What is more important for classification - taxonomy or function?
Something I've been thinking a lot about recently is how we characterize microbial communities. Now that sequencing is relatively cheap, we can generate large amounts of data about the microbes of our respective research projects. However, should we be performing amplicon sequencing (16S, 18S, ITS) or metagenomics? Should we be classifying communities by function or taxonomy?
A recent short article by Xu et al, discusses this very question. Xu et al used PICRUST to examine if either function or taxonomy was a better indicator of microbial community composition. Using several publicly available datasets, they compared 16S classification to functional classification from PICRUST and in one instance to annotated metagenomic data. They determined that adding functional information DOES NOT improve classification accuracy of microbial communities. However, the authors don't downplay the importance of functional information, emphasizing that functional information may be very important depending on the research question. The authors state that improving our ability to classify samples into biologically relevant categories is not a reason to obtain functional data over taxonomic data. So if the goal of your research question is survey a microbial community, then metagenomics might actually provide you with less useful data than plain old 16S rRNA gene sequencing for answering your question.