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The Oralome and Its Dysbiosis: New Insights Into Oral Microbiome-Host Interactions

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The Oralome and Its Dysbiosis: New Insights Into Oral Microbiome-Host Interactions UCSF UC San Francisco Previously Published Works Title The oralome and its dysbiosis: New insights into oral microbiome-host interactions. Permalink https://escholarship.org/uc/item/68k197wb Authors Radaic, Allan Kapila, Yvonne L Publication Date 2021 DOI 10.1016/j.csbj.2021.02.010 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Computational and Structural Biotechnology Journal 19 (2021) 1335–1360 journal homepage: www.elsevier.com/locate/csbj Review The oralome and its dysbiosis: New insights into oral microbiome-host interactions ⇑ Allan Radaic, Yvonne L. Kapila Kapila Laboratory, Orofacial Sciences Department, School of Dentistry, University of California, San Francisco (UCSF), San Francisco, CA, USA article info abstract Article history: The oralome is the summary of the dynamic interactions orchestrated between the ecological community Received 15 October 2020 of oral microorganisms (comprised of up to approximately 1000 species of bacteria, fungi, viruses, Received in revised form 13 February 2021 archaea and protozoa - the oral microbiome) that live in the oral cavity and the host. These microorgan- Accepted 16 February 2021 isms form a complex ecosystem that thrive in the dynamic oral environment in a symbiotic relationship Available online 27 February 2021 with the human host. However, the microbial composition is significantly affected by interspecies and host-microbial interactions, which in turn, can impact the health and disease status of the host. In this Keywords: review, we discuss the composition of the oralome and inter-species and host-microbial interactions that Dysbiosis take place in the oral cavity and examine how these interactions change from healthy (eubiotic) to dis- Host-microbe interactions Complex diseases ease (dysbiotic) states. We further discuss the dysbiotic signatures associated with periodontitis and car- Oral microbiome ies and their sequalae, (e.g., tooth/bone loss and pulpitis), and the systemic diseases associated with these Oral biofilm oral diseases, such as infective endocarditis, atherosclerosis, diabetes, Alzheimer’s disease and head and neck/oral cancer. We then discuss current computational techniques to assess dysbiotic oral microbiome changes. Lastly, we discuss current and novel techniques for modulation of the dysbiotic oral microbiome that may help in disease prevention and treatment, including standard hygiene methods, prebiotics, pro- biotics, use of nano-sized drug delivery systems (nano-DDS), extracellular polymeric matrix (EPM) dis- ruption, and host response modulators. Ó 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creative- commons.org/licenses/by-nc-nd/4.0/). Contents 1. Introduction . ..................................................................................................... 1336 2. Microbial habitats in the human body . .................................................................................. 1336 3. The oral microbiome and the oralome . .................................................................................. 1336 3.1. Oral bacterial microbiome – the bacteriome. ........................................................................ 1336 3.1.1. The oral bacterial biofilm. ............................................................................. 1336 3.2. Oral viral biome – the virobiome/virome . ........................................................................ 1337 3.3. Oral fungal microbiome - the mycobiome. ........................................................................ 1337 3.4. Oral protozoa biome – the protozoome. ........................................................................ 1338 3.5. Oral archaea biome – the archaeome . ........................................................................ 1338 3.6. Interspecies interactions . ........................................................................................ 1338 3.7. Oral host-microbial interactions – the oralome . ..................................................... 1340 3.7.1. Eubiosis . ............................................................................................. 1340 4. Oral biofilm dysbiosis signatures of common diseases . ............................................................... 1341 4.1. Dental caries and periodontal disease . ........................................................................ 1341 4.2. Atherosclerosis . ........................................................................................ 1344 4.3. Alzheimer’s disease . ........................................................................................ 1344 ⇑ Corresponding author at: Department of Orofacial Sciences, University of California San Francisco, School of Dentistry, 513 Parnassus Avenue, S616C, Box 0422, San Francisco, CA 94143, USA. E-mail address: [email protected] (Y.L. Kapila). https://doi.org/10.1016/j.csbj.2021.02.010 2001-0370/Ó 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). A. Radaic and Y.L. Kapila Computational and Structural Biotechnology Journal 19 (2021) 1335–1360 4.4. Diabetes . ........................................................................................ 1345 4.5. Pregnancy complications ........................................................................................ 1345 4.6. Head and neck cancer . ........................................................................................ 1346 4.7. Other cancers. ........................................................................................ 1348 4.7.1. Pancreatic cancer . ............................................................................. 1348 4.7.2. Colorectal cancer . ............................................................................. 1348 5. Current computational techniques to evaluate oral biofilm dysbiosis . ............................................ 1348 6. Current and novel techniques for modulating oral biofilm dysbiosis . ............................................ 1350 6.1. Oral hygiene . ........................................................................................ 1350 6.2. Antimicrobial peptides (AMPs). ........................................................................ 1350 6.3. Use of nanosized-drug delivery systems . ........................................................................ 1351 6.4. Prebiotics . ........................................................................................ 1351 6.5. Probiotics . ........................................................................................ 1352 6.6. Extracellular polymeric matrix (EPM) disruption . ..................................................... 1352 6.7. Host response modulators (HRM) . ........................................................................ 1353 7. Clinical trials. ..................................................................................................... 1353 8. Summary and future outlook . .................................................................................. 1354 CRediT authorship contribution statement . ............................................................... 1354 Declaration of Competing Interest . .................................................................................. 1354 Acknowledgements . .................................................................................. 1354 References . ..................................................................................................... 1354 1. Introduction on the oral bacteria within the microbiome, while other oral biomes (i.e. fungi, archaea, protozoa and the viral biomes) receive More than three centuries ago, Antony van Leeuwenhoek was much less attention. Although there is limited literature on these the first person to observe microbes, possibly bacteria, from his other biomes, they remain relevant [1,9,13,14]. Thus, we will own dental plaque with the use a microscope that he constructed discuss each of these biomes in the context of the oral cavity. [1]; thereby laying down the foundations of microbiology. Since then, new discoveries have highlighted that these microbes inter- 3.1. Oral bacterial microbiome – the bacteriome act with their human host. A recent estimate shows that 3.8 Â 1013 microorganisms colonize the human body, accounting Due to changes in shear forces, nutrient/energy supply, temper- for about half of the total cells on a human body [2]. In aggregate, ature, pH, and oxygen content in different environments, bacteria these organisms are known as the human microbiome [3,4]. have evolved by leveraging specific survival strategies, including co-aggregation of different cells into communities embedded in 2. Microbial habitats in the human body extracellular matrices –biofilms [10]. Despite the existence of planktonic bacteria in the oral cavity, most of the oral microbiome The NIH Human Microbiome Project (HMP), which was exists in a biofilm state, known as the oral biofilm. launched in 2007, comprised 18 different studies to map and characterize the human microbiome and its role in human health 3.1.1. The oral bacterial biofilm and disease. It is well appreciated that the
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