Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection

Abstract

Background: Cholera is a public health problem worldwide, and the risk factors for infection are only partially understood.

Methods: We prospectively studied household contacts of patients with cholera to compare those who were infected to those who were not. We constructed predictive machine learning models of susceptibility, using baseline gut microbiota data. We identified bacterial taxa associated with susceptibility to Vibrio cholerae infection and tested these taxa for interactions with V. cholerae in vitro.

Results: We found that machine learning models based on gut microbiota, as well as models based on known clinical and epidemiological risk factors, predicted V. cholerae infection. A predictive gut microbiota of roughly 100 bacterial taxa discriminated between contacts who developed infection and those who did not. Susceptibility to cholera was associated with depleted levels of microbes from the phylum Bacteroidetes. By contrast, a microbe associated with cholera by our modeling framework, Paracoccus aminovorans, promoted the in vitro growth of V. cholerae. Gut microbiota structure, clinical outcome, and age were also linked.

Conclusion: These findings support the hypothesis that abnormal gut microbial communities are a host factor related to V. cholerae susceptibility.

Figure 1.

Study design for prospective observation of household contacts of patients with cholera. Index cases were hospitalized on day 1 with symptomatic Vibrio cholerae O1 infection, and their household contacts were enrolled on day 2. Daily clinical assessments and rectal swab sampling of household contacts for V. cholerae culture were conducted during the observation period on days 2–10 and day 30. On the day of enrollment, day 7, and day 30, vibriocidal antibody titers were measured, and rectal swab specimens for 16S ribosomal RNA (rRNA) gene sequencing were obtained.

Figure 2.

Predictive model performance. A, Hold-out models were trained on an initial set of 48 household contacts and tested on a set of 28 household contacts recruited at a later date. Model goodness was assessed using area under the curve (AUC) scores. We evaluated models built using clinical and epidemiological factors (clinical, AUC = 0.60; P = not significant), relative abundance of operational taxonomic units (OTUs; Microbiota, AUC = 0.80; P < .01), or a combination of these data types (combined, AUC = 0.81; P < .01). P values were computed with permutation tests. B, The same set of models was tested using a cross-validation scheme, in which contacts were repeatedly split into training and testing sets. AUCs are shown as a function of OTUs included in the model. Bold lines represent the mean cross-validated AUC, and shaded bands represent the standard error of the mean. Microbiota-based model reached maximum performance at 88 OTUs (AUC = 0.74; P < .01). The dashed gray lines indicate the theoretical performance of a model randomly guessing contact susceptibility. FPR, false-positive rate; TPR, true-positive rate.

Figure 3.

Abundances of predictive gut microbiota in uninfected and infected contacts. Slope graphs are separated into operational taxonomic units (OTUs) with negative model coefficients (uninfected associated; left) and positive model coefficients (infected associated; right). Numbers in brackets indicate the GreenGenes identifiers of representative 16S ribosomal RNA gene sequences. Each gray line depicts an OTU’s mean relative abundance in uninfected or infected contacts. Members of the Bacteroidetes phylum (green) were overrepresented among predictive gut microbiota (P < .05, by a false-discovery rate–corrected binomial test), members of the genus Streptococcus (red) have previously been associated with early stages of cholera [18], and members of the genera Blautia/Ruminococcus (highlighted in blue) have been previously associated with protection from Vibrio cholerae in mice [16].

Figure 4.

Vibrio cholerae (VC) growth in the presence of Paracoccus aminovorans (PA) cell-free spent culture supernatant (SCS). A, VC demonstrated increased growth in SCS of PA. The first initials on the x-axis represent the cultured organism grown in the SCS from the organism represented by the second set of initials, or in fresh medium. B, Colony-forming units (CFU) of V. cholerae grown in SCS and Luria-Bertani (LB) broth. Median values with interquartile ranges are shown. P values are based on a 2-sided Mann-Whitney U test. VH, Vibrio harveyi (control).