Host variables confound gut microbiota studies of human disease

Low concordance between studies that examine the microbiota in human diseases is a pervasive challenge that limits capacity to identify causal relationships between host-associated microbes and pathology. Risks of obtaining false positives in human microbiota research are exacerbated by wide inter-individual heterogeneity in microbiota composition(1) likely due to population-wide differences in human lifestyle and physiological variables(2) that exert differential impacts on the microbiota. Herein, we infer the greatest, generalized sources of heterogeneity in human gut microbiota profiles and, further, identify human lifestyle and physiological characteristics that, if not evenly matched between cases and controls, confound microbiota analyses to produce spurious microbial associations with human diseases. Surprisingly, we identify alcohol consumption frequency and bowel movement quality as unexpectedly strong sources of gut microbiota variance that differ in distribution between healthy and diseased subjects and can confound study designs. We demonstrate that for numerous prevalent, high-burden human diseases, matching cases and controls for confounding variables reduces observed microbiota differences and incidence of spurious associations. Thus, we present a list of recommended host variables to capture in human microbiota studies for the purpose of matching comparison groups, which we anticipate will increase robustness and reproducibility in resolving true disease-associated gut microbiota members in human disease.