How Your Gut Microbiome Affects Energy, Mood, Immunity & Digestion

Your gut microbiome influences far more than digestion—it impacts immunity, hormones, mood, and long-term health. This comprehensive guide explores what disrupts microbial balance, the signs of gut dysbiosis, and what to do if symptoms persist. Learn how to support your microbiome naturally through targeted diet and lifestyle changes.

To understand how your gut influences so many areas of health, we first need to explore the remarkable world of the microbiome—what it is, how it works, and why it matters more than ever.

What Is the Microbiome?

The human body is home to trillions of microorganisms—bacteria, fungi, viruses, and other microbes—that live primarily in the gut. This vast community is known as the microbiome, and it plays a foundational role in maintaining health.

Technically, the microbiome refers to the collection of all microbial genes in the body, while “microbiota” describes the actual organisms themselves. But in everyday use, the two terms are often used interchangeably.

Most of these microbes reside in the large intestine, where they influence everything from digestion and nutrient absorption to immune function, hormone production, and even mental health. It’s estimated that the gut microbiome alone houses anywhere from 10 to 100 trillion organisms, representing thousands of different species.

According to the National Institutes of Health’s Human Microbiome Project, these microbes aren’t just passengers—they’re essential to life. They perform metabolic functions we can’t carry out on our own, and they interact with our immune cells, endocrine system, and nervous system in ways we’re only beginning to understand.

The microbiome is sometimes referred to as a “forgotten organ” due to its critical influence on overall physiology. Unlike your liver or kidneys, you can’t see it or feel it—but its impact is widespread and profound.

How the Microbiome Works in the Body

While we often think of microbes as invaders, the majority of those living inside us are not only harmless—they're essential to our survival. The gut microbiome in particular acts like a command centre, coordinating key physiological processes that affect the entire body.

One of its primary roles is to help break down complex carbohydrates and fibres that the human body can't digest on its own. In doing so, these microbes produce short-chain fatty acids (SCFAs) like butyrate, propionate, and acetate—compounds that help regulate inflammation, nourish the gut lining, and support immune function.

The microbiome also plays a key part in the production of vitamins such as B12, folate, and vitamin K2, and assists in the metabolism of hormones like oestrogen. It even helps detoxify certain compounds before they enter systemic circulation.

Perhaps most importantly, the gut microbiome is in constant communication with the immune system. Around 70% of the immune system is located in or around the gut, and microbial diversity plays a direct role in immune training and tolerance. When this balance is off, it can lead to overreactions (such as allergies or autoimmunity) or underreactions (making the body more susceptible to infections).

Emerging research has also shown the microbiome’s influence on the gut-brain axis—a bidirectional communication network between the gastrointestinal tract and the central nervous system. Through this pathway, gut microbes can affect neurotransmitter production, cortisol regulation, and even emotional wellbeing.

In short, a healthy microbiome supports more than digestion. It’s intimately involved in everything from metabolism to mood—and when it’s disrupted, the consequences can be wide-reaching.

Why the Microbiome Matters — From Digestion to Mood & Immunity

A healthy microbiome isn’t just a “nice-to-have”—it’s fundamental to long-term health. When this internal ecosystem is in balance, it helps maintain digestive integrity, immune resilience, hormonal regulation, and even neurological stability.

But when disrupted, the ripple effects can impact nearly every system in the body.

Digestive Health: The most immediate role of the microbiome is in digestion. Beneficial bacteria assist in breaking down dietary fibres, regulating bowel movements, and preventing the overgrowth of harmful organisms like candida or Clostridium difficile. An imbalanced microbiome—known as dysbiosis—can lead to bloating, constipation, diarrhoea, reflux, and food intolerances.
Immune Function: Roughly 70% of your immune system resides in the gut, making microbial balance critical to immune modulation. Beneficial microbes help “train” the immune system, teaching it to respond to threats without overreacting. A loss of microbial diversity has been linked to allergies, autoimmune conditions, and increased susceptibility to infections.
Hormonal Balance: Gut bacteria assist in metabolising and eliminating hormones such as oestrogen. Imbalances in this system—sometimes called the estrobolome—can contribute to conditions like PMS, PCOS, endometriosis, and oestrogen dominance. The gut also affects cortisol regulation through its interaction with the stress-response system.
Neurological and Mental Health: The gut produces around 90% of the body’s serotonin, along with other neurotransmitters like dopamine and GABA. Disruptions in gut health have been associated with anxiety, depression, brain fog, and even neurodegenerative conditions. This growing field of research is reshaping how we understand the link between digestion and mood.
Inflammation and Chronic Disease: Poor microbial diversity is strongly associated with systemic inflammation, a key driver of chronic diseases like heart disease, type 2 diabetes, obesity, and even some forms of cancer. By restoring balance in the microbiome, we can reduce this underlying inflammatory burden.

From the immune system to emotional resilience, the microbiome plays a pivotal role in helping the body adapt, recover, and thrive. Supporting it isn’t just a digestive strategy—it’s a foundational part of disease prevention and optimal health.

What Damages the Microbiome?

While the human microbiome is incredibly adaptive, it’s also vulnerable to the pressures of modern life. A number of common lifestyle factors can disrupt microbial balance—reducing diversity, feeding pathogenic strains, and damaging the gut lining itself.

Antibiotic Use: Broad-spectrum antibiotics don’t discriminate. While they kill off harmful bacteria, they also wipe out beneficial strains that are essential to gut health. Repeated courses, especially without probiotic support, can lead to long-term dysbiosis and increase the risk of fungal overgrowth.
Poor Diet: A diet low in plant fibres and high in processed foods, refined sugar, and artificial additives directly undermines the microbiome. Harmful microbes thrive on sugar and starch, while beneficial bacteria rely on diverse fibres and resistant starches to survive.
Environmental Toxins: Chlorine and fluoride in tap water, glyphosate residues on non-organic produce, and even common household cleaning products can negatively impact gut flora. These substances don’t just affect us—they affect the microbes within us.
Chronic Stress: Ongoing emotional stress alters the gut environment via the gut-brain axis. Cortisol and other stress hormones can increase gut permeability, reduce microbial diversity, and weaken the gut’s protective barrier. It’s not just about digestion—mental health directly influences microbial health.
Medications Beyond Antibiotics: Certain non-antibiotic medications—including acid blockers (PPIs), NSAIDs, birth control pills, and antipsychotics—have all been shown to negatively impact gut flora. Long-term use, especially without microbiome support, may contribute to imbalances.
Over-Sterilisation & Lack of Exposure to Nature: Overuse of antibacterial products, lack of contact with soil and animals, and limited time outdoors reduces our microbial exposure. This “hygiene hypothesis” may partly explain the rise in allergies, autoimmune issues, and immune dysregulation.

These factors don’t exist in isolation—they tend to compound each other. For many people, gut dysfunction is the slow result of years of cumulative strain. The good news is that the microbiome is dynamic and can be supported back into balance with the right interventions.

*Processed & junk foods, refined sugar, and artificial additives directly undermines the microbiome.*

Signs of Microbial Imbalance (Gut Dysbiosis)

Gut dysbiosis refers to a disruption in the normal balance of the gut microbiota—typically involving an overgrowth of harmful bacteria, a loss of beneficial strains, or reduced microbial diversity overall. This imbalance can manifest in a wide range of symptoms, many of which go far beyond the digestive system.

Common digestive symptoms include:

Bloating, cramping, and excessive gas
Irregular bowel movements (constipation, diarrhoea, or both)
Food intolerances or sensitivities (especially to gluten, dairy, or high FODMAP foods)
Reflux or heartburn
A feeling of fullness after only a small amount of food

But dysbiosis doesn’t stop at digestion. Because the microbiome interacts with the immune system, hormones, and nervous system, symptoms often appear elsewhere in the body.

Systemic signs of gut imbalance may include:

Persistent fatigue or “crashing” energy in the afternoon
Brain fog or poor concentration
Anxiety, low mood, or irritability
Skin conditions like eczema, rosacea, or acne
Frequent infections or slow recovery from illness
Menstrual irregularities or symptoms of hormonal imbalance
Autoimmune flare-ups or chronic inflammation

While these symptoms can have many contributing factors, the gut is often involved—even when there are no obvious digestive complaints. In fact, many people don’t connect their mood, skin, or energy issues with the state of their microbiome until they start addressing it directly.

In clinical practice, we often see significant improvements in systemic symptoms once gut health is restored. It’s not just about the gut—it’s about the whole system it supports.

How to Support & Rebuild a Healthy Microbiome

Restoring the microbiome is less about quick fixes and more about consistent, foundational change. While gut protocols and supplements can be helpful, the real transformation often comes from daily habits—what you eat, how you live, and how you respond to stress.

Here are the most important strategies we focus on in clinic when helping someone rebalance their gut flora:

1. Prioritise Prebiotic Fibre Beneficial bacteria feed on fermentable fibres found in whole plant foods. These include soluble fibres and resistant starches that humans can’t digest—but your microbes can. Good sources include:

Apples and pears (with the skin)
Leeks, onions, and garlic
Legumes, oats, and flaxseed
Cooked and cooled potatoes or rice (for resistant starch)

Rather than flooding the system with fibre all at once, it’s often best to increase gradually—especially if symptoms like bloating are present.

2. Add Fermented Foods Daily Fermented foods provide live beneficial bacteria and help reinforce microbial diversity. Unlike many supplements, they contain multiple strains and work synergistically with whole foods. Some of the best options:

Unsweetened live yoghurt or kefir
Raw sauerkraut or kimchi
Miso paste (uncooked)
Kombucha (low-sugar)

Start small, and rotate types for diversity.

3. Reduce the Feed for Harmful Organisms Processed foods high in sugar and refined carbohydrates tend to promote the growth of less favourable microbes. Excess alcohol, artificial sweeteners, and frequent snacking can also disrupt balance. Cutting back on these—and replacing them with whole, unprocessed options—can shift the internal environment within days.

4. Support the Gut-Brain Connection Stress directly affects the microbiome via the vagus nerve. When stress is chronic, the gut becomes inflamed and less resilient. Supporting this connection might include:

Breathwork or meditation
Movement (especially yoga or walking)
Adaptogenic herbs like ashwagandha or rhodiola
Nervine herbs like lemon balm or chamomile
Prioritising restorative sleep

The nervous system and the gut are in constant conversation. Calming one often helps rebalance the other.

5. Rebuild After Antibiotic Use After a course of antibiotics, we often recommend a broad-spectrum probiotic to reseed beneficial bacteria, alongside a high-prebiotic diet. In some cases, targeted support may be needed—especially if symptoms persist after antibiotics.

6. Limit Environmental Stressors It’s not always possible to control every exposure, but small changes can make a difference. Using a basic water filter, choosing organic where possible, switching to natural cleaning products, and spending more time in nature can all help create a more microbiome-friendly lifestyle.

Restoring gut health doesn’t require perfection. It requires consistency and awareness. In many cases, the gut responds quickly once the right environment is created.

When Basic Interventions Aren’t Enough

For many people, small changes in diet and lifestyle are enough to restore balance. But there are cases where deeper dysfunction is present, and the microbiome can’t fully recover without more targeted support.

If symptoms persist—even after weeks of gut-friendly eating, stress management, and probiotic use—it may be a sign of an underlying condition such as:

Small Intestinal Bacterial Overgrowth (SIBO): This occurs when bacteria that normally reside in the large intestine begin to overpopulate the small intestine. It can lead to bloating, gas, fatigue, and nutrient malabsorption. SIBO often requires antimicrobial protocols (herbal or pharmaceutical) and more structured dietary changes.
Candida Overgrowth: An imbalance between yeast and bacteria in the gut can result in candida symptoms, including sugar cravings, skin issues, thrush, or digestive discomfort. Addressing this often involves antifungal herbs, dietary adjustments, and immune support.
H. pylori Infection: Helicobacter pylori is a common bacterium that can damage the stomach lining, contributing to ulcers, reflux, or chronic gastritis. It often requires testing and specific treatment to resolve.
Leaky Gut Syndrome (Increased Intestinal Permeability): When the gut lining becomes compromised, larger particles can pass into the bloodstream, triggering immune reactions. This can contribute to allergies, autoimmune issues, and systemic inflammation. Rebuilding the gut lining may require amino acid support (like glutamine), anti-inflammatory herbs, and microbiome repair.

These conditions often present subtly and overlap with more general symptoms, which is why working with a practitioner can help identify what’s really going on beneath the surface.

At EarthWise, we take a layered approach—starting with the foundations and moving into targeted protocols only when needed. Gut healing doesn’t have to be extreme, but it does need to be personalised.

Final Thoughts & Practical Next Steps

The microbiome is more than a health trend. It’s one of the most influential systems in the human body—and one of the most responsive to change.

Whether you’re dealing with persistent digestive issues, unexplained fatigue, skin problems, or mood fluctuations, it’s worth considering what your gut might be trying to tell you. Restoring microbial balance isn’t just about gut health—it’s about reclaiming energy, clarity, resilience, and long-term wellbeing.

If you’re just beginning this journey, start with the basics: whole foods, more fibre, less sugar, daily movement, and stress support. Small changes made consistently can shift your internal terrain in powerful ways.

If your symptoms have been ongoing—or if you suspect something deeper is going on—it may be time to explore a more structured gut repair plan. At EarthWise, we offer practitioner-formulated herbal support and education-based protocols to help you do just that, step by step.

Your microbiome is alive, adaptable, and ready to respond. The key is giving it the right conditions to thrive.