Bacteria in the digestive tract exist in two main ways—First, within a polysaccharide matrix known as a biofilm that adheres to the intestinal lining or to digestive contents, or second, floating in a non-adherent manner as single cells. In the natural world, 99 percent of all bacteria exist as biofilms,1 so the study of biofilms in the gut is proving to be particularly interesting. Biofilms may be beneficial, neutral, or harmful depending on the bacteria found within them. I’ve blogged about the harmful Candida biofilm, and today I’ll talk about beneficial biofilms.

Bacteria form biofilms as a protective mechanism against other bacteria and antibiotics, and beneficial biofilms help modify and balance the immune system. Bacteria behave differently when found in a biofilm—they behave like a multicellular organism,2 in fact. In a biofilm, bacteria can more easily communicate with each other,3 through a process known as quorum sensing, and can share nutrients and even genetic material due to their close proximity.4

In the gut, biofilms adhere to the mucosal lining of the intestine and to the contents that pass through it.5 Biofilms associated with the mucosal lining are particularly important due to their intimate interaction with the immune system, which exists in and around the intestinal lining. Further, mucosal associated biofilms—when made up of beneficial bacteria—serve to protect against invaders like pathogens, undigested food particles, and endotoxins (bacterial toxins).

Other types of important biofilms exist in the lumen (the space inside the intestine). These biofilms, also important, stick to the digestive contents passing through. They are often made up of transient bacteria, which pass through the intestines with food. When made up of beneficial bacteria, these biofilms help with the break down and production of nutrients and other metabolites important for health.6

A recent study published in the journal Current Nutrition & Food Science identified the ability of breast milk to form a healthy biofilm when used as a substrate for the growth of the beneficial infant microbe, E. coli (not to be confused with the pathogenic E. coli) when compared to infant formula or cow’s milk, both of which did not form biofilms when cultured.7

“Only breast milk appears to promote a healthy colonization of beneficial biofilms, and these insights suggest there may be potential approaches for developing substitutes that more closely mimic those benefits in cases where breast milk cannot be provided,” stated William Parker, PhD, lead researcher of the study.

This study gives yet one more reason why “breast is best,” but it also provides hope that an infant formula that more closely resembles breast milk may eventually be developed so that more babies will get the nutrition they need to set their digestive systems up the way breast milk does. In the meantime, probiotics and prebiotics are recommended for pregnant mothers, and often, for infants, to help support a healthy digestive system—the foundation for total-body health.


  1. J.W. Costerton, et al., “Bacterial biofilms in nature and disease.” Ann Rev Microbiol. 1987 Oct;41:435–65.
  2. P. Watnick and R. Kolter, “Biofilm, city of microbes.” J Bacteriol. 2000 May;182(10):2675–9.
  3. E.P. Greenberg, “Bacterial communication and group behavior.” J Clin Invest. 2003 Nov;112(9):1288–90.
  4. B. Prakash, et al., “Biofilms: A survival strategy of bacteria.” Curr Sci. 2003 Nov;85(9):1299–1307.
  5. S. Macfarlane and J.F. Dillion, “Microbial biofilms in the human gastrointestinal tract.” J Appl Microbiol. 2007 May;102(5):1187-96.
  6. S. Macfarlane and G.T. Macfarlane, “Composition and metabolic activities of bacterial biofilms colonizing food residues in the human gut.” Appl Environ Microbiol. 2006 September; 72(9): 6204–6211.
  7. A.Q. Zhang, et al., “Human whey promotes sessile bacterial growth, whereas alternative sources of infant nutrition promote planktonic growth.” Curr Nutr Food Sci. 2012 Aug;8(3):168–176.