The human gastrointestinal tract is colonized by a diverse microbial community of at least 400 bacterial species, with 30–40 species accounting for 99% of the total microflora [1–3]. Interest in the intestinal microflora has been stimulated by concern over the safety implications of antibiotic resistant bacteria in foods [4,5], fecal contamination of foods, effects of diets, food additives and veterinary drug residues [8,9] on the intestinal ecosystem, and the use of probiotics in the treatment and prevention of gastrointestinal disorders. Indigenous intestinal microfloras play important roles because they aid in the digestion of food, metabolize endogenous and exogenous compounds, produce vitamins and other essential nutrients, and help prevent pathogens from colonizing the gastrointestinal tract [11–14].
Traditionally, the population of anaerobic bacteria in the human gastrointestinal tract was characterized by microscopic, biochemical, physiological, and selective culture plating methods of fecal samples from human subjects [1,3]. In recent years, a variety of molecular techniques have been used to analyze the bacterial community in human fecal samples [10,15–19]. Molecular analysis can detect perturbations in the human intestinal microflora in a rapid and precise manner [6,20]. Previously, we developed polymerase chain reaction (PCR) methods for the detection and quantitation of predominant anaerobic bacteria in human and animal feces [21–23]. Although these investigations provided useful data, one of the limitations of our methodology was that we had to test for each bacterial species separately. Microarray technology is a powerful tool that can be used for simultaneous detection of thousands of genes or target DNA sequences on one glass slide [24,25]. Most studies using microarray methods are on gene expression. However, microarray method can also be used for the detection of bacteria and DNA-based typing of specific pathogenic bacterial strains [25,26]. The purpose of this study was to design and evaluate a microarray method for the detection of predominant bacterial species from human fecal samples.