Cited by 1,121Oral microbiology and periodontitis researchGut microbiota and healthOral Health Pathology and Treatment

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Oral microbiome: Unveiling the fundamentals

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Deo, PriyaNimish, Deshmukh, Revati·2019·Journal of Oral and Maxillofacial Pathology

DOI 10.4103/jomfp.jomfp_304_18PMC PMC6503789

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Abstract

The oral cavity has the second largest and diverse microbiota after the gut harboring over 700 species of bacteria. It nurtures numerous microorganisms which include bacteria, fungi, viruses and protozoa. The mouth with its various niches is an exceptionally complex habitat where microbes colonize the hard surfaces of the teeth and the soft tissues of the oral mucosa. In addition to being the initiation point of digestion, the oral microbiome is crucial in maintaining oral as well as systemic health. Because of the ease of sample collection, it has become the most well-studied microbiome till date. Previously, studying the microbiome was limited to the conventional culture-dependent techniques, but the abundant microflora present in the oral cavity could not be cultured. Hence, studying the microbiome was difficult. The emergence of new genomic technologies including next-generation sequencing and bioinformatics has revealed the complexities of the oral microbiome. It has provided a powerful means of studying the microbiome. Understanding the oral microbiome in health and disease will give further directions to explore the functional and metabolic alterations associated with the diseased states and to identify molecular signatures for drug development and targeted therapies which will ultimately help in rendering personalized and precision medicine. This review article is an attempt to explain the different aspects of the oral microbiome in health.

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Figure 1 General overview of the workflow for 16S rRNA gene-based and metagenomics analysis of microbial communities showing the most important steps and considerations for each stage of the process (Courtesy – Bik EM. The Hoops, Hopes and Hypes of Human Microbiome Research. Yale J Biol Med 2016;89:363-373)CC BY-NC-SA · PubMed Central

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Additional file 4 of Salivary microbiome and hypertension in the Qatari population
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Additional file 3 of Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut
Ormaasen, I., Rudi, K., Diep, D. B., & Snipen, L. (2023) · Figshare · doi:10.6084/m9.figshare.23273383
Additional file 4 of The mediating roles of the oral microbiome in saliva and subgingival sites between e-cigarette smoking and gingival inflammation
Park, B., Koh, H., Patatanian, M., Reyes-Caballero, H., Zhao, N., Meinert, J. L., Holbrook, J. T., Leinbach, L. I., & Biswal, S. (2024) · Figshare · doi:10.6084/m9.figshare.26565815
Additional file 1 of Evaluation of noninvasive biospecimens for transcriptome studies
Martorella, M., Kasela, S., Garcia-Flores, R., Gokden, A., Castel, S. E., & Lappalainen, T. (2024) · Figshare · doi:10.6084/m9.figshare.26656072
Additional file 1 of Altered oral microbiome, but normal human papilloma virus prevalence in cartilage-hair hypoplasia patients
Arponen, H., Vakkilainen, S., Tomnikov, N., Kallonen, T., Silling, S., Mäkitie, O., & Rautava, J. (2024) · Figshare · doi:10.6084/m9.figshare.25649371
Additional file 6 of Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut
Ormaasen, I., Rudi, K., Diep, D. B., & Snipen, L. (2023) · Figshare · doi:10.6084/m9.figshare.23273392
Additional file 3 of The mediating roles of the oral microbiome in saliva and subgingival sites between e-cigarette smoking and gingival inflammation
Park, B., Koh, H., Patatanian, M., Reyes-Caballero, H., Zhao, N., Meinert, J. L., Holbrook, J. T., Leinbach, L. I., & Biswal, S. (2024) · Figshare · doi:10.6084/m9.figshare.26565812
Additional file 7 of Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut
Ormaasen, I., Rudi, K., Diep, D. B., & Snipen, L. (2023) · Figshare · doi:10.6084/m9.figshare.23273395
Additional file 4 of Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota
Fleming, E. S., Pabst, V., Scholar, Z., Xiong, R., Voigt, A. Y., Zhou, W., Hoyt, A., Hardy, R., Peterson, A. K., Beach, R., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16815818
Additional file 2 of Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota
Fleming, E. S., Pabst, V., Scholar, Z., Xiong, R., Voigt, A. Y., Zhou, W., Hoyt, A., Hardy, R., Peterson, A. K., Beach, R., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16815812
Additional file 1 of Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut
Ormaasen, I., Rudi, K., Diep, D. B., & Snipen, L. (2023) · Figshare · doi:10.6084/m9.figshare.23273374
Additional file 5 of The mediating roles of the oral microbiome in saliva and subgingival sites between e-cigarette smoking and gingival inflammation
Park, B., Koh, H., Patatanian, M., Reyes-Caballero, H., Zhao, N., Meinert, J. L., Holbrook, J. T., Leinbach, L. I., & Biswal, S. (2024) · Figshare · doi:10.6084/m9.figshare.26565818
Additional file 1 of Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients
Wei, N., Zhu, G., Zhao, T., Wang, Y., Lou, H., Li, H., Yang, Z., Zhang, Z., Wang, Q., Han, M., et al. (2024) · Figshare · doi:10.6084/m9.figshare.26588028
Additional file 2 of Salivary microbiome and hypertension in the Qatari population
Murugesan, S., & Khodor, S. A. (2024) · Figshare · doi:10.6084/m9.figshare.26603104
Additional file 2 of Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut
Ormaasen, I., Rudi, K., Diep, D. B., & Snipen, L. (2023) · Figshare · doi:10.6084/m9.figshare.23273380
Additional file 4 of Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut
Ormaasen, I., Rudi, K., Diep, D. B., & Snipen, L. (2023) · Figshare · doi:10.6084/m9.figshare.23273386
Additional file 5 of Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut
Ormaasen, I., Rudi, K., Diep, D. B., & Snipen, L. (2023) · Figshare · doi:10.6084/m9.figshare.23273389
Additional file 2 of The mediating roles of the oral microbiome in saliva and subgingival sites between e-cigarette smoking and gingival inflammation
Park, B., Koh, H., Patatanian, M., Reyes-Caballero, H., Zhao, N., Meinert, J. L., Holbrook, J. T., Leinbach, L. I., & Biswal, S. (2024) · Figshare · doi:10.6084/m9.figshare.26565809
Additional file 3 of Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota
Fleming, E. S., Pabst, V., Scholar, Z., Xiong, R., Voigt, A. Y., Zhou, W., Hoyt, A., Hardy, R., Peterson, A. K., Beach, R., et al. (2021) · Figshare · doi:10.6084/m9.figshare.16815815
Additional file 1 of Salivary microbiome and hypertension in the Qatari population
Murugesan, S., & Khodor, S. A. (2024) · Figshare · doi:10.6084/m9.figshare.26603101
Oral microbiome: Physiological and pathological impact on oral and systemic health
Jovanović-Medojević, M., & Ninkovic, N. (2025) · Medicinski podmladak · doi:10.5937/mp76-61232
Concurrent bacterial infections in oral cancer: risk and mitigation strategies
Baby, B. M., Subramaniyan, Y., & Rekha, P. D. (2025) · Future Microbiology · doi:10.1080/17460913.2025.2606754
The Role of the Oral Microbiome in Circulating Metabolic Biomarkers and the Influence of Air Pollution
Luo, J., Wu, Y., Ahsan, H., Olopade, C. O., Pinto, J. M., & Aschebrook‐Kilfoy, B. (2026) · Oral Diseases · doi:10.1111/odi.70197
The Effect of Prior Radiotherapy on Postoperative Complications in Patients Undergoing Free Flap Reconstruction of the Head and Neck
Rozenbroek, P., Nguyen, K., Manzie, T., Ch’ng, S., Clark, J. R., Low, T.-H. H., Elliott, M. S., Palme, C. E., McPhail, L., & Wykes, J. (2026) · ANZ Journal of Surgery · doi:10.1111/ans.70460
Phage Therapy: A Promising Approach in the Management of Periodontal Disease
Juíz, P. J. L., Porto, M. F., Moreira, D. S., Amor, D., & Andrade, E. P. (2026) · Drugs and Drug Candidates · doi:10.3390/ddc5010006
“For example, it is well established that the oral microbiome is a complex ecosystem comprising approximately 700 bacterial species [72].”
Assessment of Knowledge in Adherence to Infection Control During Radiographic Procedures Among Dental Students and Dental Practitioners
Rajesh, P., Gokulraj, S., Appusamy, K., & Subhalakshmi, V. (2026) · Odovtos - International Journal of Dental Sciences · doi:10.15517/eg35ef88
“These microbes can colonize both the soft oral tissues and the hard tooth surfaces because of the special conditions found in the mouth (1,2).”
Periodontal pocket and intestinal microbiota in patients with chronic generalized periodontitis and its correction
Belova, I. V., Георгиевна, Т. А., Soloveva, I. V., Gazhva, S. I., Б., М. С., & Kropotov, V. S. (2026) · Экспериментальная и клиническая гастроэнтерология · doi:10.31146/1682-8658-ecg-239-7-45-52
“[1, 3].”
Microbes and ageing beyond the gut: the oral microbiome and frailty, sarcopenia and neurocognitive disorders in the elderly – a scoping review protocol
Murcia-Soriano, L. F., Venegas‐Sanabria, L. C., Arias-Blanco, D., Baracaldo, S. D. P., Borda, M. G., Sánchez, G., & Buitrago-Garcia, D. (2026) · BMJ Open · doi:10.1136/bmjopen-2025-106590
“20 There is a growing interest in the connection between oral microbiota and geriatric syndromes.”
Salivary microbiome diversity is associated with oral health and diseasePreprint
Lin, D. L., Augustine, M. D., & Ojcius, D. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.27.702135
“Similar to the gut, dysbiosis in the oral microbiome has been linked to many oral and systemic diseases, including Alzheimer’s disease, colorectal cancer, and diabetes 3 .”
Design, synthesis, reactivity, and biological activity of nitroimidazole derivatives and their copper(II) coordination compounds
Fugarolas-Gómez, W., Reyes-Carmona, L., Landeros‐Rivera, B., Almaguer‐Flores, A., & Behrens, N. B. (2026) · Frontiers in Chemical Biology · doi:10.3389/fchbi.2025.1736242
DNA methylation as a biomarker of prenatal exposures: current challenges and opportunities
Walkup, R. B., Nangle, M. A., Bergmann, P. E., & Lipinski, R. J. (2026) · Current Zoology · doi:10.1093/eep/dvag006
“Bacterial contamination from the oral microbiome is another major concern as bacterial DNA also contains methylated cytosines that can confound human DNAm analyses [ 117 ], and depending on the collection method, bacterial DNA can comprise 11%–90% of total DNA in saliva samples [ 118 , 119 ].”
Submucosal microbiota profile in peri-implant health, peri-implant mucositis, and different severity levels of peri-implantitis
Parlak, H. M., Özkul, C., Akman, A. C., Güncü, G. N., Ergünay, K., & Akyön, Y. (2026) · BMC Oral Health · doi:10.1186/s12903-026-07942-2
“Advances in next-generation sequencing, particularly 16S ribosomal RNA (rRNA) gene sequencing, have enabled high-resolution, culture-independent profiling of complex microbial communities [11, 12].”
Oral microbiome analysis in medication-related osteonecrosis of the jaw
Nishi, K., Hijioka, H., Yuichi, G. O. T. O., Kume, K., Yamashiro, K., Noma, Y., Nakamura, M., YOSHINAGA, H., Takaoka, R., & Okui, T. (2025) · Japanese Journal of Oral & Maxillofacial Surgery · doi:10.5794/jjoms.71.556
Comparison of the Antimicrobial Activity of Mouthwashes Containing Tea Tree Oil, Cannabidiol (CBD), Spilanthol, and Chlorhexidine Digluconate Against Selected Bacterial and Yeast Strains: An In Vitro Study
Kiełbratowski, M., Kuśka-Kiełbratowska, A., Kępa, M., Wiench, R., Trzcionka, A., Czuba, Z. P., & Tanasiewicz, M. (2026) · Applied Sciences · doi:10.3390/app16052193
Mapping the landscape of antimicrobial peptides in periodontology: A scoping review
Patil, N., Haran, S., Deshmukh, A., Shetty, A., & Shetty, G. (2025) · Journal of Indian Society of Periodontology · doi:10.4103/jisp.jisp_251_25
“[4] 5-7] The innate immune system plays a principal role in defending these microorganisms.”

Authors: Deo, P., & Deshmukh, R.
Affiliations: Bharati Vidyapeeth (Deemed to be University) (IN)
Venue: Journal of Oral and Maxillofacial Pathology
Publisher: Ovid Technologies (Wolters Kluwer Health)
Published: 2019
Volume: 23
Issue: 1
Pages: 122
ISSN: 0973-029X (ISSN-L)
DOI: 10.4103/jomfp.jomfp_304_18
PMC: PMC6503789
OpenAlex: W2952216579
Semantic Scholar: 011d7d246666d3378bdbf330e6a83816e349f558
Cited by: 1,121
References: 48
Citations by year: 2026: 162 · 2025: 214 · 2024: 238 · 2023: 191 · 2022: 140 · 2021: 129 · 2020: 38 · 2019: 7
FWCI: 87.84
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc-sa
Locations: Journal of Oral and Maxillofacial Pathology (publishedVersion, cc-by-nc-sa)
PubMed Central (publishedVersion, cc-by-nc-sa)
PubMed (publishedVersion)
Topics: Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Health Sciences › Dentistry › General Dentistry › Oral Health Pathology and Treatment
Keywords: oral microbiota, oral health, oral diseases, microbial colonization, oral mucosa, dental plaque, next-generation sequencing, precision medicine

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