After first gaining an understanding of “who’s there” generally using diversity-based surveys targeting the small subunit (SSU) ribosomal RNA (rRNA) gene, these microbiomes are then often examined as ...After first gaining an understanding of “who’s there” generally using diversity-based surveys targeting the small subunit (SSU) ribosomal RNA (rRNA) gene, these microbiomes are then often examined as a whole or in smaller units to understand the function of the cells, the nature of the associations and ultimately gain insight into the role of the microbiome in animal health, physiology, ecology, and behavior (Ezenwa et al., 2012; McFall-Ngai et al., 2013).