Bloating, Reflux, and Irregular Bowels — What Your Gut Is Really Trying to Tell You

Poor digestion is one of the most common — and most misunderstood — health concerns I see clinically. And in athletes, it can directly undermine training and recovery.

Bloating, indigestion, reflux, nausea, excessive wind, abdominal pain, and irregular bowels are symptoms that affect a huge number of people. For some they are a daily frustration; for others they are genuinely debilitating.

What many people don’t realise is that poor digestive function goes well beyond gut discomfort. It can also drive fatigue, persistent headaches, and difficulty concentrating — symptoms that are frequently investigated in isolation, when the gut may be the root cause all along.

What Causes Poor Digestive Function?

There are many potential drivers of these symptoms, and correctly identifying which is at play is the crucial first step. The most common causes include:

• Low stomach acid — which impairs the breakdown and absorption of key nutrients
• Lack of digestive enzymes — reducing the body’s ability to properly digest food
• Bacterial overgrowth (such as SIBO) — where bacteria proliferate in the wrong part of the digestive tract
• Microbiome disturbances (dysbiosis) — an imbalance in gut bacteria that disrupts normal digestive function
• Parasites — more common than many people assume, particularly in those who swim in open water or travel frequently

Each of these requires a different approach. Treating the wrong cause — or applying a blanket solution without investigating — is why so many people cycle through remedies without lasting relief.

Why Food Elimination Diets Often Fall Short

When digestive symptoms become problematic, many people turn to elimination diets — FODMAP, low-carb, paleo, or gluten-free protocols are among the most common. In many cases, symptoms do improve on these approaches, and there is a reason for that.

Most elimination diets are low in fermentable fibres. Reducing these fibres means less fuel for fermentation in the gut, which reduces gas, bloating, and distension. But — and this is important — it does not fix the underlying problem. It simply removes the trigger.

Unless you get to the root cause of the issue, symptom relief from elimination diets will be short-lived. And a long-term low-fibre diet is not a healthy solution.

There is also a widely held misconception worth addressing here:

💡 Did you know? Gluten — the protein found in wheat — does not actually cause bloating in most people. It is fructan, the carbohydrate component of wheat, that ferments in the gut and causes bloating and distension. This distinction matters enormously when it comes to identifying the real trigger.

The Problem With Reaching Straight for Probiotics

Another very common response to digestive symptoms is to start taking a probiotic supplement — often one marketed with billions of bacteria and impressive-sounding strains.

While probiotics can be genuinely valuable in the right context, they are not a universal solution. If the underlying issue is bacterial overgrowth or gut dysbiosis, introducing large quantities of additional bacteria can actually make symptoms significantly worse.

More bacteria is not always better. The goal is the right balance — and that requires understanding what is actually happening in your gut first.

The Long-Term Consequences of Untreated Poor Digestion

Beyond the day-to-day discomfort, the long-term implications of poor digestive function are significant. The primary concern is nutrient deficiency.

Key micronutrients that depend on effective digestive function for absorption include:

• Iron — essential for energy, oxygen transport, and immune function
• Vitamin B12 — critical for nerve function, red blood cell production, and energy metabolism
• Folate — vital for cell repair, methylation, and red blood cell formation
• Zinc — important for immune function, wound healing, and hormone balance

These nutrients are readily available from a balanced diet — but only if the digestive system is working effectively enough to absorb them. Persistent deficiencies in these nutrients, despite adequate dietary intake, are often a signal that digestive function deserves closer attention.

A Special Note for Endurance Athletes

Athletes — particularly endurance athletes — are at significantly higher risk of digestive issues than the general population, and it is an area that is frequently overlooked in sports nutrition practice.

Why athletes are more vulnerable:

• Exercise-induced gut inflammation — endurance exercise, especially running, causes mechanical stress and increased gut permeability
• Exposure to contaminated water — triathletes swimming in open waterways, trail runners drinking from taps or streams, and athletes travelling internationally are at elevated risk of parasitic or bacterial infection
• High carbohydrate intake — the large volumes of carbohydrate required to fuel endurance training can increase fermentation in the gut, particularly in those with pre-existing microbiome imbalances
• Compromised recovery — chronic training loads reduce the gut’s ability to repair and maintain its lining between sessions

 

When digestive symptoms start to interfere with training, energy levels, and recovery, it becomes far more than a comfort issue. It is a performance issue — and one that deserves a proper clinical investigation rather than a trial-and-error approach to supplements and elimination diets.

What About Testing?

There are a number of diagnostic tests available to help identify the underlying cause of digestive symptoms. Working with a qualified nutritionist or naturopath is the best way to determine which tests are appropriate for your situation — because while testing can be extremely valuable, it can also be expensive, and using the wrong test leads to wasted time and money without useful answers.

One important note: food intolerance testing is a commonly requested option, and while it has its place in certain contexts, it is not useful for identifying the cause of bloating or excess wind. If that is your primary symptom, there are more targeted and informative tests available.

Getting to the Root Cause

If you are experiencing any of the symptoms described in this post — whether occasional or persistent — the most important thing is not to normalise them. Bloating, reflux, irregular bowels, and chronic fatigue are common, but they are not inevitable, and in most cases they are very addressable once the underlying driver is identified.

A personalised approach that looks at your symptoms, diet, training load, lifestyle, and health history is far more effective than generic protocols. What works for one person may worsen symptoms in another — and that is precisely why individual assessment matters.

You do not have to keep managing symptoms. With the right investigation and support, it is possible to resolve them.

Work With Me

At Mad on Nutrition, I work with individuals and athletes to investigate the real drivers of digestive symptoms and build a personalised plan to address them — without unnecessary elimination diets or guesswork.

If you are experiencing any of the symptoms mentioned above and would like support, get in touch via the contact page or book an appointment online.

You deserve to feel well — not just manage symptoms.