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Nocardioides luti sp. nov., belonging to the family Nocardioidaceae isolated from kaolinite, exhibiting the biosynthesis potential of alkylresorcinol

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Abstract

A novel Gram-staining-positive, short rod-shaped, non-motile, and non-pigmented actinobacterial strain (KIGAM211T) was isolated from kaolinite, a soft white clay mineral, collected from Sancheong in the Republic of Korea. On the basis of 16S rRNA gene sequence analysis, strain KIGAM211T was determined to belong to the genus Nocardioides and was most closely related to N. ungokensis UKS-03T (97.5% similarity). Cells could grow between 4 and 35 °C (optimum 30 °C), 0–3% (w/v) NaCl concentration (optimum 0%) and pH 5.5–8.5 (optimum 7.0) on R2A agar. Morphological appearance of colonies was cream-white, arranged singly or in groups. Biochemical characterization of strain KAGAM211T indicated that it could hydrolyze casein, gelatin, Tweens 40 and tyrosine. Furthermore, the strain was positive for both oxidase and catalase activity. Strain KIGAM211T was characterized chemotaxonomically by MK-8 (H4) as the predominant menaquinone and phosphatidylglycerol (PG) and phosphatidylinositol (PI) as the major polar lipids. Major fatty acids were iso-C16:0 and C18:1 ω9c. The Ortholog average nucleotide identity (OrthoANI) and in silico DNA-DNA hybridization (isDDH) values between strain KIGAM211T and its most closely related strains of the Nocardioides genus were < 82% and < 24%, respectively, suggesting that strain KIGAM211T represent a novel species. The whole genome size of KIGAM211T was 4.52 Mb, comprising a total of 4,294 genes with DNA G + C content of 72.3 mol%. The genome of strain KIGAM211T also comprises the biosynthetic gene cluster for alkylresorcinol as secondary metabolite. The results of physiological, taxonomical, phylogenetic, and whole genome analyses allowed for differentiation of strain KIGAM211T from the recognized Nocardioides species. Therefore, strain KIGAM211T is considered to represent a novel species, for which the name Nocardioides luti sp. nov. (type strain KIGAM211T = KCTC 49364T = JCM 33859T) is proposed.

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Funding

This research was supported by Collaborate Research Program of the Korea Food Research Institute (KFRI) and the Korean Institute of Geoscience and Mineral Resources (KIGAM). This work was also supported by Research Assistance Program (2020) in the Incheon National University.

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Author notes

  1. DeokJun Yoon and Eui-Sang Cho contributed equally to this work and should be regarded as co-first authors.

Authors and Affiliations

  1. Department of Bioengineering and Nano-Bioengineering, Graduate School of Incheon National University, Incheon, 22012, Republic of Korea

    Deok Jun Yoon, Eui-Sang Cho, Chi Young Hwang & Myung-Ji Seo

  2. Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365, Republic of Korea

    Young-Do Nam, So-Lim Park & Seong-Il Lim

  3. Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea

    Myung-Ji Seo

  4. Institute for New Drug Development, Incheon National University, Incheon, 22012, Republic of Korea

    Myung-Ji Seo

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  1. Deok Jun Yoon
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Contributions

D J Y and E-S C performed all the experiments and drafted the manuscript. C Y H contributed to isolate the strains and analyze the morphological characteristics. Y-D N contributed to genome sequencing and analysis. S-L P and S-I L contributed to analyze the biochemical characteristics. M-J S designed all the experiments and supervised the manuscript.

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Correspondence to Seong-Il Lim or Myung-Ji Seo.

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Yoon, D.J., Cho, ES., Hwang, C.Y. et al. Nocardioides luti sp. nov., belonging to the family Nocardioidaceae isolated from kaolinite, exhibiting the biosynthesis potential of alkylresorcinol. Antonie van Leeuwenhoek 114, 983–995 (2021). https://doi.org/10.1007/s10482-021-01570-2

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