Microbiome research has had considerable success in analysing the molecular composition of microbial communities in the human body. Analyses of the gut microbiome in particular have found many associations between microbiota composition and human health or disease states. A recent focus has been on the connections between gut microbiota and human behavioural states. Links have been made repeatedly between microbiota composition and host disorders such as anorexia, autism, anxiety and depression. Microbiota even appear to have effects on general cognition and memory, both positive and negative. Some strong interpretations have been made of these findings, including claims that microbiota control behaviour in the same way puppeteers control puppets, or that microbiome findings are the final nail in the coffin of ideas about free will. I’ll discuss these claims in light of several broad problems in microbiome research, to do with causality, normality, and our evolutionary relationships with our microbes. I have presented my views on these issues to scientists, but not to philosophers. What I’m hoping for is feedback about how to develop my analysis of this field for a more philosophical audience.