Gut Health: What If It’s Not SIBO? Exploring Other Root Causes of Bloating & Digestive Issues

Gut Health: What If It’s Not SIBO?

Small Intestinal Bacterial Overgrowth (SIBO) is a hot topic in gut health and for good reason — it’s increasingly being recognised as an underlying cause of bloating, constipation, diarrhoea, reflux, abdominal pain, and even fatigue, brain fog, and hormonal imbalances.

But here’s the truth: not every digestive issue is SIBO. While SIBO is common, it’s not the only cause of gut discomfort. If you’ve been experiencing symptoms and your tests have come back negative, or your clear of SIBO and still experience gut issues, maybe your treatment hasn’t helped as it was the wrong supplements, diet or you were trying to do it yourself? There are many other possible root causes worth exploring.

Let’s break some of them down.

Other Possible Causes of Gut Symptoms

1. Parasitic or Bacterial Infections

Gut infections such as Giardia, Blastocystis hominis, or post-infectious IBS can mimic the same bloating and irregular bowel movements as SIBO. Often, these infections come after food poisoning or contaminated water and can linger for months or years if not treated properly.

2. Candida and Fungal Overgrowth

Candida (a yeast that naturally lives in our gut) can become overgrown when the microbiome is imbalanced, often after antibiotics, high sugar diets, or stress. This can lead to gas, bloating, sugar cravings, thrush, and skin issues.

3. Low Stomach Acid

We often think of reflux as too much stomach acid, but for many people it’s the opposite. Low stomach acid can affect digestion, cause bloating, and allow bacteria or pathogens to thrive higher up in the gut.

4. Food Intolerances and Sensitivities

Gluten, dairy, high-FODMAP foods, or histamine-rich foods can all cause bloating, pain, and fatigue. Sometimes, it’s not a “bug” at all — it’s your body signalling that certain foods are triggering inflammation or imbalance.

5. IBS and Motility Disorders

Irritable Bowel Syndrome (IBS) is a functional gut disorder where the muscles of the digestive tract don’t work as smoothly as they should. Slow motility (constipation), fast motility (diarrhoea), or alternating between the two can feel very similar to SIBO but have different underlying drivers.

6. Gastroparesis – The Overlooked Gut Condition

Another condition that is often confused with SIBO is gastroparesis. This is when the stomach muscles don’t empty food properly, leading to bloating, nausea, reflux, pain, and a feeling of fullness after just a few bites. Because the symptoms overlap with SIBO and IBS, gastroparesis is often missed or dismissed in conventional medicine, leaving many people feeling unheard.

As a naturopath, I work with gastroparesis by supporting gentle digestive motility, reducing inflammation, optimising mineral balance, and tailoring food choices so the gut can cope without feeling overloaded. Stress and hormone balance are also key — because nervous system health plays a huge role in how the stomach and intestines move. While this condition can be challenging, a personalised and holistic approach can make a significant difference in improving day-to-day comfort and quality of life.

7. Hormonal Imbalances

Hormones play a huge role in gut health, and disruptions can show up as bloating, constipation, diarrhoea, or reflux. Some key examples include:

• Thyroid disorders – Low thyroid function (hypothyroidism) can slow down gut motility, leading to constipation, bloating, and reflux.

• Perimenopause and menopause – Fluctuating oestrogen and progesterone affect how the gut moves, the balance of gut bacteria, and even sensitivity to certain foods. This is why many women notice more digestive symptoms as they approach midlife.

• Cortisol and stress hormones – High or low cortisol can throw digestion out of rhythm. Elevated stress hormones can reduce stomach acid, slow gut movement, and change the gut microbiome, while long-term adrenal fatigue may also cause bloating and fatigue.

8. Mineral Imbalances

Your mineral status has a powerful influence on digestion, hormones, and overall gut function. For example:

• Low magnesium can contribute to constipation and sluggish bowel movements.

• Low zinc may impair stomach acid production, affecting digestion and immunity.

• Imbalances in calcium, sodium, and potassium can affect motility, energy, and even gut sensitivity.

This is where HTMA (Hair Tissue Mineral Analysis) testing can be so valuable. It gives a clear picture of mineral balance and helps identify hidden contributors to gut issues that aren’t always picked up on standard tests.

9. Stress and the Gut-Brain Connection

Our gut and nervous system are deeply connected. Stress, anxiety, and emotional trauma can all disrupt digestion, change the microbiome, and contribute to bloating, reflux, and even food sensitivities. This is why working with emotions and nervous system balance is just as important as diet and supplements.

Why Testing Matters

When gut issues are persistent, testing can provide the missing answers.

• Comprehensive microbiome testing helps uncover if you’re dealing with SIBO, LIBO (Large Intestinal Bacterial Overgrowth), IMO (Intestinal Methanogen Overgrowth), or dysbiosis. Knowing which organisms are present allows for targeted treatment rather than guesswork.

• HTMA testing provides a deep dive into your mineral balance, highlighting how stress, diet, and even hormones are impacting your digestion and energy.

These tests can be game-changers in uncovering why symptoms aren’t resolving — and guiding a personalised plan to restore balance.

A Real-Life Example

One of my clients, a 47-year-old businesswoman, came to me feeling frustrated. She had ongoing bloating, constipation, and brain fog and was convinced she had SIBO. After careful testing, we discovered her thyroid function was low, her mineral balance (especially magnesium and zinc) needed support, and her perimenopausal hormone changes were slowing her gut motility. With targeted thyroid, mineral, and hormone support — plus gentle digestive treatment — her bowels regulated, her energy returned, and the bloating eased.

This is why it’s so important not to jump to conclusions. SIBO is just one piece of the puzzle — but your gut, minerals, hormones, and nervous system all work together.

Finding the Root Cause

The key takeaway is: gut symptoms don’t always mean SIBO. Just like there’s no “one-size-fits-all” diet, there’s no single explanation for bloating, reflux, or constipation. A thorough assessment — looking at your microbiome, minerals, hormones, nervous system, and lifestyle — helps uncover your unique root cause.

That’s where naturopathy and holistic testing come in. With the right support, you don’t have to guess. Instead, you can address what’s really happening in your gut, restore balance, and feel energised again.

✨ If you’ve been struggling with ongoing gut symptoms and wondering if it’s SIBO or something else, I’d love to help you uncover what’s really going on.

I work online seeing patients throughout Australia and overseas, in person locally.

Book your consultation

Yours in health and wellness,

Katrina xxx

Naturopath and Energy Healer

BHSc (Naturopathy)

Online | Springfield Lakes | Highfields