Follow the microbes: A new perspective on health inequalities

Rhiannon Day-Thompson is an NHS GP and NHS England Health Inequalities Fellow, with an interest in ultra-processed food and the gut microbiome. She works in Cornwall.

Office of National Statistics data has shown that UK healthy life expectancy (HLE) is now confirmed to be falling in the UK.¹ The gap in HLE between those living in the most deprived, compared to the most affluent communities, was last measured at around 20 years.² In fact according to the latest data, published in April 2026,  we can see that whilst the healthy life expectancy of the most affluent is static, the healthy life expectancy of the poorest is plummeting.³

Looking into the waiting room, I often feel like I can see this change before my eyes. I expect many other GPs working in areas of deprivation might also be feeling that the health gap is opening up like a socio-biological chasm.

But why? It feels like nothing but progress has been made over my 25-year career- immunotherapy, antiretrovirals, laparoscopy, robotics, sophisticated imaging, improved access, screening – how can the nation’s health be getting worse?

Perhaps the answer is something powerful but invisible. Something that lives in our houses, our consulting rooms, and in our bodies. Something that we have treated badly, often tried to obliterate. This element, once considered, pushes our understanding of health inequality towards a re-frame: Rather than understanding bodies as machines, in a world that promotes malfunction, we are invited to understand that bodies are complex ecosystems.

Microbes

We could say that each human is like a planet, with a population of around thirty-nine trillion microbes – the human microbiome. These microbes are not passive passengers, but active participants in metabolic, digestive, and immune function.

The microbiome could be seen as our ancient partner. When working synergistically with the human body, a healthy microbiome can be a powerful physiological ally. But, when the microbial populations shift, and the ‘behaviour’ of the microbes alters, this is called dysbiosis, resulting in a negative impact on health. In fact, it is not just the microbiome that is altered in dysbiosis, but it’s also the metabolome – the metabolic output of the microbes, and the metagenome – the adaptive genetic potential, added to our own, by that of our microbes.

The influence of microbes is far-reaching in the human body. For example, an estimated twenty percent of the small molecules in the circulation come from microbes.⁴ The microbiome is vital to the ecology within a human, significantly influencing both organs and systems. The potential functions of the microbiome are highly adaptable – much more so than the epigenetics of a human. The microbiome forms a foundational part of our inner ecosystems, in the same way that it contributes to the ecosystems of the natural world around us.

Dysbiosis

On the other hand, dysbiosis is extremely relevant in many disease states we encounter in General Practice. Conditions such as: overweight and obesity, metabolic syndrome, gastro-intestinal disorders, Metabolic dysfunction-associated steatotic liver disease (MASLD), immune-related diseases, and mood disorders such as anxiety and depression are influenced by microbes, as are many of the symptoms that characterise those 50% of all GP consultations where a diagnosis is never reached,⁵ such as brain fog, chronic pain and fatigue – conditions that dominate Deep End GP practice. Is it possible then, that dysbiosis is a missing link underlying the UK’s huge gap in healthy life expectancy?

At the moment, dysbiosis is a unifying concept rather than a diagnosis. Therefore, despite its importance, dysbiosis has neither been written into our NHS policies and guidelines, nor into our social strategies. In fact, it’s only recently that movements such as the biocide bill,⁶ are beginning to gain momentum. And yet, if there was one word to characterise the global body of the 21^st century, dysbiosis might be it.

Four Key Changes

This is because dysbiosis sits at the intersection of four key changes that the global population has experienced over the past 50-75 years. These are changes that disproportionately affect those living in deprivation.

The first, is the wholesale change in the ‘normal’ diet of human beings – which is now dominantly ultra-processed food (UPF). Large prospective cohort studies and biobank analysis demonstrate an often dose-dependent effect of UPF on both healthy life expectancy, and on life expectancy. A small number of randomised controlled trials focusing mainly on the primary outcome of weight in relation to UPF consumption, confirm that in the short-term, UPF contributes to excess weight.^7–9 Mechanistically, we are learning that a dominantly UPF diet may damage the gut lining, the gut immune system, the gut-brain axis, the metabolism, the liver and the brain. UPF-related damage occurs through multiple interacting mechanisms, but many of them are mediated by alterations or damage to the microbiome.

The second key change is widespread antibiotic use – not only in humans but also in agriculture. This never slows down. There is a year-on-year increase in global antibiotic use. In humans, for example, this increased 65% between 2000 and 2015.¹⁰ The impact of widespread antibiotic use has been shown to have dramatically changed the composition and diversity of the human microbiome.¹¹

The third and fourth key changes are reduced rates of breastfeeding and increased rates of caesarean section – both factors are known to be sub-optimal for vertical transmission of microbial species from mother to child.¹²

Some human studies have shown a possible trans-generational attrition of the microbial species.¹³ Mouse models have even shown that alterations in the microbiome of one generation can produce disease in the next.¹⁴ In the same way that we are living through a biodiversity crisis in nature, we might also be experiencing a biodiversity crisis affecting our inner ecology. In fact, certain essential microbes such as Bifidobacterium longum infantis – a bacterium which produces energy (via short-chain fatty acids) from human breast milk, which used to be ubiquitous in humans, are now dwindling to near-absence in industrial populations.^15,16 This means that even the purest form of human nutrition – human breast milk – has literally become less nutritious to human babies, because of dysbiosis. We don’t yet know the extent of these changes, or how permanent they are.

Unfortunately, those living in deprivation are much more vulnerable to dysbiosis. Why? Because UPF has become the dominant diet of deprivation – and the reasons for that include financial poverty, time poverty, lack of access and a shift in social norms driven by corporate-dominated foodscape, motivated by profit.¹⁷ This is not an issue of individual responsibility, in Public Health-speak, it’s an issue of the commercial determinants of health.¹⁸

Breastfeeding rates are consistently lower in more deprived communities,¹⁹ meaning many infants begin life with reduced exposure to the microbial and immunological foundations that breast milk provides. The next layer is the evidence that antibiotic prescriptions are more likely to be issued to those living in deprivation.²⁰

Follow the microbes… to the Health Gap

If dysbiosis is contributing to the widening health gap, it adds a layer of socio-biological context to the social determinants described by Marmot. The microbiome may be one of the major biological pathways through which the social determinants exert their effects.

At present we cannot easily measure the “health” of the microbiome, and dysbiosis remains a developing concept, rather than a clinical diagnosis. But absence of measurement is not absence of reality. The signals are already visible in epidemiology, in mechanistic research, and in the day-to-day experience of GPs.

Perhaps a new take on the UK’s health inequality gap could be a focus on dysbiosis. We could seek to understand how the microbiome signatures of those living in deprivation compare to those living in affluence, and how that might link to health outcomes. The health gap could be viewed as a story of altered ecology within the human body, most visible in deprivation.

References

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