Human gut microbiota predicts susceptibility to Vibrio cholerae infection

Cholera continues to cause epidemics of severe diarrheal disease in the developing world. We prospectively tracked household contacts of cholera patients to examine the role of the gut microbiota in susceptibility to infection. Machine learning models constructed using human gut microbiota were a superior marker of susceptibility to infection than models built from epidemiological factors including youth, vibriocidal titer, and blood type. Predictive gut taxa were linked to subject age, however, supporting models that microbiota maturity can be linked to enteric health. Broadly, susceptibility among contacts was associated with depleted levels of microbes typically found in healthy subjects and increased levels of normally rare bacteria. One rare microbe enriched among susceptible subjects, Paracoccus aminovorans, was confirmed to promote the in vitro growth of Vibrio cholerae. Thus, cholera susceptibility may be partially characterized by the presence of bacteria that facilitate pathogen colonization. More broadly, our work provides some of the first evidence in prospective human cohorts that gut microbiota can be linked to infectious disease susceptibility. See code and metadata on https://github.com/LAD-LAB/Midani_Cholera_JID_2018