The Gut, Illness, and Weight Gain: The Dirty Truth About Your Microbiome

What’s Living in Your Gut (And Why It Matters)

Your body is not just yours. You’re basically a walking, talking ecosystem for trillions of microorganisms—bacteria, fungi, viruses, and even parasites—that call your gut home. These microbes are collectively known as the microbiome and play an essential role in digestion, immunity, metabolism, and even mental health. In fact, your microbiome is so vital that scientists consider it an organ in its own right.

Think of your microbiome as an exclusive nightclub where good bacteria are the VIPs and harmful bacteria are the troublemakers. If too many gate-crashing bad microbes show up (a state called dysbiosis), the bouncers get overwhelmed, and chaos ensues—leading to inflammation, disease, and even weight gain.

Your microbiome is initially shaped by factors like your DNA, birth method (vaginal vs. C-section), and early diet (hello, breast milk prebiotics!). But as you grow, your gut’s guest list can be altered by diet, environment, stress, medications (especially antibiotics), and lifestyle choices.

Food: The Microbiome’s Make-or-Break Factor

Your gut bacteria have a major sweet tooth for fibre—the kind found in vegetables, fruit, nuts, seeds, and whole grains. A high-fibre diet feeds good bacteria, promoting the production of short-chain fatty acids (SCFAs) like butyrate, which help reduce inflammation and protect against disease (BMJ, 2021).

On the flip side, diets high in processed foods, sugar, artificial sweeteners, and unhealthy fats act like an open bar for harmful bacteria. Artificial sweeteners such as aspartame and sucralose can throw your gut out of whack (BMJ Gut, 2022), while food additives like emulsifiers (found in many packaged foods) are linked to inflammation and an increased risk of metabolic disorders.

The Hidden Dangers of Artificial Sweeteners

Artificial sweeteners might seem like the perfect fix for those avoiding sugar, but they come with a major downside—they disrupt the gut microbiome. Research has shown that aspartame, sucralose, and saccharin alter gut bacteria in ways that increase glucose intolerance and insulin resistance, leading to higher risks of weight gain, metabolic disorders, and type 2 diabetes (Nature, 2023). Some studies even suggest that artificial sweeteners may trick the brain into craving more calories, making it easier to overeat.

Better alternatives? Swap artificial sweeteners for natural options like stevia and monk fruit, which don’t seem to have the same negative effects on gut bacteria. These plant-based sweeteners provide sweetness without spiking blood sugar or interfering with microbial balance.

The Western Diet: A Gut Disaster

A low-fibre, high-fat, and high-sugar diet—typical of Western eating patterns—can lead to a decline in microbial diversity, which is bad news for metabolism and immune function. Research links this imbalance to obesity, diabetes, and even mental health conditions like depression and anxiety (BMJ, 2023).

Moral of the story? Feed your gut well, and it will return the favour.

Antibiotics: Lifesavers with a Dark Side

Antibiotics revolutionised medicine, saving millions of lives. But their overuse is now creating superbugs—bacteria resistant to antibiotics—leading to 23,000 deaths annually in the U.S. alone (CDC, 2024). Even more concerning? Some researchers predict 10 million deaths annually from antibiotic resistance by 2050—making it deadlier than cancer (Lancet, 2023).

But that’s not all. Frequent antibiotic use wipes out not only bad bacteria but also the good ones, damaging the microbiome. This has been linked to a rise in autoimmune diseases, allergies, autism, and metabolic disorders. And it’s not just direct antibiotic use—industrial farming practices that rely on antibiotics also contribute to gut imbalance when we consume antibiotic-treated foods (BMC Vet Res, 2017).

Pesticides and Herbicides: Gut-Wrecking Chemicals

Modern farming has made food more abundant, but pesticides and herbicides, particularly glyphosate (a key ingredient in Roundup), are a gut health nightmare. Research suggests glyphosate disrupts gut bacteria, with 54% of core gut bacterial species showing sensitivity to it (PMC, 2022).

People with high pesticide exposure (e.g., farmers, agricultural workers) tend to have lower gut diversity, which is linked to inflammatory and autoimmune conditions (Frontiers, 2021). Even low-dose pesticide residues in food and water may have long-term health consequences, including metabolic and neurological disorders (Nature, 2023).

The Gut-Illness Connection: Why Microbiome Health Matters

A dysfunctional microbiome isn’t just about bloating or digestive issues—it’s linked to major chronic diseases, including:

• Obesity & Metabolic Disorders – An unbalanced gut microbiome influences how you store fat, absorb nutrients, and regulate hunger hormones. Certain bacterial strains are associated with weight gain and insulin resistance(Nature, 2024).

• Cardiovascular Disease – Some gut bacteria produce compounds that increase inflammation and plaque buildup in arteries, raising the risk of heart disease (JAMA Cardiology, 2023).

• Mental Health Disorders – The gut-brain axis is real. An imbalance in gut bacteria has been linked to depression, anxiety, and neurodevelopmental disorders (EHP, 2023).

• Autoimmune Diseases – Conditions like rheumatoid arthritis, lupus, and multiple sclerosis are increasingly associated with gut dysbiosis and chronic inflammation triggered by an imbalanced microbiome (Lancet, 2024).

What You Can Do to Improve Your Gut Health

1. Eat for Your Microbiome

• Prioritise high-fibre foods (veggies, nuts, seeds, whole grains).

• Incorporate fermented foods (yoghurt, kefir, sauerkraut, kimchi).

• Reduce processed foods, artificial sweeteners, and additives. Switch to stevia or monk fruit instead.

2. Rethink Antibiotics

• Thank goodness for modern medicine but only take antibiotics when necessary.

• Choose organic, antibiotic-free meat and dairy whenever possible and if you’re like me, when on sale.

3. Avoid Pesticide-Heavy Foods

• Buy organic when you can, especially for high-residue produce like berries and leafy greens.

• Wash produce thoroughly and consider a vinegar soak to reduce pesticide residues.

4. Probiotics & Prebiotics: Friends with Benefits

• Probiotics (good bacteria) can be found in fermented foods and supplements.

• Prebiotics (food for good bacteria) are found in high-fibre plant foods.

• Work with an integrative health practitioner to find the right probiotic strains for you.

Bottom Line? Your Gut Holds the Key to Health

If you’ve been struggling with stubborn weight, fatigue, digestive issues, or chronic illness, your gut might be sending you a distress signal. The microbiome is one of the most powerful, yet underappreciated, regulators of health—and it’s something you can actively improve through diet and lifestyle choices.

So, what’s it going to be? Feed your microbiome the right way, and it will pay you back in spades. If you’re interesting in learning more about gut health and the gut brain connection, learn more about my Gut Health course here.