8 Signs Your Microbiome Is Unbalanced

Ever feel constantly bloated or fatigued? It could be a sign that your gut microbiome is unbalanced. Your gut microbiome is the community of over a hundred different species of bacteria and other microorganisms living in your gut. Far from harmful, these bacteria support digestion and nutrition.

But if they become unbalanced, it can lead to a range of signs and symptoms which may disrupt your everyday life. Spotting these symptoms early can help you take preventative action, correcting any issues with your diet or lifestyle before they become a bigger problem. This might prompt you to get a gut health check.

Here are eight of the most common signs your microbiome may be out of balance — and what they can tell you about your health.

8 Signs and Symptoms of Unbalanced Gut Bacteria

1. Persistent Bloating and Gas

Bloating is normal from time to time. We all eat certain foods that bloat us or produce a lot of gas. The difference is whether you’re bloating occasionally or consistently.

Chronic bloating is often caused by gas-producing bacteria in your gut. If you’ve got the wrong balance or too many (and the wrong diet), these bacteria could go into overdrive, producing excessive amounts of gas, leading to bloating. High-FODMAP foods often feed these bacteria, exacerbating the issue.

2. Irregular Bowel Movements

Changes in bowel habit almost always indicate a problem. Constipation, diarrhoea, or alternating patterns may mean there is a disruption in gut motility. If the change in bowel habit is not caused by unbalanced gut bacteria, chances are it could result in an imbalance. Diarrhoea, in particular, can mean beneficial gut bacteria are flushed out.

If you experience diarrhoea, following up with fermented and high fibre foods can help support your gut bacteria by replenishing those lost beneficial bacteria. But if the problem persists, make sure to speak to your GP in case there is a more serious underlying issue.

3. Constant Fatigue and Low Energy

Constantly feeling tired? Having to drag yourself through each day? It’s a common symptom of gut bacteria imbalances. Beneficial gut bacteria don’t just aid digestion; they also produce key nutrients your body needs to thrive.

B-vitamins, iron, and magnesium, in particular, reduce feelings of tiredness and supply our bodies with the energy they need.

Inflammation is another factor. When “bad” bacteria proliferate, they can inflame the bowel. Inflammation drains the body’s energy reserves, leaving us feeling depleted.

4. Increased Food Sensitivities

Food sensitivities are often confused with true food allergies, but they’re one of the clearest signs your microbiome may be unbalanced.

A food allergy triggers an immediate immune response (which can be severe). A food sensitivity, on the other hand, is usually delayed and far more subtle. Symptoms like bloating, cramps, nausea, headaches, and brain fog can appear hours after eating.

These delayed reactions can be related to your microbiome. When beneficial bacteria are reduced, food isn’t broken down properly, leading to fermentation, inflammation, and possible increased sensitivity over time.

5. Brain Fog, Anxiety, or Low Mood

Your gut and brain talk to each other. Known as the gut-brain axis, this bidirectional communication influences everything from your mental sharpness to your mood.

How? Well, gut microbes play a role in serotonin, dopamine, and GABA production and regulation. These neurotransmitters are partly responsible for your mood, motivation, and cognition. If they’re disrupted, you’ll notice the effects.

6. Ongoing Skin Problems

Like your brain, your skin is closely tied to your gut. Skin conditions like acne, eczema, rosacea, and rashes can occur due to inflammation and immune signalling from the gut.

Often, the tell-tale sign is that topical treatments alone fail. Only by correcting the gut imbalances can the problem be resolved.

7. Frequent Infections or Weak Immunity

Around 70-80% of the immune system resides in the gut. That makes sense as it’s the first-line defence against any harmful bacteria and microorganisms we ingest.

Beneficial bacteria usually compete against harmful microorganisms, forming part of this defence. But if they’re disrupted, people often notice frequent infections or slow healing.

8. Unexplained Weight or Appetite Changes

Microbes try to create their perfect environment in the gut. That can mean influencing your appetite hormones, causing you to feel more or less hungry (or even crave specific foods).

Another symptom of an unbalanced gut is difficulty losing or gaining weight (despite stable habits). The cause is often altered nutrient absorption or changes in fat storage due to the gut bacteria.

What Causes the Microbiome to Become Unbalanced

It can seem that no matter what you do, your gut microbiome is disrupted. But there are a few factors that may increase the risk of your gut microbiome becoming unbalanced. These include:

• Ultra-processed diets: Low in fibre and high in additives that may damage the gut lining and feed harmful bacteria.

• Chronic stress: Raises cortisol, disrupts gut bacteria, and slows digestion.

• Antibiotic overuse: Wipes out beneficial microbes alongside infections.

• Alcohol: Damages the gut lining and promotes harmful bacteria.

• Poor sleep: Weakens immune regulation and microbial balance.

• Low fibre intake: Starves beneficial bacteria, allowing harmful species to dominate.

Can You Fix an Unbalanced Microbiome?

Yes! If you have any of the symptoms above, you can fix your gut microbiome. With the right diet and lifestyle changes, you can restore a healthy balance.

But it helps to know the current state of your microbiome before you start. The Functional Gut Clinic is the UK’s first advanced microbiome testing centre. We offer a range of testing options along with expert-led interpretation and personalised treatment plans.

Book your assessment today to discover what’s going wrong with your gut microbiome.

Take a look at this article: Fermented Foods for Gut Health