Beyond the gut: Exploring the full spectrum of the human microbiome with nutritional therapy
The gut microbiome: A big chapter, but just part of the story
Introduction
The gut microbiome has taken centre stage in health conversations, social media trends, and general wellness advice. From kefir and kombucha to probiotic supplements and other fermented foods, the spotlight has been quite firmly fixed on the bacteria in the lower parts of our digestive system. While this focus is well-deserved, the gut microbiome does indeed play a critical role in digestion, immunity, and even mental health, it tells only part of the story.
In my clinical consultations, I work with clients who often arrive having only heard of “gut health” in the context of, for example, bloating, IBS or skin complaints. But when we zoom out, the human body is home to a network of interconnected microbiomes, from the mouth to the skin, the lungs to the vagina, each with its own unique ecosystem and a role in our overall health. A holistic, person-centred approach demands we consider and balance all of them, not just the gut.
What is a microbiome?
The term “microbiome” refers to the collection of microorganisms: Bacteria, fungi, viruses, and other microbes, that live in a particular environment. In the body, these environments include the gastrointestinal tract, skin, mouth, respiratory system, and reproductive organs. Each site hosts a distinct microbial community, influenced by diet, lifestyle, genetics, environment and overall health status.
These microbiomes don’t function in isolation; they’re in constant communication, directly or indirectly affecting one another. When one microbiome is disrupted, there can be knock-on effects throughout the body, something I regularly observe in clinic.
The key microbiomes and why they matter
Let’s start where most people begin:
The gut microbiome
The largest and most studied microbiome, research studies are many (in quantity and sometimes, quality). It influences digestion, nutrient absorption, immune modulation, and even neurotransmitter production (hello, gut-brain axis!).
However, many gut-related issues often have upstream or downstream roots in other microbiomes. This is why I dig deeper with my clients to look at patterns that might begin elsewhere in the body.
Where else do I look?
The oral microbiome
The mouth is the gateway to the gut. It’s easy to forget that digestion begins here, not just mechanically, but microbiologically. An imbalance in the oral microbiome can lead to gum disease or other dental issues, but also potentially contribute to whole body inflammation and dysbiosis (disruption to the microbe balance in the gut). For example, pathogenic (unhelpful) bacteria from the mouth can find their way to the gut and alter its microbial composition.
I often see links between poor oral hygiene or high-sugar diets and stubborn digestive symptoms. This highlights the need to start from the top of the digestive tract, not just the middle.
The skin microbiome
Your skin isn’t just a protective barrier, it’s a living, breathing ecosystem. Conditions like eczema, acne, and psoriasis often reflect not just a local imbalance but general internal dysfunction, particularly in the gut and liver. Topical treatments alone may offer limited relief, if the root cause lies within.
In practice, I work with clients to support the skin microbiome from the inside out, often (but not exclusively) considering blood sugar regulation, gut support and inflammatory load, whilst also considering other targeted support, all depending on the individual.
The vaginal microbiome
For women, the vaginal microbiome, typically dominated by Lactobacillus species, plays a vital role in protecting against infections, supporting fertility and maintaining hormonal balance. Infections, antibiotic use, hormonal contraception and even stress are just some examples of things that may disrupt this delicate balance.
I work with clients experiencing recurrent thrush, bacterial vaginosis, or UTIs who see improvement only after we rebalance the gut and vaginal microbiota in tandem.
The lung microbiome
The lungs were long thought to be sterile, but we now know they host their own community of microbes. This lung microbiome may play a role in respiratory conditions like asthma and COPD and may be influenced by the gut via the “gut-lung axis”.
This connection may present in my practice, especially in children and adults with persistent coughs or respiratory sensitivity. Reducing bodily inflammation and ensuring particular vitamins are optimised in terms of both intake and absorption can have a positive knock-on effect on respiratory resilience.
The microbiome web: Interconnected and dynamic
What’s clear is that these microbiomes don’t operate in silos. A change in one can trigger a ripple effect through others:
Gut-skin axis: Gut dysbiosis can lead to increased intestinal permeability, the more technical (and my preferred) terminology for what is often referred to as "leaky gut", which may contribute to systemic inflammation and skin flare-ups.
Oral-gut link: Gum disease and H. pylori infections have been associated with changes in gut microbial profiles.
Gut-brain axis: Mental health conditions such as anxiety and depression have been linked with gut microbiome imbalance.
Vagina-gut axis: A gut that’s in dysbiosis may increase susceptibility to vaginal infections due to a transference of bacteria or immune modulation (stimulants or suppressants to the immune system).
This is why in my nutritional therapy practice, my approach is never to isolate one symptom or system. Instead, I work holistically, looking at diet, lifestyle, environment, stress, and sleep, to understand how these microbiomes are interacting and what might need recalibration. I use a functional medicine approach, often with targeted lab testing which can help to clarify what’s going inside and speed up the process of my clients feeling better.
Final thoughts
The gut may be getting the headlines, but it's just one part of the microbial puzzle. A truly holistic view of health acknowledges the complex and wonderful interplay between all our microbiomes. By broadening the conversation with my clients beyond the gut, we move from symptom-chasing to systems-thinking; a philosophy that lies at the heart of my practice.
Whether you’re managing chronic symptoms, aiming to optimise your wellbeing, or simply curious about your body's inner ecosystem, nutritional therapy can provide clarity on your full microbiome picture and personalised strategies to support your health.
It’s tough to make and sustain change alone. Having me in your corner can make it simple, doable, and most of all, enjoyable. Contact me if you’d like some support.
References
Clemente, J.C. et al., 2012. The impact of the gut microbiota on human health: an integrative view. Cell, 148(6), pp.1258-1270.
Kilian, M. et al., 2016. The oral microbiome – an update for oral healthcare professionals. British Dental Journal, 221, pp.657–666.
Belkaid, Y. and Tamoutounour, S., 2016. The influence of skin microorganisms on cutaneous immunity. Nature Reviews Immunology, 16(6), pp.353–366.
Ma, B. et al., 2012. Vaginal microbiome: rethinking health and disease. Annual Review of Microbiology, 66, pp.371–389.
Dickson, R.P. et al., 2014. The lung microbiome and health. Lancet Respiratory Medicine, 2(1), pp.13–21.
Cryan, J.F. et al., 2019. The microbiota-gut-brain axis. Physiological Reviews, 99(4), pp.1877–2013.