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Comparative genomics with evolutionary lineage in Streptomyces bacteria reveals high biosynthetic potentials

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Abstract

Genome mining in silico approaches allow scientists to proficiently evaluate the genomic potency of secondary bioactive chemical producers and find new bioactive compounds in different bacteria. Streptomyces is one of the most ubiquitous bacterial genera in the environments, and well-known as prolific producers of diverse and valuable natural products (NPs) with significant biological activities. Mining and prioritizing of NP biosynthetic gene clusters (BGCs) would be the most important stage in the identification of novel compounds. Comparative genomics and genetic similarity network analysis of 62 Streptomyces public reference genomes demonstrated that individuals of these species exhibit a huge number of distinct NP BGCs, the most of which are cryptic and unconnected to any reported NPs with high phylogenetic variation among individuals. It was assumed that substantial heterogeneity across the varieties of species of Streptomyces drives outstanding biosynthetic and metabolic potential, making them plausible candidates for the identification of novel molecules.

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The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding author.

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Funding

This study was supported by the National Key R&D Program of China (2018YFA0900400 and 2019YFA0905700), National Natural Science Foundation of China (32270088 and 32170038), the Open Project Program of the State Key Laboratory of Bio-based Material and Green Papermaking (KF201825) and the 111 Project (B16030).

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Authors and Affiliations

  1. Helmholtz International Lab for Anti-Infectives, State Key Laboratory of Microbial Technology, Shandong University-Helmholtz Institute of Biotechnology, Shandong University, Qingdao, 266237, People’s Republic of China

    Khorshed Alam, Jinfang Hao, Muhammad Nazeer Abbasi, Muhammad Hayat, Muhammad Shoaib, Youming Zhang & Aiying Li

  2. Department of Microbiology, Rajshahi Institute of Biosciences (RIB), Affiliated University of Rajshahi, Rajshahi, 6212, Bangladesh

    Md. Mahmudul Islam

  3. Chattogram Laboratories, Bangladesh Council of Scientific and Industrial Research (BCSIR), Chattogram, 4220, Bangladesh

    Saiful Islam

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  1. Khorshed Alam
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  2. Md. Mahmudul Islam
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  3. Saiful Islam
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  4. Jinfang Hao
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  5. Muhammad Nazeer Abbasi
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  7. Muhammad Shoaib
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  8. Youming Zhang
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  9. Aiying Li
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Contributions

AL conceived the concept and funds, supervised the work, and validated the results. KA conducted all experiments, analyzed the data, and wrote the original draft of manuscript. KA, MMI, SI conducted software, JH, MNA, MH conducted validation, MS conducted formal analysis, YZ visualization and writing and data analysis. All authors read and approved the manuscript.

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Correspondence to Aiying Li.

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Alam, K., Islam, M.M., Islam, S. et al. Comparative genomics with evolutionary lineage in Streptomyces bacteria reveals high biosynthetic potentials. World J Microbiol Biotechnol 39, 64 (2023). https://doi.org/10.1007/s11274-022-03433-y

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