Levilactobacillus brevis 3LB genome sequenced from koumiss, revealing metabolic dominance and non-pathogenic profile.

Fermented milk products like koumiss are rich sources of beneficial lactic acid bacteria (LAB), which contribute to their nutritional value and potential probiotic effects. Understanding the genetic makeup of these strains is crucial for assessing their safety and functional potential. Current research often lacks comprehensive genomic data for specific strains isolated from traditional fermented foods, hindering the identification of key metabolic pathways and adaptation mechanisms. This study addresses this gap by providing a high-quality draft genome sequence for Levilactobacillus brevis 3LB, a strain from Kazakhstani koumiss, to elucidate its biological capabilities and safety profile.

Researchers performed genomic DNA sequencing of Levilactobacillus brevis 3LB (strain B-RKM 0546) isolated from fermented milk koumiss. Sequencing utilized the Illumina MiSeq platform, followed by de novo genome assembly using SPAdes Genome Assembler v3.15.5. The assembled draft genome was then subjected to comprehensive functional annotation and analysis, including GO (Gene Ontology), COG (Clusters of Orthologous Groups), KEGG (Kyoto Encyclopedia of Genes and Genomes), RAST (Rapid Annotation using Subsystem Technology), and CAZymes (Carbohydrate-Active enzymes) analyses. A genomic safety assessment was also conducted to identify potential virulence factors or pathogenic traits.

The assembled draft genome of Levilactobacillus brevis 3LB measured 2,307,466 bp with 150x coverage and a 46.01% GC content, consisting of 63 contigs. Annotation revealed 2260 coding genes, 61 transfer RNA genes, 7 ribosomal RNA genes, and 2 CRISPR loci. Functional analysis consistently showed a dominance of genes related to metabolism, information storage and processing, and cellular processes. > GO analysis identified 786 genes for metabolism, 549 for information storage, and 361 for cellular processes. COG categories highlighted transcription (228 genes), translation and ribosome biogenesis (166 genes), and carbohydrate metabolism (166 genes), with cellular motility being least represented (8 genes). KEGG analysis confirmed metabolism (446 genes) and genetic information processing (296 genes) as dominant. RAST annotation further emphasized carbohydrate metabolism (19.82%), protein synthesis (16.37%), and amino acid synthesis (9.85%). CAZymes analysis identified 52 genes for carbohydrate modification, including 26 glycoside hydrolases and 20 glycosyltransferases. Crucially, genomic safety analysis confirmed Levilactobacillus brevis 3LB is not a human pathogen.