Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States

Audrie Lin,Upinder Singh,Elisabeth M Bik,David A Relman,Elizabeth K Costello,Rashidul Haque,Les Dethlefsen,Ramy K Aziz

doi:10.1371/journal.pone.0053838

Abstract

BackgroundOur current understanding of the composition and stability of the human distal gut microbiota is based largely on studies of infants and adults living in developed countries. In contrast, little is known about the gut microbiota and its variation over time in older children and adolescents, especially in developing countries.Methodology/Principal FindingsWe compared the diversity, composition, and temporal stability of the fecal microbiota of healthy children, ages 9 to 14 years, living in an urban slum in Bangladesh with that of children of the same age range in an upper-middle class suburban community in the United States. We analyzed >8,000 near full-length 16S rRNA gene sequences and over 845,000 pyrosequencing reads of the 16S rRNA V1–V3 region. The distal gut of Bangladeshi children harbored significantly greater bacterial diversity than that of U.S. children, including novel lineages from several bacterial phyla. Bangladeshi and U.S. children had distinct fecal bacterial community membership and structure; the microbiota of Bangladeshi children was enriched in Prevotella, Butyrivibrio, and Oscillospira and depleted in Bacteroides relative to U.S. children (although similar to Bangladeshi adults). Furthermore, community membership and structure in Bangladeshi children was significantly less stable month-to-month than U.S. children.Conclusions/SignificanceTogether, these results suggest that differing environmental or genetic factors may shape the microbiota of healthy children in the two countries. Further investigation is necessary to understand the mechanisms and factors that underlie these differences, and to incorporate these findings into new strategies for the prevention and treatment of childhood and adolescent diseases.

Highlights

Of the 1.2 billion global adolescent population, 88% live in developing nations where the incidence of environmental enteropathy – a multifaceted, subclinical intestinal disorder encompassing repeated episodes of infectious gastroenteritis, chronic inflammation, and malnutrition – ranges from 50–95% [1,2,3]
We found that Bangladeshi children harbor greater bacterial diversity and evenness in the distal gut than U.S children
Our results are similar to previous observations of higher bacterial diversity in children living in rural Burkina Faso compared to children from urban Italy [6]

Summary

Introduction

Of the 1.2 billion global adolescent population, 88% live in developing nations where the incidence of environmental enteropathy – a multifaceted, subclinical intestinal disorder encompassing repeated episodes of infectious gastroenteritis, chronic inflammation, and malnutrition – ranges from 50–95% [1,2,3]. The human gut microbiota has been characterized in depth using molecular approaches from individuals in only a few low-income areas of the developing world [5]. Recent work highlights the importance of geography in explaining the gut microbiota composition of adults and children [6,7] and underscores the need to select additional geographic settings in an effort to characterize the global extent of human-associated microbial diversity [8]. The influence of geography on the temporal stability of the composition of the gut microbiota within healthy individuals has not previously been examined, in part because of the difficulty in obtaining serial samples from a consistently healthy reference population in areas with high rates of environmental enteropathy or other gastrointestinal conditions. Little is known about the gut microbiota and its variation over time in older children and adolescents, especially in developing countries

Methods

Results

Conclusion