Genome analysis of Lactobacillus plantarum and Lactobacillus brevis isolated from traditionally fermented Ethiopian kocho and their probiotic properties

Abstract

Probiotics are essential for promoting health, with lactic acid bacteria (LAB) from traditional fermented foods like Ethiopian kocho offering valuable benefits. The objective of this study was to systematically analyse the genomic characteristics, bacteriocin production, and probiotic potential of LAB strains isolated from fermented Ethiopian kocho. The research involved isolating LAB from kocho, assessing their tolerance to acid and bile salts, evaluating antimicrobial activity, determining antibiotic susceptibility, and conducting whole-genome sequencing (WGS) to investigate genetic relatedness. Out of 150 LAB isolates, 7 (4.67%) exhibited remarkable acid tolerance, surviving at rates between 50.52-74.05% and 33.33-62.40% after 3 and 6 hours of exposure to pH 2, respectively. These seven acid-tolerant isolates also demonstrated exceptional resistance to 0.3% bile salt, maintaining survival rates ranging from 88.96% to 98.10% over 24 hours. In addition, the isolates displayed inhibitory effects against several important foodborne pathogenic bacteria, underscoring their potential as natural antimicrobial agents. Antibiotic susceptibility testing revealed that all isolates were susceptible to ampicillin, tetracycline, and erythromycin, whereas the most potent isolates exhibited significant resistance to kanamycin. Notably, four of the seven isolates showed resistance to streptomycin, while the remaining three were sensitive. The WGS analysis revealed that the isolates belonged to the Lactobacillus genus, including six Lactobacillus plantarum strains and one Lactobacillus brevis strain. Genomic analysis using the Bayesian Analysis of Gene Essentiality (BAGEL) tool predicted the presence of two class II bacteriocins across all seven strains, further supporting their potential as functional probiotic candidates. Overall, our findings highlight the probiotic potential of the seven Lactobacillus strains, demonstrating their acid and bile salt tolerance, antimicrobial properties, and genetic predisposition for bacteriocin production.