Research & Education

Viva la Commensal Biofilm

Gastrointestinal biofilms are an important topic and those comprised of pathogenic microbes are getting much well-deserved attention in the integrative medical community. However in keeping with the sIgA topic I want to give a shout-out to commensal biofilms which are vital to GI health and deserve similar attention. 

Biofilms are everywhere allowing bacteria to survive -- good or bad. They are found at the solid-liquid interface in most environments. Indeed dental plaque is a biofilm as is the slime on an icky bathtub. Biofilms are comprised of bacteria (and/or other microbes) and an extracellular matrix of excreted polymeric polysaccharides. 

Simply put: bugs + goo = slime (biofilm). 

Slime is nothing to joke about! Biofilms allow pathogenic organisms to be antibiotic resistant up to 1000-fold by one estimate. But biofilms comprised of commensals can be our friends modulating our immune response supporting GI integrity and reducing inflammation. 

Research on commensal GI biofilm shows that E. coli bifidobacteria and L. reuteri are apparently efficient producers with the former mediated by sIgA and mucin. Research suggests commensal biofilms may be anti-inflammatory modulate cytokine production and crowd out pathogenic biofilms.

One study in rats with human-type flora showed improved bifidobacteria biofilm mucus thickness villous height crypt depth and mucin-producing goblet cell numbers when supplemented with inulin-type fructans. How cool is that? 

How can we tell if our GI commensal biofilm is healthy? 

On a stool test I would be concerned if I didn't see enough bifidobacteria lactobacillus commensal E. coli or sIgA. Glutamine vitamin A and S. boulardii support sIgA production; whereas the inulin mentioned above plus probiotic supplementation will help facilitate commensal bacterial growth. Finally treating inflammation and minimizing unwarranted antibiotic use should also benefit biofilm status. 

I think we can say that biofilms are little ecosystems unto themselves where "the sum is greater than the parts. And when we're thinking about protection of our all-important GI microbiota the commensal biofilm is once slimy surface we don't want to slip away!


by Dr. Kara Fitzgerald



Dr. Fitzgerald received her doctorate of naturopathic medicine from National College of Natural Medicine in Portland Oregon. She completed the first CNME-accredited post-doctorate position in nutritional biochemistry and laboratory science at Metametrix Clinical Laboratory under the direction of Richard Lord Ph.D. Her residency was completed at Progressive Medical Center a large integrative medical practice in Atlanta Georgia. Dr. Fitzgerald is lead author and editor with J. Alexander Bralley Ph.D. of The Metametrix Institute's Case Studies in Integrative and Functional Medicine. She is a contributing author to Laboratory Evaluations for Integrative and Functional Medicine and the Institute for Functional Medicine's updated Textbook for Functional Medicine. She has also published in a number of peer reviewed journals. Dr. Fitzgerald is on faculty and a Curriculum Advisory Committee member at Institute for Functional Medicine. She is an adjunct faculty member at University of Bridgeport in the school of Human Nutrition and a member of The Institute for Therapeutic Discovery. Dr. Fitzgerald regularly lectures internationally for several organizations. Formerly at Advanced Diagnostic Pain Treatment Center at Yale-New Haven she is now in private practice in Sandy Hook Connecticut. She may be reached at or