8.8. Metagenomics

Metagenomic approaches began as an attempt to study the functional significance of all organisms in a habitat, and the term was first used to describe soil microbes and their collective proteins (Handelsman et al., 1998). In honey bees, usage has so far focused on identifying pathogen taxa (Cox-Foster et al., 2007; Runckel et al., 2011, Cornman et al., 2012) and, more recently, on targeted surveys of bacterial associates in honey bee guts (Martinson et al., 2011; Mattila et al., 2012). There are six key decision points in metagenomic surveys and, rather than choose any specific recipe, we will instead list those decisions and their outcomes: