Whole-genome analysis of a probiotic strain Lactocaseibacillus – identification of genetic determinants for bacteriocin production as a basis for standardization of mono- and multicomponent probiotics

Thu, 20 Aug 2026 15:28:01 +0000

Objective.

Conducting a whole-genome study and bioinformatic analysis of a Lacticaseibacillus strain to confirm taxonomic affiliation, identify genetic determinants of metabolic activity, stress resistance, and bacteriocin production as a criterion for the standardization of mono- and multi-component probiotics.

Materials and Methods.

The object of the study was a strain isolated from a coloproctology patient in 2024. Cultivation was carried out on MRS medium under microaerophilic conditions. Wholegenome sequencing was performed on the Oxford Nanopore Technologies MinION platform (R10.4.1 flow cells). De novo genome assembly was performed using Flye, quality assessment using QUAST. Taxonomic verification was carried out using Kraken2 and ANI calculation. Functional annotation was performed using Bakta, bacteriocin search using BAGEL4 and antiSMASH. The distribution of proteins into functional categories was performed based on the annotated pool of CDS.

Results.

One strain was included in the study, finally identified as Lacticaseibacillus rhamnosus. A complete genome assembly was obtained (2.98 Mb, 1 contig, GC 46.7%, Busco 99.3%). Taxonomic affiliation to L. rhamnosus was confirmed (ANI 99.0% using the reference strain NCTC1364). It was found that the strain is most closely related to LOCK908. Genes for metabolic plasticity (iolH, iolR, murR), vitamin biosynthesis (thi-cluster) and amino acids (trpACFB, trpS2), stress resistance (dnaK, dnaJ, yidC) and colonization (epsH) were identified. A cluster for the biosynthesis of class IIc bacteriocins (15 ORFs) was identified, including a core peptide with homology to enterocin X and carnocin CP52, as well as modules for modification, regulation, immunity, transport, and leader peptide processing. The phagederived gene ORF8 was found, which is significant for the development of a combined preparation with phages.

Conclusions.

The strain L. rhamnosus MRIVS-38065 is characterized by high metabolic plasticity, metabolic autonomy, the presence of a fully functional bacteriocin cluster, and a developed adaptive potential. The set of genes identified in this strain serves as a criterion to justify classifying this strain as a promising probiotic candidate and the feasibility of its use in mono- and multi-component preparations, as well as in combined biotherapeutic systems.

Bozhkova A.G. on КМАХ

Whole-genome analysis of a probiotic strain Lactocaseibacillus – identification of genetic determinants for bacteriocin production as a basis for standardization of mono- and multicomponent probiotics

Objective.

Materials and Methods.

Results.

Conclusions.