 The rise of metagenomics is also linked to other changes in biological sciences more generally, especially the rise of systems biology starting around the year 2000 (which is itself closely linked to the development of genomics since the 1990s). O’Malley and Dupré (2005) point out that there is an important distinction to be made when looking at fields like systems biology, because there is not only a change in epistemology but also one in ontology. They therefore distinguish between pragmatic and systems-theoretic biologists. For the former, the idea of a ‘system’ is merely an epistemic tool. For the latter, the system becomes the new fundamental ontological unit. Doolittle and Zhaxybayeva (2010) claim that the same can be seen in metagenomics where there is a drive to see the community or the ecosystem as the new fundamental unit, and not the single species (see also Dupré &amp; O’Malley 2007).