Biosynthetic gene cluster profiling predicts the positive association between antagonism and phylogeny in Bacillus

Liming Xia, Youzhi Miao, A’li Cao, Yan Liu, Zihao Liu, Xinli Sun, Yansheng Xue, Zhihui Xu, Weibing Xun, Qirong Shen, Nan Zhang () and Ruifu Zhang ()
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Liming Xia: Nanjing Agricultural University
Youzhi Miao: Nanjing Agricultural University
A’li Cao: Nanjing Agricultural University
Yan Liu: Nanjing Agricultural University
Zihao Liu: Nanjing Agricultural University
Xinli Sun: Nanjing Agricultural University
Yansheng Xue: Nanjing Agricultural University
Zhihui Xu: Nanjing Agricultural University
Weibing Xun: Nanjing Agricultural University
Qirong Shen: Nanjing Agricultural University
Nan Zhang: Nanjing Agricultural University
Ruifu Zhang: Chinese Academy of Agricultural Sciences

Nature Communications, 2022, vol. 13, issue 1, 1-11

Abstract: Abstract Understanding the driving forces and intrinsic mechanisms of microbial competition is a fundamental question in microbial ecology. Despite the well-established negative correlation between exploitation competition and phylogenetic distance, the process of interference competition that is exemplified by antagonism remains controversial. Here, we studied the genus Bacillus, a commonly recognized producer of multifarious antibiotics, to explore the role of phylogenetic patterns of biosynthetic gene clusters (BGCs) in mediating the relationship between antagonism and phylogeny. Comparative genomic analysis revealed a positive association between BGC distance and phylogenetic distance. Antagonistic tests demonstrated that the inhibition phenotype positively correlated with both phylogenetic and predicted BGC distance, especially for antagonistic strains possessing abundant BGCs. Mutant-based verification showed that the antagonism was dependent on the BGCs that specifically harbored by the antagonistic strain. These findings highlight that BGC-phylogeny coherence regulates the positive correlation between congeneric antagonism and phylogenetic distance, which deepens our understanding of the driving force and intrinsic mechanism of microbial interactions.

Date: 2022
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DOI: 10.1038/s41467-022-28668-z

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