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

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  • 1 School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia;
  • 2 School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia;
  • 3 Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador;
  • 4 School of Public Health, University of Washington, Seattle, Washington;
  • 5 Centro de Biomedicina, Universidad Central del Ecuador, Quito, Ecuador.

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.

Author Notes

Address correspondence to Konstantinos T. Konstantinidis, School of Civil and Environmental Engineering, Georgia Institute of Technology, 310 Ferst Dr. NW, Atlanta, GA 30332, E-mail: kostas.konstantinidis@gatech.edu or Karen Levy, School of Public Health, University of Washington, Box 351618, 2980 15th Avenue NE, Seattle, WA 98105, E-mail: klevyx@uw.edu.

Disclaimer: The content in this article is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Financial support: This study was supported by the National Institute for Allergy and Infectious Diseases (grant nos. K01AI103544 and R01AI137679) at the U.S. National Institutes of Health. M. S.- G. was supported by a doctoral scholarship from Colciencias, Colombian government.

Authors’ addresses: Maria J. Soto-Girón and Angela Peña-Gonzalez, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, E-mails: dendroapsis@gmail.com and angela.viviana.pena@gmail.com. Janet K. Hatt and Konstantinos T. Konstantinidis, School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA, E-mails: janet.hatt@ce.gatech.edu and kostas.konstantinidis@gatech.edu. Lorena Montero, Maritza Páez, Estefania Ortega, and Gabriel Trueba, Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador, E-mails: lpmonterot@gmail.com, mpaezllerena86@gmail.com, estefania1058@gmail.com, and gtrueba@usfq.edu.ec. Shanon Smith, Rollins School of Public Health, Emory University, Atlanta, GA, E-mail: shanon.smith@emory.edu. Karen Levy, School of Public Health, University of Washington, Seattle, WA, E-mail: klevyx@uw.edu. William Cevallos, Centro de Biomedicina, Universidad Central del Ecuador, Quito, Ecuador, E-mail: wcevallos@usfq.edu.ec.

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