Pamela Gilford, MA, CCN

Acceptance of the germ theory of disease unleashed a two-century war between humanity and the unseen microbial world. First, better sanitation, and after WWII, the advent of antibiotic treatment, saved millions of lives. Bacteria were the enemy; babies were even bathed in a toxic, chlorinated wash now withdrawn from the market. The presence of bacteria in the GI tract was treated as nature's "mistake." Who cared that oral antibiotics killed off some gut flora? Oral delivery avoided that unpleasant shot in the buttocks.

The mysterious rise in autoimmune disease since the development of modern antibiotic therapy has been one clue that humans might not be winning the war against microbes (see references below). A slow reassessment of the microbes, grudgingly referred to as "GI commensals" (harmless organisms) began. The genesis of pathogenicity has been discovered to be a two-way street between the human immune system and microbes, now referred to as a "relationship". Multi-celled, "higher" organisms clearly coevolved with one-celled organisms to mutual benefit. Microbes help us digest our food and provide certain vitamins. The microbes that line most of our GI tract defend our GI mucosal lining against invading pathogens, and as they begin to colonize the sterile gut of a newborn, they "educate" the child's immune system.

Multi-celled host organisms (like us) provide food, water, physical safety, and transportation. How else could microorganisms have extended their range without transportation? Humans have been particularly helpful. If this notion seems odd, think about syphilis coming to the New World with the first ocean explorers, and more recently, HIV and ebola making the crossing.

Although the variety of our GI flora has been known for a long time (See Theodor Rosebury's Life on Man, 1969), the advent of DNA tools to catalog species has spurred new interest in how human metabolism interacts with GI flora. The National Institute of Health's huge Human Microbiome Project is now nearing completion (see Evidence-based probiotic supplements for medical use are eagerly anticipated, although the first truly "evidence-based"probiotic was probably Lactobacillus GG, or Culturelle, discovered in cheek swabs by two researchers from Tufts University (see references below). Goldin and Gorbach patented Culturelle in 1985 for treatment of diarrhea caused by Clostridia difficile in children and has since been the subject of several hundred studies. Subsequent DNA analysis has granted this strain of bacteria a species designation of Lactobacillus rhamnosus and it is now incorporated into many commercial probiotic blends.

Studies have shown that variations in the species composition of gut microflora are related to the risk of obesity and that probiotic treatment often improves mood (see references below). Inflammation, which can be modulated by healthy gut flora, has become definitively linked to the epidemic of depression worldwide, as well as the genesis of many chronic diseases (see – many articles).

Clinical Endocrinology News reports that 64% of family physicians are stressed and uncomfortable when faced with treating autoimmune disease (see reference below) The fact that available allopathic therapies come with substantial side effects does not improve the practitioners' or patients' comfort levels. The frustration of both in finding safe therapies for autoimmune and chronic disease has certainly contributed to the growing popularity of integrative or CAM approaches. An article in Science magazine from November 2013 (see reference below) cited research by Mathis and Littman who found that Prevotella copri was present in 75% of RA patients' intestines. Later, they were able to trigger inflammation in mice by inoculating with the bacterium. Such studies add weight to clinicians' observations that probiotic treatments and even fecal implants can often halt the progress of chronic diseases.

We have been discussing our microbial passengers and an important part of the organic acids test is the assessment of the level of metabolites of pathogenic microbes, including yeast and Clostridia bacteria. The COMP stool test cultures both beneficial and potentially pathogenic microbes and microscopic examination can catch both yeast and one-celled parasites. When we added the Candida marker to the IgG food allergy test, we discovered a very useful tool for determining if a patient has become sensitive to his/her own native fungal flora. At The Great Plains Laboratory, we believe that the metabolic and and toxic element assessments we offer assist in directing treatment protocols that can mediate many chronic conditions, eliminate harmful microbes, and reinforce beneficial gut flora for improvement in overall health.

Clinical References:

  • Hunter, P. 2012. The changing hypothesis of the gut. The intestinal microbiome is increasingly seen as vital to human health. Science and Society DOI 10.1038/embor.2012.68 |Published online 15.05.2012, EMBO reports(2012)13,498-500
  • Thomas Jefferson University. 2014. Can antibiotics cause autoimmunity? ScienceDaily. March 31, 2014:
  • Chalmers, R.A., Valman. H.B., and Liberman, M.M., Measurement of 4-hydroxyphenylacetic aciduria as a screening test for small-bowel disease. Clin Chem 25:1791, 1979
  • Whiteman, H. 2014. Antibiotic use in children linked to juvenile idiopathic arthritis. Medical News Today. November 16, 2014:
  • Parry, W. 2011. Overuse of antibiotics is seen behind many human ills. LiveScience. August 24, 2011:
  • Golden, B.R. and Gorbach, S.L. 2008. Clinical indications for probiotics: An overview. Clinical Infectious Dieases 46(12): S96-S100.
  • Mason, J. 2013. Can probiotics keep my gastrointestinal system happy? Tufts Now. September 16, 2013:
  • Baumler, M.D. 2013. Gut bacteria. Today's Dietitian. June 2013:
  • Wells, J.M. and Allison, C. Molecular genetics of intestinal anaerobes. In: Human Colonic Bacteria. Role in Nutrition, Physiology, and Pathology. Gibson and MacFarlane, ed. CRC Press. Ann Arbor. 1995. Page28
  • 10. Conway, P. Microbial ecology of the human large intestine. In: Human Colonic Bacteria. Role in Nutrition, Physiology, and Pathology. Gibson and MacFarlane, ed. CRC Press. Ann Arbor. 1995. Pages 1-24