Human microbiome: Diet, precision medicine and wellbeing

Conor Purcell talks to Dr Harriet Schellekens of APC Microbiome Ireland

Over the past decade, research into the nature of the human microbiome has undergone a revolution, accompanied by much publicity. We now know this vast network of hundreds, if not thousands, of species of microbes that live in our bodies, operate together via a complex ecosystem of processes.

Scientists are now beginning to understand how interactions between these bacterial species may be contributing to not only our physical health – or illnesses – but also to our mental wellbeing.

Recent books authored by leading researchers in the field – including Gut Feelings, published earlier this year, and The Psychobiotic Revolution, by a team at the world-leading APC Microbiome Ireland research centre at University College Cork – have helped bring new results from this emerging field to the public.

Dr Harriet Schellekens is a researcher at APC Microbiome Ireland who has a particular interest in the relationship between the human microbiome and mental health.


Conor Purcell: What does a healthy microbiome look like?

Dr Harriet Schellekens: A healthy microbiome is definitely a diverse microbiome, which includes many different species and different strains, from a variety of sources. The composition of your microbiome can change – its diversity can change – and not only in the abundance of one particular strain, but across different microbes.

Essentially, the more you have, the better. What we have found is that in order to maintain healthy populations of all these different microbes, a diverse and varied diet is required.

I always like to use the analogy of a village. You know, if you have a village, you need a baker, you need supermarkets, locksmiths, teachers, and a whole bunch of other people and services. Usually, if you miss one of these, the society can breakdown, or at least begin to function poorly. Just look at life during the pandemic without schools functioning.

So, it’s the same with our microbiome, you need to have all these different components – multiple different microbes – that carry out different functions and interact with each other on a variety of levels. And to do that we need to feed ourselves properly.

How can we achieve a healthy microbiome through our diet?

Basically, we need to eat a diet with a large variety of natural foods. Looking at the scientific literature, it is now absolutely clear that processed foods are just terrible for us. And while some processed foods may contain fruits and vegetables, they are not present in the way nature intended. The act of processing foods takes away their beneficial qualities.

In addition, high-fibre diets are perfect for our microbiome, as digestible fibres can reach all the way to the large intestine, where we have the majority of our microbes. So we are talking about unprocessed foods again – fruits and vegetables are absolutely full of natural fibres.

It has also become absolutely clear that eating too much meat, especially red meat and processed meat like sausages and burgers, is a big problem. Processing implies the presence of a lot of additives, which just aren’t good for your microbiome. I think vegetarianism has a dual function, firstly contributing to good gut health, and therefore overall health, and secondly contributing to the health of the planet, through sustainability.

What is the link between the microbiome and mental health?

At APC we have been looking at mechanisms, or pathways, by which the microbiome can alter our brain function, potentially improving cognitive function, and also reducing anxiety and depression.

One particular interest of mine is stress eating, which is really interesting in the context of the pandemic, because we think that many people have began to eat more and put on weight. We know there’s a strong link between stress, mood, and food intake.

So we are trying to investigate the mechanisms which specifically drive that, asking questions like can the presence of specific microbes alter the way we perceive rewarding foods. Are there specific microbes that change our food intake behaviour, and change the desire for certain foods, ultimately determining our food choice and dietary decisions?

So you are suggesting our microbiome can alter our decision-making?

Yes, we think so. This is at the cutting edge of our research. What we’re trying to investigate is the relationship between the presence of certain microbes, food choice, and mood.

It is a complex topic, with a lot of variables, because our behaviour is influenced by lots of different factors, including our own genetics. We are not saying that the make-up of the microbiome alone determines how we make dietary choices – our dietary choices are also influenced by visual cues in our day-to-day lives – but we think it may have an impact.

For example, we know there are bacteria in our microbiome that have very strong, potent effects on specific mechanisms. So we now think it might be possible to identify microbiome communities, or specific probiotic strains, that can make you make healthier food choices, and reduce your stress levels. If we could identify that and be sure about it, wouldn’t that be something that people might want?

What prospects are there in the future for precision medicine targeting individual microbiomes?

There was a recent study on a collection of obese human individuals where they gave supplementation of inulin – which can be found in leeks and chicory by the way – which showed positive effects on emotional competence and cognitive flexibility. What was really interesting was that some of the individuals responded well, and some did not. We are interpreting this to suggest that the baseline microbiomes for these individuals were completely different, meaning the supplementation worked depending on the composition of the individual microbiome during the study.

So, via studies like this, our knowledge is rapidly accumulating, and this particular study reinforced the connection between the composition of the individual microbiome and mental health.

Essentially, based on which microbes exist – which people live in the village – we may be able to determine what kind of response to expect from stimulation through supplementation. We need to tease out which stimuli work with which compositions of microbiome. There is a long road ahead, but we are hopeful that this direction will eventually form some kind of precision medicine targeting individual microbiomes.

Dr Conor Purcell writes about science, society and culture. He can be found on twitter @ConorPPurcelland some of his other articles at