Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans

Abstract

Disability after childhood diarrhea is an important burden on global productivity. Recent studies suggest that gut bacterial communities influence how humans recover from infectious diarrhea, but we still lack extensive data and mechanistic hypotheses for how these bacterial communities respond to diarrheal disease and its treatment. Here, we report that after Vibrio cholerae infection, the human gut microbiota undergoes an orderly and reproducible succession that features transient reversals in relative levels of enteric Bacteroides and Prevotella. Elements of this succession may be a common feature in microbiota recovery from acute secretory diarrhea, as we observed similar successional dynamics after enterotoxigenic Escherichia coli (ETEC) infection. Our metagenomic analyses suggest that multiple mechanisms drive microbial succession after cholera, including bacterial dispersal properties, changing enteric oxygen and carbohydrate levels, and phage dynamics. Thus, gut microbiota recovery after cholera may be predictable at the level of community structure but is driven by a complex set of temporally varying ecological processes. Our findings suggest opportunities for diagnostics and therapies targeting the gut microbiota in humans recovering from infectious diarrhea.IMPORTANCE Disability after diarrhea is a major burden on public health in the developing world. Gut bacteria may affect this recovery, but it remains incompletely understood how resident microbes in the digestive tract respond to diarrheal illness. Here, we observed an orderly and reproducible succession of gut bacterial groups after cholera in humans. Genomic analyses associated the succession with bacterial dispersal in food, an altered microbial environment, and changing phage levels. Our findings suggest that it may one day be feasible to manage resident bacterial populations in the gut after infectious diarrhea.

Metagenomics of Two Severe Foodborne Outbreaks Provides Diagnostic Signatures and Signs of Coinfection Not Attainable by Traditional Methods

“…These findings indicated that different types of diarrhea, e.g., acute versus moderate infection, may be characterized by different gut microbiota signatures, potentially opening new possibilities for the diagnosis and typing of diarrheal infections. Consistent with these interpretations, a recent longitudinal study of gut microbial community recovery observed that preexisting taxa dropped in abundance and new taxa appeared in great abundance following acute diarrheal disease due to Vibrio cholerae and enterotoxigenic Escherichia coli (ETEC) infection, before the preexisting taxa returned in abundance postinfection (26). It is also possible that the differences noted between our and previous studies might be due, at least in part, to the methods employed by the different studies; e.g., the 16S rRNA gene used in previous studies typically offers limited resolution at the species and subspecies levels due to high sequence conservation (27), while the causative agent was unknown in most of the samples analyzed by Pop and colleagues, limiting further conclusions and interpretations.…”

Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose?

“…Given the diversity of the sample set, a relatively low number of OTU indicated that majority of them were genuine. Rectal samples were shown to closely approximate the stool samples (David et al, 2015). This was the case in our study, where typical adult stool taxa were identified including Bacteroides, Prevotella, Erysipelotrichaceae, Table S1).…”

Dynamic Interactions of a Conserved Enterotoxigenic Escherichia coli Adhesin with Intestinal Mucins Govern Epithelium Engagement and Toxin Delivery

“…Intriguingly, recent studies have demonstrated that during the peak of the severe cholera-like illness caused by ETEC, this pathogen emerges in diarrheal stool in a predominant clonal population that coincides with transient displacement of the commensal microbiota (43,44). However, within days, ETEC bacteria are supplanted as the commensal microbiota re-emerges and the infection resolves.…”