Bioprospecting for the soil-derived actinobacteria and bioactive secondary metabolites on the Western Qinghai-Tibet Plateau

Lifang Liu; Yuyu Liu; Shaowei Liu; Arina A Nikandrova; Arina N Imamutdinova; Dmitrii A Lukianov; Ilya A Osterman; Petr V Sergiev; Benyin Zhang; Dejun Zhang; Feina Li; Chenghang Sun

doi:10.3389/fmicb.2023.1247001

Bioprospecting for the soil-derived actinobacteria and bioactive secondary metabolites on the Western Qinghai-Tibet Plateau

Front Microbiol. 2023 Oct 11:14:1247001. doi: 10.3389/fmicb.2023.1247001. eCollection 2023.

Authors

Lifang Liu¹, Yuyu Liu^{1

2}, Shaowei Liu^{1

2}, Arina A Nikandrova^{3

4}, Arina N Imamutdinova^{3

5}, Dmitrii A Lukianov^{3

5}, Ilya A Osterman^{3

5}, Petr V Sergiev^{3

5}, Benyin Zhang⁶, Dejun Zhang⁶, Feina Li^{7

8}, Chenghang Sun^{1

2

6

9}

Affiliations

¹ Department of Microbial Chemistry, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
² Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
³ Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russia.
⁴ Department of Biology, Lomonosov Moscow State University, Moscow, Russia.
⁵ Department of Chemistry, Lomonosov Moscow State University, Moscow, Russia.
⁶ College of Eco-Environmental Engineering, Qinghai University, Xining, China.
⁷ Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China.
⁸ Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China.
⁹ State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China.

Abstract

Introduction: The increase in incidence of multidrug-resistant bacteria and the inadequacy of new antimicrobial drugs have led to a widespread outbreak of bacterial antimicrobial resistance. To discover new antibiotics, biodiversity, and novelty of culturable actinobacteria dwelled in soil of the Western Qinghai-Tibet Plateau were investigated. By integrating antibacterial assay with omics tools, Amycolatopsis sp. A133, a rare actinobacterial strain and its secondary metabolites were further studied.

Method: Culture-dependent method was used to obtain actinobacterial strains from two soil samples collected from Ali region in Qinghai-Tibet Plateau. The cultural extractions of representative strains were assayed against "ESKAPE" pathogens by paper-disk diffusion method and the double fluorescent protein reporter "pDualrep2" system. An Amycolatopsis strain coded as A133 was prioritized and its secondary metabolites were further analyzed and annotated by omics tools including antiSMASH and GNPS (Global Natural Social Molecular Networking). The predicted rifamycin analogs produced by Amycolatopsis sp. A133 were isolated and identified by chromatographic separation, such as Sephadex LH-20 and HPLC, and spectral analysis, such as NMR and UPLC-HRESI-MS/MS, respectively.

Results: A total of 406 actinobacteria strains affiliated to 36 genera in 17 families of 9 orders were isolated. Out of 152 representative strains, 63 isolates exhibited antagonistic activity against at least one of the tested pathogens. Among them, 7 positive strains were identified by the "pDualrep2" system as either an inhibitor of protein translation or DNA biosynthesis. The cultural broth of Amycolatopsis sp. A133 exhibited a broader antimicrobial activity and can induce expression of TurboRFP. The secondary metabolites produced by strain A133 was annotated as rifamycins and zampanolides by antiSMASH and GNPS analysis. Five members of rifamycins, including rifamycin W, protorifamycin I, rifamycin W-M1, proansamycin B, and rifamycin S, were purified and identified. Rifamycin W-M1, was found as a new member of the naturally occurring rifamycin group of antibiotics.

Discussion: Assisted by omics tools, the successful and highly efficient discovery of rifamycins, a group of clinically used antibiotics from actinobacteria in Ali area encouraged us to devote more energy to explore new antibiotics from the soils on the Western Tibetan Plateau.

Keywords: Amycolatopsis; GNPs; Qinghai-Tibet Plateau; actinobacteria; rifamycins.

Grants and funding

The research work was partly supported by CAMS Innovation Fund for Medical Sciences (CIFMS 2021-I2M-1-028); the Kunlun Talented People, High-end Innovation and Entrepreneurship Talents Plan of Qinghai Province; The Open Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University (2023-KF-06); the National Natural Sciences Foundation of China (NSFC, Grant No. 32200001); Beijing National Natural Science Foundation (BJNSF, Grant No. 7222256); the Ministry of Science and Higher Education of the Russian Federation (Agreement No. 075–15-2021-1085).