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Oral microbiome: Unveiling the fundamentals
Open accessAbstract
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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“After the colon, the oral microbiome represents the second most diverse microbiota in the human host, with over 700 bacterial species presently identified.35”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [35]
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“due to improved understanding of the crucial role played by the oral microbiome in initiating food digestion and maintaining oral and systemic health.”
From The oral microbiome: Role of key organisms and complex networks in oral health and disease (2021) · cites this paper as [35]
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“73 Emerging research suggests a potential bidirectional relationship between the oral microbiome and thyroid-related metabolic processes.”
Santos, H. S. D. B., Pagnussatti, M. E. L., & Arthur, R. A. (2025) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-79146-8_3 · Cited by 7
First molecular detection of Entamoeba gingivalis subtypes in individuals from Turkey
Örsten, S., Şahin, C., Yılmaz, E., & Akyön, Y. (2023) · Pathogens and Disease · doi:10.1093/femspd/ftad017 · Cited by 6
“In addition to bacteria, the oral cavity can also harbour protozoa such as Entamoeba gingivalis and Trichomonas tenax , which received less attention in periodontal studies (Deo and Deshmukh 2019 ).”
Salivary microbiome of healthy women of reproductive age
Cauwenberghs, E., Oerlemans, E. F. M., Wittouck, S., Allonsius, C. N., Gehrmann, T., Ahannach, S., Boeck, I. D., Spacova, I., Bron, P. A., Donders, G. G. G., et al. (2023) · mBio · doi:10.1128/mbio.00300-23 · Cited by 6
“T he oral cavity forms a complex microbial habitat due to its various anatomical sites, including the tongue, cheek, throat, and saliva (1).”
BackgroundRole of Human Oral Microbiome in Diseases
Upadhyay, M., Swaroop, A., Sinhal, V. K., Srivastava, A., Garg, S. K., Singh, V., & Arora, P. (2024) · Journal of Pure and Applied Microbiology · doi:10.22207/jpam.18.1.52 · Cited by 4
Probiotic Effect of Streptococcus dentisani on Oral Pathogens: An In Vitro Study
Bedoya‐Correa, C. M., Betancur-Giraldo, S., Franco, J., & Arango-Santander, S. (2024) · Pathogens · doi:10.3390/pathogens13050351 · Cited by 6
“It is considered a dynamic ecosystem with environmental fluctuations and multiple interactions where commensal bacteria limit the colonization of pathogens, thus maintaining homeostasis [3,4].”
BackgroundKumar, S., Malviya, R., Sridhar, S. B., Wadhwa, T., Shareef, J., & Meenakshi, D. U. (2024) · Annales Pharmaceutiques Françaises · doi:10.1016/j.pharma.2024.12.004 · Cited by 6
Anti-biofilm effect of clove oil against Candida albicans: A systematic review
Sangeeta, J. P., Aishwarya, O. B., Omkar, D. B., & Madhura, N. B. (2024) · Journal of Oral and Maxillofacial Pathology · doi:10.4103/jomfp.jomfp_225_24 · Cited by 6
From Dysbiosis to Disease: The Microbiome’s Influence on Uveitis Pathogenesis
Samalia, P. D., Solanki, J., Kam, J., Angelo, L., & Niederer, R. L. (2025) · Microorganisms · doi:10.3390/microorganisms13020271 · Cited by 8
“The oral microbiome consists of the microorganisms inhabiting the human oral cavity [33] and is the second largest microbiota, comprising over 700 species of bacteria [34].”
Bartsch, S., Scholz, K. J., Al‐Ahmad, A., & Cieplik, F. (2025) · Advances in experimental medicine and biology · doi:10.1007/978-3-031-79146-8_16 · Cited by 8
Sterzenbach, T., Pioch, A., Dannemann, M., Hannig, C., & Weber, M.-T. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.599137 · Cited by 6
“Furthermore many species of the oral microbiome are difficult to cultivate or are yet uncultivable (Deo and Deshmukh, 2019).”
BackgroundThrombus-associated microbiota in acute ischemic stroke patients
Walker, M., Uranga, C., Lévy, S., Kelly, C. M., & Edlund, A. (2022) · Surgical Neurology International · doi:10.25259/sni_104_2022 · Cited by 6
“e confirmation of bacterial signatures representing the human microbiota, specifically the oral microbiota,[6,21] is significant and merits further investigation.”
BackgroundPedro, N., Brucato, N., Cavadas, B., Lisant, V., Camacho, R. C., Kinipi, C., Leavesley, M., Pereira, L., & Ricaut, F. (2022) · Molecular Ecology · doi:10.1111/mec.16702 · Cited by 7
“The core oral microbiome of PNG agrees with the normal microbiota in the oral cavity obtained in other studies (Aas et al., 2005; Deo & Deshmukh, 2019; Dewhirst et al., 2010).”
BackgroundRaman, S. R., Liu, C., Herremans, K. M., Riner, A. N., Vudatha, V., Freudenberger, D. C., McKinley, K. L., Triplett, E. W., & Trevino, J. (2022) · Microorganisms · doi:10.3390/microorganisms10112291 · Cited by 6
Hypothesis of a potential BrainBiota and its relation to CNS autoimmune inflammation
Elkjaer, M. L., Simon, L. M., Frisch, T., Bente, L.-M., Kacprowski, T., Thomassen, M., Reynolds, R., Baumbach, J., Röttger, R., & Illés, Z. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1043579 · Cited by 6
Impact of Refined and Unrefined Sugar and Starch on the Microbiota in Dental Biofilm
Chhaliyil, P., Fischer, K. F., Schoel, B., & Chhalliyil, P. (2022) · Journal of International Society of Preventive and Community Dentistry · doi:10.4103/jispcd.jispcd_104_22 · Cited by 6
“T he oral microbiome is comprised hundreds of microbial species that co-inhabit and functionally interact in oral biofilms, which later matures into dental plaque accompanied by inflammation, periodontitis, and systemic diseases.[1,2]”
BackgroundFathi-Hafshejani, P., Tinker, H. B., Freel, K., Mahjouri‐Samani, M., & Hasim, S. (2023) · ACS Applied Bio Materials · doi:10.1021/acsabm.2c00707 · Cited by 6
Towards multiomic analysis of oral mucosal pathologies
Einhaus, J. F., Han, X., Feyaerts, D., Sunwoo, J. B., Gaudilliere, B. L., Ahmad, S. H., Aghaeepour, N., Bruckman, K. C., Ojcius, D. M., Schürch, C. M., et al. (2023) · Seminars in Immunopathology · doi:10.1007/s00281-022-00982-0 · Cited by 8
“, in deepening periodontal pockets under accumulated calculus) [40, 41].”
BackgroundCross-kingdom Microbial Interactions Within the Oral Cavity and Their Implications for Oral Disease
Wijesinghe, G. K., Nobbs, A. H., & Bandara, N. (2023) · Current Clinical Microbiology Reports · doi:10.1007/s40588-023-00191-9 · Cited by 7
Understanding the Relationship of the Human Bacteriome with COVID-19 Severity and Recovery
Zafar, H., & Saier, M. H. (2023) · Cells · doi:10.3390/cells12091213 · Cited by 6
“The human oral bacteriome is the second largest bacterial community in the human body, after that of the gut, and it includes around 700 recognized species [61,62].”
BackgroundOral microbiome: a doubtful predictor but potential target of cardiovascular diseases
Cheng, C. K., & Huang, Y. (2023) · Medical Review · doi:10.1515/mr-2023-0015 · Cited by 6
“Oral dysbiosis refers to the imbalance between symbionts and pathobionts in oral cavity, posing potential threats to host health [1].”
BackgroundMicrobial Extracellular Vesicles in Host-Microbiota Interactions
Abubaker, S., Miri, S., Mottawea, W., & Hammami, R. (2024) · Results and problems in cell differentiation · doi:10.1007/978-3-031-62036-2_19 · Cited by 7
Oral Microbiome and Cognition Among Black Cancer Caregivers
Yang, I. H., Alford, T., Brewster, G. S., Geurs, N. C., Wharton, W., Yeager, K. A., & Houser, M. C. (2024) · Nursing Research · doi:10.1097/nnr.0000000000000785 · Cited by 6
“The oral cavity, however, has a characteristic microbiome, with over 700 bacterial species, second only to the colon (Deo & Deshmukh, 2019).”
Urvashi, U., Choksket, S., Jain, A. R., Sharma, D., Grover, V., & Korpole, S. (2020) · Anaerobe · doi:10.1016/j.anaerobe.2020.102239 · Cited by 6
Abstracts of III International Scientific and Practical Conference
Гордієнко, К. О. (2021) · doi:10.46299/isg.2021.ii.iii · Cited by 8
Kamil, W. N. W. A., Zainal, M., Mokhtar, M., Bandara, N., Dashper, S. G., & Arzmi, M. H. (2025) · Biofouling · doi:10.1080/08927014.2025.2518281 · Cited by 5
“This complex oral microbiome comprises interconnected communities, including those formed by yeast and bacteria (Deo and Deshmukh 2019; Sharma et al. 2023).”
The Relationship Between Neuropsychiatric Disorders and the Oral Microbiome
Kalinowski, J., Ahsan, T., Ayed, M., & Esposito, M. M. (2025) · Bacteria · doi:10.3390/bacteria4030030 · Cited by 5
“The oral cavity, which hosts the second-largest microbiome after the gut, harbors over 700 microorganisms, including bacteria, fungi, viruses, and protozoa, that are crucial in maintaining oral and systemic health [1].”
Brown, J. L., Johnston, W., Butcher, M. C., Burleigh, M. C., & Ramage, G. (2025) · npj Antimicrobials and Resistance · doi:10.1038/s44259-025-00156-6 · Cited by 7
Špiljak, B., Ozretić, P., Brailo, V., Škrinjar, I., Brzak, B. L., Rogulj, A. A., Butić, I., Andrašević, A. T., & Juras, D. V. (2025) · Archives of Microbiology · doi:10.1007/s00203-025-04611-w · Cited by 5
“The oral cavity harbors one of the most diverse microbial ecosystems in the human body, encompassing more than 700 bacterial species alongside fungi, viruses, and archaea (Radaic and Kapila 2021 ; Rajasekaran et al. 2024 ; Dewhirst et al. 2010 ; Deo and Deshmukh 2019).”
Li, L., Zhu, J., Yan, Y., Li, Z., & Du, H. (2026) · Microorganisms · doi:10.3390/microorganisms14030634 · Cited by 6
Çelik, M. N., Dazıroğlu, M. E. Ç., Atabılen, B., Nanì, M. F., Romano, B., Ağagündüz, D., & Capasso, R. (2026) · Food Research International · doi:10.1016/j.foodres.2026.118945 · Cited by 8
Medication Use Among Patients Reporting Xerostomia of an Academic Dental Clinic
Krajewski, M. P., Mo, Q., Lu, C., Cantos, A., Feuerstein, S. G., Brandt, M. J., & Wahler, R. G. (2022) · Journal of Pharmacy Technology · doi:10.1177/87551225221108599 · Cited by 5
“268 Journal of Pharmacy Technology 38(5)”
InfluentialMéabed, E. M. H., & HENIN, R. (2022) · Afro-Egyptian Journal of Infectious and Endemic Diseases · doi:10.21608/aeji.2022.171351.1264 · Cited by 5
“The oral cavity is the second largest gathering of microorganisms after the colon, it shelters 700 species [1].”
BackgroundSynergistic effects of arginine and fluoride on human dental biofilm control
Kuriki, N., Asahi, Y., Okamoto, M., Noiri, Y., Ebisu, S., Machi, H., Suzuki, M., & Hayashi, M. (2024) · Journal of Dentistry · doi:10.1016/j.jdent.2024.105307 · Cited by 5
Microbial Changes Occurring During Oronasal Fistula Wound Healing
Goudy, S. L., Bradley, H. L., Gacasan, C. A., Toma, A. I., Naudin, C. R., Wuest, W. M., Tomov, M. L., Serpooshan, V., Coskun, A. F., & Jones, R. M. (2025) · Microorganisms · doi:10.3390/microorganisms13020327 · Cited by 5
Evolution of Holobionts: The Hologenome Concept
ROSENBERG, E. B. (2021) · The microbiomes of humans, animals, plants, and the environment · doi:10.1007/978-3-030-65317-0_9 · Cited by 6
Changes in Oral Microbial Diversity in a Piglet Model of Traumatic Brain Injury
Jeon, J. H., Lourenco, J. M., Fagan, M. M., Welch, C. B., Sneed, S. E., Dubrof, S., Duberstein, K. J. J., Callaway, T. R., West, F. D., & Park, H. J. (2022) · Brain Sciences · doi:10.3390/brainsci12081111 · Cited by 5
Toyama, N., Ekuni, D., Yokoi, A., Fukuhara, D., Islam, M. M., Sawada, N., Nakashima, Y., Nakahara, M., Sumita, I., & Morita, M. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.957890 · Cited by 5
“Previous studies did not incorporate the association between alpha diversity and periodontal status because the techniques used, standardization methods, and sample sizes varied (Deo and Deshmukh, 2019).”
Background
Metadata
- Authors
- Deo, P., & Deshmukh, R.
- Affiliations
- Bharati Vidyapeeth (Deemed to be University) (IN)
- Venue
- Journal of Oral and Maxillofacial Pathology
- Published
- 2019
- Volume
- 23
- Issue
- 1
- Pages
- 122
- ISSN
- 0973-029X (ISSN-L)
- 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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