Our gut houses the microbiological equivalent of a large biodynamic vegetable patch that has a profound effect on our health. The old adage “You are what you eat”, could perhaps be, “You are what you grow in your gut garden”. Our gut microbiome, is the 1000 or so species of microbe that are normally present for most of our life. Our microbiome is a bit like our genome in that each of us has a unique microbiome and it encodes basic properties that influence our health and well-being. A key difference is that we acquire our genome more or less instantaneously at conception and are stuck with it for life. In contrast we acquire our microbiome over a far more protracted period and it is more malleable – for good or for bad. Studies comparing the microbiome of healthy and sick people have revealed a wide range of metabolic, immunological and even neuropsychiatric conditions where a dysfunctional microbiome is part of the underlying problem. We are exploring forces that shape host-microbiome interaction in mouse and human models with a view to developing intervention strategies across a range of such dysbioses. A systematic exploration of nutrient intake in mice has shown that feeding behaviour and diet composition interact to alter microbial community composition in a predictable fashion. Our model is that the nutritional landscape sets a framework in which host-microbe interactions that lead to pathophysiological outcomes including visceral inflammation and metabolic dysfunction occur. This gives rise to two basic, and synergistic, opportunities for improving healthcare in diseases involving dysbiosis: Microbiome profiling to provide diagnoses that inform personalized intervention strategies, and; Modulation of host-microbiome interaction to improve health.