Culture-independent methods are changing the way scientists interrogate microbes in complex environments such as the human body. Specifically, targeted sequencing of the conserved 16S rRNA gene is relatively simple, inexpensive, and high-throughput. However, the analysis of such data quantifies each microbe as a fraction of the total read count, which can lead to misinterpretations of microbes that differ between communities associated with disease. To address this limitation, quantitative microbiome profiling (QMP) methods have been developed.