“…Such advances require the development of theoretical and conceptual frameworks such as those discussed in §3 to drive hypothesis generation and predictions that can be tested through the careful design of empirical studies. The field of microbiome research therefore transcends disciplines, as exemplified by the diversity of methodological and analytical approaches described in the contributions to the special feature, including mathematical modelling [9,[16][17][18], DNA and RNA sequencing [7,10,14,18], flow cytometry [14], infection tests in model and non-model pathosystems [7,18], physico-chemical and volatile analysis [7], and measures of hormone activity to assess host physiological responses to its environment [10]. A major theme pervading this special feature is the link between mathematical model simulations and empirical studies [9,11,16,17].…”