Abstract
The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Lactobacillus salivarius, a species commonly isolated from the gastrointestinal tract of humans and animals, has been described as having potential probiotic properties and results of previous studies have revealed considerable functional diversity existing on both the chromosomes and plasmids. Our study consists of comparative genomic analyses of the functional and phylogenomic diversity of 42 genomes of strains of L. salivarius using bioinformatic techniques. The main aim of the study was to describe intra-species diversity and to determine how this diversity is spread across the replicons. We found that multiple phylogenomic and non-phylogenomic methods used for reconstructing trees all converge on similar tree topologies, showing that different metrics largely agree on the evolutionary history of the species. The greatest genomic variation lies on the small plasmids, followed by the repA-type circular megaplasmid, with the chromosome varying least of all. Additionally, the presence of extra linear and circular megaplasmids is noted in several strains, while small plasmids are not always present. Glycosyl hydrolases, bacteriocins and proteases vary considerably on all replicons while two exopolysaccharide clusters and several clustered regularly interspaced short palindromic repeats-associated systems show a lot of variation on the chromosome. Overall, despite its reputation as a mammalian gastrointestinal tract specialist, the intra-specific variation of L. salivarius reveals potential strain-dependant effects on human health.
Highlights
The genus Lactobacillus is a diverse, paraphyletic group with a combined species and subspecies count of over 200 [1]
They are the largest group within the lactic acid bacteria (LAB) and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties [2]
It is difficult to explain the absence of plasmid sequences in JCM1230 in the current study: the megaplasmid might have been artificially excluded by a procedural artefact during the DNA extraction/preparation procedure or, alternatively, since 100 kb is the smallest repA-type megaplasmid in the Li et al [25] dataset, the strain may have lost the megaplasmid in vitro during laboratory passage
Summary
The genus Lactobacillus is a diverse, paraphyletic group with a combined species and subspecies count of over 200 [1]. Lactobacilli are Gram-positive, rod-shaped, non-sporeforming bacteria that inhabit a wide range of niches from soil and plants to the gastrointestinal tracts of humans and animals [2, 3]. They are the largest group within the lactic acid bacteria (LAB) and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties [2]. Numerous studies have focused on the comparative genomics of individual species of the genus Lactobacillus, highlighting considerable intraspecific genomic diversity among strains [8–19]. One species that has been repeatedly isolated from the gastro-intestinal tracts of humans and animals and that has potential probiotic properties is the facultatively heterofermentative species, Lactobacillus salivarius [20–22]
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