Model organisms are an important tool for the development and validation of analytical approaches for proteomics and for the study of basic mechanisms of biological processes. The Initiative on Model Organism Proteomics (iMOP) organized a session during the 11th HUPO world congress in Boston in 2012, highlighting the potential of proteomics studies in model organism for the elucidation of important mechanisms regulating the interaction of humans with its environment. Major subjects were the use of model organisms for the study of molecular events triggering the interaction of host organisms with the surrounding microbiota and the elucidation of the complex influence of nutrition on the health of human beings.