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Bajagai YS, Trotter M, Williams TM, Costa DFA, Whitton MM, Ren X, Wilson CS, Stanley D. The role of microbiota in animal health and productivity: misinterpretations and limitations. ANIMAL PRODUCTION SCIENCE 2022. [DOI: 10.1071/an21515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Xu H, Tian J, Hao W, Zhang Q, Zhou Q, Shi W, Qin M, He X, Chen F. Oral Microbiome Shifts From Caries-Free to Caries-Affected Status in 3-Year-Old Chinese Children: A Longitudinal Study. Front Microbiol 2018; 9:2009. [PMID: 30210479 PMCID: PMC6121080 DOI: 10.3389/fmicb.2018.02009] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 08/09/2018] [Indexed: 01/14/2023] Open
Abstract
As one of the most prevalent human infectious diseases, dental caries results from dysbiosis of the oral microbiota driven by multiple factors. However, most of caries studies were cross-sectional and mainly focused on the differences in the oral microbiota between caries-free (CF) and caries-affected (CA) populations, while little is known about the dynamic shift in microbial composition, and particularly the change in species association pattern during disease transition. Here, we reported a longitudinal study of a 12-month follow-up of a cohort of 3-year-old children. Oral examinations and supragingival plaque collections were carried out at the beginning and every subsequent 6 months, for a total of three time points. All the children were CF at enrollment. Children who developed caries at 6-month follow-up but had not received any dental treatment until the end of the study were incorporated into the CA group. Children who remained CF at the end of the study were incorporated into the CF group. Using Illumina Miseq Sequencing of the 16S rRNA gene, we monitored the shift of supragingival microbiome during caries initiation and progression in children who developed caries over the 12-month study period. Intriguingly, principle coordinates analyses revealed two major shifting patterns in microbial structures during caries initiation and progression in CA group, but not in CF group. Dynamic co-occurring OTU network study showed that compared to CF group, there was significant increase in both number and intensity of correlations between microbial taxa, as well as the formation of tight clusters of specific bacteria in CA group. Furthermore, there were enhanced correlations, positive ones between CA-enriched taxa, and negative ones between CF-enriched and CA-enriched species within CA group. Our data suggested coordinated microbial interactions could be essential to caries pathogenesis. Most importantly, our study indicated that significant microbial shifts occur not only during caries development, but even in the sub-clinical state. Using supragingival microbiome profiles, we were able to construct a caries-onset prediction model with a prediction accuracy of 93.1%. Our study indicated that the microbial shifts prior to the onset of caries might potentially be used for the early diagnosis and prediction of caries.
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Affiliation(s)
- He Xu
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Jing Tian
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Wenjing Hao
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Qian Zhang
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
| | - Qiong Zhou
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Weihua Shi
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Man Qin
- Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology, Beijing, China
| | - Xuesong He
- The Forsyth Institute, Cambridge, MA, United States
| | - Feng Chen
- Central Laboratory, Peking University School and Hospital of Stomatology, Beijing, China
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Zhang X, Sun Z, Yang Q. Application of Denaturing Gradient Gel Electrophoresis to the Analysis of Bacterial Communities Associated With Asymptomatic and Symptomatic Pericoronitis. J Oral Maxillofac Surg 2017; 76:483-489. [PMID: 28893542 DOI: 10.1016/j.joms.2017.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 07/12/2017] [Accepted: 08/05/2017] [Indexed: 11/18/2022]
Abstract
PURPOSE Denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial communities associated with asymptomatic and symptomatic pericoronitis. The aim of the study was to compare the fingerprinting patterns of these 2 clinical conditions. MATERIALS AND METHODS The microbiota of mandibular third molar pockets associated with asymptomatic or symptomatic pericoronitis cases were collected and profiled by the polymerase chain reaction DGGE method. Banding patterns were compared by cluster analysis techniques. RESULTS Thirteen symptomatic pericoronitis and 7 asymptomatic pericoronitis samples were collected. Comparative analysis of the 2 clinical conditions showed bands that were common to the symptomatic and asymptomatic cases, but most DGGE bands appeared to be unique to the clinical condition. No single band occurred in all profiles. The mean number of bands detected in the 16S rDNA community profiles was 23.8 ± 4.2 (range, 19 to 34) for samples from symptomatic cases and 24.1 ± 2.4 (range, 21 to 29) for those from asymptomatic cases. Cluster analysis and multidimensional scaling analysis of the DGGE banding pattern showed a distinction in the similarity of banding patterns according to the presence or absence of symptoms. CONCLUSIONS These results suggest that the diversity of pericoronal pocket microbiota in asymptomatic pericoronitis cases differs markedly from that of symptomatic cases.
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Affiliation(s)
- Xin Zhang
- Doctor, Department of Dental Emergency, Beijing Stomatological Hospital and School of Stomatology, Capital Medical University, Beijing, China
| | - Zheng Sun
- Professor, Department of Oral Medicine, Beijing Stomatological Hospital and School of Stomatology, Capital Medical University, Beijing, China
| | - Qiubo Yang
- Professor, Beijing Institute for Dental Research, Beijing Stomatological Hospital and School of Stomatology, Capital Medical University, Beijing, China.
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M Weerasekera M, H Sissons C, Wong L, A Anderson S, R Holmes A, D Cannon R. Denaturing gradient gel electrophoresis profiles of bacteria from the saliva of twenty four different individuals form clusters that showed no relationship to the yeasts present. Arch Oral Biol 2017; 82:6-10. [PMID: 28577425 DOI: 10.1016/j.archoralbio.2017.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 04/25/2017] [Accepted: 05/20/2017] [Indexed: 10/19/2022]
Abstract
OBJECTIVES The aim was to investigate the relationship between groups of bacteria identified by cluster analysis of the DGGE fingerprints and the amounts and diversity of yeast present. METHODS Bacterial and yeast populations in saliva samples from 24 adults were analysed using denaturing gradient gel electrophoresis (DGGE) of the bacteria present and by yeast culture. RESULTS Eubacterial DGGE banding patterns showed considerable variation between individuals. Seventy one different amplicon bands were detected, the band number per saliva sample ranged from 21 to 39 (mean±SD=29.3±4.9). Cluster and principal component analysis of the bacterial DGGE patterns yielded three major clusters containing 20 of the samples. Seventeen of the 24 (71%) saliva samples were yeast positive with concentrations up to 103cfu/mL. Candida albicans was the predominant species in saliva samples although six other yeast species, including Candida dubliniensis, Candida tropicalis, Candida krusei, Candida guilliermondii, Candida rugosa and Saccharomyces cerevisiae, were identified. The presence, concentration, and species of yeast in samples showed no clear relationship to the bacterial clusters. CONCLUSION Despite indications of in vitro bacteria-yeast interactions, there was a lack of association between the presence, identity and diversity of yeasts and the bacterial DGGE fingerprint clusters in saliva. This suggests significant ecological individual-specificity of these associations in highly complex in vivo oral biofilm systems under normal oral conditions.
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Affiliation(s)
- Manjula M Weerasekera
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Department of Microbiology, Faculty of Medical Sciences,University of Sri Jayewardenepura, Sri Lanka.
| | - Chris H Sissons
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Lisa Wong
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Sally A Anderson
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand
| | - Ann R Holmes
- Sir John Walsh Research Institute and Department of Oral Sciences, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
| | - Richard D Cannon
- Sir John Walsh Research Institute and Department of Oral Sciences, Faculty of Dentistry, University of Otago, Dunedin, New Zealand
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Xia M, Qi Q. Bacterial analysis of combined periodontal-endodontic lesions by polymerase chain reaction-denaturing gradient gel electrophoresis. J Oral Sci 2015; 55:287-91. [PMID: 24351916 DOI: 10.2334/josnusd.55.287] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
We used denaturing gradient gel electrophoresis (DGGE) to compare bacterial profiles in periodontium and root canals of teeth with combined periodontal-endodontic lesions. Samples of dental plaque and necrotic pulp were collected from thirteen extracted teeth with advanced periodontitis. Genomic DNA was extracted for polymerase chain reaction (PCR) analysis using universal bacterial primers. The PCR products were then loaded onto DGGE gels to obtain fractionated bands. Characteristic DGGE bands were excised and DNA was cloned and sequenced. The number of bands, which indicates the number of bacterial species, was compared between dental plaques and necrotic pulp tissues from the same tooth. Although the difference was statistically significant (P < 0.01), there was no positive correlation; similarity (Dice coefficient) was 13.1% to 62.5%. Some bacteria species were present in both the periodontal pockets and root canals of the same tooth; however, periodontal bacteria did not always invade the root canals, and some bacteria in root canals were not present in periodontal pockets of the same tooth. In some teeth, unique bacteria in root canals had not passed from periodontal pockets. A basic local alignment search tool (BLAST) sequence search in Genbank indicated that new bacteria species were present in periodontal pockets and root canals. Their characteristics must thus be further analyzed.
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Wang S, Guo L, Seneviratne CJ, Huang B, Han J, Peng L, Liu X, Zhang C. Biofilm formation of salivary microbiota on dental restorative materials analyzed by denaturing gradient gel electrophoresis and sequencing. Dent Mater J 2014; 33:325-31. [PMID: 24598237 DOI: 10.4012/dmj.2013-152] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The microbial diversity of biofilms formed on the surfaces of amalgam, glass-ionomer cement, and resin composite was analyzed by denaturing gradient gel electrophoresis (DGGE). The V2-V3 region of salivary microbial 16S rDNA gene sequences of planktonic and biofilm bacteria, after 1 day and 1 week of incubation, was amplified by polymerase chain reaction (PCR) and analyzed by DGGE. The amounts of strongly adherent phylotypes after 1 day and 1 week on the three dental restorative materials were more than those on hydroxyapatite. Streptococcus salivarius was detected in both loosely adherent and strong adherent groups of all 1-day samples. At 1 week, the amounts of loosely adherent and strongly adherent phylotypes present on the three restorative materials ranked in this ascending order: glass-ionomer cement < resin composite < amalgam. Results of DGGE analysis suggested that glass-ionomer cement was the best material of choice in terms of suppressing bacterial phylotypes in biofilms.
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Affiliation(s)
- Shuai Wang
- Comprehensive Dental Care (Endodontics), Faculty of Dentistry, The University of Hong Kong
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Abstract
Limited information is available about the effects of HIV and subsequent antiretroviral treatment on host-microbe interactions. This study aimed to determine the salivary microbial composition for 10 HIV-seropositive subjects, before and 6 months after highly active antiretroviral therapy (HAART), compared with that for 10 HIV-seronegative subjects. A conventional culture and two culture-independent analyses were used and consistently demonstrated differences in microbial composition among the three sets of samples. HIV-positive subjects had higher levels of total cultivable microbes, including oral streptococci, lactobacilli, Streptococcus mutans, and Candida, in saliva than did HIV-negative subjects. The total cultivable microbial levels were significantly correlated with CD4+ T cell counts. Denaturing gradient gel electrophoresis (DGGE), which compared the overall microbial profiles, showed distinct fingerprinting profiles for each group. The human oral microbe identification microarray (HOMIM) assay, which compared the 16S rRNA genes, showed clear separation among the three sample groups. Veillonella, Synergistetes, and Streptococcus were present in all 30 saliva samples. Only minor changes or no changes in the prevalence of Neisseria, Haemophilus, Gemella, Leptotrichia, Solobacterium, Parvimonas, and Rothia were observed. Seven genera, Capnocytophaga, Slackia, Porphyromonas, Kingella, Peptostreptococcaceae, Lactobacillus, and Atopobium, were detected only in HIV-negative samples. The prevalences of Fusobacterium, Campylobacter, Prevotella, Capnocytophaga, Selenomonas, Actinomyces, Granulicatella, and Atopobium were increased after HAART. In contrast, the prevalence of Aggregatibacter was significantly decreased after HAART. The findings of this study suggest that HIV infection and HAART can have significant effects on salivary microbial colonization and composition.
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Salazar CR, Sun J, Li Y, Francois F, Corby P, Perez-Perez G, Dasanayake A, Pei Z, Chen Y. Association between selected oral pathogens and gastric precancerous lesions. PLoS One 2013; 8:e51604. [PMID: 23308100 PMCID: PMC3538744 DOI: 10.1371/journal.pone.0051604] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Accepted: 11/02/2012] [Indexed: 12/13/2022] Open
Abstract
We examined whether colonization of selected oral pathogens is associated with gastric precancerous lesions in a cross-sectional study. A total of 119 participants were included, of which 37 were cases of chronic atrophic gastritis, intestinal metaplasia, or dysplasia. An oral examination was performed to measure periodontal indices. Plaque and saliva samples were tested with real-time quantitative PCR for DNA levels of pathogens related to periodontal disease (Porphyromonas gingivalis, Tannerella forsythensis, Treponema denticola, Actinobacillus actinomycetemcomitans) and dental caries (Streptococcus mutans and S. sobrinus). There were no consistent associations between DNA levels of selected bacterial species and gastric precancerous lesions, although an elevated but non-significant odds ratio (OR) for gastric precancerous lesions was observed in relation to increasing colonization of A. actinomycetemcomitans (OR = 1.36 for one standard deviation increase, 95% Confidence Interval = 0.87-2.12), P. gingivalis (OR = 1.12, 0.67-1.88) and T. denticola (OR = 1.34, 0.83-2.12) measured in plaque. To assess the influence of specific long-term infection, stratified analyses by levels of periodontal indices were conducted. A. actinomycetemcomitans was significantly associated with gastric precancerous lesions (OR = 2.51, 1.13-5.56) among those with ≥ median of percent tooth sites with PD ≥ 3 mm, compared with no association among those below the median (OR = 0.86, 0.43-1.72). A significantly stronger relationship was observed between the cumulative bacterial burden score of periodontal disease-related pathogens and gastric precancerous lesions among those with higher versus lower levels of periodontal disease indices (p-values for interactions: 0.03-0.06). Among individuals with periodontal disease, high levels of colonization of periodontal pathogens are associated with an increased risk of gastric precancerous lesions.
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Affiliation(s)
- Christian R. Salazar
- Department of Epidemiology and Health Promotion, New York University College of Dentistry, New York, New York, United States of America
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, United States of America
| | - Jinghua Sun
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, New York, United States of America
| | - Yihong Li
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, New York, United States of America
| | - Fritz Francois
- Department of Medicine, New York University School of Medicine, New York, New York, New York, United States of America
- New York University Cancer Institute, New York University School of Medicine, New York, New York, New York, United States of America
| | - Patricia Corby
- Department of Periodontology and Implant Dentistry, New York University College of Dentistry, New York, New York, New York, United States of America
| | - Guillermo Perez-Perez
- Department of Microbiology, New York University School of Medicine, New York, NY, United States of America
| | - Ananda Dasanayake
- Department of Epidemiology and Health Promotion, New York University College of Dentistry, New York, New York, United States of America
| | - Zhiheng Pei
- Department of Medicine, New York University School of Medicine, New York, New York, New York, United States of America
- Department of Pathology, New York University School of Medicine, New York, New York, New York, United States of America
| | - Yu Chen
- Department of Medicine, New York University School of Medicine, New York, New York, New York, United States of America
- New York University Cancer Institute, New York University School of Medicine, New York, New York, New York, United States of America
- Division of Epidemiology, Department of Environmental Medicine, New York University School of Medicine, New York, New York, New York, United States of America
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Weerasekera MM, Sissons CH, Wong L, Anderson S, Holmes AR, Cannon RD. Use of denaturing gradient gel electrophoresis for the identification of mixed oral yeasts in human saliva. J Med Microbiol 2012; 62:319-330. [PMID: 23065546 DOI: 10.1099/jmm.0.050237-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A PCR-denaturing gradient gel electrophoresis (DGGE) method was established for the simultaneous presumptive identification of multiple yeast species commonly present in the oral cavity. Published primer sets targeting different regions of the Saccharomyces cerevisiae 26-28S rRNA gene (denoted primer sets N and U) and the 18S rRNA gene (primer set E) were evaluated with ten Candida and four non-Candida yeast species, and twenty Candida albicans isolates. Optimized PCR-DGGE conditions using primer set N were applied to presumptively identify, by band matching, yeasts in the saliva of 25 individuals. Identities were confirmed by DNA sequencing and compared with those using CHROMagar Candida culture. All primer sets yielded detectable DGGE bands for all species tested. Primer set N yielded mainly single bands and could distinguish all species examined, including differentiating Candida dubliniensis from C. albicans. Primer set U was less discriminatory among species but yielded multiple bands that distinguished subspecies groups within C. albicans. Primer set E gave poor yeast discrimination. DGGE analysis identified yeasts in 17 of the 25 saliva samples. Six saliva samples contained two yeast species: three contained C. albicans and three C. dubliniensis. C. dubliniensis was present alone in one saliva sample (total prevalence 16 %). CHROMagar culture detected yeasts in 16 of the yeast-containing saliva samples and did not enable identification of 7 yeast species identified by DGGE. In conclusion, DGGE identification of oral yeast species with primer set N is a relatively fast and reliable method for the simultaneous presumptive identification of mixed yeasts in oral saliva samples.
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Affiliation(s)
- Manjula M Weerasekera
- Department of Microbiology, Faculty of Medical Sciences, University of Sri Jayewardenepura, Nugegoda 10250, Sri Lanka.,Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington 6242, New Zealand
| | - Chris H Sissons
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington 6242, New Zealand
| | - Lisa Wong
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington 6242, New Zealand
| | - Sally Anderson
- Dental Research Group, School of Medicine and Health Sciences, University of Otago, Wellington 6242, New Zealand
| | - Ann R Holmes
- Department of Oral Sciences, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
| | - Richard D Cannon
- Department of Oral Sciences, Faculty of Dentistry, University of Otago, Dunedin 9016, New Zealand
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Wei X, Pushalkar S, Estilo C, Wong C, Farooki A, Fornier M, Bohle G, Huryn J, Li Y, Doty S, Saxena D. Molecular profiling of oral microbiota in jawbone samples of bisphosphonate-related osteonecrosis of the jaw. Oral Dis 2012; 18:602-12. [PMID: 22443347 PMCID: PMC7167636 DOI: 10.1111/j.1601-0825.2012.01916.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 01/31/2012] [Accepted: 02/03/2012] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Infection has been hypothesized as a contributing factor to bisphosphonate (BP)-related osteonecrosis of the jaw (BRONJ). The objective of this study was to determine the bacterial colonization of jawbone and identify the bacterial phylotypes associated with BRONJ. MATERIALS AND METHODS Culture-independent 16S rRNA gene-based molecular techniques were used to determine and compare the total bacterial diversity in bone samples collected from 12 patients with cancer (six, BRONJ with history of BP; six, controls without BRONJ, no history of BP but have infection). RESULTS Denaturing gradient gel electrophoresis profile and Dice coefficient displayed a statistically significant clustering of profiles, indicating different bacterial population in BRONJ subjects and control. The top three genera ranked among the BRONJ group were Streptococcus (29%), Eubacterium (9%), and Pseudoramibacter (8%), while in the control group were Parvimonas (17%), Streptococcus (15%), and Fusobacterium (15%). H&E sections of BRONJ bone revealed layers of bacteria along the surfaces and often are packed into the scalloped edges of the bone. CONCLUSION This study using limited sample size indicated that the jawbone associated with BRONJ was heavily colonized by specific oral bacteria and there were apparent differences between the microbiota of BRONJ and controls.
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Affiliation(s)
- X Wei
- New York University College of Dentistry, New York, NY, USA
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Pushalkar S, Ji X, Li Y, Estilo C, Yegnanarayana R, Singh B, Li X, Saxena D. Comparison of oral microbiota in tumor and non-tumor tissues of patients with oral squamous cell carcinoma. BMC Microbiol 2012; 12:144. [PMID: 22817758 PMCID: PMC3507910 DOI: 10.1186/1471-2180-12-144] [Citation(s) in RCA: 219] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 07/20/2012] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Bacterial infections have been linked to malignancies due to their ability to induce chronic inflammation. We investigated the association of oral bacteria in oral squamous cell carcinoma (OSCC/tumor) tissues and compared with adjacent non-tumor mucosa sampled 5 cm distant from the same patient (n = 10). By using culture-independent 16S rRNA approaches, denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing, we assessed the total bacterial diversity in these clinical samples. RESULTS DGGE fingerprints showed variations in the band intensity profiles within non-tumor and tumor tissues of the same patient and among the two groups. The clonal analysis indicated that from a total of 1200 sequences characterized, 80 bacterial species/phylotypes were detected representing six phyla, Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Actinobacteria and uncultivated TM7 in non-tumor and tumor libraries. In combined library, 12 classes, 16 order, 26 families and 40 genera were observed. Bacterial species, Streptococcus sp. oral taxon 058, Peptostreptococcus stomatis, Streptococcus salivarius, Streptococcus gordonii, Gemella haemolysans, Gemella morbillorum, Johnsonella ignava and Streptococcus parasanguinis I were highly associated with tumor site where as Granulicatella adiacens was prevalent at non-tumor site. Streptococcus intermedius was present in 70% of both non-tumor and tumor sites. CONCLUSIONS The underlying changes in the bacterial diversity in the oral mucosal tissues from non-tumor and tumor sites of OSCC subjects indicated a shift in bacterial colonization. These most prevalent or unique bacterial species/phylotypes present in tumor tissues may be associated with OSCC and needs to be further investigated with a larger sample size.
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Affiliation(s)
- Smruti Pushalkar
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
| | - Xiaojie Ji
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
- Department of Chemical and Biological Sciences, Polytechnic Institute of NYU, New York, NY, USA
| | - Yihong Li
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
| | - Cherry Estilo
- Dental Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Ramanathan Yegnanarayana
- Laboratory of Epithelial Cancer Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Bhuvanesh Singh
- Laboratory of Epithelial Cancer Biology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Xin Li
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
| | - Deepak Saxena
- Department of Basic Sciences and Craniofacial Biology, New York University College of Dentistry, 345 E, 24th Street, Room 921B, New York, NY, 10010, USA
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Thomas RZ, Zijnge V, Ciçek A, de Soet JJ, Harmsen HJM, Huysmans MCDNJM. Shifts in the microbial population in relation to in situ caries progression. Caries Res 2012; 46:427-31. [PMID: 22739571 DOI: 10.1159/000339482] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 04/24/2012] [Indexed: 11/19/2022] Open
Abstract
The shift in microbial diversity from young to mature plaque, related to caries activity on sound and restored surfaces, was studied using denaturing gradient gel electrophoresis. During a 20-week in situ study on caries progression 8 subjects wearing restored and unrestored dentin and enamel sections, biofilm was sampled after 1 and 20 weeks (young or mature plaque). A higher microbial diversity (mature plaque) was seen in caries-active compared to caries-free subjects. Rothia dentocariosa and Scardovia inopinata were absent from all caries-free sites, but appeared in 50% of the caries-active sites.
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Affiliation(s)
- R Z Thomas
- Center for Dentistry and Oral Hygiene, University Medical Center Groningen, The Netherlands.
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Ji X, Pushalkar S, Li Y, Glickman R, Fleisher K, Saxena D. Antibiotic effects on bacterial profile in osteonecrosis of the jaw. Oral Dis 2012; 18:85-95. [PMID: 21883710 PMCID: PMC3232327 DOI: 10.1111/j.1601-0825.2011.01848.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Oral infection is considered to play a critical role in the pathogenesis of bisphosphonate-related osteonecrosis of the jaw (BRONJ), and antibiotic therapy has become a mainstay of BRONJ therapy. This study was aimed to investigate the effect of antibiotics on bacterial diversity in BRONJ tissues. MATERIALS AND METHODS The bacterial profile from soft tissues associated with the BRONJ lesion was determined using 16S rRNA-based denaturing gradient gel electrophoresis (DGGE) and sequencing. Twenty BRONJ subjects classified as stage 0-2 were enrolled in this study, and patient groups were divided into an antibiotic cohort (n=10) treated with systemic antibiotic and a non-antibiotic cohort (n=10) with no prior antibiotic therapy. RESULTS The DGGE fingerprints indicated no significant differences in bacterial diversity of BRONJ tissue samples. Patients on antibiotics had higher relative abundance of phylum Firmicutes with bacterial species, Streptococcus intermedius, Lactobacillus gasseri, Mogibacterium timidum, and Solobacterium moorei, whereas patients without antibiotics had greater amounts of Parvimonas micra and Streptococcus anginosus. Thirty percent of bacterial populations were uncultured (yet-to be cultured) phylotypes. CONCLUSION This study using limited sample size indicated that oral antibiotic therapy may have a limited efficacy on the bacterial population associated with BRONJ lesions.
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Affiliation(s)
- X Ji
- Department of Chemical and Biological Sciences, Polytechnic Institute of New York University, USA
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Jiang W, Jiang Y, Li C, Liang J. Investigation of supragingival plaque microbiota in different caries status of Chinese preschool children by denaturing gradient gel electrophoresis. MICROBIAL ECOLOGY 2011; 61:342-352. [PMID: 20927511 DOI: 10.1007/s00248-010-9753-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 09/16/2010] [Indexed: 05/30/2023]
Abstract
This study aimed to detect differences in the richness of total supragingival plaque microbiota as well as the species composition of oral streptococci involved in the different stages of dental caries. Forty-five plaque samples were collected from caries-moderate (CM, 4 ≤ dmfs ≤ 6), caries-susceptible (CS, dmfs ≥ 10), and age-matched caries-free children separately. Total DNA was isolated directly from each sample, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses using universal and primers specific for oral streptococci were carried out. Using 16S rDNA PCR-DGGE, 34 different species of bacteria were identified in a culture-independent manner and classified into 11 genera according to phylogenetic analysis. Among them, Mitis group streptococci and Campylobacter, which were present in health status, no longer appeared in caries-susceptible samples. In addition, Capnocytophaga, Burkholderia, and Prevotella were found significantly less frequently in the CS group samples (P < 0.05), while there were no significant differences among the prevalence of Neisseria, Leptotrichia, Haemophilus, Mutans group streptococci, Corynebacterium, and Actinomyces in the three groups. Further DGGE analysis of rnpB gene amplicons obtained with oral streptococci species-specific primers showed that a total of 23 species of oral streptococci were identified. Streptococcus sanguinis, Streptococcus mitis, and Streptococcus oralis showed a significantly higher prevalence in healthy children (P < 0.05), while that of Streptococcus mutans and Streptococcus sobrinus did not vary among the three groups. Overall, these results suggest that supragingival plaque microbiota as a whole undergoes a more complicated shift in the caries process.
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Affiliation(s)
- Wei Jiang
- Department of Endodontics and Operative Dentistry, School of Stomatology, Ninth People's Hospital, Shanghai Key Laboratory of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
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Pushalkar S, Mane SP, Ji X, Li Y, Evans C, Crasta OR, Morse D, Meagher R, Singh A, Saxena D. Microbial diversity in saliva of oral squamous cell carcinoma. ACTA ACUST UNITED AC 2011; 61:269-77. [PMID: 21205002 DOI: 10.1111/j.1574-695x.2010.00773.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the oral cavity, chronic inflammation has been observed at various stages of oral squamous cell carcinomas (OSCC). Such inflammation could result from persistent mucosal or epithelial cell colonization by microorganisms. There is increasing evidence of the involvement of oral bacteria in inflammation, warranting further studies on the association of bacteria with the progression of OSCC. The objective of this study was to evaluate the diversity and relative abundance of bacteria in the saliva of subjects with OSCC. Using 454 parallel DNA sequencing, ∼58,000 PCR amplicons that span the V4-V5 hypervariable region of rRNAs from five subjects were sequenced. Members of eight phyla (divisions) of bacteria were detected. The majority of classified sequences belonged to the phyla Firmicutes (45%) and Bacteroidetes (25%). Further, 52 different genera containing approximately 860 (16.51%) known species were identified and 1077 (67%) sequences belonging to various uncultured bacteria or unclassified groups. The species diversity estimates obtained with abundance-based coverage estimators and Chao1 were greater than published analyses of other microbial profiles from the oral cavity. Fifteen unique phylotypes were present in all three OSCC subjects.
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Affiliation(s)
- Smruti Pushalkar
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, NY, USA
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Comparison of endodontic bacterial community structures in root-canal-treated teeth with or without apical periodontitis. J Med Microbiol 2010; 59:1360-1364. [DOI: 10.1099/jmm.0.018887-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial occurrence in treated root canals, even in patients without post-treatment apical periodontitis, raises the possibility that factors other than mere bacterial presence can be determinants for a favourable outcome of endodontic treatment. Because these factors may be related to the bacterial communities colonizing the root canal, including virulence, density and interactions, the objective of this study was to compare the community structures found in root-canal-treated teeth with (12 samples) and without (11 samples) apical periodontitis lesions by means of a PCR-denaturing gradient gel electrophoresis fingerprinting approach. Results confirmed a polymicrobial composition even in treated patients without post-treatment disease. A large microbial community diversity was observed for treated teeth both with or without disease, but no specific pattern was detected for diseased teeth. Nevertheless, the number of bands from samples with apical periodontitis lesions was statistically significantly higher (P=0.04) than that from samples collected from root-canal-treated teeth without post-treatment apical periodontitis. Furthermore, predominant bands in samples from patients with apical disease were also observed.
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Liu G, Saxena D, Deng H, Norman RG, Chen Z, Abrams WR, Malamud D, Li Y. Effect of protease inhibitors on the quantitative and qualitative assessment of oral microorganisms. FEMS Microbiol Lett 2010; 312:63-70. [PMID: 20831596 DOI: 10.1111/j.1574-6968.2010.02100.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Protease inhibitor cocktails are routinely added to clinical samples used for proteomic studies to inactivate proteases. As these same samples are often used for microbial studies, we determined whether the addition of protease inhibitors could affect the quantitative or qualitative assessment of microbial profiles. Twenty-two saliva samples were collected and processed immediately with or without the addition of a protease inhibitor cocktail. Conventional cultivation methods were used to evaluate total bacterial growth. Total genomic DNA was isolated and a specific 16S rRNA gene-targeted region was PCR-amplified and separated by denaturing gradient gel electrophoresis. A combination of 1D sodium dodecyl sulfate polyacrylamide gel electrophoresis and LC-MS/MS methods was used to determine the effect of the protease inhibitors on the integrity of salivary proteins and peptides. Interestingly, no significant differences were observed in either the bacterial growth and composition or the integrity of salivary proteins between the two groups. Correlation coefficients between the paired samples for total cultivable microbiota (r(2) =0.847), total mutans streptococci (r(2) =0.898), total oral lactobacilli (r(2) =0.933), and total Streptococcus mutans (r(2) =0.870) also exceeded expected values. The results suggest that the addition of a protease inhibitor cocktail in saliva samples does not impact the growth of oral microbiota or compromise the ability to characterize its composition.
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Affiliation(s)
- Gaoxia Liu
- Department of Basic Sciences, New York University College of Dentistry, New York, NY 10010-4086, USA
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18
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Drinking habits are associated with changes in the dental plaque microbial community. J Clin Microbiol 2009; 48:347-56. [PMID: 19955272 DOI: 10.1128/jcm.00932-09] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Caries and gingivitis are the most prevalent oral infectious diseases of humans and are due to the accumulation of dental plaque (a microbial biofilm) on the tooth surface and at the gingival margin, respectively. Several in vitro and in vivo studies have shown that many natural components of foods and beverages inhibit the adhesion of and/or exert activity against oral bacteria. These biological activities have mainly been attributed to the polyphenol fraction. In order to explore the possibility that diet can alter the dental plaque community, in this study we evaluated the composition of the microbiota of supra- and subgingival plaque samples collected from 75 adult subjects with different drinking habits (drinkers of coffee, red wine, or water for at least 2 years) by analyzing the microbial population through the separation of PCR-amplified fragments using the denaturing gradient gel electrophoresis (DGGE) technique. The mean numbers of bands of the DGGE profiles from all three categories were evaluated. There were no significant differences between the two kinds of plaque collected from the control group (water drinkers), and this group showed the highest number of bands (supragingival plaque, 18.98 +/- 3.16 bands; subgingival plaque, 18.7 +/- 3.23 bands). The coffee and wine drinker groups generated the lowest numbers of bands for both supragingival plaque (coffee drinkers, 8.25 +/- 3.53 bands; wine drinkers, 7.93 +/- 2.55 bands) and subgingival plaque (coffee drinkers, 8.3 +/- 3.03 bands; wine drinkers, 7.65 +/- 1.68 bands). The differences between coffee drinkers or wine drinkers and the control group (water drinkers) were statistically significant. A total of 34 microorganisms were identified, and the frequency of their distribution in the three subject categories was analyzed. A greater percentage of subjects were positive for facultative aerobes when supragingival plaque was analyzed, while anaerobes were more frequent in subgingival plaque samples. It is noteworthy that the frequency of identification of anaerobes was significantly reduced when the frequencies for coffee and wine drinkers were compared with the frequencies for subjects in the control group. The DGGE profiles of the organisms in both plaque samples from all groups were generated and were used to construct dendrograms. A number of distinct clusters of organisms from water, coffee, and wine drinkers were formed. The clustering of some of the DGGE results into cohort-specific clusters implies similarities in the microbiotas within these groups and relevant differences in the microbiotas between cohorts. This supports the notion that the drinking habits of the subjects may influence the microbiota at both the supragingival and the subgingival levels.
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Icoz I, Saxena D, Andow DA, Zwahlen C, Stotzky G. Microbial populations and enzyme activities in soil in situ under transgenic corn expressing cry proteins from Bacillus thuringiensis. JOURNAL OF ENVIRONMENTAL QUALITY 2008; 37:647-62. [PMID: 18396552 DOI: 10.2134/jeq2007.0352] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transgenic Bt crops produce insecticidal Cry proteins that are released to soil in plant residues, root exudates, and pollen and that may affect soil microorganisms. As a continuation of studies in the laboratory and a plant-growth room, a field study was conducted at the Rosemount Experiment Station of the University of Minnesota. Three Bt corn varieties that express the Cry1Ab protein, which is toxic to the European corn borer (Ostrinia nubilalis Hübner), and one Bt corn variety that expresses the Cry3Bb1 protein, which is toxic to the corn rootworm complex (Diabrotica spp.), and their near-isogenic non-Bt varieties were evaluated for their effects on microbial diversity by classical dilution plating and molecular (polymerase chain reaction-denaturing gradient gel electrophoresis) techniques and for the activities of some enzymes (arylsulfatases, acid and alkaline phosphatases, dehydrogenases, and proteases) involved in the degradation of plant biomass. After 4 consecutive years of corn cultivation (2003-2006), there were, in general, no consistent statistically significant differences in the numbers of different groups of microorganisms, the activities of the enzymes, and the pH between soils planted with Bt and non-Bt corn. Numbers and types of microorganisms and enzyme activities differed with season and with the varieties of corn, but these differences were not related to the presence of the Cry proteins in soil. The Cry1Ab protein of Bt corn (events Bt11 and MON810) was detected in most soils during the 4 yr, whereas the Cry3Bb1 protein was not detected in soils of Bt corn (event MON863) expressing the cry3Bb1 gene.
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Affiliation(s)
- I Icoz
- Lab. of Microbial Ecology, Dep. of Biology, New York Univ., New York, NY 10003, USA
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Kuramitsu HK, He X, Lux R, Anderson MH, Shi W. Interspecies interactions within oral microbial communities. Microbiol Mol Biol Rev 2007; 71:653-70. [PMID: 18063722 PMCID: PMC2168648 DOI: 10.1128/mmbr.00024-07] [Citation(s) in RCA: 373] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
While reductionism has greatly advanced microbiology in the past 400 years, assembly of smaller pieces just could not explain the whole! Modern microbiologists are learning "system thinking" and "holism." Such an approach is changing our understanding of microbial physiology and our ability to diagnose/treat microbial infections. This review uses oral microbial communities as a focal point to describe this new trend. With the common name "dental plaque," oral microbial communities are some of the most complex microbial floras in the human body, consisting of more than 700 different bacterial species. For a very long time, oral microbiologists endeavored to use reductionism to identify the key genes or key pathogens responsible for oral microbial pathogenesis. The limitations of reductionism forced scientists to begin adopting new strategies using emerging concepts such as interspecies interaction, microbial community, biofilms, polymicrobial disease, etc. These new research directions indicate that the whole is much more than the simple sum of its parts, since the interactions between different parts resulted in many new physiological functions which cannot be observed with individual components. This review describes some of these interesting interspecies-interaction scenarios.
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Affiliation(s)
- Howard K Kuramitsu
- Department of Oral Boiology, School of Dental Medicine, State University of New York, Buffalo, New York, USA
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Li Y, Ismail AI, Ge Y, Tellez M, Sohn W. Similarity of bacterial populations in saliva from African-American mother-child dyads. J Clin Microbiol 2007; 45:3082-5. [PMID: 17634300 PMCID: PMC2045297 DOI: 10.1128/jcm.00771-07] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Revised: 05/20/2007] [Accepted: 06/12/2007] [Indexed: 11/20/2022] Open
Abstract
Using PCR-based denaturing gradient gel electrophoresis analyses of oral bacterial samples in 20 mother-child dyads, this study demonstrated a high degree of similarity of bacterial compositions between the mothers and their children; the two may share as much as 94% of their oral bacterial spectra, including cariogenic species.
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Affiliation(s)
- Yihong Li
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, 345 E. 24th St., New York, NY 10010, USA.
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Li Y, Ge Y, Saxena D, Caufield PW. Genetic profiling of the oral microbiota associated with severe early-childhood caries. J Clin Microbiol 2006; 45:81-7. [PMID: 17079495 PMCID: PMC1828962 DOI: 10.1128/jcm.01622-06] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The determination of the composition of the microbial community in the oral cavity is usually based on cultivation methods; however, nearly half of the bacteria in the saliva and the dental plaque are not cultivable. In this study, we evaluated the difference in oral microbial diversity between children with severe early-childhood caries (S-ECC) and caries-free (CF) controls by means of a cultivation-independent approach called denaturing gradient gel electrophoresis (DGGE). Pooled dental plaque samples were collected from 20 children aged 2 to 8 years. Total microbial genomic DNA was isolated from those subjects, and a portion of the 16S rRNA gene locus was PCR amplified by using universal primers. We observed that the mean species richness of the bacterial population was greater in the CF children (n = 12) (42 +/- 3.7) than in the S-ECC children (n = 8) (35 +/- 4.3); the difference was statistically significant (P = 0.005). The overall diversity of plaque samples as measured by the Shannon index was 3.5 for the S-ECC group and 3.7 for the CF group (P = 0.004). Differences in DGGE profiles were distinguished on the basis of a cluster analysis. Sequence analysis of excised DGGE bands consisted of 2.7 phylotypes, on average. After adjusting for the number of observed bands, we estimated that the S-ECC group exhibited 94.5 total phylotypes and that the CF group exhibited 113.4. These results suggest that the microbial diversity and complexity of the microbial biota in dental plaque are significantly less in S-ECC children than in CF children.
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Affiliation(s)
- Y Li
- Department of Basic Science and Craniofacial Biology, New York University College of Dentistry, New York, NY 10010, USA.
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