Abstract
BackgroundLactobacillus salivarius strains are increasingly being exploited for their probiotic properties in humans and animals. Dissemination of antibiotic resistance genes among species with food or probiotic-association is undesirable and is often mediated by plasmids or integrative and conjugative elements. L. salivarius strains typically have multireplicon genomes including circular megaplasmids that encode strain-specific traits for intestinal survival and probiotic activity. Linear plasmids are less common in lactobacilli and show a very limited distribution in L. salivarius. Here we present experimental evidence that supports an unusually complex multireplicon genome structure in the porcine isolate L. salivarius JCM1046.ResultsJCM1046 harbours a 1.83 Mb chromosome, and four plasmids which constitute 20% of the genome. In addition to the known 219 kb repA-type megaplasmid pMP1046A, we identified and experimentally validated the topology of three additional replicons, the circular pMP1046B (129 kb), a linear plasmid pLMP1046 (101 kb) and pCTN1046 (33 kb) harbouring a conjugative transposon. pMP1046B harbours both plasmid-associated replication genes and paralogues of chromosomally encoded housekeeping and information-processing related genes, thus qualifying it as a putative chromid. pLMP1046 shares limited sequence homology or gene synteny with other L. salivarius plasmids, and its putative replication-associated protein is homologous to the RepA/E proteins found in the large circular megaplasmids of L. salivarius. Plasmid pCTN1046 harbours a single copy of an integrated conjugative transposon (Tn6224) which appears to be functionally intact and includes the tetracycline resistance gene tetM.ConclusionExperimental validation of sequence assemblies and plasmid topology resolved the complex genome architecture of L. salivarius JCM1046. A high-coverage draft genome sequence would not have elucidated the genome complexity in this strain. Given the expanding use of L. salivarius as a probiotic, it is important to determine the genotypic and phenotypic organization of L. salivarius strains. The identification of Tn6224-like elements in this species has implications for strain selection for probiotic applications.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-771) contains supplementary material, which is available to authorized users.
Highlights
Lactobacillus salivarius strains are increasingly being exploited for their probiotic properties in humans and animals
Probes associated with the replication origin of pMP1046A hybridised to a band that migrated to a constant position between the 194 kb and 242.5 kb linear λ DNA markers, which was in keeping with the expected 219,748 bp size indicated by DNA sequencing
The plasmids of L. salivarius probably confer on their host many of the genes associated with niche adaptation and which are known to modulate the phenotype of a strain significantly
Summary
Lactobacillus salivarius strains are increasingly being exploited for their probiotic properties in humans and animals. L. salivarius strains typically have multireplicon genomes including circular megaplasmids that encode strain-specific traits for intestinal survival and probiotic activity. The probiotic and immunomodulatory activity of L. salivarius strains has been recently reviewed [5] and are considered to be strain-specific traits [6]. Linear phage genomes are harboured by strains of Escherichia coli [25], Yersinia enterocolitica [26], Klebsiella oxytoca [27] as well as the probiotic cheese strain Lactobacillus paracasei NFBC 338 [28]. We previously identified linear megaplasmids in two porcine L. salivarius isolates, JCM1046 and JCM1047, and one human intestinal isolate AH43348 [12]
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