Lacticaseibacillus paracasei: Occurrence in the Human Gut Microbiota and K-Mer-Based Assessment of Intraspecies Diversity

Abstract

Alignment-free approaches employing short k-mers as barcodes for individual genomes have created a new strategy for taxonomic analysis and paved a way for high-resolution phylogeny. Here, we introduce this strategy for the Lacticaseibacillus paracasei species as a taxon requiring barcoding support for precise systematics. Using this approach for phylotyping of L. paracasei VKM B-1144 at the genus level, we identified four L. paracasei phylogroups and found that L. casei 12A belongs to one of them, rather than to the L. casei clade. Therefore, we propose to change the specification of this strain. At the genus level we found only one relative of L. paracasei VKM B-1144 among 221 genomes, complete or available in contigs, and showed that the coding potential of the genome of this “rare” strain allows its consideration as a potential probiotic component. Four sets of published metagenomes were used to assess the dependence of L. paracasei presence in the human gut microbiome on chronic diseases, dietary changes and antibiotic treatment. Only antibiotics significantly affected their presence, and strain-specific barcoding allowed the identification of the main scenarios of the adaptive response. Thus, suggesting bacteria of this species for compensatory therapy, we also propose strain-specific barcoding for selecting optimal strains for target microbiomes.

Variability of Genetic Characters Associated with Probiotic Functions in Lacticaseibacillus Species

“…Each gene locus in the list was aligned by Blastn to the completely annotated genomes of the species Lacticaseibacillus casei , L. paracasei , L. rhamnosus , and L. zeae , which were represented by 5, 54, 38, and 2 entries, respectively, in NCBI at the time of analysis. Strain 12A was included in the analyses as a member of the L. paracasei species because it was found to be erroneously identified as L. casei [ 12 ].…”

Analysis of the Genome Architecture of Lacticaseibacillus paracasei UNQLpc 10, a Strain with Oenological Potential as a Malolactic Starter

“…Lactobacillus paracasei belongs to the L. casei group and is found in diverse niches [38] including food (raw or fermented), plants [39], birds [40], and the gut of mammals [41], including human gut of healthy adults and of breast-fed infants [42,43]. The advance in molecular techniques and their application in winemaking has allowed for the identification of this species as part of the wine microbiota [2].…”

The IMPB RAS is 50 years old. Bioinformatics Laboratory

“…На уровне рода мы обнаружили только одного родственника L. paracasei ВКМ В-1144 среди 221 генома, полного или имеющегося в контигах, и показали, что кодирующий потенциал генома этого «редкого» штамма позволяет рассматривать его как потенциальный пробиотический компонент. Четыре набора опубликованных метагеномов использовались для оценки зависимости присутствия L. paracasei в микробиоме кишечника человека от хронических заболеваний, диетических изменений и лечения антибиотиками [29]. В данном исследовании наиболее значимым представляется результат, свидетельствующий о благоприятном изменении состава родной микробиоты.…”