Microbes run the world... but they don't care for the names we give them. Molecular functional abilities of individual microbes in micriobiomes living in different environmental conditions are clearly different. Thus, the question of “who is there?” is not as relevant as “what are they doing?”
Focusing on microbial molecular functionality, instead of names or classes, allows for a better description of microbial and microbiome-ial abilities and similarities. The recent emergence of high-throughput genomic sequencing, coupled with the growing analytical capacities, has unlocked new horizons in our understanding of the microbial world. However, making sense of this deluge of data requires efficient and accurate computational techniques. The identification of microbial clades resident in a particular niche is only an estimate of the microbiome’s functional potential. We developed a sequencing read-based approach that can be applied to individual microbes and microbiomes to facilitate assessment of functional diversity. By adopting this point of view in analyzing metagenomic data we hope to map emergent functionalities of condition (or niche) -specific microbiomes.