrihabitans
and 67.3% with
Ald. kunmingensis
, while the POCP values ranged from 56.9 to 63.6%. On the basis of results obtained here, strain YC3-6
T
is concluded to represent a novel species of the genus
Antrihabitans
, for which the name
Antrihabitans stalagmiti
sp. nov. (type strain, YC3-6
T
= KACC 19963
T
= DSM 107561
T
) is proposed. Based on overall genome relatedness and chemotaxonomic differences, it is also proposed that
R. cavernicola
Lee et al. 2020 be transferred to a new genus
Spelaeibacter
as
Spelaeibacter cavernicola
gen. nov., comb. nov.</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><pmid>35179674</pmid><doi>10.1007/s10482-022-01718-8</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-8043-9544</orcidid></addata></record> |
| fulltext | fulltext |
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| ispartof | Antonie van Leeuwenhoek, 2022-04, Vol.115 (4), p.521-532 |
| issn | 0003-6072 1572-9699 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2630930425 |
| source | SpringerLink Journals - AutoHoldings |
| subjects | Amino acids Biomedical and Life Sciences Clusters Genomes Life Sciences Medical Microbiology Microbiology Morphology New genera New species Nucleotides Original Paper Phylogeny Physical characteristics Plant Sciences Rhodococcus Roncocreagris cavernicola rRNA 16S Similarity Sodium chloride Soil Science & Conservation Taxonomic revision |
| title | Antrihabitans stalagmiti sp. nov., isolated from a larva cave and a proposal to transfer Rhodococcus cavernicola Lee et al. 2020 to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov. comb. nov |
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