Genetic Signatures of Dairy Lactobacillus casei Group

Abstract

Lactobacillus casei/Lactobacillus paracasei group of species contains strains adapted to a wide range of environments, from dairy products to intestinal tract of animals and fermented vegetables. Understanding the gene acquisitions and losses that induced such different adaptations, implies a comparison between complete genomes, since evolutionary differences spread on the whole sequence. This study compared 12 complete genomes of L. casei/paracasei dairy-niche isolates and 7 genomes of L. casei/paracasei isolated from other habitats (i.e., corn silage, human intestine, sauerkraut, beef, congee). Phylogenetic tree construction and average nucleotide identity (ANI) metric showed a clustering of the two dairy L. casei strains ATCC393 and LC5, indicating a lower genetic relatedness in comparison to the other strains. Genomic analysis revealed a core of 313 genes shared by dairy and non-dairy Lactic Acid bacteria (LAB), within a pan-genome of 9,462 genes. Functional category analyses highlighted the evolutionary genes decay of dairy isolates, particularly considering carbohydrates and amino acids metabolisms. Specifically, dairy L. casei/paracasei strains lost the ability to metabolize myo-inositol and taurine (i.e., iol and tau gene clusters). However, gene acquisitions by dairy strains were also highlighted, mostly related to defense mechanisms and host-pathogen interactions (i.e., yueB, esaA, and sle1).This study aimed to be a preliminary investigation on dairy and non-dairy marker genes that could be further characterized for probiotics or food applications.

An assessment of Cuminum cyminum (Boiss) Essential Oil, NaCl, Bile Salts and their combinations in probiotic yogurt

“…(Al-Okbi and Mohamed, 2012;Lucatto et al, 2020). Lactobacillus casei is a gram-positive, mesophilic, microaerophilic, catalase-negative, and spore-free bacterium and a facultative hetero-formative bacterium with high acid production capacity (Fontana et al, 2018). L. casei is a probiotic strain linked with antihypertensive antioxidant, antihypocholesterolemic and anticarcinogenic, characteristics (Balthazar et al, 2018;Garcia et al, 2019).…”

Genome Analysis and Physiological Characterization of Four Streptococcus thermophilus Strains Isolated From Chinese Traditional Fermented Milk

“…The comparative analysis of genome sequences was carried out among all the S. thermophilus strains available in the public database. This kind of comparative phylogenetic analysis that is used for inspection of probiotic potentials has already been done for other bacterial species, such as Lactobacillus acidipiscis, Lactobacillus crispatus, Lactobacillus casei, and Lactobacillus helveticus (Ojala et al, 2014;Fontana et al, 2018Fontana et al, , 2019Kazou et al, 2018). Furthermore, important technological properties of the four strains were investigated including milk acidification, antibiotic resistance, EPS and γ-aminobutyric acid (GABA) production ability, and in vitro survival capacity in the gastrointestinal tract (GIT).…”

Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data

“…In our research, Bacillus pumilus , Bacillus amyloliquefaciens , Lactobacillus casei , and Lactococcus lactis contained strains that were not considered to be of the same species, and which were instead classified into two groups based on 95% ANI (Supplementary Figure S1). For example, when mapping a shotgun read simulated from the genome of the L. casei type strain (GCF_000019245.4) to a genome of L. casei (GCF_000829055.1) in another group, we found that the read mapping coverage was very low, to the extent that it cannot be regarded as the same species (Supplementary Figure S2; Fontana et al, 2018). Although L. casei did not have any officially named subspecies, the nine strains analyzed were divided in two groups consisting of seven and two strains, with the latter two strains being L. casei LC5 and L. casei ATCC 393.…”