Fig. 3.

Study designs for identifying microbes that modulate complex disease risk. Microbial inheritance patterns provide an opportunity to identify etiologic agents of disease. By delineating the set of microbial inhabitants in each individual at the strain level, microbial inheritance patterns can be compared with disease incidence to identify strains whose presence/absence explains (correlates with) disease variation. As an illustrative example, every subject in this figure harbors a set of three microbial strains identified by their individual lower and uppercase letters (e.g., “a” is one strain and “A” is another). Healthy individuals are shown with a blue outline whereas affected individuals are shown in solid blue. Microbes that significantly increase disease risk are presented in red boldface (i.e., v, X, T, x, H, M). (A) A classic case-control design is difficult to power when searching for microbes that alter disease risk because, on average, unrelated individuals are expected to share no or very few strains. Sampling a broad enough population to have replicate observations of each strain would likely be prohibitively expensive. (B) Focusing on families increases the likelihood of identifying multiple individuals that share the same strain to enable identification of microbes enriched in either affected or unaffected individuals. Powering familial studies requires large families with multiple affected and unaffected individuals. (C) Geographic disease clusters provide a study design with high potential statistical power. Unrelated individuals are not expected to share microbial strains so identifying the same strain in multiple unrelated affected individuals would be highly significant and indicative of a shared environmental source of the identified strains.