Whole-genome sequence of Bacillus subtilis ka15: a potent starter isolated from Kawal, a fermented condiment

TL;DR

This paper presents the whole-genome sequence of a Bacillus subtilis strain isolated from a fermented condiment called Kawal.

Contribution

The study provides a detailed genomic characterization of a new Bacillus subtilis strain with potential use as a starter culture.

Findings

The genome size is 4,312,934 bp with 244 contigs and a 43.5% GC content.

The genome contains 4,588 coding genes, 82 tRNAs, 28 rRNAs, and 5 ncRNAs.

Abstract

Bacillus subtilis named ka15 was isolated from Kawal, a fermented condiment produced from the Senna obtusifolia leaves. The genomic sequence size is 4,312,934 bp with 244 contigs, 43.5% average content of GC, 82 tRNAs, 28 rRNAs, 5 ncRNAs and 4,588 coding genes.

Full text

ANNOUNCEMENT

Bacillus subtilis is recommended as a starter in the production of African condiments and fermented foods (1, 2). It has antimicrobial, anticancer, antioxidant, and vitamin production properties (3). However, some Bacillus species probiotics or starter cultures that are sold have antibiotic resistance genes (4). This is why the experimental and in silico analyses of these strains are necessary in order to assess their bioactivity and toxicity before their use in food. The present work provides a genome sequence project of Bacillus subtilis ka15, which was isolated from Kawal.

The Kawal is a fermented condiment extracted from the natural alkaline fermentation of the Senna obtusifolia leaves (5). The Bacillus subtilis ka15 isolate has been isolated from a Kawal sample and was bought on the bargain market Abéché (Tchad) and identified on the basis of 16S RNA (GenBank accession number: OP798035.1). The isolate was cultured on Luria-Bertani (LB) agar for 24 h at 37°C to extract its genomic DNA. After 24 h, a single colony was selected and incubated for 24 h at 37°C in a Luria-Bertani broth until it reached an optical density of 0.6 at 600 nm (OD600) (6). Then, it was submitted to the extraction of genomic DNA using the Wizard Genomic DNA purification Kit (Promega). The genomic DNA concentration was determined by using an Invitrogen Qubit 4.0 fluorometer. Genomic DNA libraries were prepared with the use of the Nextera XT Library (Illumina, San Diego, USA) with 1 ng input DNA kit, accordingly to the manufacturer’s instructions. The sequencing of the entire genome was made by Illumina MiSeq platform using 2 × 250 bp paired-end reads. The raw sequence was processed using Trimmomatic (V.0.39) (7). De novo genome assembly was performed using SPAdes (3.11.1 version) (8) and annotated using the National Center for Biotechnology Information-Prokaryotic Genome Annotation Pipeline (NCBI-PGAP) (https://www.ncbi.nlm.nih.gov/genome/annotation_prok/), 6.9 (2025) version (9, 10), via the NCBI genomic submission gate. The search for genes of virulence, resistance to antibiotics, and antimicrobial peptides was performed with VirulenceFinder v2.0 (11), PathogenFinder v1.1 (12), PlasmidFinder v2.1 (13), ResFinder v 4.6.0. (14), and antiSMASH (version 7) (15). Default parameters were used, except where otherwise noted. Biosynthesis of antimicrobial peptide gene clusters, such as bacillilaene, subtilosin A, bacilysin, bacillibactin, surfactin, and fengycin, was identified in the genomic sequence. No coding gene for putative virulence factors, no plasmid, and no antibiotic resistance genes were identified. The genomic sequence was 4,312,934 bp long and spread over 244 contigs. It had a 43.5% GC content and contained a total of 4,703 genes, including 4,588 CDS, 28 rRNAs (11 5S, 10 16S, 7 23S), 82 tRNAs, and 5 ncRNAs.