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Pyrosequencing analysis of the Oral Microflora of healthy adults
Abstract
A good definition of commensal microflora and an understanding of its relation to health are essential in preventing and combating disease. We hypothesized that the species richness of human oral microflora is underestimated. Saliva and supragingival plaque were sampled from 71 and 98 healthy adults, respectively. Amplicons from the V6 hypervariable region of the small-subunit ribosomal RNA gene were generated by PCR, pooled into saliva and plaque pools, and sequenced by means of the Genome Sequencer 20 system at 454 Life Sciences. Data were evaluated by taxonomic and rarefaction analyses. The 197,600 sequences generated yielded about 29,000 unique sequences, representing 22 taxonomic phyla. Grouping the sequences in operational taxonomic units (6%) yielded 3621 and 6888 species-level phylotypes in saliva and plaque, respectively. This work gives a radically new insight into the diversity of human oral microflora, which, with an estimated number of 19,000 phylotypes, is considerably higher than previously reported.
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“The reduction in pathogenic periodontal bacteria in biofilms by mechanical instrumentation [13] through nonsurgical periodontal treatment has been shown to have limited long-term benefits [14,15].”
From A Cross-Talk between Diet and the Oral Microbiome: Balance of Nutrition on Inflammation and Immune System’s Response during Periodontitis (2022) · cites this paper as [15]
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Pyrosequencing enumerates and contrasts soil microbial diversity
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Occlusal Caries: Biological Approach for Its Diagnosis and Management
Carvalho, J. C., Dige, I., Mačhiulskienė, V., Qvist, V., Bakhshandeh, A., Parolo, C. C. F., & Maltz, M. (2016) · Caries Research · doi:10.1159/000448662 · Cited by 2,159
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Wade, W. G. (2013) · Pharmacological Research · doi:10.1016/j.phrs.2012.11.006 · Cited by 1,347
Environmental and Gut Bacteroidetes: The Food Connection
Thomas, F., Hehemann, J., Rebuffet, E., Czjzek, M., & Michel, G. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00093 · Cited by 1,398
“Bacteroidetes have also been found in the normal microbiota of the oral cavity, either in the saliva or dental plaque (Keijser et al., 2008; Nasidze et al., 2009a,b).”
BackgroundDefining the healthy “core microbiome” of oral microbial communities
Zaura, E., Keijser, B. J., Huse, S. M., & Crielaard, W. (2009) · BMC Microbiology · doi:10.1186/1471-2180-9-259 · Cited by 1,323
“Since saliva is easily and noninvasively accessible it is a popular sample in oral epidemiology and microbiome diversity [4,16] studies.”
InfluentialSelf-citationSegata, N., Haake, S. K., Mannon, P., Lemon, K. P., Waldron, L., Gevers, D., Huttenhower, C., & Izard, J. (2012) · Genome Biology · doi:10.1186/gb-2012-13-6-r42 · Cited by 1,076
“The oral microbiome as revealed in this investigation was generally consistent with earlier studies [11,13,14,22,66,67].”
ResultGriffen, A. L., Beall, C. J., Campbell, J. H., Firestone, N. D., Kumar, P., Yang, Z. K., Podar, M., & Leys, E. J. (2011) · The ISME Journal · doi:10.1038/ismej.2011.191 · Cited by 1,006
“Some recent sequencing efforts have estimated much higher numbers of species and a higher fraction of uncharacterized species (Keijser et al., 2008; Pushalkar et al., 2011).”
BackgroundNext-Generation Sequencing: From Basic Research to Diagnostics
Voelkerding, K. V., Dames, S. A., & Durtschi, J. (2009) · Clinical Chemistry · doi:10.1373/clinchem.2008.112789 · Cited by 903
Salivary Biomarkers: Toward Future Clinical and Diagnostic Utilities
Yoshizawa, J., Schafer, C. A., Schafer, J. J., Farrell, J. J., Paster, B. J., & Wong, D. T. (2013) · Clinical Microbiology Reviews · doi:10.1128/cmr.00021-13 · Cited by 704
“org) reside in the mouth, investigators using next-generation sequencing (NGS) suggest that this number could be as high as 10,000 (43, 44, 45, 46).”
BackgroundBacterial diversity in the oral cavity of 10 healthy individuals
Bik, E. M., Long, C. D., Armitage, G. C., Loomer, P., Emerson, J., Mongodin, E. F., Nelson, K. E., Gill, S. R., Fraser-Liggett, C. M., & Relman, D. A. (2010) · The ISME Journal · doi:10.1038/ismej.2010.30 · Cited by 651
“Two recent 16S rRNA gene-tag pyrosequencing-based studies have suggested that there are B250–300 species-level phylotypes in the mouth of any given individual, and that they segregate based on mucosal versus dental surfaces (Keijser et al., 2008; Zaura et al., 2009).”
BackgroundThe oral microbiome and the immunobiology of periodontal disease and caries
Costalonga, M., & Herzberg, M. C. (2014) · Immunology Letters · doi:10.1016/j.imlet.2014.08.017 · Cited by 645
“The power to comprehensively study bacterial community composition through determination of thousands of sequences per sample was facilitated by the advent of 454 pyrosequencing of V regions of 16S rRNA genes [18,20].”
BackgroundMicrobiota restoration: natural and supplemented recovery of human microbial communities
Reid, G., Younes, J. A., van der Mei, H. C., Gloor, G. B., Knight, R. D., & Busscher, H. J. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2473 · Cited by 607
Human oral microbiota and its modulation for oral health
Zhang, Y., Wang, X., Li, H., Ni, C., Du, Z., & Yan, F. (2018) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2018.01.146 · Cited by 582
Insights into the human oral microbiome
Verma, D., Garg, P. K., & Dubey, A. K. (2018) · Archives of Microbiology · doi:10.1007/s00203-018-1505-3 · Cited by 586
“The microbial diversity of the oral cavity has been extensively studied through traditional Sanger-based sequencing during 2005–2010 (Aas et al. 2005; DeLillo et al. 2006; Sakamoto et al. 2008; Faveri et al. 2008; Ribeiro et al. 2011; Keijser et al. 2008; Bik et al. 2010; Dewhirst et al. 2010).”
BackgroundThe oral metagenome in health and disease
Belda‐Ferre, P., Alcaraz, L. D., Cabrera‐Rubio, R., Romero, H., Simón‐Soro, Á., Pignatelli, M., & Mira, Á. (2011) · The ISME Journal · doi:10.1038/ismej.2011.85 · Cited by 540
“, 2010) and when short pyrosequencing reads of the 16S rRNA gene were used, uncertainties in taxonomic assignment (Keijser et al., 2008; Lazarevic et al., 2009) and inflated diversity due to pyrosequencing errors (Quince et al.”
BackgroundMethodThe role of natural salivary defences in maintaining a healthy oral microbiota
Pedersen, A. M. L., & Belstrøm, D. (2019) · Journal of Dentistry · doi:10.1016/j.jdent.2018.08.010 · Cited by 496
Periodontal disease and the oral microbiota in new‐onset rheumatoid arthritis
Scher, J. U., Úbeda, C., Equinda, M. J., Khanin, R., Buischi, Y. D. P., Viale, A. J., Lipuma, L., Attur, M. G., Pillinger, M. H., Weissmann, G., et al. (2012) · Arthritis & Rheumatism · doi:10.1002/art.34539 · Cited by 480
“As has been previously described by others (23,24), our assessment showed that the periodontal microbiota of healthy control subjects was dominated by 7 phyla, including Bacteroidetes (21.”
ResultDiversity of Endodontic Microbiota Revisited
Siqueira, J. F., Jr., & Rôças, I. N. (2009) · Journal of Dental Research · doi:10.1177/0022034509346549 · Cited by 464
“A recent study with pyrosequencing, a high-throughput molecular approach that allows for extensive sequencing of microbial populations, revealed about 5600 and 10,000 species-level phylotypes representing 22 phyla in saliva and plaque, respectively (Keijser et al., 2008).”
BackgroundFrom Structure to Function: the Ecology of Host-Associated Microbial Communities
Robinson, C. J., Bohannan, B. J. M., & Young, V. B. (2010) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00014-10 · Cited by 473
Dental plaque biofilms: communities, conflict and control
Marsh, P. D., Moter, A., & DeVine, D. (2010) · Periodontology 2000 · doi:10.1111/j.1600-0757.2009.00339.x · Cited by 432
Illumina-based analysis of microbial community diversity
Degnan, P. H., & Ochman, H. (2011) · The ISME Journal · doi:10.1038/ismej.2011.74 · Cited by 422
“…barcodes): 967F 50-XXX CAACGCGAAGAACCTTACC-30 and 1046R 50-XXX CGACAGCCATGCANCACCT-30 (Short 1 V6 (S1V6); 98 bp in Escherichia coli) (Sogin et al., 2006), and 917F 50-XXX GAATTGACGGGGRCCCGC-30 and 1061R 50-XXX CACGRCACGAGCTGACGAC-30 (Long V6 (LV6); 163 bp in E. coli) (Keijser et al., 2008).”
MethodDeep Sequencing of the Oral Microbiome Reveals Signatures of Periodontal Disease
Liu, B., Faller, L. L., Klitgord, N., Mazumdar, V., Ghodsi, M., Sommer, D. D., Gibbons, T. R., Treangen, T. J., Chang, Y.-C., Li, S., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0037919 · Cited by 411
“The total diversity of the global oral microbiome can be estimated to be around 25,000 phylotypes [25].”
BackgroundBacterial biogeography of the human digestive tract
Stearns, J. C., Lynch, M. D. J., Senadheera, D. B., Tenenbaum, H. C., Goldberg, M. B., Cvitkovitch, D. G., Croitoru, K., Moreno‐Hagelsieb, G., & Neufeld, J. D. (2011) · Scientific Reports · doi:10.1038/srep00170 · Cited by 411
Said, H. S., Suda, W., Nakagome, S., Chinen, H., Oshima, K., Kim, S., Kimura, R., Iraha, A., Ishida, H., Fujita, J., et al. (2013) · DNA Research · doi:10.1093/dnares/dst037 · Cited by 394
Gihring, T. M., Green, S. J., & Schadt, C. W. (2011) · Environmental Microbiology · doi:10.1111/j.1462-2920.2011.02550.x · Cited by 382
“This approach – rarefaction with sequence number equalization – has been employed with rRNA gene cloning (see Schloss and Handelsman, 2005) and pyrosequencing (e.g. Keijser et al., 2008; Dickie, 2010; Liggenstoffer et al., 2010) libraries.”
Changes in Abundance of Oral Microbiota Associated with Oral Cancer
Schmidt, B. L., Kuczynski, J., Bhattacharya, A., Huey, B., Corby, P. M. A., Queiroz, E. L. S., Nightingale, K., Kerr, A. R., DeLacure, M. D., Veeramachaneni, R., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0098741 · Cited by 385
“(TIF) Figure S5 Diversity of Firmicutes, Fusobacteria, Bacteroidetes, Proteobacteria and Actinobacteria genera in cancer, pre-cancers and healthy normal samples.”
BackgroundInfluentialOral Biofilms: Emerging Concepts in Microbial Ecology
Filoche, S. K., Wong, L., & Sissons, C. H. (2009) · Journal of Dental Research · doi:10.1177/0022034509351812 · Cited by 370
Saliva microbiomes distinguish caries-active from healthy human populations
Yang, F., Zeng, X., Ning, K., Liu, K.-L., Lo, C., Wang, W., Chen, J., Wang, D., Huang, R., Chang, X., et al. (2011) · The ISME Journal · doi:10.1038/ismej.2011.71 · Cited by 371
“For example, Proteobacteria were more abundant in our data sets when in silico pooled (healthy Chinese adults), wherever Firmicutes were more abundant at a sample pooled from 91 healthy adult individuals in Amsterdam (Keijser et al., 2008).”
BackgroundResultInfluentialCurrent concepts in the pathogenesis of periodontitis: from symbiosis to dysbiosis
Abdulkareem, A. A., Al-Taweel, F. B. H., Al-Sharqi, A. J. B., Gul, S. S., Sha, A. M., & Chapple, I. (2023) · Journal of Oral Microbiology · doi:10.1080/20002297.2023.2197779 · Cited by 438
“In addition, the increased proportions of Bacteroidetes (mainly the Prevotella genus), and Spirochaetes were detected with increasing age [104], with a significant abundance reported in the adult population [105].”
BackgroundCommunity structures of fecal bacteria in cattle from different animal feeding operations
Shanks, O. C., Kelty, C. A., Archibeque, S., Jenkins, M., Newton, R. J., McLellan, S. L., Huse, S. M., & Sogin, M. L. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.02988-10 · Cited by 359
“quences from previous studies (1, 16, 26, 31, 52, 55, 58), and (iii) the small size”
Lessons learned and unlearned in periodontal microbiology
Teles, R. P., Teles, F., Frias‐Lopez, J., Paster, B. J., & Haffajee, A. D. (2013) · Periodontology 2000 · doi:10.1111/prd.12010 · Cited by 387
“complex ecosystems and was only recently introduced for the study of the oral microbiota (172, 410).”
BackgroundOral cavity contains distinct niches with dynamic microbial communities
Xu, X., He, J., Xue, J., Wang, Y., Li, K., Zhang, K., Guo, Q., Liu, X., Zhou, Y., Cheng, L., et al. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.12502 · Cited by 335
“Several studies have been performed to define the ‘normal’ residents at different oral niches including saliva (Nasidze et al., 2009), supragingival plaque (Keijser et al., 2008), subgingival plaque (Bik et al., 2010) and mucosa (Zaura et al., 2009).”
Kumar, P., Mason, M. R., Brooker, M. R., & O'Brien, K. A. (2012) · Journal Of Clinical Periodontology · doi:10.1111/j.1600-051x.2012.01856.x · Cited by 352
“…coverage allows a more comprehensive examination of taxonomically heterogeneous community than was previously possible and has revealed a significantly greater level of microbial diversity than was previously apparent with Sanger sequencing(Charlson et al., 2010, Keijser et al., 2008, Li et al.).”
Resultd’Enfert, C., Kaune, A.-K., Alaban, L. R., Chakraborty, S., Cole, N. L., Delavy, M., Kosmala, D., Marsaux, B., Fróis-Martins, R., Morelli, M., et al. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa060 · Cited by 377
Oligotyping analysis of the human oral microbiome
Eren, A. M., Borisy, G. G., Huse, S. M., & Mark Welch, J. L. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1409644111 · Cited by 347
Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis
Ling, Z., Kong, J., Liu, F., Zhu, H., Chen, X., Wang, Y., Li, L., Nelson, K. E., Xia, Y., & Xiang, C. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-488 · Cited by 356
“This technique has been successfully used in various ecosystems including deep mines [46], soil [47], fermented seafood [48], skin [49], chronic wounds [50], and oral microbiota [42].”
BackgroundMethodThe Oral Microbiota: Community Composition, Influencing Factors, Pathogenesis, and Interventions
Li, X., Liu, Y., Yang, X., Li, C., & Song, Z. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.895537 · Cited by 365
Fibronectin: a multidomain host adhesin targeted by bacterial fibronectin-binding proteins
Henderson, B. E., Nair, S. P., Pallas, J. A., & Williams, M. A. (2010) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2010.00243.x · Cited by 326
“The development of massively parallel DNA sequencing is revealing the scale of mammalian bacterial colonization (Keijser et al., 2008; McKenna et al., 2008) and suggests that Homo sapiens is colonized by between 103 and 104 bacterial phylotypes.”
BackgroundBacterial biofilm: structure, function, and antimicrobial resistance
Dufour, D., Leung, V., & Levesque, C. M. (2010) · Endodontic Topics · doi:10.1111/j.1601-1546.2012.00277.x · Cited by 330
Crielaard, W., Zaura, E., Schuller, A. A., Huse, S. M., Montijn, R. C., & Keijser, B. J. F. (2011) · BMC Medical Genomics · doi:10.1186/1755-8794-4-22 · Cited by 330
“Recent advances in sequencing technology, such as 454 pyrosequencing, have revealed an unexpectedly high diversity of the human oral microbiome: dental plaque pooled from 98 healthy adults comprised about 10000 microbial phylotypes [1].”
InfluentialChen, H., & Jiang, W. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00508 · Cited by 317
“At species level, it had been estimated that the number of species–level phylotypes were between 500 and 10000 (Keijser et al., 2008; Lazarevic et al., 2009), and each oral niches harbored 266 “species-level” phylotypes on average (Zaura et al., 2009).”
BackgroundSiddiqui, H. A., Nederbragt, A. J., Lagesen, K., Jeansson, S. L., & Jakobsen, K. S. (2011) · BMC Microbiology · doi:10.1186/1471-2180-11-244 · Cited by 327
“Our OTU calculations on female urine displayed richness levels that were in the same range as reported for commensal vaginal microbiota (1584 OTUs) [79], but lower than those reported for oral (3011 to 5669 OTUs) [4,92] and fecal samples (up to 5200 OTUs) [90].”
BackgroundMethodInfluentialThe oral microbiome diversity and its relation to human diseases
He, J., Li, Y., Cao, Y., Xue, J., & Zhou, X. (2015) · Folia Microbiologica · doi:10.1007/s12223-014-0342-2 · Cited by 314
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing
Lazarević, V., Whiteson, K., Huse, S. M., Hernández, D., Farinelli, L., Østerås, M., Schrenzel, J., & François, P. (2009) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2009.09.012 · Cited by 313
“Species coverage was within the 91–100% range for all HOMD bacterial phyla except Chloroflexi which is very rare in oral microbiota (Keijser et al., 2008) and has a single representative in the HOMD.”
BackgroundResultInfluentialThe interpersonal and intrapersonal diversity of human-associated microbiota in key body sites
Ursell, L. K., Clemente, J. C., Rideout, J. R., Gevers, D., Caporaso, J. G., & Knight, R. D. (2012) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2012.03.010 · Cited by 320
The Oral Microbiome in Health and Its Implication in Oral and Systemic Diseases
(2016) · Advances in Applied Microbiology · doi:10.1016/bs.aambs.2016.08.002 · Cited by 306
ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences
Sun, Y., Cai, Y., Liu, L., Yu, F., Farrell, M. L., McKendree, W., & Farmerie, W. G. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp285 · Cited by 303
“(5) were among the first to study oral microbial populations.”
BackgroundMethodArweiler, N. B., & Netuschil, L. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-31248-4_4 · Cited by 302
Structure of the human gastric bacterial community in relation to Helicobacter pylori status
Maldonado‐Contreras, A., Goldfarb, K. C., Godoy‐Vitorino, F., Karaöz, U., Contreras, M., Blaser, M. J., Brodie, E., & Domínguez-Bello, M. G. (2010) · The ISME Journal · doi:10.1038/ismej.2010.149 · Cited by 311
“…on Hugenholtz taxonomy (as of April 2007) (Hugenholtz, 2002; DeSantis et al., 2006a, b) and we reclassified the detected taxa using RDP to compare with results in other publications (Eckburg et al., 2005; Gill et al., 2006; Andersson et al., 2008; Dethlefsen et al., 2008; Keijser et al., 2008).”
BackgroundMethodResultInfluentialInvestigation of archaeal and bacterial diversity in fermented seafood using barcoded pyrosequencing
Roh, S. W., Kim, K., Nam, Y., Chang, H.-W., Park, E., & Bae, J. (2009) · The ISME Journal · doi:10.1038/ismej.2009.83 · Cited by 295
“, 2008), and human oral microflora (Keijser et al., 2008).”
BackgroundRaman spectroscopy in cell biology and microbiology
Pezzotti, G. (2021) · Journal of Raman Spectroscopy · doi:10.1002/jrs.6204 · Cited by 296
The generation and maintenance of diversity in microbial communities
Fierer, N., & Lennon, J. T. (2011) · American Journal of Botany · doi:10.3732/ajb.1000498 · Cited by 301
Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis
Mark Welch, J. L., Dewhirst, F. E., & Borisy, G. G. (2019) · Annual Review of Microbiology · doi:10.1146/annurev-micro-090817-062503 · Cited by 284
“In a quest for yet greater sequencing depth at lower cost, work shifted to short-read, highthroughput sequencing, using technologies that could generate hundreds of thousands to millions of sequencing reads at a time, where each individual read was only a few hundred nucleotides in length (12, 19, 44, 48, 58, 81, 105).”
BackgroundMicrobial Geography of the Oral Cavity
Simón‐Soro, Á., Tomás, I., Cabrera‐Rubio, R., Catalan, M. D., Nyvad, B., & Mira, Á. (2013) · Journal of Dental Research · doi:10.1177/0022034513488119 · Cited by 284
“A further complication is given by the use of different salivasampling protocols in different laboratories, including paperpoints, mouthrinses, and oral swabs (Keijser et al., 2008; HMP, 2012).”
BackgroundChen, C., Hemme, C. L., Beleno, J., Shi, Z. J., Ning, D., Qin, Y., Tu, Q., Jorgensen, M. G., He, Z., Wu, L., et al. (2018) · The ISME Journal · doi:10.1038/s41396-017-0037-1 · Cited by 273
Analysis of Oral Microbiota in Children with Dental Caries by PCR-DGGE and Barcoded Pyrosequencing
Ling, Z., Kong, J., Jia, P., Wei, C., Wang, Y., Pan, Z., Huang, W., Li, L., Chen, H., & Xiang, C. (2010) · Microbial Ecology · doi:10.1007/s00248-010-9712-8 · Cited by 268
“In this sense, the oral microbiota from saliva and plaque of children in our study were more representative than that from the previous study [30].”
BackgroundResultInfluentialDental Caries from a Molecular Microbiological Perspective
Nyvad, B., Crielaard, W., Mira, Á., Takahashi, N., & Beighton, D. (2012) · Caries Research · doi:10.1159/000345367 · Cited by 262
“Indeed, since the first use of NGS for oral communities in 2008 [Keijser et al., 2008], there has been an avalanche of NGS studies directed towards oral infections.”
BackgroundInfluentialOttesen, A., Peña, A. G., White, J. R., Pettengill, J., Li, C., Allard, S. M., Rideout, S. L., Allard, M. W., Hill, T. A., Evans, P. S., et al. (2013) · BMC Microbiology · doi:10.1186/1471-2180-13-114 · Cited by 268
“The convenience and affordability of next generation sequencing technologies, improved bioinformatic pipelines, and converging reference databases has enabled the description of culture independent microflora associated with numerous environmental and human microbiomes [3-5].”
BackgroundKumar, P., Brooker, M. R., Dowd, S. E., & Camerlengo, T. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020956 · Cited by 255
“The unprecedented sampling depth provided by this deep-sequencing approach allows the identification of several numerically minor or rare species within a community and has revealed a significantly greater level of microbial diversity than was previously apparent with Sanger sequencing [12,13].”
BackgroundResultBiofilm in endodontics: A review
Jhajharia, K., Parolia, A., Shetty, K., & Mehta, L. K. (2015) · Journal of International Society of Preventive and Community Dentistry · doi:10.4103/2231-0762.151956 · Cited by 262
“More than 1000 different bacterial species have been identified in the oral cavity by culture and independent molecular microbiology, but with advanced massively parallel DNA pyrosequencing techniques, the number may be higher.[61,62]”
BackgroundBacterial and Host Interactions of Oral Streptococci
Kreth, J., Merritt, J. L., & Qi, F. (2009) · DNA and Cell Biology · doi:10.1089/dna.2009.0868 · Cited by 241
“However, a recent report using pyrosequencing analysis estimated the number of phylotypes to be greater than 19,000 (Keijser et al., 2008).”
Study of inter- and intra-individual variations in the salivary microbiota
Lazarević, V., Whiteson, K., Hernández, D., François, P., & Schrenzel, J. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-523 · Cited by 242
“Among them 19 were neither reported in previous studies of oral microbiotas assessed by high-throughput sequencing [6,9,10,17] nor listed in the Human Oral Microbiome Database (HOMD; http:// www.”
BackgroundStearns, J. C., Davidson, C. J., McKeon, S., Whelan, F. J., Fontes, M. E., Schryvers, A. B., Bowdish, D. M. E., Kellner, J. D., & Surette, M. G. (2015) · The ISME Journal · doi:10.1038/ismej.2014.250 · Cited by 234
“The oropharynx is known to contain mainly Prevotella, Veillonella and Streptococcus (Keijser et al., 2008; Lazerevic et al., 2009; Nasidze et al., 2009), with the latter being more prevalent here than previously shown.”
BackgroundResultPark, E., Chun, J., Cha, C., Park, W.-S., Jeon, C. O., & Bae, J. (2011) · Food Microbiology · doi:10.1016/j.fm.2011.10.011 · Cited by 232
“, 2008), human samples such as oral microflora (Keijser et al., 2008), skin (Fierer et al.”
BackgroundBacterial Community Development in Experimental Gingivitis
Kistler, J. O., Booth, V., Bradshaw, D. J., & Wade, W. G. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071227 · Cited by 231
“dentocariosa has previously been identified as a common constituent of the oral microbiome in health, particularly on tooth surfaces [13,15,50] and the genus Rothia has been associated with oral health.”
BackgroundChun, J., Kim, K. Y., Lee, J.-H., & Choi, Y. (2010) · BMC Microbiology · doi:10.1186/1471-2180-10-101 · Cited by 225
“Previously published pyrosequencing data for human saliva and plaque bacterial communities [6] were obtained from the public domain and also processed using the same bioinformatic pipeline based on the JAVA programming language.”
MethodSalivary biomarkers in cancer detection
Wang, X., Kaczor‐Urbanowicz, K. E., & Wong, D. T. (2016) · Medical Oncology · doi:10.1007/s12032-016-0863-4 · Cited by 237
“The recent advances in next generation sequencing allowed the identification of about 19,000 phylotypes in the oral cavity [34].”
BackgroundNon-pathogenic Neisseria: members of an abundant, multi-habitat, diverse genus
Liu, G., Tang, C. M., & Exley, R. M. (2015) · Microbiology · doi:10.1099/mic.0.000086 · Cited by 230
“While most oral microbiome studies have been conducted on Caucasians or Asians (Keijser et al., 2008; Ling et al., 2013; Said et al., 2014; Zaura et al., 2009), an interesting investigation focused on isolated communities, with oral swabs taken from six adult Amerindian participants of Guahibo ethnicity living in an i…”
BackgroundInfluentialComposition and development of oral bacterial communities
Palmer, R. J., Jr. (2013) · Periodontology 2000 · doi:10.1111/j.1600-0757.2012.00453.x · Cited by 222
“the molecular equivalent of a species) were defined at 3% genetic difference (38).”
BackgroundLife at the hyperarid margin: novel bacterial diversity in arid soils of the Atacama Desert, Chile
Neilson, J. W., Quade, J., Ortiz, M., Nelson, W. M., Legatzki, A., Tian, F., LaComb, M., Betancourt, J. L., Wing, R. A., Soderlund, C. A., et al. (2012) · Extremophiles · doi:10.1007/s00792-012-0454-z · Cited by 218
“The 16S rDNA V6 region of DNA community extracts from the three samples was amplified using the following universal primers: a 1:1 mixture of forward primers 909/917F (50-AAACTYAAARRAATTGACGG-30 and 50-GAATTGACGGGGRCCCGCA-30) (Keijser et al. 2008) and reverse primer 1070R (50-AGCTGACGACARCCAT) combined with 454 platfo…”
MethodMicrobial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing
Hasan, N. A., Young, B. A., Minard-Smith, A. T., Saeed, K., Li, H., Heizer, E. M., McMillan, N. J., Isom, R., Abdullah, A., Bornman, D. M., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0097699 · Cited by 207
“Overall abundance and distribution of phyla and genera were in agreement with results of studies of human saliva reported by other investigators [34,63,64].”
ResultThe Relationship of the Oral Microbiotia to Periodontal Health and Disease
Curtis, M. A., Zenobia, C., & Darveau, R. P. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.09.008 · Cited by 210
“Of the 197,600 sequences that were analyzed, they were suggested to represent 22 phyla comprising 3621 and 6888 species-level phylotypes in the saliva and plaque, respectively (Keijser et al., 2008).”
BackgroundMicrobiology of sugar‐rich environments: diversity, ecology and system constraints
Lievens, B., Hallsworth, J. E., Pozo, M. I., Belgacem, Z. B., Stevenson, A. W., Willems, K., & Jacquemyn, H. (2014) · Environmental Microbiology · doi:10.1111/1462-2920.12570 · Cited by 202
Stahringer, S. S., Clemente, J. C., Corley, R. P., Hewitt, J., Knights, D., Walters, W. A., Knight, R., & Krauter, K. S. (2012) · Genome Research · doi:10.1101/gr.140608.112 · Cited by 180
“Although no mechanical disruption method was used in the extraction of the DNA from saliva, we readily detected known ‘‘hard to lyse’’ species including Actinomyces and Streptococcus in comparable abundances to previously published studies that used zirconia beads to disrupt bacterial cell walls (Keijser et al. 2008).”
ResultPhylogenetic and metabolic diversity of bacteria associated with cystic fibrosis
Guss, A. M., Roeselers, G., Newton, I. L. G., Young, C. R., Klepac‐Ceraj, V., Lory, S., & Cavanaugh, C. M. (2010) · The ISME Journal · doi:10.1038/ismej.2010.88 · Cited by 200
“For example, anaerobic organism phylotypes, including those typically found in the oral cavity (Aas et al., 2005; Keijser et al., 2008), were detected at relatively high frequency (Figure 1 and Supplementary Figure S1).”
BackgroundAggregatibacter (Actinobacillus) actinomycetemcomitans: a triple A* periodontopathogen?
Henderson, B., Ward, J. M., & Ready, D. (2010) · Periodontology 2000 · doi:10.1111/j.1600-0757.2009.00331.x · Cited by 239
Vonaesch, P., Morien, E., Andrianonimiadana, L., Sanke‐Waîgana, H., Mbecko, J., Huus, K. E., Naharimanananirina, T., Gondje, B. P., Nigatoloum, S. N., Vondo, S. S., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1806573115 · Cited by 201
Human viruses in periodontitis
Slots, J. (2010) · Periodontology 2000 · doi:10.1111/j.1600-0757.2009.00325.x · Cited by 208
Microbiota diversity and gene expression dynamics in human oral biofilms
Benítez‐Páez, A., Belda‐Ferre, P., Simón‐Soro, Á., & Mira, Á. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-311 · Cited by 193
“Although some studies, using NGS methods and 16S rRNA-based analysis, estimate that microbial diversity of the oral cavity is composed by thousands of species [1], more recent data have limited these estimates to a few hundreds [2-4].”
ResultLorenzo, F. D., Castro, C. D., Silipo, A., & Molinaro, A. (2019) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuz002 · Cited by 195
Meurman, J. H. (2010) · Journal of Oral Microbiology · doi:10.3402/jom.v2i0.5195 · Cited by 194
“For example, pyrosequencing of the oral cavity and salivary samples has greatly improved our understanding in the wider perspective of the complex microbiota of the mouth (72).”
BackgroundKoch, C. D., Gladwin, M. T., Freeman, B. A., Lundberg, J. O., Weitzberg, E., & Morris, A. (2017) · Free Radical Biology and Medicine · doi:10.1016/j.freeradbiomed.2016.12.015 · Cited by 186
Antimicrobial peptides of the oral cavity
Gorr, S. (2009) · Periodontology 2000 · doi:10.1111/j.1600-0757.2009.00310.x · Cited by 189
Unterseher, M., Jumpponen, A., Öpik, M., Tedersoo, L., Moora, M., Dormann, C. F., & Schnittler, M. (2010) · Molecular Ecology · doi:10.1111/j.1365-294x.2010.04948.x · Cited by 186
“With respect to exhaustiveness of species inventories, detection of microbes from the environment has greatly benefited from the next generation sequencing (NGS) approach that however also has shed further light on the poverty of applicable taxonomic concepts (Sogin et al. 2006; Keijser et al. 2008; Buée et al. 2009;…”
BackgroundMicrobial signature profiles of periodontally healthy and diseased patients
Lourenço, T. G. B., Heller, D., Silva‐Boghossian, C. M., Cotton, S. L., Paster, B. J., & Colombo, A. P. V. (2014) · Journal of Clinical Periodontology · doi:10.1111/jcpe.12302 · Cited by 185
“…Rothia spp. and Streptococcus spp. were more prevalent in H, corroborating the data reported by other studies (Aas et al. 2005, Kumar et al. 2005, Keijser et al. 2008, Colombo et al. 2009, 2012, Bik et al. 2010, Huang et al. 2011, Griffen et al. 2012, Liu et al.2012, Abusleme et al. 2013, Ge et…”
ResultAntimicrobial peptides and periodontal disease
Gorr, S., & Abdolhosseini, M. (2011) · Journal Of Clinical Periodontology · doi:10.1111/j.1600-051x.2010.01664.x · Cited by 185
Siqueira, J. F., Jr., & Rôças, I. N. (2009) · Oral Surgery Oral Medicine Oral Pathology Oral Radiology and Endodontology · doi:10.1016/j.tripleo.2009.01.044 · Cited by 176
The Oral Microbiome of Children: Development, Disease, and Implications Beyond Oral Health
Gomez, A., & Nelson, K. E. (2017) · Microbial Ecology · doi:10.1007/s00248-016-0854-1 · Cited by 175
“Diversity surveys on healthy oral microbiomes do suggest a core group of phylotypes [8, 9], different from those found under diseased conditions [5, 10].”
BackgroundDiversity of human small intestinal Streptococcus and Veillonella populations
van den Bogert, B., Erkuş, O., Boekhorst, J., de Goffau, M. C., Smid, E. J., Zoetendal, E. G., & Kleerebezem, M. (2013) · FEMS Microbiology Ecology · doi:10.1111/1574-6941.12127 · Cited by 181
“Interestingly, both bacterial populations are abundant not only in the small intestine but also in the microbiota of the stomach (Bik et al., 2006), esophagus (Pei et al., 2004), throat (Andersson et al., 2008), and oral cavity (Keijser et al., 2008).”
BackgroundSun, Y., Cai, Y., Huse, S. M., Knight, R. D., Farmerie, W. G., Wang, X., & Mai, V. (2011) · Briefings in Bioinformatics · doi:10.1093/bib/bbr009 · Cited by 172
“It has been reported that microbial communities are much more diverse than expected [19, 20], which suggests that the underlying assumption of MSA might not be valid because parts of the sequence are not homologous due to insertions and deletions, or because so much change has occurred that bases that are the same are…”
BackgroundMethodWarinner, C., Speller, C., Collins, M. J., & Lewis, C. M. (2015) · Journal of Human Evolution · doi:10.1016/j.jhevol.2014.10.016 · Cited by 178
“Despite shorter read lengths and a shift of focus to individual 16S rRNA gene hypervariable regions rather than the entire gene, the increased sequencing depth has revealed a great diversity of low abundance taxa within the human microbiome, expanding the known taxonomic complexity of the oral microbiome alone by more…”
Bacterial Profile of Dentine Caries and the Impact of pH on Bacterial Population Diversity
Kianoush, N., Adler, C. J., Nguyen, K.-A. T., Browne, G. V., Simonian, M. R., & Hunter, N. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092940 · Cited by 173
“The carious lesions we investigated contained between 15% to 50% of the total number of OTUs recorded from pyrosequencing analysis of plaque and saliva samples from healthy sites [60] and healthy mucosal biofilms [58], respectively.”
BackgroundResultAntifungal drug resistance of oral fungi
Niimi, M., Firth, N. A., & Cannon, R. D. (2010) · Odontology · doi:10.1007/s10266-009-0118-3 · Cited by 170
Comparison of ITS1 and ITS2 rDNA in 454 sequencing of hyperdiverse fungal communities
Bazzicalupo, A., Bálint, M., & Schmitt, I. (2012) · Fungal ecology · doi:10.1016/j.funeco.2012.09.003 · Cited by 165
Wade, W. G. (2011) · Journal Of Clinical Periodontology · doi:10.1111/j.1600-051x.2010.01679.x · Cited by 167
Pyrosequencing as a tool for better understanding of human microbiomes
Siqueira, J. F., Jr., FOUAD, A. F., & Rôças, I. N. (2012) · Journal of Oral Microbiology · doi:10.3402/jom.v4i0.10743 · Cited by 184
“Using 454 GS FLX pyrosequencing, an analysis of 71 saliva and 98 supragingival samples revealed a total of 28,978 unique V6 tag sequences from 22 known phyla (91).”
MethodKönönen, E., Fteita, D., Gürsoy, U. K., & Gürsoy, M. (2022) · Journal of Oral Microbiology · doi:10.1080/20002297.2022.2079814 · Cited by 177
“In healthy adults, the detection rates of the genus Prevotella are high in saliva and dental plaque [17,27].”
BackgroundRobinson, C. M., & Pfeiffer, J. K. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085550 · Cited by 171
Comparison of the microbiological features of chronic and aggressive periodontitis
Armitage, G. C. (2010) · Periodontology 2000 · doi:10.1111/j.1600-0757.2010.00357.x · Cited by 157
Oral microbiota in human health and disease: A perspective
Santacroce, L., Passarelli, P. C., Azzolino, D., Bottalico, L., Charitos, I. A., Cazzolla, A. P., Colella, M., Topi, S., Godoy, F. G., & D’Addona, A. (2023) · Experimental Biology and Medicine · doi:10.1177/15353702231187645 · Cited by 178
“Most organisms are optionally anaerobic or necessarily anaerobic, 7,44,45 and most oxygen in the oral cavity is dissolved in the saliva and is readily available to microorganisms for their metabolic needs.”
BackgroundCephas, K., Kim, J., Mathai, R. A., Barry, K. A., Dowd, S. E., Meline, B. S., & Swanson, K. S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0023503 · Cited by 158
“The prevalence of the genera Porphyromonas and Prevotella was lower than that reported by other researchers [5,6,14,22].”
Result
Metadata
- Authors
- Keijser, B. J. F., Zaura, E., Huse, S. M., van der Vossen, J. M. B. M., Schuren, F. H. J., Montijn, R. C., ten Cate, J. M., & Crielaard, W.
- Affiliations
- Marine Biological Laboratory (US)
- TNO Quality of Life, Business Unit Food and Biotechnology Innovations, Microbial Genomics Group, Zeist, The Netherlands;
- Venue
- Journal of Dental Research
- Publisher
- SAGE Publications
- Published
- 2008-11
- Volume
- 87
- Issue
- 11
- Pages
- 1016-1020
- ISSN
- 0022-0345 (ISSN-L)
- 1544-0591
- OpenAlex
- W2103805072
- Cited by
- 669
- References
- 27
- Citations by year
- 2026: 6 · 2025: 14 · 2024: 33 · 2023: 16 · 2022: 39 · 2021: 26 · 2020: 30 · 2019: 24 · 2018: 47 · 2017: 45 · 2016: 41 · 2015: 42 · 2014: 49 · 2013: 50 · 2012: 65
- FWCI
- 53.33
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Journal of Dental Research (publishedVersion)
- PubMed (publishedVersion)
- UvA-DARE (University of Amsterdam) (publishedVersion)
- UvA-DARE (University of Amsterdam) (submittedVersion)
- VU Research Portal (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- Topics
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Keywords
- oral microbiota, species richness, saliva, supragingival plaque, 16S rRNA gene, operational taxonomic units, phylotypes, microbial diversity, healthy adults
- MeSH terms
- Adult, Dental Plaque, DNA, Bacterial, Humans, RNA, Bacterial, RNA, Ribosomal, 16S, Saliva, Bacterial Typing Techniques, Sequence Analysis, DNA
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