Fig. 3

Network architecture for the hosts (top) level. Three main places describe the health states the microbiotas can assume: the non-resistant (in green), mildly resistant (in yellow) and severely resistant (in red) states respectively (a). Transitions can move microbiota tokens, each having the network structure from Fig. 4, to the next place. The state of non-resistance holds two microbiota tokens depicted in a compact form, i.e., with their name only. This happens according to the value of their point prevalence score which a synchronous channel (d) reads from networks at the lower level, possibly taking the relative microbiota to the next step along resistance progression (the structures in e track the changing numerosity of microbiota instances in each place). Synchronous channels take care of the antibiotic administration and microbiota integration events (b), activating network structures at the lower level (Fig. 4b and f, respectively) according to time delays and number of microbiota instances injected in the network by the dedicated structure (c)