Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling

• Type of Material: Article
• Authors: Minjae Kim, Georgia Institute of Technology, Atlanta; Luis M Rodriguez-R, University of Innsbruck; Janet K Hatt, Georgia Institute of Technology, Atlanta; Osman Kayali, Georgia Institute of Technology, Atlanta; Rassul Nalá, Instituto Nacional de Saúde, Marracuene; Anne Dunlop, Emory University; Patricia Brennan, Emory University; Elizabeth Corwin, Emory University; Alicia Smith, Emory University; Joe Brown, University of North Carolina at Chapel Hill; Konstantinos T Konstantinidis, Georgia Institute of Technology, Atlanta
• Language: English
• Date: 2022-08-18
• Publisher: Springer Nature
• Publication Version: Final Published Version
• Copyright Statement: © The Author(s) 2022
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1038/s43705-022-00154-z
• Title of Journal or Parent Work: ISME Communications
• Volume: 2
• Keywords: Public health; Microbiome
• Research Categories: Health Sciences, Nursing; Environmental Sciences; Biology, Microbiology; Health Sciences, Obstetrics and Gynecology

Abstract

The infant gut microbiome has lifelong implications on health and immunity but there is still limited understanding of the microbiome differences and similarities between children in low- and middle-income countries (LMICs) vs. high-income countries (HICs). Here, we describe and compare the microbiome profile of children aged under 48 months in two urban areas: Maputo, Mozambique and Atlanta, USA using shotgun metagenomics. The gut microbiome of American children showed distinct development, characterized by higher alpha diversity after infancy, compared to the same age group of African children, and the microbiomes clustered separately based on geographic location or age. The abundances of antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly higher in Maputo children, driven primarily by several primary and opportunistic pathogens. Most notably, about 50% of Maputo children under the age of two were positive for enterotoxigenic (ETEC) and typical enteropathogenic (EPEC) Escherichia coli diagnostic genes while none of the Atlanta age-matched children showed such a positive signal. In contrast, commensal species such as Phocaeicola vulgatus and Bacteroides caccae were more abundant in Atlanta, potentially reflecting diets rich in animal protein and susceptibility to inflammatory diseases. Overall, our results suggest that the different environments characterizing the two cities have significant, distinctive signatures on the microbiota of children and its development over time. Lack of safe water, sanitation, and hygiene (WASH) conditions and/or unsafe food sources may explain the higher enteric pathogen load among children in Maputo.