Multireplicon genome architecture of Lactobacillus salivarius

Abstract

Lactobacillus salivarius subsp. salivarius strain UCC118 is a bacteriocin-producing strain with probiotic characteristics. The 2.13-Mb genome was shown by sequencing to comprise a 1.83 Mb chromosome, a 242-kb megaplasmid (pMP118), and two smaller plasmids. Megaplasmids previously have not been characterized in lactic acid bacteria or intestinal lactobacilli. Annotation of the genome sequence indicated an intermediate level of auxotrophy compared with other sequenced lactobacilli. No single-copy essential genes were located on the megaplasmid. However, contingency amino acid metabolism genes and carbohydrate utilization genes, including two genes for completion of the pentose phosphate pathway, were megaplasmid encoded. The megaplasmid also harbored genes for the Abp118 bacteriocin, a bile salt hydrolase, a presumptive conjugation locus, and other genes potentially relevant for probiotic properties. Two subspecies of L. salivarius are recognized, salivarius and salicinius, and we detected megaplasmids in both subspecies by pulsed-field gel electrophoresis of sizes ranging from 100 kb to 380 kb. The discovery of megaplasmids of widely varying size in L. salivarius suggests a possible mechanism for genome expansion or contraction to adapt to different environments.

Fig. 1.

Genome atlas of L. salivarius UCC118. The color coding of the genomic features in circle 1 and 2 represents different Clusters of Orthologous Groups categories.

Fig. 2.

Genes for completing the pentose phosphate pathway are on pMP118. Numbers and arrows in red or green represent genes and pathways encoded by pMP118 or the chromosome, respectively. Features in amber have genes coded by both replicons.

Fig. 3.

Megaplasmids of varying size are found in L. salivarius. (A) PFGE of genomic DNA of 10 L. salivarius strains. (B) Corresponding Southern hybridization with the pMP118 repA probe. (+) or (−) indicate treatment with S1 nuclease. Arrowheads to left indicate λ DNA concatamers used as size standard. Detailed strain information is provided in Supporting Text. The estimated size of megaplasmids are as follows: AH4231, 210 kb; UCC118, 242 kb; UCC119, 195 kb; DSM20492, 240 kb; DSM20555, 380 kb; NICMB8816, 180 kb; NCIMB8817, 145 kb; DSM20554, 260 kb; NCIMB702343, 160 kb; JCM1230, 100 kb.