Microarray-based amplification product detection and identification

Abstract

Microorganisms play important roles in ecosystem functioning in both the environment and within host organisms. However, the diversity of microbial communities (an estimated 2,000-50,000 microbial species per gram of soil) [1-4] and the human intestine is estimated to contain at least 500 phylotypes [5], and their mostly unculturable status (>99 % [6-8]) make them difficult to study. As such, culture-independent approaches are essential to study even a fraction of microorganisms in the environment. Microarrays can examine tens of thousands of genes at one time in a simple, rapid, high-throughput, and parallel manner, making them ideal for the study of microbial communities. Microarrays can also provide quantitative information if amplification of target DNA is not required prior to analysis. Due to the large amount of data generated from each array, array-based analyses can be more cost-effective than other molecular methods. In addition, arrays are an ideal tool for comparing microbial communities from different sites, conditions, or times since samples are interrogated against a defined set of genes or microorganisms contained on the array. These features make microarrays excellent tools for assessing microbial community structure, functions, activities, and dynamics in natural settings. This chapter discusses various types of arrays and their applications to issues of clinical interest.