Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

Mihai Pop, Alan W Walker, Joseph Paulson, Brianna Lindsay, Martin Antonio, M Anowar Hossain, Joseph Oundo, Boubou Tamboura, Volker Mai, Irina Astrovskaya, Hector Bravo, Richard Rance, Mark Stares, Myron M Levine, Sandra Panchalingam, Karen Kotloff, Usman N Ikumapayi, Chinelo Ebruke, Mitchell Adeyemi, Dilruba AhmedFiroz Ahmed, Meer Alam, Ruhul Amin, Sabbir Siddiqui, John B Ochieng, Emmanuel Ouma, Jane Juma, Euince Mailu, Richard Omore, J Glenn Morris, Robert F Breiman, Debasish Saha, Julian Parkhill, James P Nataro, O Colin Stine

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168 Citations (Scopus)
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BACKGROUND: Diarrheal diseases continue to contribute significantly to morbidity and mortality in infants and young children in developing countries. There is an urgent need to better understand the contributions of novel, potentially uncultured, diarrheal pathogens to severe diarrheal disease, as well as distortions in normal gut microbiota composition that might facilitate severe disease.

RESULTS: We use high throughput 16S rRNA gene sequencing to compare fecal microbiota composition in children under five years of age who have been diagnosed with moderate to severe diarrhea (MSD) with the microbiota from diarrhea-free controls. Our study includes 992 children from four low-income countries in West and East Africa, and Southeast Asia. Known pathogens, as well as bacteria currently not considered as important diarrhea-causing pathogens, are positively associated with MSD, and these include Escherichia/Shigella, and Granulicatella species, and Streptococcus mitis/pneumoniae groups. In both cases and controls, there tend to be distinct negative correlations between facultative anaerobic lineages and obligate anaerobic lineages. Overall genus-level microbiota composition exhibit a shift in controls from low to high levels of Prevotella and in MSD cases from high to low levels of Escherichia/Shigella in younger versus older children; however, there was significant variation among many genera by both site and age.

CONCLUSIONS: Our findings expand the current understanding of microbiota-associated diarrhea pathogenicity in young children from developing countries. Our findings are necessarily based on correlative analyses and must be further validated through epidemiological and molecular techniques.

Original languageEnglish
Article numberR76
Number of pages12
JournalGenome Biology
Publication statusPublished - 27 Jun 2014

Bibliographical note

This work was funded in part by the William and Melinda Gates Foundation, award 42917 to JPN and OCS; US National Institutes of Health grants 5R01HG005220 to HCB, 5R01HG004885 to MP; US National Science Foundation Graduate Research Fellowship award DGE0750616 to JNP; AWW and JP are funded by The Wellcome Trust (Grant No. WT098051).


  • intestinal microbiota
  • Diarrheal Disease
  • Dysentery
  • ribosomal database project
  • Microbiota composition


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