Oleg Paliy, Vijay Shankar and Marketa Sagova-Mareckova
from: Bioinformatics and Data Analysis in Microbiology (Edited by: Özlem Taştan Bishop). Caister Academic Press, U.K. (2014)
Environmental microbial communities are known to be highly diverse, often comprising hundreds and thousands of different species. Such great complexity of these populations, as well as the fastidious nature of many of the microorganisms, makes culture-based techniques both inefficient and challenging to study these communities. The analyses of such communities are best accomplished by the use of high-throughput molecular methods such as phylogenetic microarrays and next generation sequencing. Phylogenetic microarrays have recently become a popular tool for the compositional analysis of complex microbial communities, owing to their ability to provide simultaneous quantitative measurements of many community members. This chapter describes the currently available phylogenetic microarrays used in the interrogation of complex microbial communities, the technology used to construct the arrays, as well as several key features that distinguish them from other approaches. We also discuss optimization strategies for the development and usage of phylogenetic microarrays as well as data analysis techniques and available options read more ...