The coupling of taxonomy and function in microbiomes

Microbiologists are transitioning from the study and characterization of individual strains or species to the profiling of whole microbiomes and microbial ecology. Equipped with high-throughput methods for studying the taxonomic and functional characteristics of diverse samples, they are just beginning to encounter the conceptual, theoretical, and experimental problems of comparing taxonomy to (micro-ecological) function, and extracting useful measures from such comparisons (i.e. diversity, stability, or ‘‘health’’). Although still unresolved, these problems are well studied in macro-ecology (the ecology of non-microbes) and are reiterated here as an historical precautionary for microbial ecologists. Beyond expected and unresolved terminological vagueness, we argue that assessments and comparisons of taxonomic and functional profiles in micro-ecology suffer from theoretically unresolvable arbitrariness and ambiguities. We divide these into problems of scale, individuation, and commensurability. We argue that there is no technically/theo-retically ‘‘correct’’ scale, individuation, or comparison of taxonomy and function, but there are nonetheless better and worse methodologies for profiling.