There is one approach to environmental sampling that circumvents the need for prior knowledge of the relevant ecological parameters. This is to use metagenomes to biotically characterize environments by the contents of their bacterial communities [16]. For example, Arumugam et al. [17] characterized human gut communities and classified them into three ‘enterotypes’ according to species composition and abundance, as well as functional aspects of the communities. Thus, without having to know ahead of time the environmental parameters by which ecotypes have diverged, one could test whether hypothesized ecotypes of a particular taxon are different in their associations with these enterotype communities. Likewise, a community analysis of various freshwater beach and surface water communities might reveal cryptically different bacterial community types, and one could then test whether the environmental ecotypes of Escherichia are significantly different in their community-type associations.