Cholera patient metagenomes. human gut metagenome

To understand the roles of antibiotics and lytic phages on Vibrio cholerae infections and disease outcomes, we conducted a national prospective longitudinal study in the cholera endemic setting of Bangladesh. Stool samples were collected at hospital admission from diarrheal disease patients and screened for Vibrio cholerae or V. cholerae phage. Among positive samples, we sequenced shotgun metagenomes to quantify the relative abundances of V. cholerae, phages, and gut microbiome taxa, while accounting for antibiotic exposure determined by mass spectrometry.