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Microbiology and Biotechnology Letters

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Bioactive Compounds / Food Microbiology  |  Probiotics and Foodborne Microorganisms

Microbiol. Biotechnol. Lett. 2019; 47(1): 25-33

https://doi.org/10.4014/mbl.1807.07008

Received: July 13, 2018; Accepted: October 8, 2018

Comparative Genomic Analysis of Lactobacillus rhamnosus BFE5264, a Probiotic Strain Isolated from Traditional Maasai Fermented Milk

Haeyoung Jeong 1, 2, Sanghaeng Choi 3, Gun-Seok Park 3, Yosep Ji 4, Soyoung Park 4, Wilhelm Holzapfel 4, Julius Mathara 5 and Jihee Kang 3*

1Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea, 2Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea, 3AtoGen Co., Ltd., 11-8, Techno 1-ro, Yuseong-gu, Daejeon, 34015, Republic of Korea., 4Advanced Green Energy and Environment, Handong Global University, Pohang, Gyungbuk, Republic of Korea, 5Dept of Food Science and Technology, Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000 – 00200, Nairobi, Kenya

Lactobacillus rhamnosus BFE5264, isolated from a Maasai fermented milk product (“kule naoto”), was previously shown to exhibit bile acid resistance, cholesterol assimilation, and adhesion to HT29-MTX cells in vitro. In this study, we re-annotated and analyzed the previously reported complete genome sequence of strain BFE5264. The genome consists of a circular chromosome of 3,086,152 bp and a putative plasmid, which is the largest one identified among L. rhamnosus strains. Among the 2,883 predicted protein-coding genes, those with carbohydrate-related functions were the most abundant. Genome analysis of strain BFE5264 revealed two consecutive CRISPR regions and no known virulence factors or antimicrobial resistance genes. In addition, previously known highly variable regions in the genomes of L. rhamnosus strains were also evident in strain BFE5264. Pairwise comparison with the most studied probiotic strain L. rhamnosus GG revealed strain BFE5264-specific deletions, probably due to insertion sequence-mediated recombination. The latter was associated with loss of the spaCBA pilin gene cluster and exopolysaccharide biosynthetic genes. Comparative genomic analysis of the sequences from all available L. rhamnosus strains revealed that they were clustered into two groups, being within the same species boundary based on the average nucleotide identities. Strain BFE5264 had a sister group relationship with the group that contained strain GG, but neither ANI-based hierarchical clustering nor core-gene-based phylogenetic tree construction showed a clear distinctive pattern associated with the isolation source, implying that the genotype alone cannot account for their ecological niches. These results provide insights into the probiotic mechanisms of strain BFE5264 at the genomic level.

Keywords: Lactobacillus, lactobacillus rhamnosus, genome anlysis, comparative genomic analysis, probiotic, complete genome

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