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BackgroundStreptococcus salivarius is an abundant isolate of the human oral microbiota. Since both pH and glucose availability fluctuate frequently in the oral cavity, the goal of this study was to investigate regulation by CodY, a conserved pleiotropic regulator of Gram positive bacteria, in response to these two signals. The chemostat culture system was employed to precisely control the growth parameters, and the transcriptomes of wild-type S. salivarius 57.I and its CodY-null derivative (ΔcodY) grown at pH 7 and 5.5, with limited and excessive glucose supply were determined.ResultsThe transcriptomic analysis revealed that CodY was most active at pH 7 under conditions of glucose limitation. Based on whether a CodY binding consensus could be located in the 5′ flanking region of the identified target, the transcriptomic analysis also found that CodY shaped the transcriptome via both direct and indirect regulation. Inactivation of codY reduced the glycolytic capacity and the viability of S. salivarius at pH 5.5 or in the presence of H2O2. Studies using the Galleria mellonella larva model showed that CodY was essential for the toxicity generated from S. salivarius infection, suggesting that CodY regulation was critical for immune evasion and systemic infections. Furthermore, the CodY-null mutant strain exhibited a clumping phenotype and reduced attachment in biofilm assays, suggesting that CodY also modulates cell wall metabolism. Finally, the expression of genes belonging to the CovR regulon was affected by codY inactivation, but CodY and CovR regulated these genes in opposite directions.ConclusionsMetabolic adaptation in response to nutrient availability and growth pH is tightly linked to stress responses and virulence expression in S. salivarius. The regulation of metabolism by CodY allows for the maximal utilization of available nutrients and ATP production. The counteractive regulation of the CovR regulon could fine tune the transcriptomes in response to environmental changes.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4781-z) contains supplementary material, which is available to authorized users.

Streptococcus salivarius is an abundant isolate of the oral cavity. The genome of S. salivarius 57.I consists of a 2-Mb chromosome and a 40,758-bp circular molecule, designated YMC-2011. Annotation of YMC-2011 revealed 55 open reading frames, most of them associated with phage production, although plaque formation is not observed in S. salivarius 57.I after lytic induction using mitomycin C. Results from Southern hybridization and quantitative real-time PCR confirmed that YMC-2011 exists extrachromosomally, with an estimated copy number of 3 to 4. Phage particles were isolated from the supernatant of mitomycin C-treated S. salivarius 57.I cultures, and transmission electron microscopic examination indicated that YMC-2011 belongs to the Siphoviridae family. Phylogenetic analysis suggests that phage YMC-2011 and the cos-type phages of Streptococcus thermophilus originated from a common ancestor. An extended Ϫ10 element (p L ) and a 70 -like promoter (p R ) were mapped 5= to Ssal_phage00013 (encoding a CI-like repressor) and Ssal_phage00014 (encoding a hypothetical protein), respectively, using 5= rapid amplification of cDNA ends, indicating that YMC-2011 transcribes at least two mRNAs in opposite orientations. Studies using promoter-chloramphenicol acetyltransferase reporter gene fusions revealed that p R , but not p L , was sensitive to mitomycin C induction, suggesting that the switch from lysogenic growth to lytic growth was controlled mainly by the activity of these two promoters. In conclusion, a lysogenic state is maintained in S. salivarius 57.I, presumably by the repression of genes encoding proteins for lytic growth.IMPORTANCE The movement of mobile genetic elements such as bacteriophages and the establishment of lysogens may have profound effects on the balance of microbial ecology where lysogenic bacteria reside. The discovery of phage YMC-2011 from Streptococcus salivarius 57.I suggests that YMC-2011 and Streptococcus thermophilus-infecting phages share an ancestor. Although S. salivarius and S. thermophilus are close phylogenetically, S. salivarius is a natural inhabitant of the human mouth, whereas S. thermophilus is commonly found in the mammary mucosa of bovine species. Thus, the identification of YMC-2011 suggests that horizontal gene transfer via phage infection could take place between species from different ecological niches.KEYWORDS Streptococcus salivarius, temperate phage, lysogeny, plasmid, Siphoviridae family P hages, prokaryotic viruses, are the most abundant biological entities on the planet (1). Although phages have been isolated from the oral cavity (2, 3), relatively little is known about the phages of oral streptococci, compared to those of other lactic acid bacteria, particularly Lactococcus lactis and Streptococcus thermophilus. To date, the better characterized phages of oral streptococci are the virulent phage M102AD of Streptococcus mutans (4) and the temperate phage SM1 of Streptococcus mitis (5). A Streptococcus salivarius-infecting phage of the family Cystoviridae wa...

Streptococcus salivarius 57.I is one of the most abundant and highly ureolytic bacteria in the human mouth. It can utilize urea as the sole nitrogen source via the activity of urease. Complete genome sequencing of S. salivarius 57.I revealed a chromosome and a phage which are absent in strain SK126.Streptococcus salivarius, a member of the salivarius group of the viridans group streptococci, is one of the early colonizers of the epithelium and a common isolate of the human oral cavity (10). When S. salivarius gains entrance to the bloodstream, it may cause severe systemic infections (13). Although not all S. salivarius strains synthesize urease, the ureolytic activity of S. salivarius strain 57.I is the major alkali generation machinery in the oral cavity that plays an essential role in maintaining oral pH homeostasis and balancing dental plaque ecology (5, 17). Here we report the complete genome and annotation of the ureolytic strain 57.I and compared the genome with that of strain SK126.The complete genome sequence of S. salivarius strain 57.I was determined via a whole-genome shotgun approach employing Roche 454 pyrosequencing on a GS-FLX at 454 Life Sciences. A total of 272,194 high-quality reads were assembled by using Roche's Newbler assembler with approximately 50ϫ sequence coverage of the entire genome. The order of the contigs was arranged initially based on the gene order of S. salivarius strain SK126 chromosome (ACLO00000000), and the gaps between contigs were then finished by the multiplex PCR and primer walking method. The resulting sequence was edited by the phred/phrap/consed software package (8,9,11,12). The protein-coding genes, tRNAs, and rRNA were predicted by Glimmer 3.0, tRNA-SE, and RNAmmer (7, 14, 15), respectively. The functions of all genes were predicted by searching against the NCBI nonredundant protein database, cluster of orthologous groups (COGs), and InterProScan, and the metabolic pathways were reconstructed by using the Kyoto Encyclopedia of Genes and Genomes (KEGG) (1, 16, 18).The genome has one circular DNA molecule with a GC content of 39.93% and one phage DNA with a 41.24% GC content. The chromosome DNA is 2,138,805 bp in length, carrying 1,942 predicted open reading frames (ORFs), 68 predicted tRNA genes encoding all 20 amino acids, and 6 rRNA operons containing 5S, 16S, and 23S RNA genes. Additionally, there are two clusters of regularly interspaced short palindromic repeats (CRISPRs) and two potential CRISPRs in the chromosome. The phage DNA is 40,758 bp in length and encodes 55 proteins. Comparative genomic analysis of S. salivarius strains 57.I and SK126 revealed 164 ORFs that are unique in S. salivarius strain 57.I. These genes include the ure operon of 11 genes, encoding all proteins required for assembly of a functional urease (2, 3, 6), the cadDX operon, encoding a system for cadmium and zinc resistance (4), and a cluster of genes encoding sugar transferases involved in extracellular polysaccharide synthesis (Ssal_01171-01174 and Ssal_01176-01177), indicating that th...

Dental plaque rich in alkali-producing bacteria is less cariogenic, and thus, urease-producing Streptococcus salivarius has been considered as a therapeutic agent for dental caries control. Being one of the few ureolytic microbes in the oral cavity, S. salivarius strain 57.I promotes its competitiveness by mass-producing urease only at acidic growth pH. Here, we demonstrated that the downregulation of the transcription of the ure operon at neutral pH is controlled by a two-component system, VicRKX, whereas the upregulation at acidic pH is mediated by the global transcription regulator of nitrogen metabolism, GlnR. In the absence of VicR-mediated repression, the α subunit of RNA polymerase gains access to interact with the AT-rich sequence within the operator of VicR, leading to further activation of transcription. The overall regulation provides an advantage for S. salivarius to cope with the fluctuation of environmental pH, allowing it to persist in the mouth successfully.