A recent explosion in the number of studies taking advantage of the power of next-generation sequencing to explore metagenomic or 16S rRNA taxonomic diversity of microbial environments means that, we need to stop and think about how we best interpret these data.

Currently, 16S rRNA gene studies provide us with the most effective way of fingerprinting the species richness of a community, with weak links to culture-derived functional relationships. However, the vast increase in the number of bacterial taxa known only from 16S rRNA sequence has started to sever this link, which can only be corrected through more experimental functional characterization requiring improved culturing techniques. A diversity study that uses core-genome processes and key metabolic functions would be an improvement, especially in the absence of the sequence of every genome for every cell in a system. But even then, we know only the potential of the system, not how it is regulated or what is expressed under any given circumstance, for which metatranscriptomics is required (Gilbert et al., 2008). When appropriately applied, core-genome fingerprints could provide a genuine understanding of the population structure with defined niches, insight to functional variation and how these vary between ecosystems. Currently, our understanding is still very limited, but we do have some ideas about how to proceed.

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