Intestinal microbial communities associated with acute enteric infections and disease recovery

Abstract

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.

Fig. 1

Differences in operational taxonomic units (OTUs) among individuals with and without enteric infections. Rarefaction curve representing the number of OTUs by the number of sequences sampled in intestinal communities from patients with Shiga toxin-producing Escherichia coli (STEC), Salmonella, Shigella, and Campylobacter infections relative to uninfected family members

Fig. 2

Phyla abundance in communities from a healthy family members and b patients with enteric infections. Only phyla that were shared between the two groups are highlighted for comparison; bars represent averages within each phyla and black dots represent outliers

Fig. 3

Microbiota profiles among intestinal communities from patients with and without enteric infections. The dendrogram was constructed using the Neighbor-joining method based on the Bray-Curtis dissimilarity index with 1000 bootstrap replications. Hierarchical clustering identified five distinct groups (clusters I–V). Communities from healthy family members (Controls) are labeled in green outside the phylogeny, while patients infected with Salmonella, Campylobacter, Shigella, and Shiga toxin-producing E. coli (STEC) are represented by different colors

Fig. 4

Principle coordinate analysis depicting the shift in microbial communities following recovery. Intestinal communities of 13 patients with a Campylobacter (n = 3), b Salmonella (n = 6), and c Shigella (n = 4) infections were compared during the acute enteric infection (red) and post-recovery (green). A comparison was also made to the intestinal communities among healthy family members (pink). The number of individuals sampled during the acute infection stage did not always equal the number of samples received following recovery due to missing samples or loss to follow-up; hence, the time points were pooled for the analysis