Evaluating Methods for Studying Microbial Biodiversity
As mentioned above, nearly all of the publications addressing the evaluation of methods for studying microbial biodiversity (theme Methods) focused on evaluating laboratory methods for characterizing microorganisms or their DNA. Nevertheless, we could distinguish between methods that were evaluated based on environmental samples and those that were evaluated based on strains from collections. For the former, we noted whether multiple independent samples were employed in the study, and for the latter, we noted whether an independent collection of strains was used to validate the method (Fig. 2). Among the 94 publications analyzed under this theme, 85% were based on environmental samples (aliquots of water or soil, for example) and the remainder were based on strains from collections to evaluate methods of characterization. For the studies employing environmental samples, about 75% exploited multiple samples as the basis for evaluating the method. In the other 25% of studies, the evaluation of the method was based on only a single environmental sample. None of the studies employing strains from laboratories or national collections validated their conclusion with results from a second independent collection of strains. In some cases, independent collections have been combined to determine the genetic diversity within a given species. Tamplin et al. (259) used two laboratory collections (53 environmental and 78 clinical isolates) to determine the genetic variability within Vibrio vulnificus.
https://mmbr.asm.org/content/66/4/592