Abstract
BackgroundThe 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.Results16S 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.ConclusionsThese 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 materialThe online version of this article (doi:10.1186/s40168-015-0109-2) contains supplementary material, which is available to authorized users.
Highlights
The intestinal microbiome represents a complex network of microbes that are important for human health and preventing pathogen invasion
Enteric disease cases identified via active surveillance are representative of the Michigan population As part of the Enteric Research Investigative Network (ERIN) Cooperative Research Center (CRC) at Michigan State University, we developed an active surveillance system to identify patients with enteric infections at four participating hospitals and the Michigan Department of Health and Human Services (MDHHS)
To ensure that the ERIN surveillance network is representative of statewide enteric infection frequencies and that our results are generalizable, we compared the frequency of all ERIN cases (n = 615) identified between January 1, 2011 and May 7, 2014 to all cases (n = 7435) identified throughout the State of Michigan during the same time period
Summary
The intestinal microbiome represents a complex network of microbes that are important for human health and preventing pathogen invasion. Prior studies have demonstrated that intestinal communities are stable over time [9] and that several factors including diet, lifestyle, age, probiotic and antibiotic use, infection, and chronic conditions [10,11,12], can significantly alter the diversity and abundance of the intestinal microbiota. Commensal microbes were suggested to alter pathogen virulence gene expression profiles by modifying environmental conditions [15]. These data underlie the importance of intestinal communities in both promoting and inhibiting pathogen proliferation; additional studies are needed to identify which communities are most susceptible to and protective against infection and how they change with infection
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