Next-generation sequencing approaches to understanding the oral microbiome

Until recently, the focus in dental research has been on studying a small fraction of the oral microbiome—so-called opportunistic pathogens. With the advent of next-generation sequencing (NGS) technologies, researchers now have the tools that allow for profiling of the microbiomes and metagenomes at unprecedented depths. The major advantages of NGS are the high throughput and the fact that specific taxa do not need to be targeted. The relatively low cost and the availability of sequencing facilities have contributed to nearly exponential growth of NGS datasets. The quality and interpretation of the NGS data could be undermined at numerous steps—from sample collection, storage, and DNA extraction to PCR bias, sequencing errors, choice of algorithms for data processing, and statistical analyses. Making sense out of this data deluge is and will be the major challenge. The community analyses based on systems ecology principles will bring us closer to an understanding of the underlying forces that facilitate the stability (or imbalance) of the microbiome. The next logical step will take us beyond the microbiome. The integration of bacterial, viral, fungal "meta-omes" such as the meta-transcriptome, meta-proteome, and meta-metabolome, together with the host as a major co-factor, should be the ultimate goal in unraveling the complexity of the oral interactome.