Abstract
Although the genotypic and phenotypic properties of the Lactobacillus casei group have been studied extensively, the taxonomic structure has been the subject of debate for a long time. Here, we performed a large-scale comparative analysis by using 183 publicly available genomes supplemented with a Lactobacillus strain isolated from the human upper respiratory tract. On the basis of this analysis, we identified inconsistencies in the taxonomy and reclassified all of the genomes according to their most closely related type strains. This led to the identification of a catalase-encoding gene in all 10 L.casei sensu stricto strains, making it the first described catalase-positive species in the Lactobacillus genus. Moreover, we found that 6 of 10 L.casei genomes contained a SecA2/SecY2 gene cluster with two putative glycosylated surface adhesin proteins. Altogether, our results highlight current inconsistencies in the taxonomy of the L.casei group and reveal new clade-associated functional features. IMPORTANCE The closely related species of the Lactobacillus casei group are extensively studied because of their applications in food fermentations and as probiotics. Our results show that many strains in this group are incorrectly classified and that reclassifying them to their most closely related species type strain improves the functional predictive power of their taxonomy. In addition, our findings may spark increased interest in the L.casei species. We find that after reclassification, only 10 genomes remain classified as L.casei. These strains show some interesting properties. First, they all appear to be catalase positive. This suggests that they have increased oxidative stress resistance. Second, we isolated an L.casei strain from the human upper respiratory tract and discovered that it and multiple other L.casei strains harbor one or even two large, glycosylated putative surface adhesins. This might inspire further exploration of this species as a potential probiotic organism.
Highlights
The genotypic and phenotypic properties of the Lactobacillus casei group have been studied extensively, the taxonomic structure has been the subject of debate for a long time
In addition to the public genomes classified as belonging to the L. casei group, we screened all of the unclassified Lactobacillus genomes for L. casei group members by comparing their 16S rRNA gene sequences to a filtered version of the RDP database (v11) [14]
This resulted in a total of 184 L. casei group strains studied, thereby significantly improving the number of genomic assemblies studied since the latest comparative genomics study, where only 10 [2] or 34 [9] genomes were used
Summary
The genotypic and phenotypic properties of the Lactobacillus casei group have been studied extensively, the taxonomic structure has been the subject of debate for a long time. Lactobacillus is the largest genus of lactic acid bacteria, comprising Ͼ200 species [1] These species are naturally present on human and animal mucosal surfaces (e.g., the gastrointestinal and vaginal tracts) and in many food-related environments, including fruits, vegetables, wine, milk, and meat, where they can become dominant if able to ferment large doses of sugar with concomitant production of lactic acid and related metabolites. These bacteria are important model microorganisms for metabolic fermentation, cell wall biosynthesis, and microbe-host interaction studies. With the price reduction of whole-genome sequencing and the rising availability of public genomes (210 L. casei group members as of February 2017), a more in-depth insight into the genetic differences and taxonomy of L. casei group members can be obtained by using computational comparative genomics
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