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Treerat P, McGuire B, Palmer E, Dahl EM, Karstens L, Merritt J, Kreth J. Oral microbiome diversity: The curious case of Corynebacterium sp. isolation. Mol Oral Microbiol 2022; 37:167-179. [PMID: 35859343 PMCID: PMC9578355 DOI: 10.1111/omi.12381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/29/2022] [Accepted: 07/14/2022] [Indexed: 01/28/2023]
Abstract
Oral microbiome sequencing efforts revealed the presence of hundreds of different microbes. Interindividual differences at strain and species resolution suggest that microbiome diversity could lead to mechanistically distinct gene regulation as well as species-related differences in phenotypes. Commonly, gene regulation and related phenotypes are studied in a few selected strains of a particular species with conclusions that are mostly generalized. The aim of this study was to isolate several species of Corynebacterium using an established protocol that led to the previous isolation of C. durum. Characterization of C. durum interspecies interactions revealed a specific mechanism for chain elongation in Streptococcus sanguinis that was the result of corynebacterial fatty acid production and secretion. While the protocol was successfully applied to isolate what we presumed to be additional Corynebacterium based on several phenotypic traits that seem to be identical to C. durum, genome sequencing of the newly isolated strains placed them closer to Actinomyces. Both Corynebacterium and Actinomyces are suborders of the Actinobacteridae and related species. Our study suggests to take several comprehensive strategies into consideration when taxonomically identifying closely related microorganisms. Furthermore, it seems to be important to test common core phenotypes in bacterial ecology to understand the behavior of specific groups of microbes, rather than simply relying upon genome sequence homology to establish relationships in the microbiome.
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Affiliation(s)
- Puthayalai Treerat
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian McGuire
- Department of Pediatric Dentistry, Oregon Health & Science University, Portland, Oregon, USA
- Portsmouth Pediatric Dentistry and Orthodontics, 150 Griffin Rd #1, Portsmouth, NH 03801, USA
| | - Elizabeth Palmer
- Department of Pediatric Dentistry, Oregon Health & Science University, Portland, Oregon, USA
| | - Erin M. Dahl
- Department of Medical Informatics and Clinical Epidemiology, Division of Bioinformatics and Computational Biomedicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Lisa Karstens
- Department of Medical Informatics and Clinical Epidemiology, Division of Bioinformatics and Computational Biomedicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, Oregon Health & Science University, Portland, Oregon, USA
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Bedoya-Correa CM, Rincón-Rodríguez RJ, Parada-Sanchez MT. Acidogenic and aciduric properties of Streptococcus mutans serotype c according to its genomic variability. Eur J Oral Sci 2021; 129:e12824. [PMID: 34865249 DOI: 10.1111/eos.12824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/27/2021] [Indexed: 11/24/2022]
Abstract
Streptococcus mutans (S. mutans) has a wide genetic diversity that contributes to its phenotypic heterogeneity, and may be related to attributes associated with acidogenicity and aciduricity. The aim of this study was to evaluate the acidogenic and aciduric properties of S. mutans serotype c isolates from saliva of schoolchildren according to the genomic variability. S. mutans isolates were identified by polymerase chain reaction. Fifty S. mutans serotype c isolates were genotyped by pulsed field gel electrophoresis and tested for their ability to produce and resist acid. Three specific genotypes were identified in the caries-active group and only one in the caries-free group. Although isolates were similarly acidogenic, an exclusive caries-active genotype had the greatest glycolytic activity. In contrast, isolates exhibited variable aciduricity, and three caries-active genotypes were the least aciduric. We concluded that there is genetic variability within serotype c. Acid production was similar regardless of the caries status but correlated with the number of genotypes. In addition, resistance to acid could be an important characteristic for the establishment and colonisation of specific genotypes in children with caries. However, it is important to evaluate children's intrinsic characteristics and other phenotypic properties to explain the physiopathological behaviour of the different genotypes.
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Bottner A, He RY, Sarbu A, Nainar SMH, Dufour D, Gong SG, Lévesque CM. Streptococcus mutans isolated from children with severe-early childhood caries form higher levels of persisters. Arch Oral Biol 2019; 110:104601. [PMID: 31734540 DOI: 10.1016/j.archoralbio.2019.104601] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/12/2019] [Accepted: 11/04/2019] [Indexed: 10/25/2022]
Abstract
OBJECTIVES Dental caries is the most common chronic infectious disease in children. Streptococcus mutans, the main cariogenic bacterial species, produces persisters, nongrowing dormant variants of regular cells associated with chronicity of diseases. We hypothesized that the recurrent nature of caries, particularly within populations with high-caries risk, is due partly to specific phenotypic features of S. mutans such as its ability to form persisters. We aimed to investigate the genotypic and phenotypic differences between the S. mutans from children with severe early-childhood caries (S-ECC) and those without caries. METHODS S. mutans from plaque samples of caries-free (CF) and S-ECC children were tested for their ability to adapt to a lethal pH in an acid tolerance response assay. The persister levels of S. mutans isolates was quantified in both groups. RESULTS S. mutanswas identified in all 23 S-ECC but only 6 of the 21 CF subjects. In most subjects, only one dominant S. mutans genotype was detected. No statistically significant differences in the mean survival percentage of S. mutans were observed between the two groups at a lethal pH of 3.5. However, the dominant genotype within a particular S-ECC subject exhibited a higher percentage of cell survival compared to those in the CF group. In S-ECC patients, S. mutans isolates displayed a ∼15-fold higher persistence phenotype than S. mutans isolates from CF patients. CONCLUSIONS The ability of S. mutans to produce high levels of persisters may contribute to part of an individual's ability to control caries disease activity and recurrent lesions.
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Affiliation(s)
- Aaron Bottner
- Orthodontics, Faculty of Dentistry, University of Toronto, Canada
| | - Richard Y He
- Microbiology, Faculty of Dentistry, University of Toronto, Canada
| | - Andrea Sarbu
- Microbiology, Faculty of Dentistry, University of Toronto, Canada
| | - S M Hashim Nainar
- Pediatric Dentistry, Faculty of Dentistry, University of Toronto, Canada
| | - Delphine Dufour
- Microbiology, Faculty of Dentistry, University of Toronto, Canada
| | - Siew-Ging Gong
- Orthodontics, Faculty of Dentistry, University of Toronto, Canada.
| | - Céline M Lévesque
- Pediatric Dentistry, Faculty of Dentistry, University of Toronto, Canada
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Exploring the Genomic Diversity and Cariogenic Differences of Streptococcus mutans Strains Through Pan-Genome and Comparative Genome Analysis. Curr Microbiol 2017; 74:1200-1209. [PMID: 28717847 DOI: 10.1007/s00284-017-1305-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2017] [Accepted: 07/11/2017] [Indexed: 10/19/2022]
Abstract
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.
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Okamoto M, Naito M, Miyanohara M, Imai S, Nomura Y, Saito W, Momoi Y, Takada K, Miyabe-Nishiwaki T, Tomonaga M, Hanada N. Complete genome sequence of Streptococcus troglodytae TKU31 isolated from the oral cavity of a chimpanzee (Pan troglodytes). Microbiol Immunol 2017; 60:811-816. [PMID: 27921343 DOI: 10.1111/1348-0421.12453] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/21/2016] [Accepted: 11/24/2016] [Indexed: 11/27/2022]
Abstract
Streptococcus troglodytae TKU31 was isolated from the oral cavity of a chimpanzee (Pan troglodytes) and was found to be the most closely related species of the mutans group streptococci to Streptococcus mutans. The complete sequence of TKU31 genome consists of a single circular chromosome that is 2,097,874 base pairs long and has a G + C content of 37.18%. It possesses 2082 coding sequences (CDSs), 65 tRNAs and five rRNA operons (15 rRNAs). Two clustered regularly interspaced short palindromic repeats, six insertion sequences and two predicted prophage elements were identified. The genome of TKU31 harbors some putative virulence associated genes, including gtfB, gtfC and gtfD genes encoding glucosyltransferase and gbpA, gbpB, gbpC and gbpD genes encoding glucan-binding cell wall-anchored protein. The deduced amino acid identity of the rhamnose-glucose polysaccharide F gene (rgpF), which is one of the serotype determinants, is 91% identical with that of S. mutans LJ23 (serotype k) strain. However, two other virulence-associated genes cnm and cbm, which encode the collagen-binding proteins, were not found in the TKU31 genome. The complete genome sequence of S. troglodytae TKU31 has been deposited at DDBJ/European Nucleotide Archive/GenBank under the accession no. AP014612.
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Affiliation(s)
- Masaaki Okamoto
- Department of Translational Research, Tsurumi University School of Dental Medicine
| | - Mariko Naito
- Division of Microbiology and Oral Infection, Department of Molecular Microbiology and Immunology, Nagasaki University Graduate School of Biomedical Sciences, 1-7-1 Sakamoto, Nagasaki 852-8588
| | - Mayu Miyanohara
- Department of Translational Research, Tsurumi University School of Dental Medicine
| | - Susumu Imai
- Department of Translational Research, Tsurumi University School of Dental Medicine
| | - Yoshiaki Nomura
- Department of Translational Research, Tsurumi University School of Dental Medicine
| | - Wataru Saito
- Department of Operative Dentistry, 2-1-3, Tsurumi, Tsurumi-ku, Yokohama 230-8501
| | - Yasuko Momoi
- Department of Operative Dentistry, 2-1-3, Tsurumi, Tsurumi-ku, Yokohama 230-8501
| | - Kazuko Takada
- Department of Oral Microbiology, Nihon University School of Dentistry at Matsudo, 2-870-1 Sakaecho-Nishi, Matsudo, Chiba, 271-8587
| | | | - Masaki Tomonaga
- Language and Intelligence Section, Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Nobuhiro Hanada
- Department of Translational Research, Tsurumi University School of Dental Medicine
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Lessons Learned from Clinical Studies: Roles of Mutans Streptococci in the Pathogenesis of Dental Caries. ACTA ACUST UNITED AC 2013. [DOI: 10.1007/s40496-013-0008-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Olson AB, Kent H, Sibley CD, Grinwis ME, Mabon P, Ouellette C, Tyson S, Graham M, Tyler SD, Van Domselaar G, Surette MG, Corbett CR. Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation. BMC Genomics 2013; 14:895. [PMID: 24341328 PMCID: PMC3897883 DOI: 10.1186/1471-2164-14-895] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 12/09/2013] [Indexed: 12/30/2022] Open
Abstract
Background The Streptococcus Anginosus Group (SAG) represents three closely related species of the viridans group streptococci recognized as commensal bacteria of the oral, gastrointestinal and urogenital tracts. The SAG also cause severe invasive infections, and are pathogens during cystic fibrosis (CF) pulmonary exacerbation. Little genomic information or description of virulence mechanisms is currently available for SAG. We conducted intra and inter species whole-genome comparative analyses with 59 publically available Streptococcus genomes and seven in-house closed high quality finished SAG genomes; S. constellatus (3), S. intermedius (2), and S. anginosus (2). For each SAG species, we sequenced at least one numerically dominant strain from CF airways recovered during acute exacerbation and an invasive, non-lung isolate. We also evaluated microevolution that occurred within two isolates that were cultured from one individual one year apart. Results The SAG genomes were most closely related to S. gordonii and S. sanguinis, based on shared orthologs and harbor a similar number of proteins within each COG category as other Streptococcus species. Numerous characterized streptococcus virulence factor homologs were identified within the SAG genomes including; adherence, invasion, spreading factors, LPxTG cell wall proteins, and two component histidine kinases known to be involved in virulence gene regulation. Mobile elements, primarily integrative conjugative elements and bacteriophage, account for greater than 10% of the SAG genomes. S. anginosus was the most variable species sequenced in this study, yielding both the smallest and the largest SAG genomes containing multiple genomic rearrangements, insertions and deletions. In contrast, within the S. constellatus and S. intermedius species, there was extensive continuous synteny, with only slight differences in genome size between strains. Within S. constellatus we were able to determine important SNPs and changes in VNTR numbers that occurred over the course of one year. Conclusions The comparative genomic analysis of the SAG clarifies the phylogenetics of these bacteria and supports the distinct species classification. Numerous potential virulence determinants were identified and provide a foundation for further studies into SAG pathogenesis. Furthermore, the data may be used to enable the development of rapid diagnostic assays and therapeutics for these pathogens.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Michael G Surette
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada.
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Argimón S, Konganti K, Chen H, Alekseyenko AV, Brown S, Caufield PW. Comparative genomics of oral isolates of Streptococcus mutans by in silico genome subtraction does not reveal accessory DNA associated with severe early childhood caries. INFECTION GENETICS AND EVOLUTION 2013; 21:269-78. [PMID: 24291226 DOI: 10.1016/j.meegid.2013.11.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 11/07/2013] [Accepted: 11/08/2013] [Indexed: 11/29/2022]
Abstract
Comparative genomics is a popular method for the identification of microbial virulence determinants, especially since the sequencing of a large number of whole bacterial genomes from pathogenic and non-pathogenic strains has become relatively inexpensive. The bioinformatics pipelines for comparative genomics usually include gene prediction and annotation and can require significant computer power. To circumvent this, we developed a rapid method for genome-scale in silico subtractive hybridization, based on blastn and independent of feature identification and annotation. Whole genome comparisons by in silico genome subtraction were performed to identify genetic loci specific to Streptococcus mutans strains associated with severe early childhood caries (S-ECC), compared to strains isolated from caries-free (CF) children. The genome similarity of the 20 S. mutans strains included in this study, calculated by Simrank k-mer sharing, ranged from 79.5% to 90.9%, confirming this is a genetically heterogeneous group of strains. We identified strain-specific genetic elements in 19 strains, with sizes ranging from 200 to 39 kb. These elements contained protein-coding regions with functions mostly associated with mobile DNA. We did not, however, identify any genetic loci consistently associated with dental caries, i.e., shared by all the S-ECC strains and absent in the CF strains. Conversely, we did not identify any genetic loci specific with the healthy group. Comparison of previously published genomes from pathogenic and carriage strains of Neisseria meningitidis with our in silico genome subtraction yielded the same set of genes specific to the pathogenic strains, thus validating our method. Our results suggest that S. mutans strains derived from caries active or caries free dentitions cannot be differentiated based on the presence or absence of specific genetic elements. Our in silico genome subtraction method is available as the Microbial Genome Comparison (MGC) tool, with a user-friendly JAVA graphical interface.
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Affiliation(s)
- Silvia Argimón
- New York University College of Dentistry, Department of Cariology and Comprehensive Care, 345 East 24th St, New York, NY 10010, USA.
| | - Kranti Konganti
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, 227 East 30th St, New York, NY 10016, USA
| | - Hao Chen
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, 227 East 30th St, New York, NY 10016, USA
| | - Alexander V Alekseyenko
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, 227 East 30th St, New York, NY 10016, USA
| | - Stuart Brown
- Center for Health Informatics and Bioinformatics, New York University School of Medicine, 227 East 30th St, New York, NY 10016, USA
| | - Page W Caufield
- New York University College of Dentistry, Department of Cariology and Comprehensive Care, 345 East 24th St, New York, NY 10010, USA
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Palmer SR, Miller JH, Abranches J, Zeng L, Lefebure T, Richards VP, Lemos JA, Stanhope MJ, Burne RA. Phenotypic heterogeneity of genomically-diverse isolates of Streptococcus mutans. PLoS One 2013; 8:e61358. [PMID: 23613838 PMCID: PMC3628994 DOI: 10.1371/journal.pone.0061358] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 03/07/2013] [Indexed: 11/18/2022] Open
Abstract
High coverage, whole genome shotgun (WGS) sequencing of 57 geographically- and genetically-diverse isolates of Streptococcus mutans from individuals of known dental caries status was recently completed. Of the 57 sequenced strains, fifteen isolates, were selected based primarily on differences in gene content and phenotypic characteristics known to affect virulence and compared with the reference strain UA159. A high degree of variability in these properties was observed between strains, with a broad spectrum of sensitivities to low pH, oxidative stress (air and paraquat) and exposure to competence stimulating peptide (CSP). Significant differences in autolytic behavior and in biofilm development in glucose or sucrose were also observed. Natural genetic competence varied among isolates, and this was correlated to the presence or absence of competence genes, comCDE and comX, and to bacteriocins. In general strains that lacked the ability to become competent possessed fewer genes for bacteriocins and immunity proteins or contained polymorphic variants of these genes. WGS sequence analysis of the pan-genome revealed, for the first time, components of a Type VII secretion system in several S. mutans strains, as well as two putative ORFs that encode possible collagen binding proteins located upstream of the cnm gene, which is associated with host cell invasiveness. The virulence of these particular strains was assessed in a wax-worm model. This is the first study to combine a comprehensive analysis of key virulence-related phenotypes with extensive genomic analysis of a pathogen that evolved closely with humans. Our analysis highlights the phenotypic diversity of S. mutans isolates and indicates that the species has evolved a variety of adaptive strategies to persist in the human oral cavity and, when conditions are favorable, to initiate disease.
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Affiliation(s)
- Sara R. Palmer
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
| | - James H. Miller
- Center for Oral Biology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Jacqueline Abranches
- Center for Oral Biology, University of Rochester Medical Center, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Lin Zeng
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
| | - Tristan Lefebure
- Université de Lyon, CNRS, Ecologie des Hydrosystèmes Naturels et Anthropisés; Université Lyon, Villeurbanne, France
- Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Vincent P. Richards
- Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - José A. Lemos
- Center for Oral Biology, University of Rochester Medical Center, Rochester, New York, United States of America
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Michael J. Stanhope
- Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Robert A. Burne
- Department of Oral Biology, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JDB. Strategic protein target analysis for developing drugs to stop dental caries. Adv Dent Res 2013; 24:86-93. [PMID: 22899687 DOI: 10.1177/0022034512449837] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Dental caries is the most common disease to cause irreversible damage in humans. Several therapeutic agents are available to treat or prevent dental caries, but none besides fluoride has significantly influenced the disease burden globally. Etiologic mechanisms of the mutans group streptococci and specific Lactobacillus species have been characterized to various degrees of detail, from identification of physiologic processes to specific proteins. Here, we analyze the entire Streptococcus mutans proteome for potential drug targets by investigating their uniqueness with respect to non-cariogenic dental plaque bacteria, quality of protein structure models, and the likelihood of finding a drug for the active site. Our results suggest specific targets for rational drug discovery, including 15 known virulence factors, 16 proteins for which crystallographic structures are available, and 84 previously uncharacterized proteins, with various levels of similarity to homologs in dental plaque bacteria. This analysis provides a map to streamline the process of clinical development of effective multispecies pharmacologic interventions for dental caries.
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Affiliation(s)
- J A Horst
- Division of Pediatric Dentistry, Department of Orofacial Sciences, University of California, San Francisco, CA, USA.
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11
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Burne RA, Zeng L, Ahn SJ, Palmer SR, Liu Y, Lefebure T, Stanhope MJ, Nascimento MM. Progress dissecting the oral microbiome in caries and health. Adv Dent Res 2013; 24:77-80. [PMID: 22899685 DOI: 10.1177/0022034512449462] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recent rapid advances in "-omics" technologies have yielded new insights into the interaction of the oral microbiome with its host. Associations of species that are usually considered to be acid-tolerant with caries have been confirmed, while some recognized as health-associated are often present in greater proportions in the absence of caries. In addition, some newly identified bacteria have been suggested as potential contributors to the caries process. In spite of this progress, two major challenges remain. The first is that there is a great deal of heterogeneity in the phenotypic capabilities of individual species of oral bacteria. The second is that the most abundant taxa in oral biofilms display remarkable phenotypic plasticity, i.e., the bacteria associated most strongly with health or with caries can morph rapidly in response to alterations in environmental pH, carbohydrate availability and source, and oxygen tension and redox environment. However, new technologic advances coupled with "old-fashioned microbiology" are starting to erode the barriers to a more complete understanding of oral biofilm physiology and ecology, and in doing so are beginning to provide insights for the creation of novel cost-effective caries control therapies.
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Affiliation(s)
- R A Burne
- Department of Oral Biology, University of Florida College of Dentistry, 1395 Center Drive, Gainesville, FL 32610, USA.
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12
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Lambrou GI, Koultouki E, Adamaki M, Moschovi M. Resolving Sample Traces in Complex Mixtures with Microarray Analyses. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
This chapter reviews the microarray technology and deal with the majority of aspects regarding microarrays. It focuses on today’s knowledge of separation techniques and methodologies of complex signal, i.e. samples. Overall, the chapter reviews the current knowledge on the topic of microarrays and presents the analyses and techniques used, which facilitate such approaches. It starts with the theoretical framework on microarray technology; second, the chapter gives a brief review on statistical methods used for microarray analyses, and finally, it contains a detailed review of the methods used for discriminating traces of nucleic acids within a complex mixture of samples.
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Cornejo OE, Lefébure T, Pavinski Bitar PD, Lang P, Richards VP, Eilertson K, Do T, Beighton D, Zeng L, Ahn SJ, Burne RA, Siepel A, Bustamante CD, Stanhope MJ. Evolutionary and population genomics of the cavity causing bacteria Streptococcus mutans. Mol Biol Evol 2013; 30:881-93. [PMID: 23228887 PMCID: PMC3603310 DOI: 10.1093/molbev/mss278] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Streptococcus mutans is widely recognized as one of the key etiological agents of human dental caries. Despite its role in this important disease, our present knowledge of gene content variability across the species and its relationship to adaptation is minimal. Estimates of its demographic history are not available. In this study, we generated genome sequences of 57 S. mutans isolates, as well as representative strains of the most closely related species to S. mutans (S. ratti, S. macaccae, and S. criceti), to identify the overall structure and potential adaptive features of the dispensable and core components of the genome. We also performed population genetic analyses on the core genome of the species aimed at understanding the demographic history, and impact of selection shaping its genetic variation. The maximum gene content divergence among strains was approximately 23%, with the majority of strains diverging by 5-15%. The core genome consisted of 1,490 genes and the pan-genome approximately 3,296. Maximum likelihood analysis of the synonymous site frequency spectrum (SFS) suggested that the S. mutans population started expanding exponentially approximately 10,000 years ago (95% confidence interval [CI]: 3,268-14,344 years ago), coincidental with the onset of human agriculture. Analysis of the replacement SFS indicated that a majority of these substitutions are under strong negative selection, and the remainder evolved neutrally. A set of 14 genes was identified as being under positive selection, most of which were involved in either sugar metabolism or acid tolerance. Analysis of the core genome suggested that among 73 genes present in all isolates of S. mutans but absent in other species of the mutans taxonomic group, the majority can be associated with metabolic processes that could have contributed to the successful adaptation of S. mutans to its new niche, the human mouth, and with the dietary changes that accompanied the origin of agriculture.
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Affiliation(s)
- Omar E. Cornejo
- Department of Genetics, School of Medicine, Stanford University
| | - Tristan Lefébure
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Paulina D. Pavinski Bitar
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Ping Lang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Vincent P. Richards
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Kirsten Eilertson
- Department of Biological Statistics and Computational Biology, Cornell University
| | - Thuy Do
- Department of Microbiology, King’s College London Dental Institute and NIHR Biomedical Research Centre at Guy's and St. Thomas’s NHS Foundation Trust, Guy’s Hospital, London, United Kingdom
| | - David Beighton
- Department of Microbiology, King’s College London Dental Institute and NIHR Biomedical Research Centre at Guy's and St. Thomas’s NHS Foundation Trust, Guy’s Hospital, London, United Kingdom
| | - Lin Zeng
- Department of Oral Biology, University of Florida
| | | | | | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University
| | | | - Michael J. Stanhope
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
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Peterson SN, Snesrud E, Schork NJ, Bretz WA. Dental caries pathogenicity: a genomic and metagenomic perspective. Int Dent J 2011; 61 Suppl 1:11-22. [PMID: 21726221 DOI: 10.1111/j.1875-595x.2011.00025.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In this review we address the subject of dental caries pathogenicity from a genomic and metagenomic perspective. The application of genomic technologies is certain to yield novel insights into the relationship between the bacterial flora, dental health and disease. Three primary attributes of bacterial species are thought to have direct impact on caries development, these include: adherence on tooth surfaces (biofilm formation), acid production and acid tolerance. Attempts to define the specific aetiological agents of dental caries have proven to be elusive, supporting the notion that caries aetiology is perhaps complex and multi-faceted. The recently introduced Human Microbiome Project (HMP) that endeavors to characterise the micro-organisms living in and on the human body is likely to shed new light on these questions and improve our understanding of polymicrobial disease, microbial ecology in the oral cavity and provide new avenues for therapeutic and molecular diagnostics developments.
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Distribution of putative virulence genes in Streptococcus mutans strains does not correlate with caries experience. J Clin Microbiol 2011; 49:984-92. [PMID: 21209168 DOI: 10.1128/jcm.01993-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Streptococcus mutans, a member of the human oral flora, is a widely recognized etiological agent of dental caries. The cariogenic potential of S. mutans is related to its ability to metabolize a wide variety of sugars, form a robust biofilm, produce copious amounts of lactic acid, and thrive in the acid environment that it generates. The remarkable genetic variability present within the species is reflected at the phenotypic level, notably in the differences in the cariogenic potential between strains. However, the genetic basis of these differences is yet to be elucidated. In this study, we surveyed by PCR and DNA hybridization the distribution of putative virulence genes, genomic islands, and insertion sequences across a collection of 33 strains isolated from either children with severe early childhood caries (S-ECC) or those who were caries free (CF). We found this genetically diverse group of isolates to be remarkably homogeneous with regard to the distribution of the putative virulence genes and genetic elements analyzed. Our findings point to the role of other factors in the pathogenesis of S-ECC, such as uncharacterized virulence genes, differences in gene expression and/or enzymatic activity, cooperation between S. mutans strains or with other members of the oral biota, and host factors.
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