Genetic variability of mutans streptococci revealed by wide whole-genome sequencing

The Outer Surface Protease, SepM, Is Required for blp Locus Activation in Three of the Four Most Common Pherotypes of Streptococcus pneumoniae

Streptococcus pneumoniae is an important cause of disease in humans that occurs when the bacteria in the nasopharynx bypasses host defenses to invade deeper tissues. Colonization fitness thus represents an important initial step in pathogenesis. S. pneumoniae produces antimicrobial peptides called bacteriocins that provide a competitive advantage over neighboring bacteria in the nasopharynx.

Investigating CRISPR spacer targets and their impact on genomic diversification of Streptococcus mutans

CRISPR-Cas is a bacterial immune system that restricts the acquisition of mobile DNA elements. These systems provide immunity against foreign DNA by encoding CRISPR spacers that help target DNA if it re-enters the cell. In this way, CRISPR spacers are a type of molecular tape recorder of foreign DNA encountered by the host microorganism. Here, we extracted ∼8,000 CRISPR spacers from a collection of over three hundred Streptococcus mutans genomes. Phage DNA is a major target of S. mutans spacers. S. mutans strains have also generated immunity against mobile DNA elements such as plasmids and integrative and conjugative elements. There may also be considerable immunity generated against bacterial DNA, although the relative contribution of self-targeting versus bona fide intra- or inter-species targeting needs to be investigated further. While there was clear evidence that these systems have acquired immunity against foreign DNA, there appeared to be minimal impact on horizontal gene transfer (HGT) constraints on a species-level. There was little or no impact on genome size, GC content and ‘openness’ of the pangenome when comparing between S. mutans strains with low or high CRISPR spacer loads. In summary, while there is evidence of CRISPR spacer acquisition against self and foreign DNA, CRISPR-Cas does not act as a barrier on the expansion of the S. mutans accessory genome.

The safety and potential probiotic properties analysis of Streptococcus alactolyticus strain FGM isolated from the chicken cecum

Purpose

Streptococcus alactolyticus strain FGM is used to ferment Astragalus membranaceus to develop a novel feed additive for animals in China. This study aimed at characterizing the safety and potential probiotic features of the strain FGM in vitro.

Methods

The genome of S. alactolyticus strain FGM was sequenced and used for genomic in silico studies. It was evaluated for morphology, antibiotic susceptibility, hemolytic activity, acid tolerance, bile salt tolerance, adherence ability to Caco-2, and inhibitory pathogens activity.

Result

The GC content of the strain FGM was 40.38% and composed of 29 contigs. The annotation of coding genes revealed important characteristics of the germs, especially 151 genes annotated to biological adhesion. The strain FGM forecasted 43 amino acid sequences to be VF, but did not have a hemolytic gene, and neither did it show hemolytic activity in phenotypic analysis. Although 30 amino acid sequences were predicted to aid in resisting some antibiotics, the strain FGM just showed the resistance to trimoxazole and oxytetracycline, and intermediate resistance to kanamycin. FGM cells were showed the tolerance to pH 2 broth within 4 h, and 0.15~0.30% bile salt medium with the latter being attributed to the presence of bile-salt hydrolase. The strain FGM was shown to have the ability to adhere to Caco-2 cells and the adherence rate of 1.0 × 109 CFU/mL bacterial suspensions was 37.51%. Compared with Lactobacillus acidophilus, Lactobacillus reuteri, and Lactobacillus casei, the strain FGM showed a high capability to inhibit the diffusion of Escherichia coli O78 and reduce its adhesion on Caco-2 cells.

Conclusion

The results demonstrated the presence of probiotic potential and absence of adverse effects for the Streptococcus alactolyticus strain FGM in vitro, thus contributing to develop a safety and effective fermentation feed for animals.

A Novel Competence Pathway in the Oral Pathogen Streptococcus sobrinus

Streptococcus sobrinus is an etiologic cause of dental caries (tooth decay) in humans. Our knowledge of S. sobrinus is scant despite the organism's important role in oral health. It is widely believed that S. sobrinus lacks the natural competence pathways that are used by other streptococci to regulate growth, virulence, and quorum sensing. The lack of natural competence has also prevented genetic manipulation of S. sobrinus, limiting our knowledge of its pathogenicity. We discovered that most strains of S. sobrinus contain a new class of the ComRS competence system. Although S. sobrinus is typically placed among the mutans group streptococci, the S. sobrinus ComRS system is most similar to the competence pathways in the salivarius group. Unlike all other ComRS systems, the S. sobrinus pathway contains 2 copies of the transcriptional regulator ComR and has a peptide pheromone (XIP) that lacks any aromatic amino acids. Synthetic XIP enables transformation of S. sobrinus with plasmid or linear DNA, and we leverage this newfound genetic tractability to confirm that only 1 of the ComR homologs is required for induced competence while the other appears to suppress competence. Exogenous XIP increases the expression of bacteriocin gene clusters and produces an antimicrobial response that inhibits growth of S. mutans. We also identified 2 strains of S. sobrinus that appear to be "cheaters" by either not responding to or not producing XIP. We show how a recombination event in the nonresponsive strain could restore function of the ComRS pathway but delete the gene encoding XIP. Thus, the S. sobrinus ComRS pathway provides new tools for studying this pathogen and offers a lens into the evolution of ecological cheaters.

cnm-Positive Streptococcus mutans and diffusion-weighted imaging hyperintensities in acute intracerebral hemorrhage

BACKGROUND

Strains of Streptococcus mutans expressing the cell surface collagen-binding protein, Cnm, encoded by cnm (cnm-positive S. mutans), are associated with hypertensive intracerebral hemorrhage (ICH) and the occurrence of cerebral microbleeds (CMBs). Small diffusion-weighted imaging (DWI) hyperintensities in patients with acute ICH are also associated with CMBs. However, the association between cnm-positive S. mutans and DWI hyperintensities is unclear. Hence, this study aimed to investigate the association between cnm-positive S. mutans and DWI hyperintensities in patients with acute ICH.

METHODS

Patients with acute ICH were prospectively registered at three hospitals. Dental plaque specimens were collected within 4 days after admission, and cnm-positive S. mutans was detected using the polymerase chain reaction. Magnetic resonance imaging at 14 ± 5 days after admission was used to evaluate DWI hyperintensities and CMBs.

RESULTS

A total of 197 patients were enrolled in this study. cnm-positive S. mutans was detected in 30 patients (15.2%), and DWI hyperintensities were observed in 56 patients (28.4%). Patients with cnm-positive S. mutans had a higher frequency of DWI hyperintensities (50.0% vs 24.6%; p = 0.008) and a higher number of CMBs (5.5 vs 1.5; p < 0.001) than those without cnm-positive S. mutans. Multivariable logistic analysis revealed that the presence of cnm-positive S. mutans was independently associated with DWI hyperintensities (OR 2.38; 95% CI 1.01-5.61; p = 0.047) after adjusting for several confounding factors.

CONCLUSION

This study found an association between the presence of cnm-positive S. mutans and DWI hyperintensities in patients with acute ICH.

A Core Genome Multilocus Sequence Typing Scheme for Streptococcus mutans

Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries. Recent whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) approaches have been employed in epidemiological studies of specific human pathogens. However, this approach has not been reported in studies of S. mutans Here, we therefore developed a cgMLST scheme for S. mutans We surveyed 199 available S. mutans genomes as a means of identifying cgMLST targets, developing a scheme that incorporated 594 targets from the S. mutans UA159 reference genome. Sixty-eight sequence types (STs) were identified in this cgMLST scheme (cgSTs) in 80 S. mutans isolates from 40 children that were sequenced in this study, compared to 35 STs identified by multilocus sequence typing (MLST). Fifty-six cgSTs (82.35%) were associated with a single isolate based on our cgMLST scheme, which is significantly higher than in the MLST scheme (11.43%). In addition, 58.06% of all MLST profiles with ≥2 isolates were further differentiated by our cgMLST scheme. Topological analyses of the maximum likelihood phylogenetic trees revealed that our cgMLST scheme was more reliable than the MLST scheme. A minimum spanning tree of 145 S. mutans isolates from 10 countries developed based upon the cgMLST scheme highlighted the diverse population structure of S. mutans This cgMLST scheme thus offers a new molecular typing method suitable for evaluating the epidemiological distribution of this pathogen and has the potential to serve as a benchmark for future global studies of the epidemiological nature of dental caries.IMPORTANCE Streptococcus mutans is regarded as a major pathogen responsible for the onset of dental caries. S. mutans can transmit among people, especially within families. In this study, we established a new epidemiological approach to S. mutans classification. This approach can effectively differentiate among closely related isolates and offers superior reliability relative to that of the traditional MLST molecular typing method. As such, it has the potential to better support effective public health strategies centered around this bacterium that are aimed at preventing and treating dental caries.

Potential effects of Psidium sp., Mangifera sp., Mentha sp. and its mixture (PEM) in reducing bacterial populations in biofilms, adherence and acid production of S. sanguinis and S. mutans

OBJECTIVE

Psidium sp., Mangifera sp. and Mentha sp. and its mixture (PEM) are known to have antimicrobial and anti-adherence effects.

DESIGN

Here, we have investigated these individual plant extracts and its synergistic mixture (PEM) for its anti-cariogenic effect to reduce populations of single and mixed-species of Streptococcus sanguinis and Streptococcus mutans in a planktonic or/and biofilm and their others reduced virulence. Bacterial populations in the biofilm after 24 h, hydrophobic cell surface activity to n-hexadecane and pH changes at 5 min' intervals until 90 min of incubation were recorded. Total phenolic content and bioactive compounds in the crude aqueous plant extracts were analysed. Regulatory gene expressions of S. mutans adhesins genes (gtfB, gtfC, gbpB and spaP) upon treatment with PEM were investigated in planktonic and biofilm conditions.

RESULTS

All plant extracts strongly reduced S. mutans in the biofilm compared to S. sanguinis in single and mixed-species. PEM reduced S. mutans by 84% with S. sanguinis 87% in the mixed population. Psidium sp. and PEM highly reduced cell-surface hydrophobicity of the two bacteria thus reducing adherence and biofilm formation. PEM and Mangifera sp. lowered initial pH change in the mixed populations of S. sanguinis and S. mutans. PEM downregulated the S. mutans gtfB gene expression in the single species planktonic and mixed-species biofilms.

CONCLUSIONS

The effectiveness of PEM in reducing S. mutans within the biofilm, cell-surface hydrophobicity, acid production and adhesin gene (gtfB) expression in mixed-species with S. sanguinis indicates its potential as an antibacterial agent against dental caries. This is attributed to the phenolic content in the PEM.

Conserved Pheromone Production, Response and Degradation by Streptococcus mutans

Streptococcus mutans, a bacterium with high cariogenic potential, coordinates competence for natural transformation and bacteriocin production via the XIP and CSP pheromones. CSP is effective in inducing bacteriocin responses but not competence in chemically defined media (CDM). This is in contrast to XIP, which is a strong inducer of competence in CDM but can also stimulate bacteriocin genes as a late response. Interconnections between the pathways activated by the two pheromones have been characterized in certain detail in S. mutans UA159, but it is mostly unknown whether such findings are representative for the species. In this study, we used bioassays based on luciferase reporters for the bacteriocin gene cipB and the alternative sigma factor sigX to investigate various S. mutans isolates for production and response to CSP and XIP pheromones in CDM. Similar to S. mutans UA159, endogenous CSP was undetectable in the culture supernatants of all tested strains. During optimization of the bioassay using the cipB reporter, we discovered that the activity of exogenous CSP used as a standard was reduced over time during S. mutans growth. Using a FRET-CSP reporter peptide, we found that S. mutans UA159 was able to degrade CSP, and that such activity was not significantly different in isogenic mutants with deletion of the protease gene htrA or the competence genes sigX, oppD, and comR. CSP cleavage was also detected in all the wild type strains, indicating that this is a conserved feature in S. mutans. For the XIP pheromone, endogenous production was observed in the supernatants of all 34 tested strains at peak concentrations in culture supernatants that varied between 200 and 26000 nM. Transformation in the presence of exogenous XIP was detected in all but one of the isolates. The efficiency of transformation varied, however, among the different strains, and for those with the highest transformation rates, endogenous XIP peak concentrations in the supernatants were above 2000 nM XIP. We conclude that XIP production and inducing effect on transformation, as well as the ability to degrade CSP, are conserved functions among different S. mutans isolates. Understanding the functionality and conservation of pheromone systems in S. mutans may lead to novel strategies to prevent or treat unbalances in oral microbiomes that may favor diseases.

Genetic diversity of Streptococcus mutans serotype c isolated from white spot and cavitated caries lesions from schoolchildren

OBJECTIVE

To determine the genetic diversity of Streptococcus mutans (S. mutans) serotype c isolated from white spot and cavitated caries lesions of schoolchildren.

METHODS

S. mutans isolates were obtained and identify by Polymerase Chain Reaction (PCR) from 28 schoolchildren. A total of 92 S. mutans isolates, identified as serotype c by PCR, were analyzed by pulsed field gel electrophoresis after digestion of genomic DNA with SmaI enzyme. 62 isolates were obtained from white spot and cavitated caries lesions of schoolchildren that presented both lesions simultaneously and 30 isolates were from saliva and biofilm samples of schoolchildren without dental caries. Cluster analyses were performed using the Dice coefficient of the BioNumerics software version 6.0.

RESULTS

It was possible to determine the serotype in 190 isolates out of 255 isolates identified as S. mutans. Serotype c was the most frequent (n = 139), followed by serotype f (n = 31) and serotype e (n = 20). After analyzing the dendograms of the 92 serotype c isolates, this study identified three strains present in both types of lesions, two strains specific to the type of lesion: one strain from the white spot lesion and one strain from the cavitated caries lesion, and five strains specific to children with caries versus four strains for children without caries.

CONCLUSION

S. mutans serotype c genetic variability is similar in terms of the number of strains present according to the caries status and type of lesion.

Hidden Gems in the Transcriptome Maps of Competent Streptococci

Natural transformation is regarded as an important mechanism in bacteria that allows for adaptation to different environmental stressors by ensuring genome plasticity. Since the discovery of this phenomenon in Streptococcus pneumoniae, remarkable progress has been made in the understanding of the molecular mechanisms and pathways coordinating this process. Recently, the advent of high-throughput sequencing allows the posing of questions that address the system at a larger scale but also allow for the creation of high-resolution maps of transcription. Thus, while much is already known about genetic competence in streptococci, recent studies continue to reveal intricate novel regulation pathways and components. In this perspective article, we highlight the use of transcriptional profiling and mapping as a valuable resource in the identification and characterization of “hidden gems” pertinent to the natural transformation system. Such strategies have recently been employed in a variety of different species. In S. mutans, for example, genome editing combined with the power of promoter mapping and RNA-Seq allowed for the identification of a link between the ComCDE and the ComRS systems, a ComR positive feedback loop mediated by SigX, and the XrpA peptide, encoded within sigX, which inhibits competence. In S. pneumoniae, a novel member of the competence regulon termed BriC was found to be directly under control of ComE and to promote biofilm formation and nasopharyngeal colonization but not competence. Together these new technologies enable us to discover new links and to revisit old pathways in the compelling study of natural genetic transformation.

Inhibition of Streptococcus mutans and S. sobrinus biofilms by liamocins from Aureobasidium pullulans

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Liamocins are polyol lipids that specifically inhibit Streptococcus spp..

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Liamocins inhibited biofilms of S. mutans and S. sobrinus in MTP assays.

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MTP results were verified in biofilm flow cell assays.

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Liamocins are potential new inhibitors of oral streptococcal biofilms.

The aim of this study was to determine if the novel anti-streptococcal inhibitors, liamocins, also inhibit biofilm formation by S. mutans and S. sobrinus. S. mutans strain ATCC 25175 and S. sobrinus strain ATCC 33478 were tested for biofilm formation in a rapid microtiter plate (MTP) assay and the effects of added liamocins were determined. This assay measures relative biofilm growth on pin lids. Results were verified in a biofilm flow cell assay, using hydroxyapatite-coated coupons to simulate dental material. Planktonic cultures of S. mutans and S. sobrinus were inhibited by 0.1 mg liamocins/ml. When liamocins were added after the adhesion phase in a rapid microtiter plate assay, S. mutans was inhibited 53% by 5 mg liamocins/ml, while S. sobrinus was more sensitive, showing 100% inhibition at 0.5 mg liamocins/ml. When liamocins were added during the adhesion phase, biofilms of S. mutans showed 78% inhibition at 3.0 mg liamocins/ml. In a biofilm flow cell assay, liamocins added after the adhesion phase at 0.5 mg liamocins/ml inhibited biofilms of S. sobrinus, and appeared to remove biofilms over time. Liamocins were shown for the first time to inhibit biofilm formation by S. mutans and S. sobrinus. Since liamocins are specific for Streptococcus spp., they are potential new inhibitors of oral streptococcal biofilms that should not affect normal oral microflora.

CovR and VicRKX Regulate Transcription of the Collagen Binding Protein Cnm of Streptococcus mutans

Cnm is a surface-associated protein present in a subset of Streptococcus mutans strains that mediates binding to extracellular matrices, intracellular invasion, and virulence. Here, we showed that cnm transcription is controlled by the global regulators CovR and VicRKX. In silico analysis identified multiple putative CovR- and VicR-binding motifs in the regulatory region of cnm as well as in the downstream gene pgfS, which is associated with the posttranslational modification of Cnm. Electrophoretic mobility shift assays revealed that CovR and VicR specifically and independently bind to the cnm and pgfS promoter regions. Quantitative real-time PCR and Western blot analyses of ΔcovR and ΔvicK strains as well as of a strain overexpressing vicRKX revealed that CovR functions as a positive regulator of cnm, whereas VicRKX acts as a negative regulator. In agreement with the role of VicRKX as a repressor, the ΔvicK strain showed enhanced binding to collagen and laminin and higher intracellular invasion rates. Overexpression of vicRKX was associated with decreased rates of intracellular invasion but did not affect collagen or lamin binding activities, suggesting that this system controls additional genes involved in binding to these extracellular matrix proteins. As expected, based on the role of CovR in cnm regulation, the ΔcovR strain showed decreased intracellular invasion rates, but, unexpectedly collagen and laminin binding activities were increased in this mutant strain. Collectively, the results presented here expand the repertoire of virulence-related genes regulated by CovR and VicRKX to include the core gene pgfS and the noncore gene cnm IMPORTANCE Streptococcus mutans is a major pathogen associated with dental caries and also implicated in systemic infections, in particular, infective endocarditis. The Cnm adhesin of S. mutans is an important virulence factor associated with systemic infections and caries severity. Despite its role in virulence, the regulatory mechanisms governing cnm expression are poorly understood. Here, we describe the identification of two independent regulatory systems controlling the transcription of cnm and the downstream pgfS-pgfM1-pgfE-pgfM2 operon. A better understanding of the mechanisms controlling expression of virulence factors like Cnm can facilitate the development of new strategies to treat bacterial infections.

Complete Genome Sequences of Streptococcus sobrinus SL1 (ATCC 33478 = DSM 20742), NIDR 6715-7 (ATCC 27351), NIDR 6715-15 (ATCC 27352), and NCTC 10919 (ATCC 33402)

The bacterium Streptococcus sobrinus causes tooth decay in humans. We present complete circularized genome sequences for four strains of S. sobrinus, type strain SL1, strain NIDR 6715-7 and the related NIDR 6715-15, and strain NCTC 10919.

The bacterium Streptococcus sobrinus causes tooth decay in humans. We present complete circularized genome sequences for four strains of S. sobrinus, type strain SL1, strain NIDR 6715-7 and the related NIDR 6715-15, and strain NCTC 10919. The finished genomes will enable genomic comparisons between S. sobrinus and other cariogenic microbes.

Whole genome sequence and phenotypic characterization of a Cbm+ serotype e strain of Streptococcus mutans

We report the whole genome sequence of the serotype e Cbm+ strain LAR01 of Streptococcus mutans, a dental pathogen frequently associated with extra-oral infections. The LAR01 genome is a single circular chromosome of 2.1 Mb with a GC content of 36.96%. The genome contains 15 phosphotransferase system gene clusters, seven cell wall-anchored (LPxTG) proteins, all genes required for the development of natural competence and genes coding for mutacins VI and K8. Interestingly, the cbm gene is genetically linked to a putative type VII secretion system that has been found in Mycobacteria and few other Gram-positive bacteria. When compared with the UA159 type strain, phenotypic characterization of LAR01 revealed increased biofilm formation in the presence of either glucose or sucrose but similar abilities to withstand acid and oxidative stresses. LAR01 was unable to inhibit the growth of Strpetococcus gordonii, which is consistent with the genomic data that indicate absence of mutacins that can kill mitis streptococci. On the other hand, LAR01 effectively inhibited growth of other S. mutans strains, suggesting that it may be specialized to outcompete strains from its own species. In vitro and in vivo studies using mutational and heterologous expression approaches revealed that Cbm is a virulence factor of S. mutans by mediating binding to extracellular matrix proteins and intracellular invasion. Collectively, the whole genome sequence analysis and phenotypic characterization of LAR01 provides new insights on the virulence properties of S. mutans and grants further opportunities to understand the genomic fluidity of this important human pathogen.

Determination and identification of antibiotic-resistant oral streptococci isolated from active dental infections in adults

OBJECTIVE

To determine and identify antibiotic-resistant bacteria (ARB) of oral streptococci from active dental infections in adults and its association with age and gender.

MATERIAL AND METHODS

This cross-sectional study included 59 subjects from 18 to 62 years old. Ninety-eighth samples obtained from the subjects were cultivated in agar plates containing antibiotics amoxicillin/clavulanic acid (A-CA), clindamycin, and moxifloxacin (concentrations of 16, 32 or 64 µg/ml). PCR assay was performed to identify bacterial species.

RESULTS

The bacterial species that showed more antibiotic-resistance (AR) was S. mutans (45.9%), followed by S. gordonii (21.6%), S. oralis (17.6%), S. sanguinis (9.5%), S. salivarius (5.4%) and S. sobrinus (0%). Moreover, clindamycin (59.4%) showed the highest frequency of AR. Moxifloxacin and A-CA showed an susceptibility >99.1%, while clindamycin showed the lowest efficacy (93.3%); there was a significant statistically difference (p < .01). The age group between 26 and 50 years old (32.2%) and females (28.8%) showed more multiresistance. Clindamycin showed a statistical difference (p < .05) when comparing groups by gender.

CONCLUSIONS

Clindamycin was the antibiotic with the highest frequency of ARB and lower bactericidal effect. Moxifloxacin and A-CA showed the highest efficacy and the lowest ARB frequency. Streptococcus mutans was the bacterial specie that showed an increased frequency of AR.

Transmission patterns of Streptococcus mutans demonstrated by a combined rep-PCR and MLST approach

OBJECTIVE

Clinical typing methods of the oral pathogen Streptococcus mutans with molecular analysis can be very specific, but expensive. Repetitive extragenic palindromic PCR (rep-PCR) is a relatively inexpensive pre-screening alternative for isolate selection for additional analyses. This study evaluated the prediction accuracy of using rep-PCR to identify S. mutans multilocus sequence typing (MLST) sequence types (ST) among children and their family members. Potential S. mutans strain sources were evaluated for evidence of transmission.

MATERIAL AND METHODS

Ten dendrograms (rep-PCR), with 20 isolates each of the 10 most common S. mutans genotypes, were generated from different subjects. Using a cut-off of 98% similarity, 7-11 isolates of each genotype were selected for MLST analysis to determine ST match/no-match.

RESULTS

Overall, rep-PCR was 75% effective at determining MLST ST match/no-match and 90% effective when applied to related individuals. Most genotypes were further differentiated by MLST. MLST ST diversity was greatest for one genotype (genotype 12, G12) and evidence of transmission among children and their family members was identified by rep-PCR and MLST. Younger children (6 months to 4 years old) shared ST with their mothers but 50% of older children (5-9 years old) had ST not identified in their mother. Six ST were shared between different families and probable source members were identified.

CONCLUSION

This study confirms that rep-PCR offers an affordable option to predict diverse isolates for downstream applications.

CLINICAL RELEVANCE

Using a combined rep-PCR and MLST approach, it is possible to track probable transmission and strain sources for S. mutans genotypes.

PGAP-X: extension on pan-genome analysis pipeline

Background

Since PGAP (pan-genome analysis pipeline) was published in 2012, it has been widely employed in bacterial genomics research. Though PGAP has integrated several modules for pan-genomics analysis, how to properly and effectively interpret and visualize the results data is still a challenge.

Result

To well present bacterial genomic characteristics, a novel cross-platform software was developed, named PGAP-X. Four kinds of data analysis modules were developed and integrated: whole genome sequences alignment, orthologous genes clustering, pan-genome profile analysis, and genetic variants analysis. The results from these analyses can be directly visualized in PGAP-X. The modules for data visualization in PGAP-X include: comparison of genome structure, gene distribution by conservation, pan-genome profile curve and variation on genic and genomic region. Meanwhile, result data produced by other programs with similar function can be imported to be further analyzed and visualized in PGAP-X. To test the performance of PGAP-X, we comprehensively analyzed 14 Streptococcus pneumonia strains and 14 Chlamydia trachomatis. The results show that, S. pneumonia strains have higher diversity on genome structure and gene contents than C. trachomatis strains. In addition, S. pneumonia strains might have suffered many evolutionary events, such genomic rearrangements, frequent horizontal gene transfer, homologous recombination, and other evolutionary process.

Conclusion

Briefly, PGAP-X directly presents the characteristics of bacterial genomic diversity with different visualization methods, which could help us to intuitively understand dynamics and evolution in bacterial genomes. The source code and the pre-complied executable programs are freely available from http://pgapx.ybzhao.com.

Electronic supplementary material

The online version of this article (doi: 10.1186/s12864-017-4337-7) contains supplementary material, which is available to authorized users.

In silico search of inhibitors of Streptococcus mutans for the control of dental plaque

Biofilm is an extremely complex microbial community arranged in a matrix of polysaccharides and attached to a substrate. Its development is crucial in the pathophysiology of oral infections like dental caries, as well as in periodontal, pulp, and periapical diseases. Streptococcus mutans is one of the most effective microorganisms in lactic acid production of the dental biofilm. Identifying essential Streptococcus mutans proteins using bioinformatics methods helps to search for alternative therapies. To this end, the bacterial genomes of several Streptococcus mutans strains and representative strains of other cariogenic and non-cariogenic bacteria were analysed by identifying pathogenicity islands and alignments with other bacteria, and by detecting the exclusive genes of cariogenic species in comparison to the non-pathogenic ones. This study used tools for orthology prediction such as BLAST and OrthoMCL, as well as the server IslandViewer for the detection of pathogenicity islands. In addition, the potential interactome of Streptococcus mutans was rebuilt by comparing it to interologues of other species phylogenetically close to or associated with cariogenicity. This protocol yielded a final list of 20 proteins related to potentially virulent factors that can be used as therapeutic targets in future analyses. The EIIA and EIIC enzymatic subunits of the phosphotransferase system (PTS) were prioritized, as well as the pyruvate kinase enzyme, which are directly involved in the metabolism of carbohydrates and in obtaining the necessary energy for the microorganism's survival. These results will guide a subsequent experimental trial to develop new, safe, and effective molecules in the treatment of dental caries.

Exploring the Genomic Diversity and Cariogenic Differences of Streptococcus mutans Strains Through Pan-Genome and Comparative Genome Analysis

Pan-genome refers to the sum of genes that can be found in a given bacterial species, including the core-genome and the dispensable genome. In this study, the genomes from 183 Streptococcus mutans (S. mutans) isolates were analyzed from the pan-genome perspective. This analysis revealed that S. mutans has an "open" pan-genome, implying that there are plenty of new genes to be found as more genomes are sequenced. Additionally, S. mutans has a limited core-genome, which is composed of genes related to vital activities within the bacterium, such as metabolism and hereditary information storage or processing, occupying 35.6 and 26.6% of the core genes, respectively. We estimate the theoretical core-genome size to be about 1083 genes, which are fewer than other Streptococcus species. In addition, core genes suffer larger selection pressures in comparison to those that are less widely distributed. Not surprisingly, the distribution of putative virulence genes in S. mutans strains does not correlate with caries status, indicating that other factors are also responsible for cariogenesis. These results contribute to a more understanding of the evolutionary characteristics and dynamic changes within the genome components of the species. This also helps to form a new theoretical foundation for preventing dental caries. Furthermore, this study sets an example for analyzing large genomic datasets of pathogens from the pan-genome perspective.

Collagen-binding proteins of Streptococcus mutans and related streptococci

The ability of Streptococcus mutans to interact with collagen through the expression of collagen-binding proteins (CBPs) bestows this oral pathogen with an alternative to the sucrose-dependent mechanism of colonization classically attributed to caries development. Based on the abundance and distribution of collagen throughout the human body, stringent adherence to this molecule grants S. mutans with the opportunity to establish infection at different host sites. Surface proteins, such as SpaP, WapA, Cnm and Cbm, have been shown to bind collagen in vitro, and it has been suggested that these molecules play a role in colonization of oral and extra-oral tissues. However, robust collagen binding is not achieved by all strains of S. mutans, particularly those that lack Cnm or Cbm. These observations merit careful dissection of the contribution from these different CBPs towards tissue colonization and virulence. In this review, we will discuss the current understanding of mechanisms used by S. mutans and related streptococci to colonize collagenous tissues, and the possible contribution of CBPs to infections in different sites of the host.

SepM, a Streptococcal Protease Involved in Quorum Sensing, Displays Strict Substrate Specificity

Streptococcus mutans, a causative agent of dental caries, relies on multiple quorum-sensing (QS) pathways that coordinate the expression of factors needed for colonization in the oral cavity. S. mutans uses small peptides as QS signaling molecules that typically are secreted into the outside milieu. Competence-stimulating peptide (CSP) is one such QS signaling molecule that functions through the ComDE two-component signal transduction pathway. CSP is secreted through NlmTE, a dedicated ABC transporter that cleaves off the N-terminal leader peptide to generate a mature peptide that is 21 residues long (CSP-21). We recently identified a surface-localized protease, SepM, which further cleaves the CSP-21 peptide at the C-terminal end and removes the last 3 residues to generate CSP-18. CSP-18 is the active QS molecule that interacts with the ComD sensor kinase to activate the QS pathway. In this study, we show that SepM specifically cleaves CSP-21 between the Ala18 and Leu19 residues. We also show that SepM recognizes only Ala at position 18 and Leu at position 19, although some CSP-18 variants with a substitution at position 18 can function equally as well as the QS peptide. Furthermore, we demonstrate that SepM homologs from other streptococci are capable of processing CSP-21 to generate functional CSP-18.

IMPORTANCE

SepM is a membrane-associated streptococcal protease that processes competence-stimulating peptide (CSP) to generate an active quorum-sensing molecule in S. mutans. SepM belongs to the S16 family of serine proteases, and in this study, we found that SepM behaves as an endopeptidase. SepM displays strict substrate specificity and cleaves the peptide bond between the Ala and Leu residues. This is the first report of an endopeptidase that specifically cleaves these two residues.

Comparing the cariogenic species Streptococcus sobrinus and S. mutans on whole genome level

Background

Two closely related species of mutans streptococci, namely Streptococcus mutans and Streptococcus sobrinus, are associated with dental caries in humans. Their acidogenic and aciduric capacity is directly associated with the cariogenic potential of these bacteria. To survive acidic and temporarily harsh conditions in the human oral cavity with hundreds of other microbial co-colonizers as competitors, both species have developed numerous mechanisms for adaptation.

Objectives

The recently published novel genome information for both species is used to elucidate genetic similarities but especially differences and to discuss the impact on cariogenicity of the corresponding phenotypic properties including adhesion, carbohydrate uptake and fermentation, acid tolerance, signaling by two component systems, competence, and oxidative stress resistance.

Conclusions

S. sobrinus can down-regulate the SpaA-mediated adherence to the pellicle. It has a smaller number of two-component signaling systems and bacteriocin-related genes than S. mutans, but all or even more immunity proteins. It lacks the central competence genes comC, comS, and comR. There are more genes coding for glucosyltransferases and a novel energy production pathway formed by lactate oxidase, which is not found in S. mutans. Both species show considerable differences in the regulation of fructan catabolism. However, both S. mutans and S. sobrinus share most of these traits and should therefore be considered as equally virulent with regard to dental caries.

Community interactions of oral streptococci

It is now clear that the most common oral diseases, dental caries and periodontitis, are caused by mixed-species communities rather than by individual pathogens working in isolation. Oral streptococci are central to these disease processes since they are frequently the first microorganisms to colonize oral surfaces and they are numerically the dominant microorganisms in the human mouth. Numerous interactions between oral streptococci and other bacteria have been documented. These are thought to be critical for the development of mixed-species oral microbial communities and for the transition from oral health to disease. Recent metagenomic studies are beginning to shed light on the co-occurrence patterns of streptococci with other oral bacteria. Refinements in microscopy techniques and biofilm models are providing detailed insights into the spatial distribution of streptococci in oral biofilms. Targeted genetic manipulation is increasingly being applied for the analysis of specific genes and networks that modulate interspecies interactions. From this work, it is clear that streptococci produce a range of extracellular factors that promote their integration into mixed-species communities and enable them to form social networks with neighboring taxa. These "community integration factors" include coaggregation-mediating adhesins and receptors, small signaling molecules such as peptides or autoinducer-2, bacteriocins, by-products of metabolism including hydrogen peroxide and lactic acid, and a range of extracellular enzymes. Here, we provide an overview of various types of community interactions between oral streptococci and other microorganisms, and we consider the possibilities for the development of new technologies to interfere with these interactions to help control oral biofilms.