Figure 4.

Ciprofloxacin is associated with minimal microbiota changes. A, Comparison of stool samples from patients with cholera in which ciprofloxacin was or was not detected; samples with phage or trace antibiotic detection were removed. P = .158, by permutational multivariate analysis of variance (Bray-Curtis dissimilarities). Brachyspira species are in brown. B, Relative abundance of taxa previously shown to be associated with early, middle, and late phases of recovery from cholera, with (Abx+) and without (Abx-) antibiotic detection. No significant differences were detected by the Mann-Whitney U test (α = 0.05). P values were adjusted for multiple comparisons. Bars and whiskers denote medians and interquartile ranges, respectively. Analyses were restricted to samples without detection of trace antibiotic and phages. See Supplementary Table 2 for further details. Bacteroid, Bacteroides; Enterob, Enterobacteriaceae (family); Enteroc, Enterococci; Prevotel, Prevotella; Roseb, Roseburia; Streptoc, Streptococci. ^aSamples negative for ciprofloxacin were also negative for metronidazole. ^bEnterobacteriaceae is grouped with genera associated with the early phase of recovery because the family contains Escherichia, which is known to be associated with this phase.