Diarrhea in young children from low-income countries leads to large-scale alterations in wintestinal 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 Corrada Bravo, Richard Rance, Mark Stares, Myron M. Levine, Sandra Panchalingam, Karen Kotloff, Usman N. Ikumapayi, Chinelo Ebruke, Mitchell Adeyemi, Dilruba AhmedFiroz Ahmed, Meer Taifur 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

Research output: Contribution to journalArticlepeer-review

117 Scopus citations


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 (US)
Article numberR76
JournalGenome Biology
Issue number6
StatePublished - Jun 27 2014
Externally publishedYes

ASJC Scopus subject areas

  • Cell Biology
  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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