Developing a philosophical foundation for the study of the microbial side of symbiosis

Symbiotic associations have been studied extensively in recent years, focusing mainly on the potential benefits to the host. However, understanding the role played by microorganisms in the physiology and fitness of the host, an aspect of the subject that had been neglected for a long time, has now become an important goal of symbiotic studies. Among the interesting philosophical questions are the following: how should we study the impact of symbiosis on the fitness of symbiotic microorganisms? What framework should scientists use, and on what philosophical assumptions should such research be based? In other words, when does comparing fitness make sense? In this paper, I develop such a framework, and argue that these requirements comprise: (i) phenotypically similar individuals put in the same (ii) sub-environment and contrast it with another popular approach. Finally, I apply this to the symbiosis between the Euprymna scolopes squid and Vibrio fischeri bacteria to show how scientists should evaluate the fitness of symbiotic microorganisms.