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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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“After the gut, the oral cavity is the second largest colonized portion of the human body [25].”
The Oral–Gut Microbiome–Brain Axis in Cognition
Adil, N. A., Omo-erigbe, C., Yadav, H., & Jain, S. (2025) · Microorganisms · doi:10.3390/microorganisms13040814 · Cited by 65
“Estimated species diversity in the oral microbiome vary, with some studies suggesting over 700 species [14].”
InfluentialCompositional Differences in the Oral Microbiome of E-cigarette Users
Chopyk, J., Bojanowski, C. M., Shin, J. H., Moshensky, A., Fuentes, A. L., Bonde, S. S., Chuki, D., Pride, D. T., & Alexander, L. E. C. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.599664 · Cited by 65
“Given that the oral microbiome can vary both spatially and temporally, it is imperative that additional analyses are conducted (Deo and Deshmukh, 2019).”
BackgroundFernandes, G. V. O., Mosley, G. A., Ross, W., Dagher, A., Martins, B. G. D. S., & Fernandes, J. C. H. (2024) · Microorganisms · doi:10.3390/microorganisms12112214 · Cited by 58
Oral Biofilm and Its Impact on Oral Health, Psychological and Social Interaction
Meseret, A. G. (2021) · International Journal of Oral and Dental Health · doi:10.23937/2469-5734/1510127 · Cited by 56
“Therefore, oral cavity harbours the second most diverse microbial species [4-7], that are present in either planktonic or sessile form [8].”
BackgroundElgezawi, M., Haridy, R., Almas, K., Abdalla, M. A., Omar, O., Abuohashish, H. M., ElEmbaby, A., Wölfle, U. C., Siddiqui, Y., & Kaisarly, D. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23168929 · Cited by 62
“The accumulating cariogenic bacteria produce acids like lactic acid that reduce the local pH, leading first to the demineralization and later to the destruction of the organic matrix through the activation of endogenous MMPs in saliva, gingival fluid, and dentine [37,38].”
BackgroundPopulation-specific differences in the human microbiome: Factors defining the diversity
Govender, P., & Ghai, M. (2024) · Gene · doi:10.1016/j.gene.2024.148923 · Cited by 59
Structure, functions, and diversity of the healthy human microbiome
Ahrodia, T., Das, S., Bakshi, S., & Das, B. (2022) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2022.07.003 · Cited by 55
The human microbiome in clinical translation: from bench to bedside
Bautista, J., Echeverría, C. E., Maldonado-Noboa, I., Ojeda-Mosquera, S., Hidalgo-Tinoco, C., & López-Cortés, A. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1632435 · Cited by 55
“…microorganisms colonize distinct niches in the oral cavity, including the tongue, teeth, gingival crevice, hard and soft palates, and tonsillar tissues, each of which provides unique environmental conditions for microbial growth and interaction (Deo and Deshmukh, 2019; Mark Welch et al., 2020).”
Microbiome of Saliva and Plaque in Children According to Age and Dental Caries Experience
Lee, E., Park, S., Um, S., Kim, S., Lee, J., Jang, J., Jeong, H., Shin, J., Kang, J., Lee, S., et al. (2021) · Diagnostics · doi:10.3390/diagnostics11081324 · Cited by 54
“Oral cavity is the second largest microbial community in the humans after the gut; a significant relationship has been found between the microbes in the oral cavity and the onset of some systemic diseases [5,10,11].”
BackgroundUllah, N., Amin, A., Farid, A., Selim, S., Rashid, S. A., Aziz, M. I., Kamran, S. H., Khan, M. A., Khan, N. R., Mashal, S., et al. (2023) · Gels · doi:10.3390/gels9030252 · Cited by 54
“Oral microbiome is quiet diverse and is comprised of over 700 different “core” and “Transient” microbial species including Gram-positive, Gram-negative and fungal species [1], which significantly contribute towards gingivitis, periodontitis, dental caries, stomatitis, and candidiasis [2].”
BackgroundProbiotics for oral health: a critical evaluation of bacterial strains
Beattie, R. E. (2024) · Frontiers in Microbiology · doi:10.3389/fmicb.2024.1430810 · Cited by 68
The Role of Bacterial and Fungal Human Respiratory Microbiota in COVID‐19 Patients
Soltani, S., Zakeri, A., Zandi, M., Kesheh, M. M., Tabibzadeh, A., Dastranj, M., Faramarzi, S., Didehdar, M., Hafezi, H., Hosseini, P., et al. (2021) · BioMed Research International · doi:10.1155/2021/6670798 · Cited by 53
“5-7), and humidity of the oral cavity make an appropriate environment for microorganism survival and maintenance [23, 24].”
Pisani, F., Pisani, V., Arcangeli, F., Harding, A., & Singhrao, S. K. (2022) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph19159386 · Cited by 55
“Therefore, the gut–brain axis may also contribute to the bacteria observed in AD brains [70] as Gram-positive cocci and rodshaped bacteria reside in the mouth, in the gastrointestinal tract, and in the brain.”
BackgroundManaging Oral Health in the Context of Antimicrobial Resistance
Bessa, L. J., Botelho, J., Machado, V., Alves, R. C., & Mendes, J. J. (2022) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph192416448 · Cited by 57
“pinpointed [14,22], and it refers to the microbial taxa or the genomic and functional attributes associated with those taxa that are characteristic of the oral cavity under healthy conditions [23,24].”
BackgroundLinking the oral microbiome and salivary cytokine abundance to circadian oscillations
Sarkar, A., Kuehl, M. N., Alman, A. C., & Burkhardt, B. R. (2021) · Scientific Reports · doi:10.1038/s41598-021-81420-3 · Cited by 50
Muzio, L. L., Ballini, A., Cantore, S., Bottalico, L., Charitos, I. A., Ambrosino, M., Nocini, R., MALCANGI, A., Dioguardi, M., Cazzolla, A. P., et al. (2021) · BioMed Research International · doi:10.1155/2021/7312611 · Cited by 54
“The archaeal community in periodontal disease was dominated by a Methanobrevibacter oralis type phytologist and a separate subspecies ofMethanobrevibacter such asMethanobrevibacter cuticularis,Methanobrevibacter filiformi, Methanobrevibacter ruminantium, and Methanobrevibacter arboriphilius [21, 22].”
BackgroundInfluentialOptical clearing of tissues: Issues of antimicrobial phototherapy and drug delivery
Tuchin, V. V., Genina, E. A., Tuchina, E. S., Svetlakova, A. V., & Svenskaya, Y. I. (2021) · Advanced Drug Delivery Reviews · doi:10.1016/j.addr.2021.114037 · Cited by 51
Immunomodulatory role of oral microbiota in inflammatory diseases and allergic conditions
Moreno, C. M., Boeree, E., Freitas, C. M. T., & Weber, K. S. (2023) · Frontiers in Allergy · doi:10.3389/falgy.2023.1067483 · Cited by 53
“The most common oral bacterial taxa found in healthy individuals are Firmicutes, Proteobacteria, Actinobacteria, Fusobacterium, and Bacteriodetes (9, 93).”
BackgroundKabwe, M., Dashper, S. G., Bachrach, G., & Tucci, J. (2021) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuab017 · Cited by 52
Functionalized Mouth‐Conformable Interfaces for pH Evaluation of the Oral Cavity
Matzeu, G., Naveh, G. R. S., Agarwal, S., Roshko, J., Ostrovsky-Snider, N. A., Napier, B. S., & Omenetto, F. G. (2021) · Advanced Science · doi:10.1002/advs.202003416 · Cited by 49
The denture microbiome in health and disease: an exploration of a unique community
Redfern, J., Tosheva, L., Malic, S., Butcher, M. C., Ramage, G., & Verran, J. (2022) · Letters in Applied Microbiology · doi:10.1111/lam.13751 · Cited by 48
“197 environment) contains over 700 species of bacteria (Verma et al. 2018; Deo and Deshmukh 2019).”
BackgroundRole of the microbiome in oral cancer occurrence, progression and therapy
Li, Z., Liu, Y., & Zhang, L. (2022) · Microbial Pathogenesis · doi:10.1016/j.micpath.2022.105638 · Cited by 51
Polyamine biomarkers as indicators of human disease
Amin, M., Tang, S., Shalamanova, L., Taylor, R. L., Wylie, S. R., Abdullah, B. M., & Whitehead, K. A. (2021) · Biomarkers · doi:10.1080/1354750x.2021.1875506 · Cited by 51
Dental Materials for Oral Microbiota Dysbiosis: An Update
Zhu, J., Chu, W., Luo, J., Yang, J., He, L., & Li, J. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.900918 · Cited by 49
“The oral microbiota is an important part of the human microbiota, encompassing over 700 bacterial species, as well as a variety of viruses, fungi, protozoa, and archaea (Deo and Deshmukh, 2019).”
BackgroundFrom Pathogenesis to Intervention: The Importance of the Microbiome in Oral Mucositis
Bruno, J. S., Al-Qadami, G. H., Laheij, A. M. G. A., Bossi, P., Fregnani, E. R., & Wardill, H. R. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24098274 · Cited by 46
“Following the identification of aberrant immune responses in OM development, attention has turned to the oral microbiome—the collection of bacteria, viruses and fungi that inhabit surfaces and niches within the oral cavity [7].”
BackgroundOral-Gut Microbiome Axis in the Pathogenesis of Cancer Treatment-Induced Oral Mucositis
Al-Qadami, G. H., Sebille, Y. Z. A. V., Bowen, J. M., & Wardill, H. R. (2022) · Frontiers in Oral Health · doi:10.3389/froh.2022.881949 · Cited by 47
Yekani, M., Dastgir, M., Fattahi, S., Shahi, S., Dizaj, S. M., & Memar, M. Y. (2025) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1533658 · Cited by 56
Silvestre, A. L. P., Filippo, L. D. D., Besegato, J. F., de Annunzio, S. R., de Camargo, B. A. F., de Melo, P. B. G., Rastelli, A. N. D. S., Fontana, C. R., & Chorilli, M. (2020) · International Journal of Pharmaceutics · doi:10.1016/j.ijpharm.2020.120078 · Cited by 45
Pseudomonadota in the oral cavity: a glimpse into the environment-human nexus
Leão, I., de Carvalho, T. B., Henriques, V., Ferreira, C., Sampaio‐Maia, B., & Manaia, C. M. (2022) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-022-12333-y · Cited by 44
“In healthy humans, the core oral microbiome is dominated by members of six phyla, which account for more than 90% of the taxa identified (HOMD V3): Bacillota (formerly Firmicutes), Actinobacteriota (Actinobacteria), Pseudomonadota (formerly Proteobacteria), Fusobacteriota (formerly Fusobacteria), Bacteroidota (formerl…”
BackgroundInfluentialPark, B., Koh, H., Patatanian, M., Reyes-Caballero, H., Zhao, N., Meinert, J. L., Holbrook, J. T., Leinbach, L. I., & Biswal, S. S. (2023) · BMC Microbiology · doi:10.1186/s12866-023-02779-z · Cited by 45
“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 [15].”
BackgroundAmaroli, A., Ravera, S., Zekiy, A. O., Benedicenti, S., & Pasquale, C. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23031372 · Cited by 44
Effects of Antibiotic Use on Saliva Antibody Content and Oral Microbiota in Sprague Dawley Rats
Cheng, X., He, F., Si, M., Sun, P., & Chen, Q. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.721691 · Cited by 42
“Figure 6 shows that a-linolenic acid metabolism, polyketide sugar unit biosynthesis, vitamin B6 metabolism, arginine proline metabolism, and starch and sucrose metabolism, all of which are normal microbial metabolic functions (helping digestion and nutrient absorption), increased significantly in the MTZ group (Deo an…”
BackgroundFusobacterium nucleatum Subspecies Differ in Biofilm Forming Ability in vitro
Muchová, M., Balacco, D. L., Grant, M., Chapple, I., Kuehne, S., & Hirschfeld, J. (2022) · Frontiers in Oral Health · doi:10.3389/froh.2022.853618 · Cited by 45
Cláudia-Ferreira, A., Barbosa, D. J., Saegeman, V., Fernández-Rodríguez, A., Dinis‐Oliveira, R. J., Freitas, A. R., & on behalf of the ESCMID Study Group of Forensic and Post-Mortem Microbiology (ESGFOR) (2023) · Microorganisms · doi:10.3390/microorganisms11102509 · Cited by 47
“…species representative of more than 10 phyla (mainly Bacillota, Bacteroidota, Pseudomonadota, Actinomycetota, Spirochaetota, Fusobacteriota) with Streptococcus spp., Fusobacterium spp., Lactobacillus spp., Actinomyces spp., Veilonella spp. and Neisseria spp. among the most abundant genera [30,31].”
BackgroundSulaiman, Y., Pacauskienė, I. M., Šadzevičienė, R., & Anuzyte, R. (2024) · Medicina · doi:10.3390/medicina60091416 · Cited by 43
“The oral microbiome is the second most diverse microbial community after the gut bacteria [6].”
BackgroundCross Talk between Synthetic Food Colors (Azo Dyes), Oral Flora, and Cardiovascular Disorders
John, A., Yang, H., Muhammad, S., Khan, Z. I., Yu, H., Luqman, M., Tufail, M., Hussain, M. I., & Awan, M. U. F. (2022) · Applied Sciences · doi:10.3390/app12147084 · Cited by 41
Meta‐analysis of caries microbiome studies can improve upon disease prediction outcomes
Butcher, M. C., Short, B., Veena, C. L. R., Bradshaw, D., Pratten, J. R., McLean, W., Shaban, S. M. A., Ramage, G., & Delaney, C. (2022) · Apmis · doi:10.1111/apm.13272 · Cited by 41
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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