Key topics in the study of host-microbe interactions-such as the prevention of drug resistance and the exploitation of beneficial effects of bacteria-would benefit from concerted efforts with both mechanistic and evolutionary approaches. But due to differences in intellectual traditions, insights gained in one field rarely benefit the other.Here, we develop a conceptual and analytical framework for the integrated study of host-microbe interactions. This framework partitions the health effects of microbes and the effector molecules they produce into components with different evolutionary implications. It thereby facilitates the prediction of evolutionary responses to inhibition and exploitation of specific molecular mechanisms.
| INTRODUC TI ONMicrobes have profound effects on the health of their hosts, and host-microbe interactions are therefore subject to intense research from both mechanistic and evolutionary perspectives. Traditionally pursued in isolation, these lines of inquiry are now becoming increasingly intertwined (Bordenstein & Theis, 2015). This is especially so in the work on antibiotic resistance evolution, and the consequent search for molecular targets for evolution-proof drugs, including antivirulence therapeutics (Allen, Popat, Diggle, & Brown, 2014).Progress is hampered, however, by a lack of common conceptual ground; key concepts in one field, such as "virulence factor" in microbial pathogenesis research (Falkow, 1988(Falkow, , 2004 do not fit into the conceptual structure of the other, for example the trade-off paradigm in virulence evolution theory (Alizon, Hurford, Mideo, & Van Baalen, 2009) (because the former is focused on the mechanisms of host harm, whereas the latter disregards mechanism, and assumes relationships between host harm and pathogen fitness). This is unfortunate because pressing public health challenges, most notably antibiotic resistance, are complex and have several aspects that are studied in both fields.The aim of this paper is to lay a foundation for a common conceptual framework for host-microbe interactions, in which mechanistic and evolutionary traditions can be integrated. To this end, we combine the analytical approach of resistance-tolerance theory in evolutionary ecology (Råberg, Sim, & Read, 2007) with the experimental strategy for identifying virulence factors in microbial pathogenesis research (Falkow, 1988). Whilst most commonly applied to pathogens in acute infections, this type of experiment can identify a range of molecules that impact host health, whether the effect is detrimental or beneficial, the microbe obligate or opportunistic, and the condition acute or chronic. And we intend our analysis to be equally broad. The framework we propose is visual and intuitive, but it also has a simple statistical formalization based on generalized linear models, which makes it flexible and open for further developments.In the main text, we develop the concepts and their implications under the assumption that the microbe's health effect and fitness are linearly relat...