Part 2: What Does Your Gut Microbiome Say About Your Health?

The warning signs of an imbalanced gut — and why so many people are living with dysbiosis without knowing it

Part 2 of the Your Gut, Your Health series. Start at the beginning: Gut Microbiome Testing →

Most people don't think about their gut until something goes obviously wrong — persistent bloating, urgent trips to the bathroom, or chronic discomfort that disrupts daily life. But the gut microbiome can be significantly disrupted long before symptoms become dramatic. In many cases, the signs are subtle, spread across different body systems, and easy to dismiss as unrelated problems. Understanding what your microbiome might be communicating — and when to pay attention — is one of the most practical things you can do for your long-term health.

1. What Is Dysbiosis, and Why Does It Matter?

A healthy gut microbiome is defined by two key characteristics: diversity and balance. Diversity means a wide variety of microbial species coexisting, each contributing different functions. Balance means the beneficial species are thriving and the potentially harmful ones are kept in check.

Dysbiosis is the disruption of this equilibrium. It can take several forms: a reduction in microbial diversity, an overgrowth of opportunistic or pathogenic bacteria, or a loss of key beneficial species. The main pathogenic mechanisms include impaired intestinal mucosal barrier function, inflammation activation, immune dysregulation, and metabolic abnormalities.

What makes dysbiosis particularly challenging is that it is rarely a single, dramatic event. It tends to develop gradually, through the accumulation of modern lifestyle factors that wear away at microbial health over time.

2. What Causes Dysbiosis?

Diet is the most powerful driver of microbiome composition. A diet high in ultra-processed foods, refined sugars, and saturated fats consistently reduces microbial diversity and the abundance of key beneficial species. Conversely, a diet rich in diverse plant foods, fibre, and fermented foods supports a broader, more resilient microbial community.

Antibiotics are one of the most significant pharmacological disruptors of the gut microbiome. Even a single course can alter microbial composition for months, and in some cases, certain species never fully recover.

Chronic stress activates the hypothalamic-pituitary-adrenal (HPA) axis, which has direct downstream effects on gut motility, gut barrier function, and microbial composition.

Sleep disruption is an underappreciated factor. The gut microbiome follows a circadian rhythm, and irregular sleep patterns or shift work have been shown to alter microbial composition in ways that may promote metabolic disruption.

Medications beyond antibiotics — including proton pump inhibitors, metformin, NSAIDs, and some antidepressants — each have documented effects on gut microbiota composition.

3. Physical Symptoms That May Signal Gut Imbalance

Persistent bloating and abdominal discomfort are among the most common presentations. When the microbial balance shifts, fermentation patterns in the colon change — producing different amounts and types of gas, and altering gut motility.

Altered bowel habits — including constipation, diarrhoea, or unpredictable fluctuations between the two — may reflect changes in gut motility regulated by microbial metabolites and the enteric nervous system.

Food intolerances that develop in adulthood are frequently associated with gut dysbiosis. When the gut barrier is compromised, incompletely digested food particles may trigger immune responses.

Recurrent infections or slow recovery may reflect impaired mucosal immunity.

Unexplained skin conditions — including eczema, adult acne, and psoriasis flares — have been associated with gut dysbiosis through the gut-skin axis.

4. Systemic Signs That Are Often Overlooked

Persistent fatigue that doesn't resolve with rest is one of the most common systemic complaints linked to gut dysbiosis.

Brain fog and difficulty concentrating are increasingly recognised as potential manifestations of gut-brain axis dysregulation.

Mood changes, anxiety, and low mood are strongly linked to the microbiome through the gut-brain axis. Approximately 90% of the body's serotonin is produced in the gut. [Read more in Part 3: The Gut-Brain Connection →]

Hormonal imbalances may also be influenced by gut health through the estrobolome — the collection of microbial genes that metabolise and reactivate oestrogens.

Immune dysregulation — including autoimmune flares, heightened inflammatory markers, or recurrent infections — has been associated with compromised gut barrier integrity.

5. Who Is Most at Risk?

• People with a history of repeated antibiotic use
• Those who have experienced major gastrointestinal illness
• Individuals consuming a Western-pattern diet low in dietary fibre
• People under prolonged psychological or occupational stress
• Older adults — gut microbiome diversity tends to decline with age, particularly after 65

Risk factors are cumulative. Someone with a history of antibiotic use, a low-fibre diet, and chronic stress has a substantially higher likelihood of significant dysbiosis than any single factor would suggest.

6. How Is Dysbiosis Identified?

Shotgun metagenomic sequencing — the technology used in the Microba Microbiome Explorer range at Helix — provides a comprehensive species-level picture of microbial composition, diversity, and functional output. It identifies not just which microbes are present, but what they are doing metabolically, and how those patterns compare to healthy reference ranges.

As the 2025 international consensus from The Lancet Gastroenterology & Hepatology made clear, microbiome tests carry the most clinical value when prescribed and interpreted by a licensed healthcare practitioner with access to the full clinical picture.

Not Sure Which Test Is Right for You?

Use our free 2-minute screening tool to find the Microba Microbiome Explorer™ tier that best matches your symptoms and health goals.

Find My Test →

Continue Reading in This Series

• Part 1: Gut Microbiome Testing: What It Is & Who Needs One →
• Part 3: The Gut-Brain Connection: How Your Microbiome Affects Mood, Anxiety & Mental Clarity →
• Part 4: How to Improve Your Gut Microbiome: Diet, Lifestyle & Evidence-Based Strategies →
• Part 5: The Gut Microbiome & Weight Loss: What the Science Actually Says →
• Part 6: Gut Dysbiosis: Causes, Symptoms & How to Restore Balance →

References

1. Shen, Y. et al. (2025). Gut microbiota dysbiosis: Pathogenesis, diseases, prevention, and therapy. MedComm, 6(5), e70168. https://doi.org/10.1002/mco2.70168
2. Tlaskalova-Hogenova, H. et al. (2022). Gut microbiota dysbiosis: Triggers, consequences, diagnostic and therapeutic options. Microorganisms, 10(3), 578.
3. Safarchi, A. et al. (2025). Understanding dysbiosis and resilience in the human gut microbiome. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2025.1559521
4. Porcari, S. et al. (2025). International consensus statement on microbiome testing in clinical practice. The Lancet Gastroenterology & Hepatology, 10(2), 154–167.