Gut microbiome and digestive health: the root cause of bloating, IBS, skin and hormonal issues

Digestive symptoms rarely appear out of nowhere, yet they often feel that way. One day your digestion feels fine, and the next you are feeling bloated, have irregular bowel movements, other Irritable Bowel Syndrome (IBS)symptoms, or skin issues such as acne or eczema that seem unrelated at first sight.

In my work with clients, I often see a similar pattern. Many of them have already made significant changes to their diet and lifestyle, they are eating more mindfully, choosing nourishing foods, and trying to support their gut health. And still, their symptoms remain. You might recognize yourself in this.  

Maybe you have noticed more questions coming up, because the usual advice does not seem to explain what is actually happening in your body.

What I have learned over the years is that digestive health is not a separate system. It is deeply connected to the gut microbiome, the nervous system, the immune system, and even hormonal balance. When one of these systems is out of sync, the others are often affected as well.

Because the gut microbiome is highly individual, the underlying root cause can also be very personal, which is why a one-size-fits-all approach often does not fully address these symptoms. This is why understanding what is going on in your gut microbiome and digestive health is often the missing piece.

In this article, we will discover how the gut microbiome influences digestion, why imbalances can contribute to bloating, IBS, skin issues and hormonal changes, and what I commonly see in microbiome testing in practice. I will also share holistic and practical steps you can start using today.

What is the gut microbiome and why it matters for digestion, bloating, skin and hormonal health

The gut microbiome is a complex ecosystem of trillions of bacteria, fungi and other microorganisms living in your digestive tract. The gut microbiome plays a central role in digestion, immune function, skin health and hormonal balance. There is a growing body of research highlighting the important role of the gut microbiome in overall health, including its connection to digestion, skin, hormones and the nervous system.

These microbes play a key role in:

• Breaking down food

• Producing nutrients and metabolites

• Regulating inflammation

• Supporting your immune system

• Communicating with your nervous system and even your skin

When this ecosystem is balanced, digestion tends to feel stable and comfortable. When a gut microbiome imbalance occurs, symptoms like bloating, gas, constipation, diarrhea, or food sensitivities can appear.

What I often see in clients is that symptoms are not caused by one single bacteria or one single food. It is usually a pattern of imbalance in the ecosystem as a whole.

How the gut microbiome affects digestion, IBS and bloating

When the gut microbiome is out of balance, a condition called dysbiosis, several things can happen at the same time. One of these is that bacterial overgrowth can produce excess gas during fermentation of food, especially carbohydrates and fibres. This can contribute to bloating and abdominal discomfort. Dysbiosis is one of the main underlying bloating causes seen in gut microbiome imbalances. In many cases, IBS causes are linked to gut microbiome imbalance and bacterial overgrowth patterns.

In some cases, we also see overgrowth patterns such as SIBO (small intestinal bacterial overgrowth). This is when bacteria that normally live in the large intestine are found in the small intestine, leading to excessive gas production and bloating or IBS symptoms. Methane and hydrogen are often detected through a breath test. Sulphate-reducing bacteria, which can also be present in SIBO-related patterns, are best assessed through a stool test. These imbalances can slow down gut motility and are often linked to constipation, diarrhoea, bloating, or other IBS symptoms.

In clinical practice, I also see patterns where other specific bacterial groups are more dominant, such as histamine producing bacteria or mucin-degrading bacteria strains. These can contribute to inflammation, leaky gut, gas formation and digestive sensitivity.

In other cases, we also see an overgrowth of yeasts or fungi such as Candida, which can contribute to fermentation, bloating, sugar cravings and digestive imbalance. Parasites can also play a role, potentially contributing to digestive discomfort, irregular bowel movements and ongoing inflammation.

From my experience working with microbiome tests, it is rarely just one imbalance. It is often a combination of reduced diversity, overgrowth of certain strains, and a lack of beneficial bacteria that normally help regulate the system.

How gut microbiome imbalances affect acne, eczema and skin health

One of the most interesting connections I see in practice is the gut skin axis. When your gut microbiome is imbalanced, it can influence inflammation levels in the body, immune reactivity, and how the body processes histamine and toxins. This can show up in the skin as acne, eczema, psoriasis, rosacea, redness or general sensitivity.

Dysbiosis can also increase the risk of a more permeable gut lining, often referred to as increased intestinal permeability or leaky gut. This allows partially digested particles and inflammatory compounds to interact more directly with the immune system, which can contribute to skin symptoms.

This is something I frequently see in microbiome test results of clients with persistent skin issues. Not always severe imbalances, but subtle patterns that keep the system in a state of low grade inflammation.

Gut microbiome and hormone balance: how gut health affects PMS, acne and other hormonal imbalances

The gut microbiome also plays an important role in hormonal balance. Certain gut bacteria are involved in the breakdown and recycling of hormones such as estrogen, also known as the estrobolome. When your gut microbiome is out of balance, it can influence how hormones are metabolised and eliminated from the body. This may contribute to symptoms such as acne, PMS, or menstrual cycle changes, something I also frequently observe in microbiome testing with my clients.

Low-grade inflammation, often linked to gut dysbiosis, can further disrupt hormonal balance and affect how the body responds to hormones.

The liver is also closely connected to this process, as it plays a key role in breaking down and clearing hormones. When gut health is compromised, this can indirectly place more pressure on liver function and hormone metabolism through the gut-liver axis.

Common gut microbiome imbalances: what I see in microbiome test results

When I analyse microbiome tests, a few recurring patterns show up:

• Reduced diversity of gut bacteria, meaning fewer beneficial strains, which can make the gut more sensitive, less resilient, and may affect hormonal balance through reduced microbial diversity

• Low levels of protective bacteria that support gut barrier function, which can make the gut more vulnerable to irritation and digestive symptoms

• Higher levels of histamine producing bacteria, often linked to bloating, skin sensitivity, headaches, and potential hormonal symptoms due to histamine-hormone interactions

• Presence of sulfate reducing bacteria, which can contribute to gas production and digestive discomfort

• Signs that may be consistent with SIBO or bacterial overgrowth patterns, often confirmed with a SIBO breath test measuring hydrogen and methane

• Imbalance between beneficial and opportunistic bacteria, which can influence digestion, inflammation and immune response

These patterns provide valuable insight into how your gut ecosystem is functioning and what the root causes of digestive, skin and hormonal symptoms may be.

This is why I work with microbiome testing in my practice. It helps move away from guessing and towards a more personalised understanding of what your body actually needs.

What affects your gut microbiome: common causes of gut imbalance, bloating and digestive issues

There are many factors that can influence your gut microbiome over time:

• Chronic stress and a constantly activated nervous system

• Low fibre or low diversity in the diet

• Antibiotics or other certain medications

• Poor sleep quality

• Highly processed foods and low nutrient intake

• Long term digestive issues that are not addressed at the root

• Eating too quickly or in a stressed state, which can reduce digestive capacity and prevent the body from entering a proper rest and digest state

From what I see in my work with microbiome testing, it is usually not one factor, but a combination over time that leads to imbalance.

How to restore your gut microbiome naturally: holistic support for gut health

Supporting your gut microbiome is not about restriction, but about creating conditions where balance can return:

• Support digestion by eating in a calm environment and chewing well

• Prioritise regular meals to support gut motility and rhythm
               • Ideally, aim for three main meals containing protein, healthy fats, fibre and carbohydrates, and add one snack per day if needed, allowing your digestion enough time between meals.

• When you experience digestive issues such as bloating, constipation or diarrhoea, following a low FODMAP diet under the guidance of a dietitian can be very insightful, with a structured reintroduction phase later on.

• If fibre does not cause digestive symptoms for you, focus on dietary diversity by including vegetables, fruits, legumes, nuts, seeds and whole grains, gradually increasing intake if your gut is sensitive.

• Include polyphenol rich foods such as berries, grapes, green tea and colourful vegetables, which help support beneficial bacteria

• Add fermented foods if tolerated, such as yoghurt, kefir or sauerkraut

• Include omega 3 rich foods such as fatty fish, chia seeds and walnuts to support inflammation balance

• Include digestive-supporting herbal teas such as ginger, peppermint, fennel or chamomile, which can help support digestion, stimulate digestive secretions, reduce bloating and calm the nervous system

• Support your nervous system daily, since a stressed body does not digest optimally
                       • Start with taking at least three slow breaths before and after each meal, with a longer exhale, to activate the rest and digest state of your nervous system.

• Reduce factors that disrupt digestion such as highly processed foods, excessive caffeine or eating in a rushed state

• For deeper understanding of your gut health and underlying symptom patterns, a microbiome test with analysis can help provide direction for personalised support

Why gut microbiome testing can be a turning point for digestive and skin issues

Many of my clients have already tried different diets or protocols before we work together, often with temporary or limited results. A microbiome test can provide deeper insight into what is actually happening inside your gut ecosystem. Combined with symptom patterns, it can help identify whether there are signs of dysbiosis, overgrowth patterns like SIBO, histamine related imbalances, or reduced bacterial diversity.

From there, we can build a personalised plan instead of guessing what might work. This is also how I work in my practice Naéture, a holistic nutrition practice focused on gut health, skin and hormonal symptoms, where we combine nutrition, lifestyle and microbiome testing to identify the root causes behind digestive, hormonal and skin symptoms.

Your gut microbiome is connected to digestion, hormones, skin and overall health

Your gut is not just responsible for digestion. It is connected to your immune system, skin, hormones, nervous system and overall sense of wellbeing. When the microbiome is out of balance, the body will often try to communicate this through symptoms. Bloating, IBS symptoms, skin issues such as acne and eczema, and food sensitivities are all part of this language. The goal is not to suppress these signals, but to understand them.

A gut microbiome test is a simple at-home test. After this, I personally analyse the results and guide you in understanding what your gut is communicating through your symptoms, and support you in integrating a tailored plan into your daily life.

If this resonates with you and you feel like you want to understand your own gut more deeply, working in a personalised way with testing and guidance can be a valuable next step.

I would love to help you explore this further if you feel ready. You are welcome to use the buttons below to ask any questions or book your intake consultation.

Love,

Nina