Accurate detection of microorganisms in the context of a healthy reference range can be of great use to physicians. All of the 28 microorganisms successfully identified using 16S rRNA gene sequencing are associated with specific health conditions. For example, 2 of the microorganisms on our panel, Escherichia-Shigella and Ruminococcus, are associated with Crohn’s disease [32–37], while 5 other organisms, Akkermansia muciniphila, Bifidobacterium, Dialister invisus, Odoribacter and Roseburia, are inversely associated with Crohn’s disease [32,35–38] (Fig 5, S2 Table). To help diagnose and monitor this condition and distinguish it from other conditions with other microbial associations, it is essential to sequence a panel of microorganisms. The combinatorial information of which organisms are outside of the healthy range can be used by a physician to augment a treatment plan. For example, reducing the intake of animal based diets and diets high in resistant starches to reduce Ruminococcus [39–41] and the consumption of probiotics, inulin and oligofructoses to increase levels of Bifidobacterium .