AUTHOR=Kim Eiseul , Yang Seung-Min , Kim Dayoung , Kim Hae-Yeong 

TITLE=Complete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.794315

DOI=10.3389/fmicb.2021.794315

ISSN=1664-302X

ABSTRACT=<p><italic>Lacticaseibacillus casei</italic>, <italic>Lacticaseibacillus chiayiensis</italic>, and <italic>Lacticaseibacillus zeae</italic> are very closely related <italic>Lacticaseibacillus</italic> species. <italic>L. casei</italic> has long been proposed as a probiotic, whereas studies on functional characterization for <italic>L. chiayiensis</italic> and <italic>L. zeae</italic> are some compared to <italic>L</italic>. <italic>casei</italic>. In this study, <italic>L. casei</italic> FBL6, <italic>L. chiayiensis</italic> FBL7, and <italic>L. zeae</italic> FBL8 were isolated from raw milk, and their probiotic properties were investigated. Genomic analysis demonstrated the role of <italic>L. chiayiensis</italic> and <italic>L. zeae</italic> as probiotic candidates. The three strains were tolerant to acid and bile salt, with inhibitory action against pathogenic bacterial strains and capacity of antioxidants. Complete genome sequences of the three strains were analyzed to highlight the probiotic properties at the genetic level, which results in the discovery of genes corresponding to phenotypic characterization. Moreover, genes known to confer probiotic characteristics were identified, including genes related to biosynthesis, defense machinery, adhesion, and stress adaptation. The comparative genomic analysis with other available genomes revealed 256, 214, and 32 unique genes for FBL6, FBL7, and FBL8, respectively. These genomes contained individual genes encoding proteins that are putatively involved in carbohydrate transport and metabolism, prokaryotic immune system for antiviral defense, and physiological control processes. In particular, <italic>L</italic>. <italic>casei</italic> FBL6 had a bacteriocin gene cluster that was not present in other genomes of <italic>L</italic>. <italic>casei</italic>, resulting in this strain may exhibit a wide range of antimicrobial activity compared to other <italic>L</italic>. <italic>casei</italic> strains. Our data can help us understand the probiotic functionalities of the three strains and suggest that <italic>L. chiayiensis</italic> and <italic>L. zeae</italic> species, which are closely related to <italic>L. casei</italic>, can also be considered as novel potential probiotic candidate strains.</p>