Digestive Tests / The Comprehensive Digestive Stool Analysis

submitted by Dr. Gary Farr Last Updated June, 25, 2004

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Microbiology: Pathogens

Because the oxygen content of the colon is low, the vast majority of bacteria are anaerobes. There are, however, hundreds of varieties of anaerobic flora in vastly different concentrations, all growing very slowly. The significance of most of these flora remains largely unknown. Most researchers, therefore, utilize the aerobic flora as an indication of bacterial health.

Three frequently identified organisms, Lactobacilli, Bifidobacteria, and Escherichia coli, are employed as indicators of eubiosis or healthy overall flora. Lactobacilli and Bifidobacteria are well established as offering intrinsic benefit and aiding digestion while helping to prevent overgrowth of abnormal flora.

Bacterial cultures also identify and show potential pathogens. We utilize the term “potential pathogens” because individuals may harbor traditional pathogens and appear healthy, while others harbor weak or questionable pathogens and have gastrointestinal complaints.

For a full list of pathogenic and potentially pathogenic organisms, see the following chart. For a complete ist of parasitic organisms, see this chart.

While they are sometimes found linked to GI tract disturbances, some intestinal bacteria may also be involvedin the etiology of various chronic or systemic problems seemingly unrelated to GI function. These include Klebsiella, Proteus, Pseudomonas, and Citrobacter. These organisms may be involved, through molecular mimicry, in various autoimmune diseases. This has been reported in diabetes mellitus, meningitis, thyroid disease, ulcerative colitis, arthritis, ankylosing spondylitis and systemic lupus.^26,27

Some potential pathogens may cause clinical and subclinical malabsorption of nutrients and increase bowel permeability to large macromolecules. A number of clinicians speculate that this is directly related to the etiology of food and chemical sensitivity and intolerance.

Whipple’s disease, although rare, presents an interesting model of the interaction of bacterial infection, absorptive processes and systemic health. This disease is known to be caused by an unusual bacteria which resists attempts to culture it in vitro. Symptoms include severe alterations in intestinal permeability and chronic fatigue.²⁸ There is strong scientific support for the profound relation between GI tract flora, malabsorption, permeability changes and overall health.

Yeast: In the last few years, colonic yeast infections have attracted attention and controversy as a possible cause of chronic complex illness.²⁹ Many investigators suggest that an intestinal overgrowth of Candida albicans (and other intestinal yeast) may be involved in food allergy, migraine, irritable bowel, asthma, indigestion and gas, depression related to PMS, vaginitis and chronic fatigue.^30-35

Although others have dismissed these claims as speculation, we suggest that part of the problem is focusing on the terms “pathogen” and “commensal.” It may be more accurate to use the terms “strong pathogen” and “weak pathogen.” A significant and surprising amount of peer-reviewed literature supports yeast as a weak pathogen.^36-38

While the normal GI tract harbors small amounts of yeast, overgrowth as a consequence of the wide use of antibiotics, corticosteroids, birth control pills and increased dietary carbohydrates may be abnormal.³⁹ Odds’ text on Candida summarized more than 20 papers that found patients had a frequency of C. albicans in their feces more than twice as often as normal controls.⁴⁰ One study reported that chronic diarrhea and abdominal cramps may be caused by large numbers of dead or damaged yeast, as found in feces.⁴¹ Other research indicates Candida as a cause of colitis in patients with AIDS, neoplastic disease and renal transplants.^42-44

While the yeast pathogenicity debate continues, high-quality lab work is essential. Yeast may be observed directly via a microscope or indirectly through a culture. Both are necessary for proper analysis.

GI Tract and Arthritis: Researchers increasingly acknowledge that there is a link between digestive processes and arthritis. In patients with altered bowel anatomy, chronic bacterial overgrowth can lead to theformation of circulating immune complexes and synovitis.⁴⁵ Changes in bowel permeability due to local gut inflammation may expose the host immune system to microbial or food antigens and even bacterial translocation. ^46,47 In some cases, toxins derived from enteric organisms (e.g., Clostridium difficile) may play a direct role in the induction of arthritis.

Microbiology: Dysbiosis

Dysbiosis is the state of disordered microbial ecology that causes disease. It may exist in the oral cavity, gastrointestinal tract or vaginal cavity. In dysbiosis, organisms of low intrinsic virulence, including bacteria, yeasts and protozoa, induce disease by altering the nutrition or immune responses of their host.⁴⁸

The concept of intestinal flora having a major impact on human health has increasingly gained support, particularly as the widespread use of antibiotics has been observed to disrupt the normal flora.

Published research has implicated intestinal dysbiosis as contributing to vitamin B12 deficiency, steatorrhea, irritable bowel syndrome, inflammatory bowel disease, autoimmune arthropathies, colon and breast cancer, psoriasis, eczema, cystic acne and chronic fatigue.^49-54

Normal Intestinal Microflora: The microflora of the GI tract constitute a complex ecosystem of aerobic and anaerobic microorganisms.⁴⁹ There are more bacteria in the gut than human cells in the body, and the flora possess more metabolic activity than the host itself.

Flora content is surprisingly stable over time but is affected by diet, antibiotic use and health status.⁵⁵ In many ways, the gut flora can be viewed as an organ of the body, as these microbes profoundly influence physiologic processes of the host.

Certain normal metabolic functions and enzyme activities can be attributed to the microflora, and these play a role in metabolizing nutrients, vitamins, drugs, endogenous hormones and carcinogens; synthesizing short chain fatty acids; preventing colonization of pathogens; and stimulating maturation of the normal immune response.^56,57

Food allergy: Food allergy is a well documented problem, although its prevalence, testing methods and treatment modalities are controversial. J.O. Hunter proposed that food allergy is not an immunological disease but a disorder of bacterial fermentation in the colon. He theorized in The Lancet that the combined mechanisms of reduced gut enzyme concentrations, imbalanced bacterial flora and increased permeability account for many cases of food intolerance.⁶⁰

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