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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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“In healthy individuals, this microbial community remains relatively stable and is characterized by high species diver - sity and richness [3 ].”
Edsor, E., Priyadarshini, G. A. G., Shankar, P. G., Srinivasan, V. R., Vigneswaran, T., & Raja, S. P. (2021) · Journal of Pharmacy And Bioallied Sciences · doi:10.4103/jpbs.jpbs_297_21 · Cited by 3
“Blood samples were collected in brain–heart infusion broth [Figure 4]; the collected samples [Figure 5] were cultured in the laboratory [Figure 6] and studied for aerobic bacterial growth.”
Agrawal, N., Fontana, F., Tarracchini, C., Lommi, S., Ventura, M., Milani, C., & Viljakainen, H. T. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2023.1323346 · Cited by 3
“However, microbes reside in different niches of the human body: the oral cavity harboring the second most diverse microbiota after the gut (Deo and Deshmukh, 2019).”
BackgroundThe potential association between salivary gland hypofunction and systemic homeostasis
Song, W., Zhou, J. P., Wang, X., & Wang, H. (2024) · Medical Hypotheses · doi:10.1016/j.mehy.2024.111279 · Cited by 3
A Novel Method for Sampling Subgingival Microbiome: A Comparative Metatranscriptomic Study
Demusaj, D., Toma, R., Khan, T., Hu, L., Banavar, G. S., & Vuyisich, M. (2024) · BioTechniques · doi:10.2144/btn-2023-0076 · Cited by 3
Sanjar, F., Silliman, D. T., Johnson, I. J., Htut, Z., Peacock, T. J., Thompson, S. F., Dion, G. R., Nahid, M. A., Decker, J. F., & Leung, K. P. (2024) · Molecular Oral Microbiology · doi:10.1111/omi.12460 · Cited by 3
Octiara, E., ADINDA, F. R., & SEMBIRING, I. R. (2024) · International Journal of Applied Pharmaceutics · doi:10.22159/ijap.2024.v16s2.04 · Cited by 3
“The oral cavity is the second body part to contain various microbiotas after the intestines, with 700 species of microorganisms consisting of bacteria, fungi, and protozoa [1].”
BackgroundGenetic Patterns of Oral Cavity Microbiome in Patients with Sickle Cell Disease
Al-Sarraj, F. M., Albiheyri, R. S., Qari, M. H., Alotaibi, M., Al-Zahrani, M., Anwar, Y., Alghamdi, M. A., Nass, N. M., Bouback, T. A., Alotibi, I., et al. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25168570 · Cited by 3
“The oral cavity hosts a diverse group of microorganisms that live together and help each other [20,21], although some of them can be pathogenic [20].”
BackgroundHaug, M., Hopkins, A., Duong, E., Kelly, K.-S., Esfandi, J., Shokeen, B., Wu, T., & Lux, R. (2024) · Journal of the California Dental Association · doi:10.1080/19424396.2024.2409957 · Cited by 4
Doucette, H. J., Ward, R., Wheeldon, C., & Whelan, A. (2024) · PubMed Central · Cited by 3
Prasad, P., Mathew, A., Jose, S., Akbarsh, M. A., & Panicker, S. P. (2024) · Springer eBooks · doi:10.1007/978-3-031-71674-4_27 · Cited by 4
Advancing dental biofilm models: the integral role of pH in predicting S. mutans colonization
Sangha, J. S., Gogulancea, V., Curtis, T. P., Jakubovics, N. S., Barrett, P., Métris, A., & Ofiţeru, I. D. (2024) · mSphere · doi:10.1128/msphere.00743-24 · Cited by 3
Franović, B., Čandrlić, M., Blašković, M., Renko, I., Milas, K. K., Markova-Car, E., Mohar, B., Gabrić, D., Gobin, I., Vranić, S. M., et al. (2025) · Journal of Functional Biomaterials · doi:10.3390/jfb16020040 · Cited by 3
“Changes in factors such as diet, oral hygiene, or the host immune response can alter the environment, promoting conditions that favor the growth of pathogenic species within the biofilm [18].”
Digestive health: functional foods for a happy gut
Pathak, V. A., Deokar, G. S., Kshirsagar, S. J., Kulkarni, K. S., Sultanbawa, Y. F., & Nirmal, N. P. (2025) · Elsevier eBooks · doi:10.1016/b978-0-443-28862-3.00004-2 · Cited by 3
Putting the mouth back in the body – the neglected area of dental and oral travel health
Bauer, I. L. (2025) · Tropical Diseases Travel Medicine and Vaccines · doi:10.1186/s40794-024-00242-z · Cited by 3
“While there is a predominant core microbiome, external factors influence a person’s unique variable microbiome [54].”
Candida albicans impacts carbohydrate metabolism of Enterococcus faecalis in interkingdom biofilms
Fiallos, N. D. M., Zanin, I. C. J., Brunson, D. N., Kajfasz, J. K., Zeng, L., Cordeiro, R. D. A., Lemos, J. A. C., & Abranches, J. (2025) · Journal of Oral Microbiology · doi:10.1080/20002297.2025.2492194 · Cited by 3
Chen, X., Lin, W.-Y., Zhang, F., Guo, L.-Q., Ge, H., Ge, D.-Z., Tan, J., Liu, B., Wang, R., & Zhang, L. (2025) · Journal of Oral Microbiology · doi:10.1080/20002297.2025.2489603 · Cited by 3
“The oral microbiota is the second most diverse microbial community to colonize the human body after gut microbes [15].”
Oral and intestinal flora translocation and tumor development
Ye, Z., Gao, L., Guo, Z., & Wang, Q. (2025) · Journal of Cancer Research and Therapeutics · doi:10.4103/jcrt.jcrt_50_24 · Cited by 3
Association Between Periodontal Pathogens and Inflammation in Patients with Acute Coronary Syndromes
Rodean, I. P., Halațiu, V.-B., Popa, T. M., Blîndu, E., Mihăilă, T., Țolescu, C., Modiga, A., Benedek, I., & Benedek, T. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26094360 · Cited by 3
“The NGS, also known as high-throughput sequencing, allows for the simultaneous sequencing of hundreds of genes, providing a deeper coverage of the microbial community [16,17].”
Mishra, M. K., Gupta, S., Rani, P., Javeed, I., Jasrotia, S., & Sehgal, S. (2025) · Indian Journal of Otolaryngology and Head & Neck Surgery · doi:10.1007/s12070-025-05780-2 · Cited by 3
“[3] The normal microbiota in the oral cavity is functional in preventing the colonization of pathogenic bacteria and maintaining homeostasis.”
InfluentialChandrasekaran, K., & Chung, S.-M. (2025) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2025.145782 · Cited by 3
Rates of Endophthalmitis in Prefilled versus Nonprefilled Syringes for Intravitreal Injections
Zhang, C., Lai, D. A., AbouKasm, G., Ersan, S., Leung, N., Zhu, D., Patel, N. A., Flynn, H. W., & Yannuzzi, N. A. (2025) · Ophthalmology Retina · doi:10.1016/j.oret.2025.08.006 · Cited by 3
Bakr, M. M., Caswell, G. M., Ankily, M. A., Zeitoun, S. I., Ahmed, N., Meer, M., & Shamel, M. (2025) · Oral · doi:10.3390/oral5030066 · Cited by 4
“Some belong to well-known groups like Bacillota and Pseudomonadota , while others—such as Gracilibacteria and candidate division SR1—remain uncultivated and poorly understood yet are consistently found in the oral cavity and other environments, including oceans and animal intestines [8,30,31].”
Song, Y., Song, F., Liu, S., Chen, S., & Song, Z. (2022) · Journal of International Medical Research · doi:10.1177/03000605221136679 · Cited by 3
“The oral cavity has the second largest and most diverse microbiota, harboring over 700 species of bacteria.(1) The soft tissues of the oral mucosa are complex habitats where microbes colonize.”
BackgroundThe dynamic communities of oral microbiome in neonates
Guo, H., Li, J., Yao, H., Liu, Y., Ji, Y., Zhang, J., Zhao, Y. L., & Du, M. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1052525 · Cited by 3
“The oral microbiome, ranking the second in the microbiomes of the human body, plays a key role in both oral and systemic diseases, such as caries, periodontitis, preterm low birth weight, Alzheimer’s disease, and depression (Agnello et al., 2017; Zhang et al., 2018; Deo and Deshmukh, 2019; Guo et al., 2021; Wingfield…”
BackgroundHardinsyah, H., Nurkolis, F., Kurniawan, R., Gunawan, W. B., Augusta, P. S., Setyawardani, A., Agustianto, R. F., Mahira, M. F. N. A., Praditya, G. N., Lailossa, D. G., et al. (2023) · Frontiers in Nutrition · doi:10.3389/fnut.2023.1113591 · Cited by 3
Sociality does not predict oral microbiome composition or diversity in free-living prairie voles
Sabol, A. C., Close, W. L., Petrullo, L., Lambert, C., Keane, B., Solomon, N. G., Schloss, P., & Dantzer, B. (2023) · Animal Behaviour · doi:10.1016/j.anbehav.2023.02.009 · Cited by 4
Effects of storage conditions on superoxidised water
Teo, S., Huat, L. L., & Andrianto, V. K. (2023) · MOJ Food Processing & Technology · doi:10.15406/mojfpt.2023.11.00279 · Cited by 3
Antibacterial Activity of Lysimachia nummularia L. in Oro-Dental Diseases
Suciu, F., Stoicescu, I., Lupu, C. E., Popescu, A., Roșca, A. C., Roncea, F. N., Dumitrescu, D. E., Badea, V., & Badea, F. C. (2023) · Applied Sciences · doi:10.3390/app13116830 · Cited by 3
“…700 bacterial species (Gram-positive, Gram-negative) and is defined as one of the most complex microbial flora in the human body; most of these bacterial species are associated with dental plaque and may represent important elements in the etiopathogenesis of periodontitis and dental caries [12].”
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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