Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus electrodiphilus (Ramaprasad et al . 2018) as a later heterotypic synonym of Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980)
A polyphasic study was designed to determine the taxonomic status of isolate CSLK01-03 , which was recovered from an Indonesian neutral hot spring and provisionally assigned to the genus . The isolate was found to have chemotaxonomic, cultural and morphological properties typical of rhodococci. It h...
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| creator | Kusuma, Ali Budhi Fenylestari, Gita Ammar, Fadhil Nououi, Imen Goodfellow, Michael |
| description | A polyphasic study was designed to determine the taxonomic status of isolate CSLK01-03
, which was recovered from an Indonesian neutral hot spring and provisionally assigned to the genus
. The isolate was found to have chemotaxonomic, cultural and morphological properties typical of rhodococci. It has a rod-coccus lifecycle and grows from 10 to 39 °C, from pH 6.5 to 8.0 and in the presence of 0-10 % (w/v) sodium chloride. Whole-organism hydrolysates contain
-diaminopimelic acid, arabinose and galactose, the predominant menaquinone is MK-8 (H
), the polar lipid pattern consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylmethylethanolamine and two unidentified components, it produces mycolic acids, and C
is the major fatty acid. Whole-genome analyses show that the isolate and
LMG 29881
(GenBank accession: JAULCK000000000) have genome sizes of 5.5 and 5.1 Mbp, respectively. These strains and
DSM 44752
and
DSM 43338
form well-supported lineages in 16S rRNA and whole-genome trees that are close to sister lineages composed of the type strains of
and related
species. The isolate can be distinguished from its closest evolutionary neighbours using combinations of cultural and phenotypic features, and by low DNA-DNA hybridization values. Based on these data it is proposed that isolate CSLK01-03
(=CCMM B1310
=ICEBB-06
=NCIMB 15214
) be classified in the genus
as
sp. nov. The genomes of the isolate and its closest phylogenomic relatives are rich in biosynthetic gene clusters with the potential to synthesize new natural products, notably antibiotics. In addition, whole-genome-based taxonomy revealed that
LMG 29881
and
DSM 43338
belong to a single species. It is, therefore, proposed that
be recognized as a heterotypic synonym of
. |
| doi_str_mv | 10.1099/ijsem.0.006236 |
| format | Article |
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, which was recovered from an Indonesian neutral hot spring and provisionally assigned to the genus
. The isolate was found to have chemotaxonomic, cultural and morphological properties typical of rhodococci. It has a rod-coccus lifecycle and grows from 10 to 39 °C, from pH 6.5 to 8.0 and in the presence of 0-10 % (w/v) sodium chloride. Whole-organism hydrolysates contain
-diaminopimelic acid, arabinose and galactose, the predominant menaquinone is MK-8 (H
), the polar lipid pattern consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylmethylethanolamine and two unidentified components, it produces mycolic acids, and C
is the major fatty acid. Whole-genome analyses show that the isolate and
LMG 29881
(GenBank accession: JAULCK000000000) have genome sizes of 5.5 and 5.1 Mbp, respectively. These strains and
DSM 44752
and
DSM 43338
form well-supported lineages in 16S rRNA and whole-genome trees that are close to sister lineages composed of the type strains of
and related
species. The isolate can be distinguished from its closest evolutionary neighbours using combinations of cultural and phenotypic features, and by low DNA-DNA hybridization values. Based on these data it is proposed that isolate CSLK01-03
(=CCMM B1310
=ICEBB-06
=NCIMB 15214
) be classified in the genus
as
sp. nov. The genomes of the isolate and its closest phylogenomic relatives are rich in biosynthetic gene clusters with the potential to synthesize new natural products, notably antibiotics. In addition, whole-genome-based taxonomy revealed that
LMG 29881
and
DSM 43338
belong to a single species. It is, therefore, proposed that
be recognized as a heterotypic synonym of
.</description><identifier>ISSN: 1466-5026</identifier><identifier>EISSN: 1466-5034</identifier><identifier>DOI: 10.1099/ijsem.0.006236</identifier><identifier>PMID: 38214280</identifier><language>eng</language><publisher>England</publisher><subject>Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial - genetics ; Fatty Acids - chemistry ; Hot Springs ; Phospholipids - chemistry ; Phylogeny ; Rhodococcus ; RNA, Ribosomal, 16S - genetics ; Sequence Analysis, DNA</subject><ispartof>International journal of systematic and evolutionary microbiology, 2024-01, Vol.74 (1)</ispartof><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c295t-89edee965b8db6bb41959ef48a07dba838f3e73136e44b5dc3ddbfca17a86a223</citedby><cites>FETCH-LOGICAL-c295t-89edee965b8db6bb41959ef48a07dba838f3e73136e44b5dc3ddbfca17a86a223</cites><orcidid>0000-0003-2707-0247 ; 0000-0002-0243-9514 ; 0000-0002-7973-7640</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784,3746,27924,27925</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38214280$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kusuma, Ali Budhi</creatorcontrib><creatorcontrib>Fenylestari, Gita</creatorcontrib><creatorcontrib>Ammar, Fadhil</creatorcontrib><creatorcontrib>Nououi, Imen</creatorcontrib><creatorcontrib>Goodfellow, Michael</creatorcontrib><title>Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus electrodiphilus (Ramaprasad et al . 2018) as a later heterotypic synonym of Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980)</title><title>International journal of systematic and evolutionary microbiology</title><addtitle>Int J Syst Evol Microbiol</addtitle><description>A polyphasic study was designed to determine the taxonomic status of isolate CSLK01-03
, which was recovered from an Indonesian neutral hot spring and provisionally assigned to the genus
. The isolate was found to have chemotaxonomic, cultural and morphological properties typical of rhodococci. It has a rod-coccus lifecycle and grows from 10 to 39 °C, from pH 6.5 to 8.0 and in the presence of 0-10 % (w/v) sodium chloride. Whole-organism hydrolysates contain
-diaminopimelic acid, arabinose and galactose, the predominant menaquinone is MK-8 (H
), the polar lipid pattern consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylmethylethanolamine and two unidentified components, it produces mycolic acids, and C
is the major fatty acid. Whole-genome analyses show that the isolate and
LMG 29881
(GenBank accession: JAULCK000000000) have genome sizes of 5.5 and 5.1 Mbp, respectively. These strains and
DSM 44752
and
DSM 43338
form well-supported lineages in 16S rRNA and whole-genome trees that are close to sister lineages composed of the type strains of
and related
species. The isolate can be distinguished from its closest evolutionary neighbours using combinations of cultural and phenotypic features, and by low DNA-DNA hybridization values. Based on these data it is proposed that isolate CSLK01-03
(=CCMM B1310
=ICEBB-06
=NCIMB 15214
) be classified in the genus
as
sp. nov. The genomes of the isolate and its closest phylogenomic relatives are rich in biosynthetic gene clusters with the potential to synthesize new natural products, notably antibiotics. In addition, whole-genome-based taxonomy revealed that
LMG 29881
and
DSM 43338
belong to a single species. It is, therefore, proposed that
be recognized as a heterotypic synonym of
.</description><subject>Bacterial Typing Techniques</subject><subject>Base Composition</subject><subject>DNA, Bacterial - genetics</subject><subject>Fatty Acids - chemistry</subject><subject>Hot Springs</subject><subject>Phospholipids - chemistry</subject><subject>Phylogeny</subject><subject>Rhodococcus</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>Sequence Analysis, DNA</subject><issn>1466-5026</issn><issn>1466-5034</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNpdUk1v1DAUDAhES-HKEb3j7mGDHSdZ57iqSkGshFTBOXLsl66rxA5-Tqv99zjdUlVc_PE8M29sT5Z94iznrGm-2DvCMWc5Y3Uh6tfZOS_relMxUb55Xhf1Wfae6I6xVGDsXXYmZMHLQrLzV7ubgzdee61nAuuMd0gWHVkCmnJw_j4HBQ4fYMSxwwC-h3hAeEkL83IwWIfqFsGSH1REA33wIxAaO6KLC2_RmWNQAxx8TPLBultQzkBAPSgi21utovVuAb9sgAPqGLyx08EOab-6UaOagiJlACMkwRwKxuUaFKUuS_sAB0yjj8fJaqCj8-44_q97Mr76EWZC4LKp13DtvelxGPzDo7PdYDBQcsSb7RZWu2kK_j7dbW8pUipKtv6Qve3VQPjxab7Ifn-9-nX5bbP_ef39crff6KKp4kY2aBCbuuqk6equK3lTNdiXUrGt6ZQUshe4FVzUWJZdZbQwpuu14lsla1UU4iJbnXSThT8zUmxHSzpZVQ79TG3RpC-tRFk1CZqfoDp4ooB9m956VOHYctYusWkfY9Oy9hSbRPj8pD13I5pn-L-ciL-Fz8PB</recordid><startdate>20240101</startdate><enddate>20240101</enddate><creator>Kusuma, Ali Budhi</creator><creator>Fenylestari, Gita</creator><creator>Ammar, Fadhil</creator><creator>Nououi, Imen</creator><creator>Goodfellow, Michael</creator><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0003-2707-0247</orcidid><orcidid>https://orcid.org/0000-0002-0243-9514</orcidid><orcidid>https://orcid.org/0000-0002-7973-7640</orcidid></search><sort><creationdate>20240101</creationdate><title>Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus electrodiphilus (Ramaprasad et al . 2018) as a later heterotypic synonym of Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980)</title><author>Kusuma, Ali Budhi ; Fenylestari, Gita ; Ammar, Fadhil ; Nououi, Imen ; Goodfellow, Michael</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c295t-89edee965b8db6bb41959ef48a07dba838f3e73136e44b5dc3ddbfca17a86a223</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Bacterial Typing Techniques</topic><topic>Base Composition</topic><topic>DNA, Bacterial - genetics</topic><topic>Fatty Acids - chemistry</topic><topic>Hot Springs</topic><topic>Phospholipids - chemistry</topic><topic>Phylogeny</topic><topic>Rhodococcus</topic><topic>RNA, Ribosomal, 16S - genetics</topic><topic>Sequence Analysis, DNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kusuma, Ali Budhi</creatorcontrib><creatorcontrib>Fenylestari, Gita</creatorcontrib><creatorcontrib>Ammar, Fadhil</creatorcontrib><creatorcontrib>Nououi, Imen</creatorcontrib><creatorcontrib>Goodfellow, Michael</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>International journal of systematic and evolutionary microbiology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kusuma, Ali Budhi</au><au>Fenylestari, Gita</au><au>Ammar, Fadhil</au><au>Nououi, Imen</au><au>Goodfellow, Michael</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus electrodiphilus (Ramaprasad et al . 2018) as a later heterotypic synonym of Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980)</atitle><jtitle>International journal of systematic and evolutionary microbiology</jtitle><addtitle>Int J Syst Evol Microbiol</addtitle><date>2024-01-01</date><risdate>2024</risdate><volume>74</volume><issue>1</issue><issn>1466-5026</issn><eissn>1466-5034</eissn><abstract>A polyphasic study was designed to determine the taxonomic status of isolate CSLK01-03
, which was recovered from an Indonesian neutral hot spring and provisionally assigned to the genus
. The isolate was found to have chemotaxonomic, cultural and morphological properties typical of rhodococci. It has a rod-coccus lifecycle and grows from 10 to 39 °C, from pH 6.5 to 8.0 and in the presence of 0-10 % (w/v) sodium chloride. Whole-organism hydrolysates contain
-diaminopimelic acid, arabinose and galactose, the predominant menaquinone is MK-8 (H
), the polar lipid pattern consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol mannosides, phosphatidylmethylethanolamine and two unidentified components, it produces mycolic acids, and C
is the major fatty acid. Whole-genome analyses show that the isolate and
LMG 29881
(GenBank accession: JAULCK000000000) have genome sizes of 5.5 and 5.1 Mbp, respectively. These strains and
DSM 44752
and
DSM 43338
form well-supported lineages in 16S rRNA and whole-genome trees that are close to sister lineages composed of the type strains of
and related
species. The isolate can be distinguished from its closest evolutionary neighbours using combinations of cultural and phenotypic features, and by low DNA-DNA hybridization values. Based on these data it is proposed that isolate CSLK01-03
(=CCMM B1310
=ICEBB-06
=NCIMB 15214
) be classified in the genus
as
sp. nov. The genomes of the isolate and its closest phylogenomic relatives are rich in biosynthetic gene clusters with the potential to synthesize new natural products, notably antibiotics. In addition, whole-genome-based taxonomy revealed that
LMG 29881
and
DSM 43338
belong to a single species. It is, therefore, proposed that
be recognized as a heterotypic synonym of
.</abstract><cop>England</cop><pmid>38214280</pmid><doi>10.1099/ijsem.0.006236</doi><orcidid>https://orcid.org/0000-0003-2707-0247</orcidid><orcidid>https://orcid.org/0000-0002-0243-9514</orcidid><orcidid>https://orcid.org/0000-0002-7973-7640</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1466-5026 |
| ispartof | International journal of systematic and evolutionary microbiology, 2024-01, Vol.74 (1) |
| issn | 1466-5026 1466-5034 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2914253459 |
| source | MEDLINE; Microbiology Society; EZB-FREE-00999 freely available EZB journals |
| subjects | Bacterial Typing Techniques Base Composition DNA, Bacterial - genetics Fatty Acids - chemistry Hot Springs Phospholipids - chemistry Phylogeny Rhodococcus RNA, Ribosomal, 16S - genetics Sequence Analysis, DNA |
| title | Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus electrodiphilus (Ramaprasad et al . 2018) as a later heterotypic synonym of Rhodococcus ruber (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980) |
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