Why You Can’t Heal Your Gut If You Have CFS

Why You Can’t Heal Your Gut If You Have CFS

There is a fascinating overlap between chronic fatigue syndrome (CFS) and irritable bowel syndrome (IBS). Depending on the study, rates vary, but in clinical practice the overlap can be as high as 90%.

If you’re someone who has tried all the gut-focused strategies—elimination diets, supplements, time-restricted eating, probiotics, vagus nerve exercises—and still feel stuck, there may be another layer to the story.

The missing piece for some people isn’t in the gut at all. It’s in the mitochondria—the tiny power plants inside your cells.

Why Gut Healing Fails in Some Cases of CFS

When we say someone has chronic fatigue syndrome, what we really mean is that their cells have a reduced capacity to make energy (ATP). This doesn’t just affect muscles and the brain—it affects the gut too.

The gut is lined with specialized cells that require a lot of energy to perform their jobs:

• Parietal cells (stomach): These produce stomach acid. Low stomach acid contributes to poor digestion and increases the risk of SIBO (small intestine bacterial overgrowth). Betaine HCl supplements may provide temporary relief, but they don’t fix the root problem—low energy in the parietal cells.

• Paneth cells (small intestine): These produce antimicrobial peptides that keep gut bacteria in check. If they’re underpowered, bacteria can overgrow, leading to stubborn SIBO.

• Colonocytes (colon): These nourish the gut lining and support a balanced microbiome. Poor energy means weakened barrier function, more inflammation, and microbiome disruption.

No amount of antimicrobials, probiotics, prebiotics, or restrictive diets can permanently fix the gut if the cells themselves lack the energy to do their jobs. That’s why some people feel like they have “incurable” digestive issues. The truth is, they’ve been using the wrong tools.

The Real Target: Mitochondrial Health

To restore gut function in these cases, you have to go deeper and support mitochondrial function.

Think of it as two main pillars:

1. What Mitochondria Need to Thrive

Mitochondria run on more than just oxygen, glucose, and fat. They also rely on key nutrients and lifestyle inputs:

• Nutrients & cofactors: CoQ10, alpha-lipoic acid, B vitamins, glutathione, iron, copper, magnesium, carnitine, omega 3 among others.

• Lifestyle inputs: Regular physical activity, cognitive stimulation, a healthy circadian rhythm, deep restorative sleep.

(Note: Never supplement iron or copper without testing, as too much can be harmful.)

2. What Damages Mitochondria

Even with the right nutrients, mitochondria can’t thrive if they’re under constant stress from:

• Chronic inflammation

• Toxins (environmental, mold, heavy metals)

• Certain medications (e.g., statins)

• Lack of exercise or mental engagement

• Overeating and unstable blood sugar

• Hormone deficiencies (estrogen, testosterone, thyroid)

• Sleep disruption and circadian rhythm problems

• Hypoxia (low oxygen, often linked to breathing issues or poor circulation)

Both sides matter: give mitochondria what they need, and remove what holds them back.

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Lifestyle Foundations for Restoring Energy & Gut Health

This isn’t just about taking a supplement stack. Supporting your mitochondria (and therefore your gut) often requires a broader life overhaul:

• Light & circadian rhythm: Limit blue light exposure at night, prioritize morning sunlight, and stick to consistent bedtimes. Blue light at the wrong time can stress mitochondria.

• Movement: Regular, moderate physical activity is the most powerful trigger for mitochondrial biogenesis—the creation of new, healthy mitochondria.

• Nutrition:

  • Balance blood sugar with adequate protein and fiber.

  • Limit refined carbs and ultra-processed foods.

  • Consider a paleo-style diet (high in whole-food fats, moderate protein, lower carbs).

  • In severe cases, some may benefit from a ketogenic diet, but this isn’t necessary for everyone.

• Mental stimulation & connection: Engaging the brain and nervous system also supports mitochondrial health.

Final Thoughts

If you’ve been endlessly chasing gut-specific solutions with little success, it might not be your gut that’s the problem—it’s your cellular energy system. By rebuilding mitochondrial health, you give your gut cells the energy they need to actually perform their functions.

Only when energy production is restored can long-term gut healing truly take place.