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Background  The intestinal microbiome represents a complex network of microbes that are important for human health and preventing pathogen invasion. Studies that examine differences in intestinal microbial communities across individuals with and without enteric infections are useful for identifying microbes that support or impede intestinal health.    Results  16S rRNA gene sequencing was conducted on stool DNA from patients with enteric infections ( n  = 200) and 75 healthy family members to identify differences in intestinal community composition. Stools from 13 patients were also examined post-infection to better understand how intestinal communities recover. Patient communities had lower species richness, evenness, and diversity versus uninfected communities, while principle coordinate analysis demonstrated close clustering of uninfected communities, but not the patient communities, irrespective of age, gender, and race. Differences in community composition between patients and family members were mostly due to variation in the abundance of phyla  Proteobacteria ,  Bacteroidetes , and  Firmicutes . Patient communities had significantly more  Proteobacteria  representing genus  Escherichia  relative to uninfected communities, which were dominated by  Bacteroides . Intestinal communities from patients with bloody diarrhea clustered together in the neighbor-joining phylogeny, while communities from 13 patients’ post-infection had a significant increase in  Bacteroidetes  and  Firmicutes  and clustered together with uninfected communities.    Conclusions  These data demonstrate that the intestinal communities in patients with enteric bacterial infections get altered in similar ways. Furthermore, preventing an increase in  Escherichia  abundance may be an important consideration for future prevention strategies.    Electronic supplementary material  The online version of this article (doi:10.1186/s40168-015-0109-2) contains supplementary material, which is available to authorized users.

Intestinal microbial communities associated with acute enteric infections and disease recovery