A major drawback of such an approach would be the underlying assumption that all microbial groups (regardless of the taxonomic level) show a consistent abundance across all soil samples of a study which is not a reflected very well (REFs?).
FISH approaches are helpful in estimating actual abundances of taxa of interest as identified by sequencing. Example CARD-FISH Piwosz, shorten.
In order to obtain better estimates of group-specific cell numbers, Catalyzed Reporter Deposition coupled to Fluorescence In Situ Hybridization (CARD-FISH) provides the opportunity to stain and count target soil microorganisms of interest on a phylum but also species level (Eickhorst and Tippkötter, 2008; Schmidt and Eickhorst, 2013).
ools such as DeSeq2 and EdgeR that were originally built for differential gene expression analyses of RNA-seq data, now extend to amplicon-based studies. These packages