23/10/2026
Crohn’s disease isn’t just about an overactive immune system. The gut microbiome may play a much bigger role than we once thought.
Through comprehensive metagenomic stool testing, I often see recurring microbial patterns in patients with inflammatory and autoimmune gut conditions, including:
➡️ Increased potentially pro-inflammatory bacteria, including certain strains of E. coli
➡️ low to no mucin degrading bacteria’s such as akkermansia
➡️ Reduced microbial diversity, richness and less beneficial, butyrate-producing bacteria.
➡️ Changes in metabolites that influence intestinal barrier integrity and immune regulation.
➡️ An imbalance between potentially pathogenic and protective species.
Adherent-invasive E. coli (AIEC) has been associated with Crohn’s disease because it can adhere to the intestinal lining, invade cells and survive within immune cells, potentially perpetuating inflammation.
But E. coli is only one piece of a much larger microbial puzzle.
Metagenomic testing help identify dysbiosis patterns contributing to an individual’s inflammatory burden, allowing for more targeted dietary and therapeutic strategies to support microbial diversity, gut barrier function and immune regulation.
Of course, association doesn’t equal causation, and microbiome-directed interventions don’t replace conventional Crohn’s treatment. We’re still learning which microbial changes lead to meaningful clinical improvements and best outcomes are seen using both conventional and specific microbial/nutraceutical interventions.
When working with a Crohn’s patient, the goal isn’t simply to eliminate a pathogen. It’s to restore an intestinal environment that is less conducive to chronic inflammation.
Because when it comes to gastrointestinal health, what lives in your gut matters.
