Genome mining reveals the biosynthetic potential of a novel Lysinibacillus zambalensis sp. nov., isolated from a hyperalkaline spring

Abstract

A novel bacterium, designated as strain M3^T, was isolated from a hyperalkaline spring in the Philippines and identified as a new species within the genus Lysinibacillus through 16 S rRNA gene sequence and genomic analyses. Although strain M3^T shared a high 16 S rRNA gene sequence similarity (> 98.7%) with many Lysinibacillus species, the digital DNA-DNA hybridization and orthologous average nucleotide identity values between strain M3^T and its closet relative, Lysinibacillus xylanilyticus DSM 23,493^T, were 41.2% and 90.6%, respectively—both below the established threshold for prokaryotic species delineation. Genome mining of the 5.3 Mbp-draft genome of strain M3^T revealed eight biosynthetic gene clusters, which shared little sequence similarity with characterized clusters, suggesting the potential for encoding novel specialized metabolites. The cells of strain M3^T were Gram-stain-positive, aerobic, rod-shaped, non-motile, and capable of endospore formation. Optimum growth was observed at 30 °C, pH 8.0, and 0.5% (w/v) NaCl. The major respiratory quinone was menaquinone-7, and the predominant polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, and two unknown phospholipids. Its fatty acid profile showed an elevated level of iso-C_15:0, and the peptidoglycan type was determined to be A4α (L-Lys–D-Asp). This study contributes to the growing database and understanding of the genus and aims to help drive future research on the bioactive potential of the genus. Lysinibacillus zambalensis sp. nov. is proposed with strain M3^T as the type strain (= TISTR 10640^T = BIOTECH 10973^T).