Eukaryotes have evolved in the presence of microbial life and so it is unsurprising that microorganisms are functionally integrated with many aspects of animal biology. Research is revealing the numerous ways that the gut microbiome interacts with the host's central nervous system, influencing brain development, neurochemistry, emotion and social behaviour. This microbiome-gut-brain axis is bidirectional since the behaviour and emotional state of the host can in turn alter microbiome composition and function. This thesis investigates these two-way interactions between the gut microbiome and host behaviour at the molecular, organism, population and evolutionary levels. I demonstrate using animal models that the gut microbiome alters the expression of neuropeptide signalling pathways implicated in social and emotional behaviour, particularly in the frontal cortex. This is the first investigation into the effect of the microbiome on the brain's opioid system. In a large human cohort I find that sociability, neuroticism, anxiety and stress are related to differences in microbiome composition and diversity, revealing a microbial dimension to human personality. I also show in a non-captive macaque population that sociability is related to differential abundances of certain bacterial taxa. From an evolutionary perspective, I find evidence that a change in gut microbiome composition may have facilitated evolution of a larger brain and complex social behaviour. Finally, I apply evolutionary theory to the microbiome-gut-brain axis and argue against the emerging hypothesis that gut microorganisms manipulate host behaviour. This multilevel approach provides a holistic view of the microbiome-gut-brain axis, from neurogenetics, to personality, social behaviour and evolution of the social brain. Based on the novel insights from this research, I conclude that the gut microbiome is fundamental to our understanding of the mammalian brain, behaviour and evolution in ways not currently appreciated, but with implications for human psychology and well-being.