Treatment Guide

Probiotics and altered gut flora – Winning the war on terrorism in your gut

probiotics celiac glutenProteins produced from partial breakdown of microorganisms are often recognized by the body’s immune system as foreign antigens triggering production of antibodies that may be detected in the blood.

Such antibodies include proteins from the cell walls (outer membranes) or flagella of the bacteria Escherichia coli and the yeast Saccharomyces cerevisiae (Baker’s or Brewer’s yeast) that are found in Crohn’s disease. Stimulation of the immune system by these proteins can also confuse the body into thinking that it needs to continue fighting an ongoing battle against an invader. The resulting ongoing intestinal inflammation and immune stimulation associated with a leaky gut frequently initiates a self-perpetuating process whereby the body attacks or injures itself long after an infection or invading microorganism has been destroyed. This is autoimmunity. The resulting self-damage may occur locally in the gut or in distant parts of the body most typically in the brain or nerves, skin, joints and various glands such as the pancreas and thyroid.

Increased permeability of the gut due to loss of preservation of the normal barrier of the intestinal tight junctions can predispose to further injury from microorganisms and/or food proteins. This vicious cycle of gut injury combined with altered gut flora, leaky gut, food sensitivity, gut inflammation, and increased leaky gut is now being recognized as one the critical links to various bowel inflammation, neurological and autoimmune diseases.

Probiotics are increasingly being shown effective in many conditions. By replacing depleted good microorganisms and restoring the normal gut micro ecology probiotics have been shown to have a beneficial effect in numerous gastrointestinal conditions. The commonly used probiotics consist of one or more strains of live bacteria from various Lactobacillus, Acidophilus and Bifidobacteria species. The most studied commercially available probiotic is VSL#3 that contains billions of live bacteria of several species. However, the yeast Saccharomyces boulardii has also been shown to be beneficial in several intestinal conditions. Several recent studies highlight the importance of gut flora in colitis, Crohn’s disease, irritable bowel syndrome, antibiotic associated diarrhea (Clostridium difficile infection), traveler’s diarrhea, and celiac disease.

Tjellström et al from Sweden noted short chain fatty acids (SCFA), one of the healthy byproducts of normal microflora in the gut, were altered in children with celiac disease. Altered SCFA levels are believed to be associated with disturbed gut nutrition for the lining cells as well as failure to protect against certain disease causing bacteria. What they proposed is that altered gut flora result in high intestinal lining cell turnover and large amounts of undigested proteins being presented to the gut flora resulting in development of celiac disease in the genetically predisposed especially in the setting of another event such as a virus infection. They concluded “our finding may well reflect a deviant gut flora in CD, which may be a new piece in the intriguing puzzle…” VSL#3 probiotic added to wheat flour has also been shown to be able break down gliadin the toxic protein in celiac disease.

Bacterial antigens (proteins) from live bacteria were shown by Sydora et al to increase intestinal permeability and initiate injury to the gut resulting in inflammation or activation of the infection fighting immune process. They demonstrated in a mouse model that although both dead and live forms of certain bacteria could cause increased intestinal permeability or leaky gut only live bacteria triggered intestinal inflammation. Though the focus of their study was how bacteria may play a role in the development of inflammatory bowel diseases (e.g. colitis and Crohn’s disease), their findings may add to the clues the role of microorganisms in leaky gut that predisposes to a variety of gastrointestinal disorders. It also lends credence to the clinical observation, research data and patient experience that various antibiotic and/or probiotic regimens are often beneficial for many patients with gastrointestinal conditions.

Probiotics contain live bacteria or yeasts that have beneficial health effects. They restore the balance of microorganisms in the gut. They produce natural antibiotics that keep bad bacteria from overgrowing in the intestine. Probiotic bacteria produce nutrients including short chain fatty acids that are health food to the intestinal lining cells that maintain the gut barrrier thereby preventing leaky gut. Probiotic bacteria may break down toxic food proteins like gliadin whereas bad bacteria may act in concert with gliadin to injure the gut. Probiotic yeast Saccharomyces boulardii also appears to help regulate the immune system in the gut. Probiotics are helping win the war on terrorism in the gut.


Gut microflora associated characteristics in children with celiac disease. Tjellström, B, et al. American Journal of Gastroenterology 2005; 100; 2784-2788.

Bacterial antigens alone can influence intestinal barrier integrity,

but live bacteria are required for initiation of intestinal

inflammation and injury. Sydora, B. et al Inflammatory Bowel

Diseases 2006; 12:429-436.

VSL#3 probiotic preparation has the capacity to hydrolyze

gliadin polypeptides responsible for Celiac Sprue. De Angelis

M. et al. Biochim  Biophys Acta. 2006; 1762(1): 80-93

Probiotics prevent bacterial translocation and improve barrier

function in rats following chronic psychological stress. Zariee,

M. et al Gut 206; 55:1553-1560.

Copyright 2007 The Food Doc, LLC All Rights Reserved.

The Food Doc, Dr. Scot Lewey, is an expert medical doctor specializing in digestive diseases and food related illness, especially food allergies, celiac disease and colitis.

About Dr. Scot Lewey

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  1. Do you need to take probiotics continuously or is a treatment of a month long enough?

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