Homeostasis is the ability of a system to regulate its state - it is not always a good thing. Our gut microbiome profoundly influences our normal physiology through a variety of mechanisms. This is not simply a one-way effect, or something microbes ‘do to us’, rather our microbiome is part of us and the microbial community state is interdependent with our systemic body state. In chronic disease the concept of dysbiosis is that our body (including its microbiome) has adopted a stable state that is undesirable. Dysbiosis is different to other disease states in that it does not have a cause per se, but is an emergent state derived from interplay between many different factors. In managing dysbioses, two critical factors in this interplay are diet and microbial history. There is now abundant evidence that changes in our food environment and influence on early life microbial dynamics have sufficiently altered the nature of microbiome-human relationships in modern society to change patterns of public health. Chief among these are the emergence of a suite of nutrition-related diseases that include diabetes, obesity, and allergies and the prevalence of multiply antibiotic resistant bacteria in nosocomial infections. I will give an overview of the ways in which diet patterns and food components can shift the state of the human system to increase risk of dysbiotic diseases, highlighting key mechanisms we have identified in these processes.