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Isolation, characterisation and genome analysis of a novel ginsenosides hydrolysing bacterium Ginsengibacter hankyongi gen. nov., sp. nov. isolated from soil

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Abstract

A novel yellow-pigmented bacterial strain (designated BR5-29T), was isolated and its taxonomy was studied. Phylogenetic study based on the 16S rRNA and draft genome sequence placed the strain BR5-29T in a distinct lineage within the family Chitinophagaceae, sharing ≤ 93.4% sequence similarity with members of the closely related genera Ferruginibacter, Flavisolibacter, Flavitalea and Niastella. The novel isolate showed the highest sequence similarity to the genus Ferruginibacter. The draft genome of strain BR5-29T had a total length of 5,505,520 base pairs. A total of 4585 genes were identified, in which 4537 were CDS and 48 RNA genes were assigned a putative function. The genome annotation of BR5-29T showed 225 carbohydrate genes which may be responsible for the conversion of major ginsenosides to minor ginsenosides. Strain BR5-29T contained MK-7 as a predominant quinone, and iso-C15:0, iso-C15:0 G, iso-C17:0 3-OH, and C16:1 ω7c and/or C16:1 ω6c (summed feature 3) as major fatty acids. The polar lipids found in the strain BR5-29T were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), five unidentified polar lipids (L1–L5), two unidentified aminolipid and one unidentified aminophospholipid. Our pilot data demonstrate that the novel isolate shares the similar major polar lipid PE, major quinone MK-7 and major fatty acids with the described members of the family Chitinophagaceae. However, the low 16S rRNA gene sequence (< 93.4%), the little high amount of C12:0, iso-C17:0 2-OH and iso-C15:1 2-OH fatty acids, low DNA G + C content, and the presence of DPG, PG and two unidentified polar lipids (L1 and L3 differentiate the BR5-29T from its closest phylogenetic neighbors. Thus, the isolate represents a novel genus and species in the family Chitinophagaceae for which the name Ginsengibacter hankyongi gen. nov., sp. nov. is proposed. The type strain is BR5-29T (= KACC 19446T = LMG 30462T). Thus, we predict that this novel strain may prove useful for the future research analysis (target gene cloning) and mass production of Rg3.

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Funding

This work was supported by the project on survey and excavation of Korean indigenous species of the National Institute of Biological Resources (NIBR) under the Ministry of Environment, by the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2019R1I1A1A01061945), and by Korea Research Fellowship (KRF) Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (Project No. 2019H1D3A1A02070958).

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Authors and Affiliations

  1. Department of Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea

    Muhammad Zubair Siddiqi & Wan-Taek Im

  2. AceEMzyme Co., Ltd, Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Kyonggi-do, 17579, Republic of Korea

    Muhammad Zubair Siddiqi & Wan-Taek Im

  3. Department of Food and Nutrition, College of Biotechnology and Natural Resource, Chung-Ang University, Gyeonggi-do, Anseong-si, 17546, Republic of Korea

    Md. Amdadul Huq

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  1. Muhammad Zubair Siddiqi
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Contributions

Conceived and designed the experiments: MZ WTI. Performed the experiments: MZS. Analyzed the data: MZS MAH WTI. Wrote the paper: MZS.

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Correspondence to Wan-Taek Im.

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Siddiqi, M.Z., Huq, M.A. & Im, WT. Isolation, characterisation and genome analysis of a novel ginsenosides hydrolysing bacterium Ginsengibacter hankyongi gen. nov., sp. nov. isolated from soil. Antonie van Leeuwenhoek 114, 11–22 (2021). https://doi.org/10.1007/s10482-020-01485-4

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