Investigation of the intestinal microbiota in preterm infants using different methods

• Published in: Anaerobe 2010-08, Vol.16 (4), p.362-370
• Main Authors: Rougé, Carole, Goldenberg, Oliver, Ferraris, Laurent, Berger, Bernard, Rochat, Florence, Legrand, Arnaud, Göbel, Ulf B., Vodovar, Michel, Voyer, Marcel, Rozé, Jean-Christophe, Darmaun, Dominique, Piloquet, Hugues, Butel, Marie-José, de La Cochetière, Marie-France
• Format: Article
• Language: English
• Subjects: 16S rRNA gene library; Biodiversity; Birth Weight; Culture; dHPLC; DNA Fingerprinting - methods; Electrophoresis, Polyacrylamide Gel; Feces - microbiology; Gastrointestinal Tract - microbiology; Humans; Infant, Newborn; Intensive Care Units, Neonatal; Metagenome; Microbiota; Nucleic Acid Denaturation; Premature Birth; Preterm infant; Sequence Analysis, DNA - methods; TTGE
• ISSN: 1075-9964; 1095-8274
• DOI: 10.1016/j.anaerobe.2010.06.002

Modifications in microbial colonization of the human gut are believed to affect intestinal homeostasis and increase the risk of gastrointestinal diseases. The present study examined different methods for investigating the dynamic characterization of the intestinal microbiota in preterm infants. Fecal samples were collected weekly from ten preterm infants during their stay in a neonatal intensive care unit. The infants had a mean gestational age of 29 weeks (range: 28–32 weeks) and a mean birth weight of 1233 g (range: 935–1450 g). Bacterial colonization was assessed using conventional culture techniques and molecular biological methods. More specifically, the recently developed denaturing high performance liquid chromatography (dHPLC) technique was compared to established methods such as temporal temperature gradient gel electrophoresis (TTGE) and rRNA gene library sequencing. Our results indicate that the gastrointestinal tract of preterm infants, born at a gestational age of less than 33 weeks, has a low biodiversity of mainly, culturable bacteria. Finally, dHPLC was evaluated in terms of speed, labor and sensitivity for its use as a tool to analyze microbial colonization in preterm infants. We found that this technique provided major improvements over gel-based fingerprinting methods, such as TTGE, that are commonly used for studying microbial ecology. As such, it may become a common analytical tool for this purpose.