Analysis of Microbial Diversity: Regarding the (Paradoxical) Difficulty of Seeing Big in Metagenomics

Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery

“…In as much as environmental genomics enhance microbial dark matter studies, for example, by unraveling extremophiles, it also raises issues, since environmental genomics has its own blind spots. The selection of samples, of genes of interests (e.g., in metabarcoding projects, or more generally in targeted environmental genomics) and the many filtering decisions and heuristics in the subsequent bioinformatic treatments imposed by the wealth of environmental sequences (i.e., reads and contigs), as well as the increased standardization of the methods and questions of environmental genomics studies (a logical scientific development for a comparative science; Vigliotti et al. 2017 ) raise the risk that the most unexpected of life forms, even if already sequenced, remain drowned under this deluge of data.…”