Signs You Have an Imbalanced Gut Microbiome

Most of us don’t give our gut health much thought until something feels off. Whether it’s bloating, tiredness, skin flare-ups, or simply not feeling like yourself, your gut microbiome may be trying to tell you something. 

The gut is home to trillions of microorganisms that play a critical role in digestion, immune health, and even mood regulation. When this ecosystem becomes unbalanced, a state known as dysbiosis, the effects can ripple throughout the body. 

In this article, we’ll explore what a healthy gut microbiome looks like, how to spot the signs of imbalance, and most importantly, what you can do about it. 

Understanding a Balanced vs. Imbalanced Gut Microbiome 

Your gut microbiome is like a bustling city made up of bacteria, viruses, fungi, and other microbes. When the population is diverse and in harmony, everything runs smoothly. This balance supports healthy digestion, regulates the immune system, and helps produce important compounds like vitamins and neurotransmitters. 

But when this balance tips — whether due to stress, poor diet, antibiotics, illness, or other factors — certain microbes can overgrow while beneficial ones decline. This can result in a wide range of symptoms, some obvious and others more subtle. 

An imbalanced gut microbiome isn’t a diagnosis in itself, but it’s often linked to conditions like: 

• IBS (Irritable Bowel Syndrome) 

• SIBO (Small Intestinal Bacterial Overgrowth) 

• Leaky gut (intestinal permeability) 

• Skin issues like acne or eczema 

• Mood disorders such as anxiety or depression 

Let’s look more closely at the signs your microbiome might be out of sync. 

Digestive Issues as a Sign of Imbalance 

Gut health and digestion go hand in hand. If your microbiome is struggling, your digestion often feels the impact first. However, many people assume that mild discomfort is just “normal” — when in fact, it may be a signal that your gut needs attention. 

Frequent Gas, Bloating, and Indigestion 

These are among the most common signs of gut dysbiosis. Excess gas may be produced when certain bacteria ferment undigested carbohydrates in the small intestine, especially in conditions like SIBO. 

Bloating that worsens as the day goes on, or after eating certain foods (like beans, onions, or wheat), could point to microbial imbalance, possibly in the large intestine. Indigestion, a sense of heaviness, or feeling “full too quickly” may also indicate that the gut bacteria aren’t working efficiently to break down food. 

Changes in Bowel Movements: Diarrhoea or Constipation 

Your microbiome plays a crucial role in regulating how frequently — and comfortably — you go to the toilet. 

• Constipation may suggest a lack of beneficial bacteria that support gut motility. 

• Diarrhoea can occur if harmful bacteria produce toxins or disrupt the gut lining. 

Some people experience an alternating pattern of both, which is common in IBS and often linked to microbial imbalances. 

Unexplained Weight Gain or Loss 

The gut microbiome helps regulate metabolism and how your body processes energy. When it’s imbalanced, you may: 

• Struggle to lose weight despite eating well 

• Experience cravings for sugar or carbs 

• Gain weight rapidly without changes in diet or activity 

• Lose weight unintentionally due to malabsorption or inflammation 

Certain bacterial strains are known to influence how efficiently we extract calories from food, and they may also affect appetite-regulating hormones. 

Skin Problems Linked to Gut Imbalance 

The connection between the gut and skin is often underestimated, but it’s very real. Known as the gut-skin axis, this relationship explains why issues like: 

• Acne 

• Eczema 

• Rosacea 

• Psoriasis 

These skin issues may appear or flare when the gut microbiome is disrupted. Inflammation in the gut can contribute to systemic inflammation, which may manifest on the skin. Conversely, improving gut health often leads to clearer, calmer skin over time. 

Frequent Infections or Illness 

An imbalanced microbiome can weaken the immune barrier, making you more prone to: 

• Frequent colds or infections 

• Slower recovery from illness 

• Increased sensitivity to allergens 

This can also be linked to increased intestinal permeability, where the intestinal lining becomes more permeable, allowing inflammatory compounds to escape into the bloodstream and trigger immune responses. 

Chronic Fatigue and Low Energy 

Feeling tired all the time, even after a good night’s sleep? It might not be just the pace of life — your microbiome could be playing a role. 

Dysbiosis can contribute to: 

• Poor nutrient absorption (e.g. iron, B12, magnesium) 

• Chronic low-grade inflammation 

• Disrupted sleep due to gut-brain signalling 

Additionally, imbalanced bacteria can interfere with melatonin production, which affects your sleep-wake cycle and may leave you feeling sluggish or foggy during the day. 

Mood Swings, Anxiety, and Depression 

The gut and brain are intimately connected through the gut-brain axis — a complex communication network involving nerves, hormones, and immune messengers. 

An imbalanced microbiome may reduce the production of mood-supporting neurotransmitters like serotonin and GABA. As a result, people with gut dysbiosis often report: 

• Low mood or apathy 

• Anxiety or panic episodes 

• Brain fog or difficulty concentrating 

• Heightened emotional reactivity 

In fact, some studies suggest that microbiome diversity may be as important as traditional psychological factors in mood disorders. 

Food Cravings and Digestive Sensitivities 

Cravings for sugar, bread, or processed foods may not just be about willpower. Certain microbes actually influence our cravings to promote their own survival, creating a feedback loop that perpetuates dysbiosis. 

At the same time, people with an imbalanced gut often find that their digestive system becomes sensitive to previously well-tolerated foods, including: 

• Dairy 

• Gluten 

• High FODMAP foods (like garlic, apples, lentils) 

• Histamine-rich foods (e.g. aged cheese, wine) 

This can be frustrating and isolating — but identifying and addressing the underlying imbalance can bring real relief. 

How to Restore Balance to Your Gut Microbiome 

If you’re recognising yourself in several of these signs, don’t panic, your gut is incredibly adaptable. With the right support, it’s possible to nudge your microbiome back into balance and feel significantly better. 

Here are some core strategies: 

1. Nourish with Whole, Fibre-Rich Foods

• Diversity is key. Feed your beneficial bacteria with a variety of plant foods, such as: 

• Vegetables and leafy greens 

• Whole grains (e.g. oats, quinoa, brown rice) 

• Legumes (beans, lentils, chickpeas) 

• Nuts and seeds 

• Fermented foods (like kefir, sauerkraut, kimchi, live yoghurt) 

• Aim for 30+ different plant-based foods per week to encourage microbial diversity. 

2. Identify and Remove Disruptors

This might include: 

• Ultra-processed foods 

• Excess alcohol 

• Artificial sweeteners 

• Unnecessary antibiotics 

A registered dietitian can help identify which specific foods may be triggering symptoms and how to reduce them safely. 

3. Consider Probiotics (With Guidance)

Probiotics can help rebalance the gut, but they’re not a magic pill. The right strain matters, as does the reason you’re taking them. Some may help with bloating or diarrhoea, while others may support immune health or mood. 

Work with a practitioner to find a targeted approach. 

4. Prioritise Sleep and Stress Management

Remember that the gut responds to how safe and supported you feel. 

• Establish a calming bedtime routine 

• Practice gentle breathwork or yoga 

• Spend time in nature 

• Seek support for anxiety or overwhelm 

Improving mental wellbeing often improves digestive health, and vice versa. 

5. Move Your Body Regularly

Physical activity helps increase microbial diversity and supports regular bowel movements. You don’t need intense workouts just consistent movement you enjoy, like walking, stretching, or cycling. 

6. Avoid Over-restriction

Eliminating entire food groups for long periods can reduce microbial diversity, potentially worsening gut health in the long run. If you need to trial a low FODMAP diet or exclusion plan, make sure it’s short-term and professionally supervised. 

When to Seek Professional Help for Gut Imbalance 

If you’ve been experiencing persistent digestive or systemic symptoms, and home remedies aren’t helping, it’s time to speak to a qualified practitioner. 

Seek professional support if: 

• Your symptoms interfere with daily life 

• You’ve tried dietary changes without relief 

• You’ve experienced significant weight changes 

• You have co-existing mental health symptoms 

• You suspect SIBO or food intolerances 

• You’re considering major dietary restrictions 

A registered gut health nutritional therapist can help with testing (if appropriate), symptom mapping, and a personalised treatment plan that works with your lifestyle, not against it. 

Conclusion 

Your gut microbiome is a powerful and sensitive ecosystem. When it’s in balance, you may feel energetic, resilient, and well-nourished. But when it’s off-kilter, the signs can show up in surprising ways: through your digestion, mood, skin, immunity, or even your cravings. 

If you’re noticing signs of imbalance, know this: you don’t have to live with it. With the right guidance, the gut is remarkably responsive to care, nourishment, and attention.