The brain is the most complex object in the known universe so how could it be reacting to bacteria in the gut?
One route is the vagus nerve, it's an information superhighway connecting the brain and the gut.
Bacteria break down fibre in the diet into chemicals called short-chain fatty acids, which can have effects throughout the body.
The microbiome influences the immune system, which has also been implicated in brain disorders .
There is even emerging evidence that gut bugs could be using tiny strips of genetic code called microRNAs to alter how DNA works in nerve cells. At Cork University Hospital, Prof Ted Dinan is trying to uncover what happens to the microbiome in his depressed patients.
A good rule of thumb is a healthy microbiome is a diverse microbiome, containing a wide variety of different species living all over our bodies.
Prof Dinan says: "If you compare somebody who is clinically depressed with someone who is healthy, there is a narrowing in the diversity of the microbiota. "I'm not suggesting it is the sole cause of depression, but I do believe for many individuals it does play a role in the genesis of depression." And he argues some lifestyles that weaken our gut bacteria, such as a diet low in fibre, can make us more vulnerable.