Whole genome sequencing and antibacterial activity determination of two novel species of Microbispora
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    Abstract:

    [Background] The abuse of antibiotics leads to the increase and spread of drug-resistant pathogens, which has become an important factor threatening people’s health. Therefore, it is particularly important to explore new antibiotics. New species are likely to produce new bioactive substances, especially rare actinomycetes which are rarely isolated by conventional methods. [Objective] To confirm classification of two novel species of Microbispora and predict the secondary metabolic gene clusters by various molecular biological technologies, which will lay a foundation for the discovery of the medicinal actinobacteria producing novel active substances. [Methods] Taxonomic positions of isolates were preliminarily determined by the 16S rRNA gene sequence analysis. The whole genomes were sequenced and annotated by Illumina genome analyzer. On this basis, a whole-genome-based phylogenomic tree was constructed, and the ANI (average nucleotide identity) and dDDH (digital DNA-DNA hybridization) values were calculated, so as to determine the taxonomic status of novel species. Based on gene annotation, COG (clusters of orthologous genes), KEGG (Kyoto Encyclopedia of Genes and Genomes), and secondary metabolic gene cluster prediction on antiSMASH were analyzed. Antimicrobial activity was tested by cylinder plate method. [Results] The ANI and dDDH values between strain H10836 and 8 species of the genus Microbispora were 85.3%?92.1% and 33.0%?44.5%, respectively. Meanwhile, the ANI and dDDH values between strain H11081 and 8 species of the genus Microbispora were 85.2%?92.1% and 31.3%?44.5%, respectively. Therefore, all the ANI and dDDH values are well below the cut-off point recommended for delineating species. In addition, a whole-genome-based phylogenomic tree showed that strains H10836 and H11081 formed an independent monophyletic branch within the genus Microbispora. Therefore, these results of phylogenetic analysis support the conclusion that strains H10836 and H11081 could be considered to represent two potential novel species of the genus Microbispora. Furthermore, there were many kinds of biosynthetic gene clusters in the genomes of both strains H10836 and H11081 by antiSMASH analysis, and the similarities with known antibiotic synthetic gene clusters were low. The metabolites of two strains exhibited antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). [Conclusion] Strains H10836 and H11081 are two novel species with antibacterial activity, so it is worth mining their novel active natural products. The results of this experiment provide reference for further research and application of the strains.

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LIU Chaolan, LI Jianghua, GUO Yidong. Whole genome sequencing and antibacterial activity determination of two novel species of Microbispora[J]. Microbiology China, 2021, 48(5): 1662-1673

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  • Online: May 10,2021
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