Friend or foe?
Friend or foe: Metagenomics in health and disease
This complexity makes it extremely difficult to pinpoint specific pathological agents and/or mechanisms using traditional methods such as bacterial culture. However, metagenomics, in tandem with the advent of next-generation sequencing technology, is now capable of studying entire microbial communities at the same time (3). The first metagenomic profiles of the oral microbiome focused on oral diseases, revealing both the distinct and complex multispecies microbial communities within dental plaques and caries, as well as stark differences in microbiota composition between individuals who suffered from these conditions versus those who did not (3, 4). Further studies have used metagenomics approaches to further expand upon the latter, helping to construct bacterial profiles characteristic of individuals with periodontal or other inflammatory diseases (2). This is especially relevant given that oral inflammation has been linked to elevated risk of cardiovascular disease (5). Indeed, metagenomics has been used to find that bacteria in atherosclerotic plaques are also present in similar abundances in the oral cavity, indicating both a potential relationship between the two populations and the possibility that the oral microbiome could be used as a biomarker for cardiovascular disease (6).
The gut microbiota
The gut microbiota is the most widely known human-resident microbial community. While typically dominated by only two phyla, the gut microbiota is immensely diverse at lower taxonomic levels. Indeed, as of 2016, over 10 million genes have been identified and cataloged to comprise the gut microbiome (7). In the same way that the oral microbiota is partially shaped by external contacts, the composition of the gut microbiota is modulated by long-term dietary habits (7). Given its role in digestion and metabolism, it is unsurprising that the gut microbiota has been linked to obesity and metabolic diseases such as type II diabetes (7). Metagenomic approaches have been used to investigate gut microbiome properties in efforts to identify specific markers and/or profiles associated with pathology (8). Studies in lean and obese individuals, for example, have found that the latter group can exhibit greater species diversity and/or experience proportional shifts in microbiome composition (9), while metagenomic profiling of gut microbiota from diabetic patients have identified species-specific polymorphism biomarkers (10–11).