Gut Microbiome Changes with Acute Diarrheal Disease in Urban Versus Rural Settings in Northern Ecuador

Abstract

Previous studies have reported lower fecal bacterial diversity in urban populations compared with those living in rural settings. However, most of these studies compare geographically distant populations from different countries and even continents. The extent of differences in the gut microbiome in adjacent rural versus urban populations, and the role of such differences, if any, during enteric infections remain poorly understood. To provide new insights into these issues, we sampled the gut microbiome of young children with and without acute diarrheal disease (ADD) living in rural and urban areas in northern Ecuador. Shotgun metagenomic analyses of non-ADD samples revealed small but significant differences in the abundance of microbial taxa, including a greater abundance of Prevotella and a lower abundance of Bacteroides and Alistipes in rural populations. Greater and more significant shifts in taxon abundance, metabolic pathway abundance, and diversity were observed between ADD and non-ADD status when comparing urban to rural sites (Welch’s t-test, P < 0.05). Collectively our data show substantial functional, diversity, and taxonomic shifts in the gut microbiome of urban populations with, ADD supporting the idea that the microbiome of rural populations may be more resilient to ADD episodes.

Exploring the universal healthy human gut microbiota around the World

“…Although host factors such as genetics, immune regulation, or age play a role in shaping the gut microbiota [105] , [106] , [107] , environmental factors such as geography, lifestyle, or diet appear to play a dominant role [108] , [109] , [110] . Moreover, even considering populations that share the same geographical origin, like the Urban Versus Rural Settings in Northern Ecuador of Soto-Girn et al [111] , lifestyle and westernization seem to be the main driver of differences. Furthermore, other findings suggest that the microbial composition of great apes and humans would be more closely related to their host’s lifestyle than to their geography [112] .…”

Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections

“…Further, community DNA from the stool samples was extracted and used for (i) qPCR of diagnostic virulence genes and (ii) short-read shotgun metagenomic sequencing followed by bioinformatic analysis. The subset of samples ( n = 35) included in this study were selected based on the following criteria: (i) the sample was from a participant who presented with diarrhea (a diarrhea case sample, defined as three or more loose stools in 24 h), (ii) there was an E. coli strain isolated from the sample that was PCR-positive for a pathogenic DEC gene profile, and (iii) we had a shotgun metagenome available for the sample from prior analyses ( 4 , 37 , 54 ). Details of each workflow are provided below, and further details about study design, sample selection, and processing, and for culturing, isolate sequencing, and shotgun metagenome sequencing can be found in references 4 , 37 , 38 , 54 , 55 .…”

Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador

“…Second, we designed this study to encompass pathogen and gut microbiome differences for any DEC pathotype. This approach allowed us to focus on broad differences associated with DEC infections but did not capture important between-pathotype differences, though pathotype-associated gut microbiome differences have been previously explored for this dataset 19 , 90 . Lastly, there are factors associated with symptomatic versus asymptomatic carriage of DEC or other enteropathogens that we were not able to explore here.…”