Computational Analysis of Interactions of the Oral Microbiota
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Purpose of Review
The human oral microbiome is a complex site containing many hundreds of species with the community response of these species having a large effect on human health. The complexity of this site speaks to the need for applying -omics techniques to better understand which microbial species are present, their interactions and contribution to the microbiome, and how this may change as a function of disease. Here, I review several recent studies that use computational analysis to examine and model the oral microbiome and determine its role in human health.
Several studies have emerged in the past few years that use several -omics approaches to look specifically at points of interaction between microbiomes of the oral cavity and between these microbiomes and the human host. New techniques in sequencing have revealed a more detailed picture of who is present and their interactions. Network studies that attempt to link hundreds of species, transcripts, or proteins are also beginning to be inferred though their use, aside from species co-abundance networks, are still in the early stages.
The ability to collect -omics data of the oral microbiome has been well established. The future of this field will likely focus on the integration and use of this data to build models that reveal hundreds of interactions between species at the individual gene or protein level. A better understanding of these interactions, and how they contribute to disease states, will allow for better control and manipulation of the oral microbiome to improve human health.
KeywordsOral cavity Microbiome -omics Interspecies interactions Computational Modeling
Compliance with Ethical Standards
Conflict of Interest
The author declares that he has no conflict of interest.
Human and Animal Rights and Informed Consent
This article does not contain any studies with human or animal subjects performed by any of the authors.
Papers of particular interest, published recently, have been highlighted as: • Of importance •• Of major importance
- 1.Escapa IF, Chen T, Huang Y, Gajare P, Dewhirst FE, Lemon KP. New insights into human nostril microbiome from the expanded human oral microbiome database (eHOMD): a resource for the microbiome of the human aerodigestive tract. mSystems. 2018;3(6).Google Scholar
- 8.• Ebbers M, Lübcke PM, Volzke J, Kriebel K, Hieke C, Engelmann R, et al. Interplay between P. gingivalis, F. nucleatum, and A. actinomycetemcomitans in murine alveolar bone loss, arthritis onset and progression. Sci Rep. 2018;8(1):15129 This paper describes specific interspecies interactions centered on pathogens that related to oral health. CrossRefPubMedPubMedCentralGoogle Scholar
- 21.•• Jasberg H, et al. Bifidobacteria inhibit the growth of Porphyromonas gingivalis but not of Streptococcus mutans in an in vitro biofilm model. Eur J Oral Sci. 2016;124(3):251–8 This paper described aspects of interactions that could be harnessed to improve oral health. CrossRefPubMedGoogle Scholar
- 22.•• Kobayashi R, et al. Oral administration of Lactobacillus gasseri SBT2055 is effective in preventing Porphyromonas gingivalis-accelerated periodontal disease. Sci Rep. 2017;7(1):545 This paper describes the same but moves toward exploring a practical application. CrossRefPubMedPubMedCentralGoogle Scholar
- 23.Jakubovics NS, Gill SR, Iobst SE, Vickerman MM, Kolenbrander PE. Regulation of gene expression in a mixed-genus community: stabilized arginine biosynthesis in Streptococcus gordonii by coaggregation with Actinomyces naeslundii. J Bacteriol. 2008;190(10):3646–57.CrossRefPubMedPubMedCentralGoogle Scholar
- 28.• Eren AM, Borisy GG, Huse SM, Mark Welch JL. Oligotyping analysis of the human oral microbiome. Proc Natl Acad Sci U S A. 2014;111(28):E2875–84 This paper applied a more stringent type of amplicon analysis to the oral cavity to better describe which specie are present. CrossRefPubMedPubMedCentralGoogle Scholar
- 41.• Mukherjee PK, Chandra J, Retuerto M, Sikaroodi M, Brown RE, Jurevic R, et al. Oral mycobiome analysis of HIV-infected patients: identification of Pichia as an antagonist of opportunistic fungi. PLoS Pathog. 2014;10(3):e1003996 This paper describes the role of fungi in the oral microbiome and its relationship to oral health. CrossRefPubMedPubMedCentralGoogle Scholar
- 46.• Musungu BM, et al. A network approach of gene co-expression in the Zea mays/Aspergillus flavus Pathosystem to map host/pathogen interaction pathways. Front Genet. 2016;7:206 This paper was one of the first to infer a multi-species network focused on host-pathogen interactions. CrossRefPubMedPubMedCentralGoogle Scholar