With the exception of the Microbiome Quality Control (MBQC), very little has been published on best practices and reference standards for microbiome and metagenomic studies. As evidenced by recent publication trends, researchers are moving the field toward commercial development at a rapid pace. If these analyses are to ever evolve into reliable assays (e.g. for clinical diagnostics), the measurement process must be regularly assessed to ensure measurement quality. A key aspect of this validation is the routine analysis of reference materials as positive controls. A reference material (RM) is any stable, abundant, and well characterized specimen that is used to assess the quantitative and/or qualitative validity of a measurement process. The focus will be on the use of whole cell microbial reference materials to characterize metagenomic analyses from start to finish. We’ll discuss 3 key categories (environmental samples, in vitro models for microbial ecosystems, pure microbial isolates) of reference standards and the challenges in characterizing those standards.