The past few years have shown how the bacteria that reside in our gut are more than just docile passengers. From helping our bodies to actively fight other, disease-causing microbes to even altering our mental health, they play an active and crucial role in maintaining our health.

Now, new research is revealing how these microscopic riders could be having an even deeper impact on us, by actually controlling the genes in our cells, and possibly helping us fight cancer in doing so.

Published in the journal Nature Communications, the study highlights how the chemicals produced by the bacteria in our gut as they break down food can physically change the location of certain chemical markers that stick to our genome, thus potentially changing gene expression.

“Our intestine is the home of countless bacteria that help in the digestion of foods such as plant fibres,” explained study leader Dr Patrick Varga-Weisz in a statement. “They also act as a barrier to harmful bacteria and educate our immune system. How these bugs affect our cells is a key part of these processes.”

By studying mice that had lost most of their microbiome – the term used to describe the microbial community found in the gut – the researchers were able to show how the bacteria responsible for breaking down fruit and vegetables also alter gene expression in the cells that line the gut wall.

It turns out that these micro-organisms also release a specific short-chain fatty acid. This molecule moves from the bacteria into our own cells and increases the number of genetic markers known as crotonylations, which are a subgroup under the more widely known epigenetic markers. They found that the fatty acids achieved this by shutting down the activity of a protein called HDAC2, and that mice lacking any gut bacteria contained more of this protein than normal.

“Short-chain fatty acids are a key energy source for cells in the gut but we've also shown they affect crotonylation of the genome,” said first author Rachel Fellows. “Crotonylation is found in many cells but it's particularly common in the gut.”

This study, therefore, goes some way into helping explain why having a healthy and balanced diet, one that promotes the fostering of “good” bacteria in our gut, can also help cut our risk of cancer.