The methods used to discern the structure (anatomy) and function (physiology) of the indigenous microbiota can be divided according to which aspect of the microbiota they can interrogate and are positioned accordingly. At the most basic level, methods can simply describe the community structure of the microbiota, that is, which taxa are present and in what relative amounts. Methods that investigate functional potential generally catalog the coding potential of individual members of the microbiota or the entire community (the metagenome). To measure function directly a catalog of the expressed microbial genes (the metatranscriptome) or the proteins or metabolites present in the microbiome environment must be generated. So, complexity in understanding the role of microbiota is quite rejecting the interested clinician. Evidence-based medicine can offer an answer suggesting strict definition of populations, measurement techniques, and external validity.