Cited by 299Oral microbiology and periodontitis researchMicrobial Community Ecology and PhysiologyGut microbiota and health

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Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis

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Mark Welch, Jessica L., Dewhirst, Floyd E., Borisy, Gary G.·2019·Annual Review of Microbiology

DOI 10.1146/annurev-micro-090817-062503PMC PMC7153577

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Abstract

Microbial communities are complex and dynamic, composed of hundreds of taxa interacting across multiple spatial scales. Advances in sequencing and imaging technology have led to great strides in understanding both the composition and the spatial organization of these complex communities. In the human mouth, sequencing results indicate that distinct sites host microbial communities that not only are distinguishable but to a meaningful degree are composed of entirely different microbes. Imaging suggests that the spatial organization of these communities is also distinct. Together, the literature supports the idea that most oral microbes are site specialists. A clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general.

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Additional file 3 of Acquisition of oral microbiota is driven by environment, not host genetics
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Additional file 11 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
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Additional file 5 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
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Additional file 14 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557451
Additional file 15 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
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Additional file 9 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557436
Additional file 1 of Using formalin fixed paraffin embedded tissue to characterize the microbiota in p16-positive and p16-negative tongue squamous cell carcinoma: a pilot study
Zhan, Y., Tianyi, L., Xuejing, S., Xinpeng, L., Jianqun, W., Wenxia, X., & Jingshu, G. (2024) · Figshare · doi:10.6084/m9.figshare.26686749
Additional file 10 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557439
Additional file 8 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557433
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Additional file 13 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557448
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Additional file 2 of Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership
Essock-Burns, T., Lawhorn, S., Wu, L., McClosky, S., Moriano‐Gutierrez, S., Ruby, E. G., & McFall‐Ngai, M. (2024) · Figshare · doi:10.6084/m9.figshare.26579489
Additional file 3 of Using formalin fixed paraffin embedded tissue to characterize the microbiota in p16-positive and p16-negative tongue squamous cell carcinoma: a pilot study
Zhan, Y., Tianyi, L., Xuejing, S., Xinpeng, L., Jianqun, W., Wenxia, X., & Jingshu, G. (2024) · Figshare · doi:10.6084/m9.figshare.26686755
Additional file 4 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557421
Additional file 4 of Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership
Essock-Burns, T., Lawhorn, S., Wu, L., McClosky, S., Moriano‐Gutierrez, S., Ruby, E. G., & McFall‐Ngai, M. (2024) · Figshare · doi:10.6084/m9.figshare.26579495
Additional file 6 of Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership
Essock-Burns, T., Lawhorn, S., Wu, L., McClosky, S., Moriano‐Gutierrez, S., Ruby, E. G., & McFall‐Ngai, M. (2024) · Figshare · doi:10.6084/m9.figshare.26579501
Additional file 6 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557427
Additional file 7 of Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
Utter, D. R., Borisy, G. G., Eren, A. M., Cavanaugh, C. M., & Mark Welch, J. L. (2020) · Figshare · doi:10.6084/m9.figshare.13466817
Self-citation
Additional file 2 of Corncob structures in dental plaque reveal microhabitat taxon specificity
Morillo-López, V., Sjaarda, A., Islam, I., Borisy, G. G., & Mark Welch, J. L. (2022) · Figshare · doi:10.6084/m9.figshare.20968167
Self-citation
Additional file 1 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557412
Additional file 2 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557415
Additional file 7 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557430
Additional file 13 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
Shaiber, A., Willis, A. D., Delmont, T. O., Roux, S., Chen, L.-X., Schmid, A. C., Yousef, M., Watson, A. R., Lolans, K., Esen, Ö. C., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13467287
Self-citation
Additional file 8 of Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
Utter, D. R., Borisy, G. G., Eren, A. M., Cavanaugh, C. M., & Mark Welch, J. L. (2020) · Figshare · doi:10.6084/m9.figshare.13466819
Self-citation
Additional file 8 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
Shaiber, A., Willis, A. D., Delmont, T. O., Roux, S., Chen, L.-X., Schmid, A. C., Yousef, M., Watson, A. R., Lolans, K., Esen, Ö. C., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13467319
Self-citation
Additional file 2 of Acquisition of oral microbiota is driven by environment, not host genetics
Mukherjee, C., Moyer, C. O., Steinkamp, H. M., Hashmi, S. B., Beall, C. J., Guo, X., Ni, A., Leys, E. J., & Griffen, A. L. (2021) · Figshare · doi:10.6084/m9.figshare.14100136
Additional file 16 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557457
Additional file 12 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557445
Additional file 4 of Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
Shaiber, A., Willis, A. D., Delmont, T. O., Roux, S., Chen, L.-X., Schmid, A. C., Yousef, M., Watson, A. R., Lolans, K., Esen, Ö. C., et al. (2020) · Figshare · doi:10.6084/m9.figshare.13467305
Self-citation
Additional file 3 of Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study
Blostein, F., Bhaumik, D., Davis, E., Salzman, E., Shedden, K., Duhaime, M. B., Bakulski, K. M., McNeil, D. W., Marazita, M. L., & Foxman, B. (2024) · Figshare · doi:10.6084/m9.figshare.26557418
Additional file 1 of Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity
Utter, D. R., Borisy, G. G., Eren, A. M., Cavanaugh, C. M., & Mark Welch, J. L. (2020) · Figshare · doi:10.6084/m9.figshare.13466803
Self-citation
Additional file 1 of Comparative analysis of microbial composition and functional characteristics in dental plaque and saliva of oral cancer patients
Zhang, M., Zhao, Y., Umar, A., Zhang, H., Yang, L., Huang, J., Long, Y., & Yu, Z. (2024) · Figshare · doi:10.6084/m9.figshare.25546999
Additional file 4 of Using formalin fixed paraffin embedded tissue to characterize the microbiota in p16-positive and p16-negative tongue squamous cell carcinoma: a pilot study
Zhan, Y., Tianyi, L., Xuejing, S., Xinpeng, L., Jianqun, W., Wenxia, X., & Jingshu, G. (2024) · Figshare · doi:10.6084/m9.figshare.26686758
Additional file 5 of Maturation state of colonization sites promotes symbiotic resiliency in the Euprymna scolopes-Vibrio fischeri partnership
Essock-Burns, T., Lawhorn, S., Wu, L., McClosky, S., Moriano‐Gutierrez, S., Ruby, E. G., & McFall‐Ngai, M. (2024) · Figshare · doi:10.6084/m9.figshare.26579498
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Authors: Mark Welch, J. L., Dewhirst, F. E., & Borisy, G. G.
Affiliations: Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA;
Harvard University (US)
The Forsyth Institute (US)
ORCID: Dewhirst, Floyd E.
Borisy, Gary G.
Venue: Annual Review of Microbiology
Publisher: Annual Reviews
Published: 2019-09-08
Volume: 73
Issue: 1
Pages: 335-358
ISSN: 0066-4227 (ISSN-L)
1545-3251
DOI: 10.1146/annurev-micro-090817-062503
PMC: PMC7153577
OpenAlex: W2949610528
Cited by: 284
References: 111
Citations by year: 2026: 35 · 2025: 41 · 2024: 50 · 2023: 38 · 2022: 42 · 2021: 39 · 2020: 36 · 2019: 3
FWCI: 4.25
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Locations: Annual Review of Microbiology (publishedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Funders: National Institute of Dental and Craniofacial Research (R37DE016937, R01DE022586, R01DE016937)
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, biogeography, microbial ecology, oral microbiology
MeSH terms: Humans, Mouth, Spatial Analysis, Microbiota

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Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis

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