How to count our microbes

Recently Vandeputte et al. introduced the concept of Quantitative Microbiome Profiling (QMP) as a way to bypass many of the statistical and interpretative challenges that arise from the compositional structure of microbiome sequencing data. Although their proposed solution looks promising and elegantly accounts for the compositionality nature of the conventional Relative Microbiome Profiling (RMP) data, it could theoretically introduce new bias when samples contain a significant amount of free extracellular prokaryotic DNA. This free DNA is captured during the sequencing but is excluded by flow-cytometry cell count. In case the taxonomic composition of free circulating DNA differs from the composition of intact microbial cells (e.g. due to differences in susceptibility of microbial cells to environmental exposures), this might result into the introduction of a new source of bias in downstream analysis.