Gut Microbiome Composition in Young Nicaraguan Children During Diarrhea Episodes and Recovery

Abstract

Understanding how the gut microbiota is affected by diarrhea episodes may help explain alterations in intestinal function among children in low-income settings. This study examined the composition of the gut microbiome of Nicaraguan children both during diarrhea episodes and while free of diarrhea for at least 2 months. Relative abundances of bacterial taxa, phylogenetic diversity, and species richness were determined by 16S amplicon sequencing and compared between paired diarrhea and recovery samples. A total of 66 stools were provided by 25 children enrolled in a 1-year cohort study of diarrhea etiologies. Children in our cohort had a mean age of 21.9 months; 64% were breast-fed, and 10% had received an antibiotic during the diarrhea episode. Overall, phylogenetic diversity and species richness did not differ significantly between diarrhea and recovery stools. However, of children who had a bacterial enteropathogen detected in any diarrhea stool, none experienced an increase in phylogenetic diversity in recovery, whereas of those in whom no bacterial enteropathogens were detected in their diarrhea stool(s), 59% experienced an increase in phylogenetic diversity in recovery (P = 0.008). This preliminary study suggests that recovery of the gut microbiota after a diarrhea episode may take longer time than previously thought and may be pathogen specific.

Figure 1.

Selection of 25 child participants from larger population-based study.

Figure 2.

Relative abundances of phyla and families detected in the first diarrhea stool vs. recovery stool.

Figure 3.

Ratio of the natural log of relative abundances of genera that differed* between the first diarrhea stool vs. recovery stool. *P < 0.05 unadjusted Wilcoxon signed-rank test. Using Wilcoxon signed-rank test adjusted by false discovery rate (FDR), only the difference in the relative abundance of Cetobacterium was statistically significant (P = 0.0217).

Figure 4.

Phylogenetic diversity and species richness in diarrhea and recovery stools by age group (whiskers indicate the ranges of phylogenetic diversity or species richness values; *P < 0.01 paired t test).