The Fiber Paradox: Why Carnivore and Low-Carb Diets Heal IBD Symptoms (And What Happens to Your Gut Bugs)

Science overwhelmingly supports diverse plant fiber as the foundation of a healthy microbiome. Yet thousands of individuals with IBD, IBS, and autoimmune issues report that removing fiber—via Carnivore or low-carb diets—brings dramatic relief. This paradox reveals an important nuance.

Short-term healing on low-fiber diets likely comes from two mechanisms:

• Elimination of inflammatory triggers: Cutting refined sugar, grains, and seed oils removes the root irritants common to Western diets.
• Starving maladaptive microbes: In SIBO and similar conditions, starving sugar-loving bacteria reduces bloating, pain, and dysbiosis. Roughly 61% of obese patients may have SIBO, where bacteria overgrow in the small intestine.

Experts emphasize that symptomatic relief ≠ microbial healing. A gut starved of fiber will calm inflammation temporarily but loses the ability to produce Short-Chain Fatty Acids (SCFAs)—the essential fuel for gut barrier health.

People are torn between scientific guidance (more fiber) and lived experience (feeling better without it). If removing fiber feels healing, how can science claim it’s harmful long term? The contradiction creates distrust and confusion. They want to understand why carnivore-style diets relieve symptoms when fiber supposedly defines gut health.

View low-fiber or Carnivore phases as elimination diets—temporary resets that quiet inflammation and remove triggers. But once stable, rebuild capacity slowly: the gut is like a muscle that must relearn to digest fiber. Gradual reintroduction restores diversity and SCFA production—the true markers of gut health.

• Dr. Will Bulsiewicz
  • Clarity: High. Explains that Carnivore relief stems from removing processed foods, not fiber itself. Notes that long-term zero-fiber diets destroy microbial diversity. Gut healing requires gradual fiber “training.”
  • Unique Advice: Suggests using probiotics like Saccharomyces boulardii before reintroducing fiber to ease IBS-D or SIBO transitions.
• Dr. Pradip Jamnadas
  • Clarity: Moderate. Advocates fasting and whole foods. Explains that fasting kills harmful microbes while preserving beneficial ones—supporting temporary relief for those with bacterial overgrowth.
  • Unique Insight: Connects low-carb eating to reduced gut overgrowth, noting that excess carbs feed bacteria in the ileum.
• Dr. Justin Sonnenburg
  • Clarity: High. Endorses fiber for long-term stability but acknowledges short-term benefits of keto/carnivore diets for metabolic disorders.
  • Unique Warning: Cautions that layering purified fibers on high-fat diets can cause “weird metabolism” and inflammation. Prioritize whole-food fiber diversity for sustained SCFA production.

If you’re thriving on low-carb or Carnivore eating, the benefit likely comes from removing processed foods and giving your gut a rest. While symptoms are calm, begin introducing fermented foods—like sauerkraut brine or kefir—to restore live microbes and prepare your gut for future fiber reintroduction.

• Mistake: Assuming comfort equals healing.
  Fix: If you can’t reintroduce fiber without flaring, the ecosystem remains weak.
• Mistake: Reintroducing fiber too fast.
  Fix: Go slow. Cook plants well and start with small portions.
• Mistake: Using purified fiber in high-fat diets.
  Fix: Stick with whole foods to prevent abnormal fermentation and inflammation.
• Mistake: Believing meat alone sustains gut health.
  Fix: SCFAs from fiber are essential for barrier integrity; zero-fiber eventually weakens this system.

• "After 22 years of ulcerative colitis, going Carnivore removed all symptoms within a week."
• "Fiber made my IBS worse; only Carnivore stabilized me, then I could slowly add veggies back."
• "Water fasting and psyllium-kefir refeeding reset my gut completely."
• "Three years Carnivore—off meds and finally symptom-free."

The Fiber Paradox shows that symptom relief is not the same as microbial recovery. Zero-fiber diets calm inflammation by elimination, not by restoration. Long-term gut strength requires gradual fiber training and fermented food diversity to rebuild SCFA-producing bacteria and sustain resilience against chronic disease.