 It is then the composition of functional elements that the community as a whole contains which is preserved over evolutionary time. And the community could be seen as an assembly of biochemical activities and not of distinct microbial lineages (see for instance Turnbaugh et al. 2009 and also Burke et al. 2011). The metagenome then becomes a ‘genome of communities’ and not a ‘community of genomes’ (Doolittle &amp; Zhaxybayeva 2010). All of this also feeds into the more general, and currently very active, discussion about the problem of individuality in biology (Clarke 2010; Bouchard &amp; Huneman 2013; Ereshefsky &amp; Pedroso 2013; Guay &amp; Pradeu 2015; SEP entry on  the biological notion of individual).