Cited by 135Oral microbiology and periodontitis researchMicrobial Community Ecology and PhysiologyBacterial biofilms and quorum sensing

The DOI matches its Crossref record; 44 of the 44 references it cites were found in a registry or an index.

Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities: DGGE profiling for culture medium development

Open access

Tian, Y., He, X., Torralba, M., Yooseph, S., Nelson, K.E., Lux, R., McLean, J.S., Yu, G., Shi, W.·2010·Molecular Oral Microbiology

DOI 10.1111/j.2041-1014.2010.00585.xPMC PMC2951289

Open this paper in CoChat — free account

Abstract

More than 700 bacterial species have been detected in the human oral cavity. They form highly organized microbial communities and are responsible for many oral infectious diseases, such as dental caries and periodontal disease. The prevention and treatment of these diseases require a comprehensive knowledge of oral microbial communities, which largely relies on culture-dependent methods to provide detailed phenotypic and physiological analysis of these communities. However, most of the currently available laboratory media can only selectively support the growth of a limited number of bacterial species within these communities, and fail to sustain the original oral microbial diversity. In this study, using denaturing gradient gel electrophoresis (DGGE) as an index to systematically survey and analyse the selectivity of commonly used laboratory media, we developed a new medium (SHI medium) by combining the ingredients of several selected media that can support different subpopulations within the original oral microbial community derived from pooled saliva. DGGE and 454 pyrosequencing analysis showed that SHI medium was capable of supporting a more diversified community with a microbial profile closer to that of the original oral microbiota. Furthermore, 454 pyrosequencing revealed that SHI medium supported the growth of many oral species that have not before been cultured. Crystal violet assay and the confocal laser scanning microscope analysis indicated that, compared with other media, SHI medium is able to support a more complex saliva-derived biofilm with higher biomass yield and more diverse species. This DGGE-guided method could also be used to develop novel media for other complex microbial communities.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1111/j.2041-1014.2010.00585.x

Cites

44 of 44 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy
Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 20,145
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
Muyzer, G., de Waal, E. C., & Uitterlinden, A. G. (1993) · Applied and Environmental Microbiology · doi:10.1128/aem.59.3.695-700.1993 · Cited by 11,490
The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
Cole, J. R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R. J., Kulam-Syed-Mohideen, A. S., McGarrell, D. M., Marsh, T. L., Garrity, G. M., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn879 · Cited by 4,873
Defining the normal bacterial flora of the oral cavity
Aas, J. A., Paster, B. J., Stokes, L. N., Olsen, I., & Dewhirst, F. E. (2005) · Journal of Clinical Microbiology · doi:10.1128/jcm.43.11.5721-5732.2005 · Cited by 3,092
Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA
Edwards, U., Rogall, T., Blöcker, H., Emde, M., & Böttger, E. C. (1989) · Nucleic Acids Research · doi:10.1093/nar/17.19.7843 · Cited by 2,766
Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA
Liu, W., Marsh, T. L., Cheng, H. H., & Forney, L. J. (1997) · Applied and Environmental Microbiology · doi:10.1128/aem.63.11.4516-4522.1997 · Cited by 2,252
Quantification of biofilm structures by the novel computer program comstat
Heydorn, A., Nielsen, A. T., Hentzer, M., Sternberg, C., Givskov, M., Ersbøll, B. K., & Molin, S. (2000) · Microbiology · doi:10.1099/00221287-146-10-2395 · Cited by 2,185
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
Bacterial Diversity in Human Subgingival Plaque
Paster, B. J., Boches, S. K., Galvin, J. L., Ericson, R. E., Lau, C. N., Levanos, V. A., Sahasrabudhe, A., & Dewhirst, F. E. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.12.3770-3783.2001 · Cited by 2,008
Oral multispecies biofilm development and the key role of cell–cell distance
Kolenbrander, P. E., Palmer, R. J., Periasamy, S., & Jakubovics, N. S. (2010) · Nature Reviews Microbiology · doi:10.1038/nrmicro2381 · Cited by 1,309
Microbial ecology of dental plaque and its significance in health and disease
Marsh, P. D. (1994) · Advances in Dental Research · doi:10.1177/08959374940080022001 · Cited by 1,278
Attachment of a 40-base-pair G + C-rich sequence (GC-clamp) to genomic DNA fragments by the polymerase chain reaction results in improved detection of single-base changes.
Sheffield, V. C., Cox, D. R., Lerman, L. S., & Myers, R. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.1.232 · Cited by 1,273
Communication among Oral Bacteria
Kolenbrander, P. E., Andersen, R. N., Blehert, D. S., Egland, P. G., Foster, J. S., & Palmer, R. J. (2002) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.66.3.486-505.2002 · Cited by 1,022
Oral Microbial Communities: Biofilms, Interactions, and Genetic Systems
Kolenbrander, P. E. (2000) · Annual Review of Microbiology · doi:10.1146/annurev.micro.54.1.413 · Cited by 894
The breadth of bacterial diversity in the human periodontal pocket and other oral sites
Paster, B. J., Olsen, I., Aas, J. A., & Dewhirst, F. E. (2006) · Periodontology 2000 · doi:10.1111/j.1600-0757.2006.00174.x · Cited by 862
Dissecting biological “dark matter” with single-cell genetic analysis of rare and uncultivated TM7 microbes from the human mouth
Marcy, Y., Ouverney, C., Bik, E. M., Lösekann, T., Ivanova, N., Martín, H. G., Szeto, E., Platt, D., Hugenholtz, P., Relman, D. A., et al. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0704662104 · Cited by 632
Interspecies Interactions within Oral Microbial Communities
Kuramitsu, H. K., He, X., Lux, R., Anderson, M. H., & Shi, W. (2007) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00024-07 · Cited by 602
Self-citation
Dental plaque: biological significance of a biofilm and community life‐style
Marsh, P. (2005) · Journal Of Clinical Periodontology · doi:10.1111/j.1600-051x.2005.00790.x · Cited by 599
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
Targeted Access to the Genomes of Low-Abundance Organisms in Complex Microbial Communities
Podar, M., Abulencia, C. B., Walcher, M., Hutchison, D., Zengler, K., Garcia, J. A., Holland, T., Cotton, D., Hauser, L., & Keller, M. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.02985-06 · Cited by 265
Unculturable Bacteria—The Uncharacterized organisms that Cause Oral Infections
Wade, W. G. (2002) · Journal of the Royal Society of Medicine · doi:10.1258/jrsm.95.2.81 · Cited by 253
Microbial etiology of periodontitis
Nishihara, T., & Koseki, T. (2004) · Periodontology 2000 · doi:10.1111/j.1600-0757.2004.03671.x · Cited by 248
Mutualism versus Independence: Strategies of Mixed-Species Oral Biofilms In Vitro Using Saliva as the Sole Nutrient Source
Palmer, R. J., Jr., Kazmerzak, K. M., Hansen, M. C., & Kolenbrander, P. E. (2001) · Infection and Immunity · doi:10.1128/iai.69.9.5794-5804.2001 · Cited by 244
Purification and characterization of an enzyme produced by Treponema denticola capable of hydrolyzing synthetic trypsin substrates
Ohta, K., Mäkinen, K. K., & Loesche, W. J. (1986) · Infection and Immunity · doi:10.1128/iai.53.1.213-220.1986 · Cited by 225
Comparison of the Biochemical Properties of Bacteroides melaninogenicus from Human Dental Plaque and Other Sites
Shah, H. N., Bowden, G. H., Hardie, J. M., & Williams, R. A. D. (1976) · Journal of Applied Bacteriology · doi:10.1111/j.1365-2672.1976.tb00660.x · Cited by 218
Development of a Multispecies Oral Bacterial Community in a Saliva-Conditioned Flow Cell
Foster, J. S., & Kolenbrander, P. E. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.7.4340-4348.2004 · Cited by 217
A comparison of human dental plaque microcosm biofilms grown in an undefined medium and a chemically defined artificial saliva
Wong, L., & Sissions, C. H. (2001) · Archives of Oral Biology · doi:10.1016/s0003-9969(01)00016-4 · Cited by 186
Soil Microbial Community Analysis Using Denaturing Gradient Gel Electrophoresis
Nakatsu, C. H. (2007) · Soil Science Society of America Journal · doi:10.2136/sssaj2006.0080 · Cited by 149
Criteria for the infectious agents in dental caries and periodontal disease
Socransky, S. S. (1979) · Journal Of Clinical Periodontology · doi:10.1111/j.1600-051x.1979.tb02114.x · Cited by 143
The Growth of Oral Bacteria on Saliva
Jong, M. H. D., & van der Hoeven, J. S. (1987) · Journal of Dental Research · doi:10.1177/00220345870660021901 · Cited by 136
A Multi-station Dental Plaque Microcosm (Artificial Mouth) for the Study of Plaque Growth, Metabolism, pH, and Mineralization
Sissons, C. H., Cutress, T. W., Hoffman, M. P., & Wakefield, J. S. J. (1991) · Journal of Dental Research · doi:10.1177/00220345910700110301 · Cited by 131
Development of a steady-state oral microbial biof ilrn community using the constant-depth film ferrnenter
Kinniment, S. L., WIMPENNY, J. W. T., Adams, D., & Marsh, P. D. (1996) · Microbiology · doi:10.1099/13500872-142-3-631 · Cited by 117
Dependence of proliferation of Bacteroides forsythus on exogenous N-acetylmuramic acid
Wyss, C. (1989) · Infection and Immunity · doi:10.1128/iai.57.6.1757-1759.1989 · Cited by 115
Biofilm formation by Porphyromonas gingivalis and Streptococcus gordonii
Cook, G. S., Costerton, J. W., & Lamont, R. J. (1998) · Journal of Periodontal Research · doi:10.1111/j.1600-0765.1998.tb02206.x · Cited by 110
Survey of Oral Microbial Diversity using PCR-based Denaturing Gradient Gel Electrophoresis
Li, Y., Ku, C., Xu, J., Saxena, D. B., & Caufield, P. W. (2005) · Journal of Dental Research · doi:10.1177/154405910508400614 · Cited by 106
Enhanced Growth of Complex Communities of Dental Plaque Bacteria in Mucin-Limited Continuous Culture
Glenister, D. A., Salamon, K., Smith, K., Beighton, D., & Keevil, C. W. (1988) · Microbial Ecology in Health and Disease · doi:10.3109/08910608809140176 · Cited by 96
Role of Suspected Periodontopathogens in Microbiological Monitoring of Periodontitis
Dahlén, G. (1993) · Advances in Dental Research · doi:10.1177/08959374930070020701 · Cited by 83
Denaturing gradient gel electrophoresis analysis to study bacterial community structure in pockets of periodontitis patients
Zijnge, V., Harmsen, H. J. M., Kleinfelder, J. W., van der Rest, M. E., Degener, J. E., & Welling, G. W. (2003) · Oral Microbiology and Immunology · doi:10.1034/j.1399-302x.2003.180110.x · Cited by 69
Profiling and monitoring of microbial populations by denaturing high-performance liquid chromatography
Barlaan, E. A., Sugimori, M., Furukawa, S., & Takeuchi, K. (2005) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2005.01.002 · Cited by 63
Application of denaturing gradient gel electrophoresis (DGGE) to the analysis of microbial communities of subgingival plaque
Fujimoto, C., Maeda, H. A., Kokeguchi, S., Takashiba, S., Nishimura, F., Arai, H., Fukui, K., & Murayama, Y. (2003) · Journal of Periodontal Research · doi:10.1034/j.1600-0765.2003.02607.x · Cited by 61
Patterns and rates of growth of microcosm dental plaque biofilms
Sissons, C. H., Wong, L., & Cutress, T. W. (1995) · Oral Microbiology and Immunology · doi:10.1111/j.1399-302x.1995.tb00137.x · Cited by 56
The cia operon of Streptococcus mutans encodes a unique component required for calcium‐mediated autoregulation
He, X., Wu, C., Yarbrough, D. K., Sim, L., Niu, G., Merritt, J. L., Shi, W., & Qi, F. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06390.x · Cited by 48
Self-citation
The Reproducibility of Curet Sampling of Subgingival Biofilms
Teles, F., Haffajee, A. D., & Socransky, S. S. (2008) · Journal of Periodontology · doi:10.1902/jop.2008.070424 · Cited by 34
Growth stimulation of the mixed microbial flora of human dental plaques by haemin
Gilmour, M. N., & Poole, A. (1970) · Archives of Oral Biology · doi:10.1016/0003-9969(70)90022-1 · Cited by 21

Sorted by citations

The oral microbiome: Role of key organisms and complex networks in oral health and disease
Sedghi, L., DiMassa, V., Harrington, A., Lynch, S. V., & Kapila, Y. L. (2021) · Periodontology 2000 · doi:10.1111/prd.12393 · Cited by 755
Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle
He, X., McLean, J. S., Edlund, A., Yooseph, S., Hall, A. P., Liu, S.-Y., Dorrestein, P. C., Esquenazi, E., Hunter, R. C., Cheng, G., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419038112 · Cited by 525
Self-citation
The bright side of microbial dark matter: lessons learned from the uncultivated majority.
Solden, L., Lloyd, K., & Wrighton, K. (2016) · Current Opinion in Microbiology · doi:10.1016/j.mib.2016.04.020 · Cited by 253
Saccharibacteria (TM7) in the Human Oral Microbiome
Bor, B., Bedree, J. K., Shi, W., McLean, J. S., & He, X. (2019) · Journal of Dental Research · doi:10.1177/0022034519831671 · Cited by 228
Self-citation
The multi-omics promise in context: from sequence to microbial isolate
Gutleben, J., Mares, M. C. D., van Elsas, J. D., Smidt, H., Overmann, J., & Sipkema, D. (2017) · Critical Reviews in Microbiology · doi:10.1080/1040841x.2017.1332003 · Cited by 227

See all 135

Authors: Tian, Y., He, X., Torralba, M., Yooseph, S., Nelson, K. E., Lux, R., McLean, J. S., Yu, G., & Shi, W.
Affiliations: Peking University (CN)
University of California, Los Angeles (US)
J. Craig Venter Institute (US)
Corresponding author: Yu, G.
Shi, W.
ORCID: He, X.
Torralba, M.
Yooseph, S.
Lux, R.
McLean, J.S.
Shi, W.
Venue: Molecular Oral Microbiology
Publisher: Wiley
Published: 2010-09-02
Volume: 25
Issue: 5
Pages: 357-367
ISSN: 2041-1006 (ISSN-L)
DOI: 10.1111/j.2041-1014.2010.00585.x
PMC: PMC2951289
OpenAlex: W1533894881
Cited by: 133
References: 44
Citations by year: 2026: 9 · 2025: 14 · 2024: 14 · 2023: 7 · 2022: 12 · 2021: 10 · 2020: 17 · 2019: 10 · 2018: 7 · 2017: 9 · 2016: 5 · 2015: 6 · 2014: 4 · 2013: 1 · 2012: 2
FWCI: 3.34
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: doi.wiley.com/10.1002/tdm_license_1.1 (tdm, 1825 d)
Locations: Molecular Oral Microbiology (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: U.S. Department of Health and Human Services
National Institutes of Health (5r01de020102-10, n01ai30071-19-0-3)
National Institute of General Medical Sciences (GM54666, R01GM054666)
National Institute of Allergy and Infectious Diseases (N01 AI30071)
National Institute of Dental and Craniofacial Research (R01-DE020102, DE020102)
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 › Bacterial biofilms and quorum sensing
Keywords: oral microbiota, media development, culture-based methods, oral bacterial diversity, dental caries, periodontal disease
MeSH terms: Adult, Culture Media, DNA, Bacterial, Humans, Image Processing, Computer-Assisted, Mouth, Saliva, Sequence Analysis, DNA, Biofilms, Biomass, Microscopy, Confocal, Denaturing Gradient Gel Electrophoresis, Microbial Consortia

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Using DGGE profiling to develop a novel culture medium suitable for oral microbial communities: DGGE profiling for culture medium development

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks