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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 74, Issue 1

sp. nov. a new member of the lineage isolated from sediment of a neutral hot spring and reclassification of (Ramaprasad . 2018) as a later heterotypic synonym of (Kruse 1896) Goodfellow and Alderson 1977 (Approved Lists 1980) Open Access

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 .

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  • Accepted:
  • Published Online:
Keyword(s): genome mining , genomics , geyser sediment , polyphasic taxonomy , Rhodococcus indonesiensis sp. nov. and Rhodococcus ruber clade
Funding
This study was supported by the:
  • Indonesia Endowment Fund for Education
    • Principle Award Recipient: AliBudhi Kusuma
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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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)
Int J Syst Evol Microbiol 74, 006236 (2024); https://doi.org/10.1099/ijsem.0.006236
/content/journal/ijsem/10.1099/ijsem.0.006236
/content/journal/ijsem/10.1099/ijsem.0.006236
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