Bacteria living in people’s guts have been linked with depression in a significant investigation into the controversial connection between microbes and mental health.

Scientists found two varieties of bacteria were consistently present at low levels in people with depression.

After first making the discovery in a group of more than 1,000 Belgian patients, the team then confirmed their findings in a separate group of a similar size.

The researchers also investigated substances produced by microbes in the gut that may have the ability to tamper with brain chemistry.

While the findings will need to be confirmed with further experiments, the team say their work should allow scientists to zoom in on the links between human gut health and mental illness.

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“The notion that microbial metabolites can interact with our brain – and thus behaviour and feelings – is intriguing, but gut microbiome-brain communication has mostly been explored in animal models, with human research lagging behind,” said Professor Jeroen Raes, a scientist at KU Leuven who led the study.

The researchers took data about microbes in faecal samples from people involved in the Flemish Gut Flora Project, and combined it with diagnoses of depression made by GPs.

They identified bacteria that correlated with mental health, and numbers of two groups in particular – Coprococcus and Dialister – were consistently low in depressed people, regardless of whether or not they had been taking antidepressants.

The researchers noticed similarities between the depleted bacteria in these people and previous subjects with Crohn’s disease, suggesting the microbes affecting intestinal inflammation and wellbeing could be related. Their results were published in the journal Nature Microbiology.

To understand how bacteria might be tampering with people’s minds, the scientists also studied the genes of over 500 gut bacteria and gauged their abilities to produce chemicals that affect the brain.

“Many neuroactive compounds are produced in the human gut. We wanted to see which gut microbes could participate in producing, degrading or modifying these molecules,” said PhD student and team member Mireia Valles-Colomer.

One example that emerged from their study was a correlation between people’s mental wellbeing and the ability of their microbes to produce a substance similar to human neurotransmitter dopamine.

“Evidence is now accumulating to support the intriguing notion that our gut digestive systems can have significant effects on our mood. This research provides further evidence of a link between the types of bacteria in our gut and depression,” said Professor Anthony Cleare, an expert at King’s College London who was not involved in the study.

“However, as the authors acknowledge, this study shows an association rather than a causal link. It could be that having depression changes the type of bacteria in the gut (for example via dietary changes) rather than changes in the gut bacteria causing depression.”

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To clarify these links, Professor Cleare said it was vital to undertake studies in which scientists test whether altering bacterial communities in the gut could directly affect mood and treat depression.