Tricks and treats of oral microbiome
Atrandi Biosciences
Microfluidics, Single-Cell Analysis, & High-Throughput Screening
There are roughly 1000 different species of bacteria living in our mouths. They play different roles both in maintaining our oral and overall health and in causing diseases, most notably dental caries and periodontal inflammatory conditions. Interestingly, the bacteria that cause disease are present in the healthy microbiota, which is why regular oral hygiene is important in preventing the development of these conditions. On the other hand, excessive oral hygiene practices, especially the use of antimicrobial agents, can be detrimental as well, because the colonies of commensal bacteria covering the surfaces of your mouth prevent opportunistic pathogenic microorganisms from attaching.
One tricky member of the oral microbiota is Streptococcus mutans. A type of lactic acid bacteria, S. mutans quickly takes up carbohydrates entering our mouths and metabolizes them in a few different ways. One of them leads to the formation of glue-like substance that S. mutans uses to form biofilms that contribute to the plaque on our teeth. Another metabolic pathway leads to production of acids, which can dissolve the minerals in tooth enamel, leading to caries. Based mostly on microbiological research utilizing laboratory cultures, for a long time S. mutans was thought to be the key pathogen initiating and leading the progression of caries.
However, the advent of culture-independent molecular methods of identifying microbes led to conflicting findings. Namely, some people were found to have high levels of S. mutans but no caries while others had low S. mutans levels but were suffering from caries. Thus, it appears that caries can be caused by different acid-producing oral bacteria, without input from S. mutans, for example, if the oral environment is disrupted by frequent intake of carbohydrates. A recent study by Gupta et al. (2024) analyzed caries samples using functional shotgun metagenomics, that is, in addition to performing metagenomic sequencing, they also used functional gene prediction techniques to identify enzymes that produce acids from primary metabolites. They identified 117 genera, among them Lactobacillus, Chryseobacterium, and Neisseria, which produce different organic acids and are present in carious lesions.
An interesting a treat to our health from a group of oral bacteria, including members of Neisseria, Rothia, and Veillonella, is the conversion of nitrate to nitrite, which is taken up into the bloodstream and converted to nitrous oxide – a compound that helps reduce blood pressure. Nitrate is a compound found in vegetables, such as dark leafy greens and beets, as well as animal-based sources (e.g., cured and processed meat where it is used as a preservative), but it appears that nitrate from the latter sources carries a certain carcinogenic risk (Pinaffi-Langley et al. 2024). A fun little study by Govoni et al. (2008) highlighted the contribution of oral bacteria in the nitrate-to-nitrite conversion by having healthy volunteers rinse their mouths with antibacterial mouthwash prior to consuming nitrate. They observed that this rinse had no effect on nitrate accumulation in saliva and blood plasma, but the increase in plasma nitrite was markedly reduced, compared to the control group, who did not rinse with antibacterial mouthwash.
Studies of the oral microbiome so far have been generally performed using bulk 16S RNA or metagenomic sequencing methods, sometimes coupled with additional analyses, such as metabolomics. However, 16S RNA sequencing, while a cost-effective method, only allows to distinguish between different genera with certainty – closely related species or strains may have 16S RNA genes that are too similar (or identical) for the differences to be detected using this method. Bulk metagenomic analysis is superior to 16S RNA analysis alone, but rare species or strains still may remain hidden. Additionally, different strains belonging to the same species might have different characteristics and produce different metabolites, some might even be pathogenic while others are not. Reviewers of the field, such as Wade (2013), note that species-level identification is likely insufficient to understand the process of caries formation and progression. A deeper analysis of the oral microbiota is required. This could be done utilizing single-cell analysis methods. To contribute to this developing field, Atrandi Biosciences has developed the semi-permeable capsule (SPC) technology which enables microbial DNA sequencing at single-cell level, allowing for absolute quantification of strains and functional profiling.
?? Find out more here: Single Cell Metagenomics | Atrandi.com
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