Molecular characterization of the diarrheal microbiome in young children from low-income countries

Diarrhea is a major cause of mortality and morbidity in young children from developing countries, leading to as many as 15% of all deaths in children under 5 years of age. While many causes of this disease are already known, conventional diagnostic approaches fail to detect a pathogen in up to 60% of diarrheal cases. Our study is part of the larger Global Enterics Multi-center study (GEMS) and aims to characterize the diarrheal microbiome in order to both evaluate the effectiveness of modern diagnostics based on molecular techniques, and to discover potentially new pathogens. Among the discoveries of our study (also see publications below) are the effectiveness of quantitative PCR as an alternative to culture in characterizing Shigella infections, as well as the potential of members of the Streptococcus genus to cause diarrhea. Streptococci were found in our study to be statistically associated with diarrheal disease in general and more severe forms (such as dysentery) in particular. The data underlying our study as well as the software used to perform our analyses are available through the links below. All software is provided Open Source with no restrictions for reuse by academic or commercial institutions.

Key People

Many scientists and health professionals have been involved in developing the infrastructure necessary to conduct our study and to collect the samples used in our project. The specific work conducted at the University of Maryland, College Park is the result of the hard work of the following individuals:


  • O. Colin Stine - University of Maryland School of Medicine
  • James Nataro - University of Virginia
  • Alan Walker - Unversity of Aberdeen, UK
  • Volker Mai - University of Florida
  • Mihai Pop - University of Maryland, College Park
  • Héctor Corrada Bravo - University of Maryland, College Park


  • Irina Astrovskaya - University of Maryland, College Park


  • Brianna Lindsay - University of Maryland School of Medicine
  • Joseph Paulson - University of Maryland, College Park

Interactive data exploration

  • An interactive visualization of the data underlying our study is available through Epiviz here.

Principal Investigators

Students and Postdoctoral researchers: