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. 2009 Jun;75(11):3572-9.
doi: 10.1128/AEM.02764-08. Epub 2009 Apr 10.

High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray

Oleg Paliy  1 , Harshavardhan Kenche, Frank Abernathy, Sonia Michail
Affiliations

High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray

Oleg Paliy et al. Appl Environ Microbiol. 2009 Jun.

Abstract

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.

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Figures

FIG. 1.
FIG. 1.
Linearity of signal ratio measurements. Expected signal ratios among different microarrays are plotted on the x axis, and observed signal ratios are plotted on the y axis. Signal value ratios for probe sets corresponding to four bacterial species hybridized to the arrays were averaged (arithmetic means). Error bars correspond to standard deviations of signal ratios among different probe sets. The trend line represents the best fit of the linear model y = ax + b to the average data. Parameter b was forced to 0.
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