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Applied and Environmental Microbiology, June 2009, p. 3572-3579, Vol. 75, No. 11
0099-2240/09/$08.00+0     doi:10.1128/AEM.02764-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

High-Throughput Quantitative Analysis of the Human Intestinal Microbiota with a Phylogenetic Microarray{triangledown}

Oleg Paliy,1* Harshavardhan Kenche,1 Frank Abernathy,3 and Sonia Michail2,3

Department of Biochemistry and Molecular Biology,1 Department of Pediatrics, Boonshoft School of Medicine, Wright State University, Dayton, Ohio,2 Dayton Children's Hospital, Dayton, Ohio3

Received 4 December 2008/ Accepted 29 March 2009

Gut microbiota carry out key functions in health and participate in the pathogenesis of a growing number of diseases. The aim of this study was to develop a custom microarray that is able to identify hundreds of intestinal bacterial species. We used the Entrez nucleotide database to compile a data set of bacterial 16S rRNA gene sequences isolated from human intestinal and fecal samples. Identified sequences were clustered into separate phylospecies groups. Representative sequences from each phylospecies were used to develop a microbiota microarray based on the Affymetrix GeneChip platform. The designed microbiota array contains probes to 775 different bacterial phylospecies. In our validation experiments, the array correctly identified genomic DNA from all 15 bacterial species used. Microbiota array has a detection sensitivity of at least 1 pg of genomic DNA and can detect bacteria present at a 0.00025% level of overall sample. Using the developed microarray, fecal samples from two healthy children and two healthy adults were analyzed for bacterial presence. Between 227 and 232 species were detected in fecal samples from children, whereas 191 to 208 species were found in adult stools. The majority of identified phylospecies belonged to the classes Clostridia and Bacteroidetes. The microarray revealed putative differences between the gut microbiota of healthy children and adults: fecal samples from adults had more Clostridia and less Bacteroidetes and Proteobacteria than those from children. A number of other putative differences were found at the genus level.

* Corresponding author. Mailing address: 260 Diggs, Department of Biochemistry and Molecular Biology, Wright State University, 3640 Col. Glenn Hwy., Dayton, OH 45435. Phone: (937) 775-3714. Fax: (937) 775-3730. E-mail: oleg.paliy{at}wright.edu

{triangledown} Published ahead of print on 10 April 2009.

Applied and Environmental Microbiology, June 2009, p. 3572-3579, Vol. 75, No. 11
0099-2240/09/$08.00+0     doi:10.1128/AEM.02764-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Resta, S. C. (2009). Effects of probiotics and commensals on intestinal epithelial physiology: implications for nutrient handling. J. Physiol. 587: 4169-4174 [Abstract] [Full Text]  


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