Understanding the gut microbiome and lifestyle medicine

Understanding the gut microbiome and lifestyle medicine
© iStock/PeopleImages

Dr Sheena Fraser and Dr Siobhan McCormack discuss the vast and impactful workings of the gut microbiome and why the Lifestyle Medicine approach is integral to improving patient care.

The pillars of good health are something the majority of us are aware of. We know that we ‘should’ prioritise sleep, exercise regularly and eat a healthy, balanced diet, however, the barriers to such interventions often come down to a lack of understanding around the ‘why’ and ‘how’. For a long time, these barriers have also been compounded by approaches to care which entail a narrative that very often seems restrictive or finite, leaving little in the control of the patient. A discipline that seeks to shift this perspective and advocate lifestyle modalities in tandem with, or in place of, pharmaceutical interventions where necessary is Lifestyle Medicine. This evidence-based approach supports sustainable behavioural changes that optimise mental and physical wellbeing. A novel but key component within the field of Lifestyle Medicine is microbiome science, more specifically, how our gut microbiome can impact our overall health and susceptibility to chronic disease.

Drs Sheena Fraser (SF) and Siobhan McCormack (SMc) are members of the British Society of Lifestyle Medicine (BSLM) whose fascination with microbiome science has not only impacted the way they practice medicine but led them to devise an in-depth course where they teach other clinicians about the connection between gut microbes and our overall health. Lorna Rothery spoke to them about the vast influence that the gut microbiome has, current areas of research, and the benefits of integrating Lifestyle Medicine into clinical practice.

Can you give a brief overview of what the gut microbiome is?

SMc: Microbes exist on every surface on Earth including on our skin and in all the cavities of the human body, anywhere there is exposure to the Earth. Your gut is a wonderful epicentre of microbes, of which most are bacteria but can also be archaea and fungi.

The community of microbes in a given location, together with their surrounding habitat, constitute the microbial biome or ‘microbiome’ for short.

The gut runs from mouth to anus so technically the term ‘gut microbiome’ includes all the resident microbes (plus their genes and surrounding structures) anywhere along the intestine. In practice, the ‘gut microbiome’ usually refers to the bacteria in the large intestine (aka ‘colon’). Why? Because the colon is your most densely populated microbiome, and most microbes are bacteria. Interestingly, the colon is one of the most densely populated microbial habitats on earth.

Most human microbiome research to date has focused on the bacteria in the large intestine, but increasingly researchers are turning their attention to the microorganisms (such as fungi) and the other body sites (such as the skin, vagina, and mouth).

Every day the gut microbiome influences many aspects of your biology including how you digest and metabolise food, absorb minerals and process xenobiotics, such as pesticides, chemicals, and medications. Importantly, your gut microbiome is very modifiable depending on factors such as sleep, activity, and stress. What you eat is key. Changing your diet can rapidly change the composition of your gut microbiome and therefore how it functions.

SF: Everyone’s microbiome is unique; it is influenced by many different factors including your lifestyle, birth mechanism and exposure to nature. We all ‘give off’ our microbiomes as well – what we refer to as our microbial cloud – and those microbes come from our mouths, noses, skin etc. This microbial cloud is unique to us like a fingerprint.

What sparked your interest in Lifestyle Medicine and microbiome science and how has it impacted your own lifestyle and the way you practice medicine?

SF: It has been an enormous revelation for me over the last few years; I use microbiome science every day in my clinical work. I am talking to patients about their microbiomes when I am prescribing antibiotics and discussing chronic diseases; I am introducing ideas about diet to people with depression. I have had an incredibly positive response from colleagues who were initially quite anxious about me doing this but now they are making changes in their own lives, and actually referring patients to me. I advocate a whole food plant-based diet and encourage people to steer clear of nasty processed foods, and by doing so, we have reversed loads of diabetics in our practice.

I think I have always been a lifestyle medic; I grew up with parents who were very interested in good personal health, and I was taught from a very early age about the importance of good farming techniques, eating well, exercise and sleep. All these things were fundamental to my upbringing, and I have always realised that I owe a lot of my health to that upbringing. When I discovered Lifestyle Medicine back in 2018, suddenly, I just felt like I had met my tribe. Having felt in the medical profession like I was a bit of an odd one out, this really permitted me to be the lifestyle medic that I always thought I was. I promptly did the Lifestyle Medicine diploma and became a fully-fledged member of the British Society of Lifestyle Medicine.

I subsequently attended a conference where there was a talk on the microbiome, I had never heard of it before and was absolutely stunned by this talk because so much of my medical knowledge up until that point had not made sense. When you talk about autoimmune conditions, for example, nobody could tell me why anybody got an autoimmune condition. The more I found out about the microbiome, the more I realised that this really could be a massive missing link in our health, and it has certainly, I think, proven to be that.

SMc: My upbringing was very different to Sheena’s. I grew up in the 70s and 80s at the onset of the era of ultra-processed foods. My parents ran an elderly care home at the time and thought everything new was brilliant. They were very forward-thinking in many ways, and they really grabbed new opportunities. They believed convenience foods were modern and time-saving, and this made sense when running a business. Back then, ultra-processed foods were seen as a scientific advance, a way of feeding people well without the ‘hassle’ of cooking from scratch. At that time people were unaware of all the negatives associated with these products. We now know that highly processed, high-fat, high-sugar foods containing many additives, artificial sweeteners and emulsifiers wreak havoc on your gut microbes.

In 2018, I started looking into Lifestyle Medicine and read a few classic books such as Matthew Walker’s Why We Sleep. I was intrigued by the huge potential impact of lifestyle modalities on health outcomes, and the advances in the science in the last two decades is staggering. For instance, the evidence base behind the multiple health benefits of physical activity and how it works at the molecular level is now substantial and incontrovertible. The same goes for sleep, nutrition, and the health benefits of social connectivity.

The gut microbiome is yet another aspect of our biology that affects everyone, including all healthcare professionals as well as the people they are trying to help.

I find when I discuss lifestyle changes with patients, they often look relieved because they were dreading ‘yet more medications’ to be the first port of call and while these do have their place, there is so much that can be achieved by making small, simple, regular lifestyle changes.

How much do we know about the ways in which the microbiome influences the development of chronic diseases?

SMc: There are trillions of microbes residing in our gut and they are active participants in every aspect of our health and wellbeing. This dynamic metropolis within our colon is active 24/7, messaging all our organs, tissues, and cells and then receiving messages back through numerous pathways including the nervous system, immune system, and endocrine system. In the early life stages, the development of your immune system, tissues and organs is heavily influenced by your gut microbiome; 70% of your immune cells live within the gut. The enteric nervous system (dubbed our second brain) extends along the digestive tract and is in constant communication with all other cells and tissues in your body through the gut-brain axis. This bi-directional communication also seems the case for other organs such as the gut-lung axis and the gut-heart axis.

Your fat and glucose metabolism are strongly influenced by the gut microbiome. If you have a low fibre intake, your microbes will not have the raw materials required to produce short-chain fatty acids, which are the metabolic by-products of bacterial fermentation. These are hugely important metabolites which are central to health.

SF: There is a relationship between diet and lifestyle in the Western world and the development of chronic disease. Microbiomes are unique, but trends are emerging between individuals with chronic diseases. For instance, scientists are now able to understand that individuals with bowel cancer might be lacking in certain gut organisms that help protect the gut including Prevotella and Bacteriodetes. We cannot say there is an absolute microbial signature yet, but we can say that some trends are emerging among chronic diseases. Of course, drug companies are keen to latch on to this because they are interested in producing probiotics that could be designed for chronic diseases.

SMc: Flooding the microbiome with a rich and diverse repertoire of beneficial bacteria that work in harmony can help protect us from all diseases. All chronic disease is related to the microbiome; there will be some reason in the microbiome for that chronic disease. As GPs, we refer people for operations, and we use medications, but we are also mindful of the potential impact that small changes such as diet, sleep, physical activity, and reduced exposure to harmful substances can have.

Inflammation is a central factor in many non-communicable diseases; reactions to toxic molecules or potential pathogens inside the gut then set off inflammatory reactions, which then send messages and cytokines everywhere. It is this low-grade chronic inflammation that seems to be central to not only diseases such as diabetes and obesity but also neurological conditions like Alzheimer’s. It is the central underlying pathology which connects all these diseases.

You both completed the Diploma in Lifestyle Medicine and co-wrote the ‘Gut Microbiome for Clinicians’ course, have you seen a growing interest in lifestyle medicine from other clinicians?

SF: Lifestyle Medicine is really expanding, exponentially in fact since I first discovered the discipline in 2018. I started doing lectures and workshops, and initially, I was getting a lot of raised eyebrows and comments that people did not have time for this so-called social prescribing. However, a few years back I took a group of trainees for a morning of Lifestyle Medicine, and they were so excited and interested in how they could integrate it into their practice. These were GP trainees in their first year, so it was really encouraging that they understood the importance of Lifestyle Medicine. Equally, the younger generation of doctors is more accustomed to reflecting on health and wellbeing, and what works.

In terms of the microbiome, I have seen a massive interest, not just from patients but other medics, too. Siobhan and I did a talk recently at the BSLM conference and it was one of the last sessions of the day which made us a little worried that no one would show, but actually, the room was packed. I think we are in a situation now where, certainly amongst the captive audience of lifestyle medics, there is a lot of interest, particularly from juniors. We need to harness it; we need to get this out to secondary care. There are still a lot of people who are less willing to be as interested but I do not think they realise yet the importance of Lifestyle Medicine.

We also co-wrote an in-depth course on the gut microbiome and though we started with the intention of writing something fairly simple, the more we learn, the more we realise that we have to explain this fully. The course comprises over 30 hours of study and explains the terminology and basics of microbiome science right the way through to the clinical application and the link between Lifestyle Medicine and the microbiome.

SMc: The Gut Microbiome for Clinicians course content could be adapted to suit the needs of a variety of specific groups. There appears to be a lot of interest from patients and members of the general public who want to know more about this fascinating subject.

I was invited to give a talk at short notice on behalf of a charitable organisation with expertise in mindfulness for chronic pain. The course co-ordinator, who runs monthly sessions, advertised the talk and was expecting six or seven people to show up. She was delighted but surprised when 60 people attended from all over the world. It was their largest turnout to date, and it was the subject matter that drew them in. They were curious and eager to learn about the connection between the gut microbiome and chronic pain. I was overwhelmed by the positive comments and it highlighted the importance of informing people about these new perspectives on the gut, inflammation, and health.

That is when Sheena and I decided to start ‘Microbiome Medics’ as a light-hearted and non-judgemental way to inform other clinicians and any other interested parties about this emerging area of health. In essence, we are two microbiome-obsessed medics who want everyone to hear about this brilliant new area of science. It links in perfectly with Lifestyle Medicine and we have a series of podcasts in the pipeline.

We are working in an underfunded and overworked NHS. Patients diagnosed with a chronic disease might expect one medication and suddenly find they are taking many more. As GPs, we are very evidence-based and diligently follow the guidelines. However, none of us feel great about adding more and more medications to a patient’s prescription. It is natural to start looking for other evidence-based options. The positive news is that so many lifestyle options have been extensively researched and are available to everyone for free.

Given the disparities in how chronic diseases develop in different parts of the world, will this hinder research and, in the future, how we integrate microbiome-based therapies?

SF: We have lost an incredible number of microorganisms in the Western world compared to people living a much more natural existence. A lot of these microorganisms we may never get back unless we take them in probiotic form.

There are practitioners out there who will take stool samples and analyse your gut microbiome. They can tell you about trends in your microbiome, whether you have more Bacteriodetes or Firmicutes and if there are certain organisms present associated with longevity or disease. But then, of course, you are only getting a snapshot from that patient at that time; if they changed their diet over the next few days they would get a very different snapshot of their microbiome and so we do not yet have signatures that would indicate the development of certain diseases. There will come a time when we can analyse people’s gut microbiota to determine how they will react to certain drugs, and that is a big area of research at the moment.

As far as I am aware, a plant-based diet is the only thing that will reverse heart disease, nothing else in the medical world that we have available to us will reverse the stenosis in your arteries. We have got very reliant on drugs, and drug companies have grown incredibly important, and far too powerful in my view. This has had an enormous impact on medicine and the way we practice as well as on the expectations of patients and doctors. I think we need to take a step back and consider the use of medications as second-line, not first-line, treatments. Of course, we always need our emergency drugs, but for the majority of people, it is incredible what you can do with lifestyle alone.

SMc: There is no one ‘healthy’ gut microbiome. Scientists have been unable to define what constitutes a ‘healthy’ microbiome because there are an infinite number of variations in the potential collection of microbes residing in any one gut and this microbial signature is unique to each of us. It is postulated that the high fat, high sugar, high ultra-processed foods typical of the Western diet could mean that many of us have a less health promoting balance of gut microbes (dysbiosis), and this is associated with an increased risk of many chronic diseases such as obesity and diabetes. Consequently, if we just analyse the gut microbiome composition from stool samples collected from those consuming a Western diet and take the average as ‘healthy’, we could be way off the mark. We do not have a ‘perfect’ measure to compare it to, so how do we know? Scientists such as the team at The Sonnenberg Lab are trying to investigate this issue by researching the gut microbiome composition of hunter-gatherer tribes and those still living in a traditional rural way. They found these groups have very different gut microbiome compositions to those of us living in modern societies.

Sheena and I are very keen to promote the benefits of healthy eating and other Lifestyle Medicine measures but there is a lot of interest in probiotics. We urge caution in this area. Probiotics are an exciting new proposition, but they need to be regarded in a similar way to new medications. We need the appropriate evidence base for using any given probiotic for a specified clinical indication, together with the effective dose, frequency, and duration. We do not want to inadvertently swap ‘Big Pharma’ for ‘Big Biotics’. Researchers in this field have extremely high standards of evidence to abide by and in getting a product approved is a complex process.

© iStock/Oleksandra Troian
There will come a time when we can analyse people’s gut microbiota to determine how they will react to certain drugs, and that is a big area of research at the moment

Microbiome Medics are represented on the Gut Microbiota for Health Expert Panel, a group of the top UK gut microbiome experts who discuss exciting research advances.

With Lifestyle Medicine, we can use the evidence that we have now to address lifestyle modalities. There is considerable research on exercise, sleep, nutrition etc, collated over the last ten to 20 years and the incredibly positive effects they have at the molecular level. We are lucky that we have chosen this area where we do not have to wait for RCTs. It is nice that people can benefit now using the data already available to us. We have a section in our course about citizen science and lots of people out there are interested and would like to be part of a project. There are lots of university departments carrying out small trials and the amount of data that you get from analysing even a few people’s gut microbiomes is absolutely astonishing. These projects increase awareness and people’s interest which, in turn, feeds back to other universities that are looking for funding and grants.

More widely, why is it important to consider planetary health alongside the gut microbiome?

SF: I am a member of the Soil Association, and I am a big advocate for going back to that whole-food level. If we do not support farmers to take care of our topsoil that is going to have a massive knock-on effect on our health in the future. We are already in a situation where over 75% of the world’s topsoil has been lost, and it is getting worse. The quality of our topsoil is so poor in this country that animals cannot even produce enough B12. Our farming techniques are heavily reliant on fertilisers and pesticides and a lack of crop rotation has massively damaged the soil; if we do not have good soil that impacts very negatively on our health.

SMc: The 2015 Lancet Commission on planetary health highlighted the intimate connection between human health and planetary health. The BSLM is committed to safeguarding the connections between human health and planetary health, which are closely intertwined, and the gut microbiome is central to this. Genetically, humans are 99% microbial and by cell numbers, about 50% microbial, which we think really changes the perspective we have of ourselves and certainly influences the way we practice medicine.

Would you like to make any further comments?

SF: My approach to living well is not benefiting pharmaceutical companies nor the biggest earners in this world, and so I do not expect there to be a huge amount of interest in what I am doing, sadly. However, I would like to see more medics move away from that overreliance on pharmaceutical companies and realise that actually, these whole foods work. They are incredibly powerful, and it is amazing what they do for our health. If you take a patient who is unwell with lots of chronic disease, and just markedly change their diet, the outcomes can be incredible; their kidney function returns, their cholesterol falls, their sugar levels fall, and there are massive improvements in their energy levels and sense of wellbeing. It allows them to have a better quality of life and do the things they want to do.

SMc: Lifestyle Medicine is ‘Us Medicine’ – it is the blueprint for how the human body works. The BSLM is made up of a diverse group of clinicians and healthcare professionals who have come to the same conclusion – that Lifestyle Medicine constitutes the very foundation of health and needs to be integrated into everyone’s life.

This does not mean that there is no place for medications and procedures. Medical advances such as antibiotics and vaccinations have saved many lives, and it is fantastic that there are medications and operations available for a variety of conditions. However, it is not either Lifestyle Medicine or medication. Lifestyle Medicine is the cornerstone of health and needs to be practised daily. Medications are added on as and when necessary.

And the good news? Practising Lifestyle Medicine is an absolute joy. Eating delicious home-made vegetable soup, walking in the sunshine with a friend, snuggling into bed at 10pm with a good book… what is not to love!?

Unlike our friends across the pond, we Brits seem to struggle with ‘self-care’ and ‘me-time’. It seems to make some people feel uncomfortable and disengaged. However, when I talk to patients about caring for their ‘friendly gut microbes’ or ‘tending to their gut garden’ they understand straight away, and it clarifies what they need to do and why. As human beings, we love narratives, and the microbiome narrative is a truly powerful one.


Ley, R.E.; Turnbaugh, P.J.; Klein, S.; Gordon, J.I. Microbial ecology: Human gut microbes associated with obesity. Nature 2006, 444, 1022–1023

Dr Sheena Fraser and Dr Siobhan McCormack
British Society of Lifestyle Medicine

This article is from issue 24 of Health Europa Quarterly. Click here to get your free subscription today.

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