So how do microbes in the gut affect inflammation?

Lee Marais
May 3
2 min read

Certain gut bacteria – when imbalanced – can absolutely increase your risk of chronic inflammation and autoimmune diseases. This imbalance is called dysbiosis, and it can trigger the immune system to go into overdrive, especially in genetically susceptible individuals.

🚨 Gut Bacteria Linked to Inflammation & Autoimmune Risk

Here are the key culprits:

🔴 1. Prevotella copri

Problem: Often found in excess in people with rheumatoid arthritis (RA).
How it harms: It stimulates immune cells and increases production of inflammatory molecules (cytokines).
Studies: Strongly linked to early RA and can cross-react with body tissue (molecular mimicry).

🔵 2. Escherichia coli (pathogenic strains)

Problem: Some strains of E. coli (especially adherent-invasive types) are linked to inflammatory bowel disease (IBD).
How it harms: Invades gut lining, activates inflammation, and disrupts the mucosal barrier.
Increased in: Crohn’s disease, ulcerative colitis.

🟣 3. Clostridium difficile

Problem: Overgrowth often follows antibiotic use.
How it harms: Produces toxins that damage the intestinal lining and spark a strong immune response.
Linked to: Chronic inflammation and gut permeability (leaky gut), which can trigger autoimmune flares.

⚫ 4. Ruminococcus gnavus

Problem: Linked to lupus and IBD.
How it harms: Produces pro-inflammatory polysaccharides, fuels gut inflammation, and can break down the protective mucus lining.
Found in: Lupus flares and IBD relapses.

🟤 5. Bacteroides fragilis (enterotoxigenic strains)

Problem: Some strains produce toxins that lead to inflammation and may promote multiple sclerosis (MS) and colitis.
How it harms: Alters the balance of T cells (especially pro-inflammatory Th17 cells).
Not all B. fragilis are bad – non-toxigenic strains can be beneficial.

⚠️ Bonus Villains: Yeast & Fungi (like Candida albicans)

Not a bacteria, but worth mentioning. Candida overgrowth can trigger immune responses, gut inflammation, and worsen autoimmune symptoms.

💡 What Makes These Bacteria Thrive?

High-sugar, high-fat diets
Antibiotic overuse
Chronic stress
Poor sleep
Lack of fiber and prebiotics
Alcohol and food intolerances (especially gluten and casein in autoimmune patients)

✅ Helpful Gut Bacteria (The Peacekeepers)

These are the ones you want in your corner to reduce inflammation and protect against autoimmunity:

Helpful Bacteria	Benefit
Faecalibacterium prausnitzii	Major anti-inflammatory species (low in IBD, RA)
Bifidobacteria	Strengthen gut lining, regulate immunity
Akkermansia muciniphila	Protects mucosal lining, reduces obesity-linked inflammation
Lactobacillus spp.	Produces anti-inflammatory compounds
Butyrate-producing bacteria	Create short-chain fatty acids (SCFAs) that nourish the gut wall and reduce inflammation

🛠️ What You Can Do Naturally

Feed good bacteria: Prebiotics (onions, garlic, leeks, chicory, green bananas)
Use targeted probiotics (strain-specific, e.g., Lactobacillus rhamnosus GG, Bifidobacterium longum) NOT ALL PROBIOTICS ARE CREATED EQUAL!
Avoid overuse of antibiotics
Fix leaky gut with glutamine, zinc, slippery elm, and herbs
Balance for blood type – certain types handle fermented foods/probiotics better than others