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

Abstract

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.

Modeling human enteric dysbiosis and rotavirus immunity in gnotobiotic pigs

“…The decreased alpha diversity in HHGM pigs after VirHRV challenge was expected. A study evaluating microbiome and diarrhea found that diarrhea was associated with decreased phylogenetic diversity [25]. Although no samples were available for time points after PCD7, it is expected, given our data on enteropathy biomarkers, that diversity of HHGM pigs would return to normal levels.…”

“…The samples were snap frozen in liquid nitrogen in the field, immediately transferred to −80 °C, shipped on dry ice to our lab, and stored at −80 °C until assayed. All stool samples underwent 16S rRNA amplicon sequencing for characterization of the gut microbiome, as previously described [25]. ELISAs for 4 biomarkers of enteropathy (α−1 antitrypsin, neopterin, myeloperoxidase and calprotectin) were run on the samples [38, 39].…”

“…LIC were collected at necropsy, snap frozen in liquid nitrogen and shipped on dry ice to the UNC Microbiome Core Facility where 16S rRNA amplicon sequencing DNA isolation was carried out as described [25]. Briefly, samples (200 mg) were transferred to sterile 2 ml tubes containing 200 mg of 212–300 μm glass beads (Sigma-Aldrich) and 1.4 ml of Qiagen ASL buffer for bead beating and subsequently incubated at 95 °C for 5 min.…”

“…Demultiplexing and quality filtering was performed on the joined results and quality analysis reports were produced using the FastQC software. Subsequent analyses were performed using the Quantitative Insights Into Microbial Ecology (QIIME v.1.8.0) [57] as described [25, 58]. Sequences were clustered into operational taxonomic units (OTU) at 97% similarity threshold using UCLUST [59], and they were aligned in order to build a phylogenetic tree [60].…”

Characterization of the gut microbiota of Nicaraguan children in a water insecure context

“…Among children, studies have considered the relationship between a diarrhea episode, which, in some cases, was associated with an enteric pathogen infection, and changes in the gut microbiota (Becker‐Dreps et al, ; Pop et al, ; Solano‐Aguilar et al, ; Subramanian et al, ; The et al, ). For example, in a large study of West African children, Pop et al () found the gut microbiota of those with moderate‐severe diarrhea to be less diverse than that of diarrhea‐free controls.…”