Phylogenetic Microarrays

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. Introduction Microbes inhabit diverse environments. Some of these environments include the human intestinal tract and skin, soil, roots, leaf and bark surfaces of plants, ocean waters, deep see vents, and air. The ecosystems of such environments are populated by communities of microorganisms, rather than by individual species, and often contain hundreds and even thousands of different microbial members. Many of these communities play pivotal roles in ecosystem processes such as energy flow, elemental cycling, and biomass production. Energy and nutrients in these systems are processed by intricate networks of metabolic pathways through multiple community members (Duncan et al., 2004; Belenguer et al., 2006; Flint et al., 2008; De Vuyst and Leroy, 2011). The sheer complexity of such networks and the difficulty involved in culturing the individual members of these communities have challenged researchers who have tried to gain a clearer understanding of these interactions. Recent advances in molecular technologies have significantly simplified the analysis of these communities because they remove the need to culture and grow community members individually. Some of the currently available molecular techniques include highthroughput sequencing (discussed in chapter 8 of this book), terminal restriction fragment length polymorphism (discussed in Chapter 6), chequerboard DNA–DNA hybridization, quantitative real-time PCR, fluorescence in situ hybridization, and phylogenetic microarrays. Phylogenetic interrogation of small subunit ribosomal RNA (SSU rRNA) molecules using these techniques has led to considerable progress in our understanding of community structure and dynamics of various microbial ecosystems (Suau, 2003; Sekirov et al., 2010). Phylogenetic microarrays, one of the more popular choices among these techniques, have been successfully used to quantitatively profile a variety of microbial communities, including the gastrointestinal tract, sewage sludge, soil, and air (Brodie et al., 2007; Nemir et al., 2010; ValMoraes et al., 2011; Rigsbee et al., 2012). Phylogenetic Microarrays