Applications of Phylogenetic Microarrays to Profiling of Human Microbiomes

Human-associated microbial communities are known to be highly diverse, comprising between hundreds and a thousand species, depending on the body area. The sheer numbers of species as well as the fastidious nature of most of these organisms make culture-based techniques both inefficient and challenging to study these communities. As a result, 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 data for many community members. This chapter will focus on currently available phylogenetic microarrays for the interrogation of human-associated microbiota, the technologies used to construct the arrays, as well as several key features that distinguish them from other approaches. We will also discuss optimization strategies for the development and usage of phylogenetic microarrays as well as opportunities to complement microarray analysis with other techniques. 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 (Belenguer et al., 2006; De Vuyst and Leroy, 2011; Duncan et al., 2004; Flint et al., 2008). The sheer complexity of such networks and the difficulty involved in culturing the members of these communities have challenged researchers who have tried to gain a clearer understanding of these interactions. Significant progress has been achieved recently in the study of microbial communities that inhabit the various niches of the human body. These microbial consortia, usually referred collectively as the human microbiota, have been estimated to harbour microbial cells ten times the number of human cells in the body, along with a cumulative microbial gene count that is approximately 100-fold larger than the human genome (Gill et al., 2006). Every exposed surface of the human body is colonized by a unique microbiota, including the mouth, skin, respiratory, gastrointestinal, and genitourinary tracts (Costello et al., 2009). Renewed interest in the human microbiota is associated with the recognition of the important relationships these microbes form with our bodies. For example, microbiota of the gut participate in host energy metabolism by breaking down complex polysaccharides in the diet. Human associated microbes also protect the host from pathogen invasion through competition for resources or directly by inhibiting pathogen growth. Moreover, microbiota modulate the proper development and