Great Plains Laboratory Logo

Digestive Disorders & Dysbiosis

Many chronic disorders come from digestive problems and inadequate nutrient absorption. Even with a very complete and balanced diet, nutrients have to be properly digested to transport vitamins to different parts of the body. Proper gastrointestinal functioning also ensures elimination of toxic molecules, microbes and undigested food particles from the body to prevent infections, toxic reactions, allergies, and other health problems.

The negative role of abnormal intestinal microorganisms in gastrointestinal disorders is widely known. However, research also shows the relationship between the gastrointestinal and other systems in the body, such as the neurological, hepatic, and immune systems. For example, excessive yeast produces toxic metabolites, which can pass through the blood-brain barrier and alter neurological functioning causing "brain fog," behavior problems, and learning difficulties. Excessive bacteria byproducts can interfere with neurotransmitters and cause chronic fatigue. Beneficial bacteria, on the other hand, helps with vitamin absorption and preventing infections.

Click here to view the Recommendations By Disorder Chart (PDF)

Gastrointestinal Bacteria Facts

  • There are 500 or more different species
  • 30-40 different species predominate
  • There are approximately 1-10 X 1013 or 10-100 trillion bacteria cells inside a typical colon
  • Comparable to the 100 trillion cells in human body
  • Anaerobic bacteria predominate
  • 90% of species may be unidentified
  • Bacteria constitute about 50% of the content of feces
  • There are about a million times more bacteria in the colon than in the stomach

Clostridia, 3-(3-hydroxy-phenyl)-3-hydroxypropionic acid (HPHPA) & Psychosis By William Shaw, Ph.D.

The role of Clostridia difficile in the etiology of pseudomembranous colitis has been well-documented. My work indicates that overgrowth of the gastrointestinal tract by multiple Clostridia species may be as important as yeast/fungal overgrowth in the etiology of a wide range of disorders. Sidney Finegold, MD, the chief of the Anaerobic Bacteria Laboratory at UCLA, estimates that there may be over a 100 species of Clostridia in the GI tract.

Several years ago, I began a collaborative study of evaluating urine samples of patients with schizophrenia obtained by Dr. Walter Gattaz, a research psychiatrist at the Central Mental Health Institute of Germany in Mannheim. These samples were very valuable since they were obtained from patients who were drug-free. Thus, any biochemical abnormalities would be due to their disease and not a drug effect. Five of the twelve samples from the patients with schizophrenia contained a very high concentration of a compound identified by GC/MS as a tyrosine derivative, which I have now identified as 3-(3-hydroxy-phenyl)-3-hydroxypropionic acid.
(Shaw, William. "Increased urinary excretion of a 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), an abnormal phenylalanine metabolite of Clostridia spp. in the gastrointestinal tract, in urine samples from patients with autism and schizophrenia." Nutritional Neuroscience. 13. (2010): 135-43. Print.)

During the same period of time, I performed urine organic acid testing on a child being evaluated for a conduct disorder at an outpatient psychiatric clinic. The concentration of HPHPA in the urine was elevated compared to urine samples in normal children. Several weeks later this child had an acute psychotic reaction and was admitted to the children's hospital. The concentration of HPHPA in the urine was much higher during the acute psychotic episode than in the previous sample and remained extremely elevated until the acute psychosis resolved. A colleague in the field of metabolic diseases suggested that this compound might be derived from microorganisms in the intestine. Since the amino acid tyrosine is the raw material used by the body for the production of neurotransmitters, I suspected that this product might be very important in altering key biochemical pathways for neurotransmitters in the brain.

Treatment of Patients with Elevated HPHPA

Patients with values of HPHPA greater than 500 mmol/mol creatinine in the urine almost always have severe neurological, psychiatric, or gastrointestinal disorders such as autism, severe depression, psychotic behavior or schizophrenia, muscle paralysis, or colitis or sometimes a combination of these disorders. Treatment of a severely autistic child with six weeks of oral Vancomycin therapy resulted in an estimated six months in developmental progress as assessed by a developmental psychologist.

Psychotic individuals with high HPHPA have been successfully treated using Vancomycin instead of antipsychotic medication. However, even individuals in the high normal range may benefit from therapeutic intervention. One patient with acute schizophrenia had a value that was 150 times the median normal value in addition to elevated yeast metabolites as well.

Several of the patients with high urine concentrations of HPHPA had positive stool immunoassay tests for Clostridium difficile, raising suspicion that Clostridia species were responsible for the production of this compound. Treatment of a wide variety of patients with elevations of this compound with drugs that kill Clostridia such as Vancomycin and Flagyl resulted in nearly complete elimination of this compound in urine samples.

Effects of Flagyl Therapy

Diagnosis & Sex


Length of time (Days) from start of Flagyl Therapy

Urinary 3-(3-hydroxy-phenyl)-3-hydroxypropionic

Autism, male














21 (stopped Flagyl)














Previous C. difficile infection and uncontrolled diarrhea, female








Autism, male












Autism male












*Measured in mmol/mol creatinine.

Table 1 - Effects of Flagyl Therapy on Urinary Excretion of 3-(3-hydroxy-phenyl)-3-hydroxypropionic acid

Note that in the first patient in the table the values for HPHPA began to increase back to their previous values after discontinuation of Flagyl.

I suspect that the reason for this "rebound" is that the Clostridia, the producers of this particular compound, are spore formers. The spores are completely resistant to the drug, which in this case is Flagyl. When the administration of Flagyl is stopped, these spores re-colonize the gastrointestinal tract. One of the ways to prevent this re-colonization is to re-seed the intestine with L acidophilus.

The marked decrease in 3-(3-hydroxy-phenyl)-3-hydroxypropionic acid followed treatment with metronidazole and Vancomycin, the antibacterial agents most commonly recommended for C. difficile and other Clostridia infections. Phenylpropionic acid and monohydroxyphenylpropionic acid, which are very closely related biochemically to this compound, are produced by several species of Clostridia.

Clostridia were the only organisms that produced phenylpropionic acid after they evaluated 67 different isolates of microbes from nine different genera of bacteria and Candida albicans. Furthermore, they found that metronidazole, clindamycin, and combined therapy of ticarcillin, clavulanate, and oxacillin abolished gut flora producing phenylpropionic acid; these drug therapies generally kill Clostridia. Cefalzolin, cefuroxime, ampicillin, chloramphenicol, and gentamicin did not abolish phenylpropionic production. This latter group of drugs are generally ineffective against Clostridia species.

Richard Jaeckle, MD, a psychiatrist and allergist in Austin, Texas has treated a number of psychotic individuals using antifungal therapy and finds that psychotic patients with elevated CPK, uric acid and white cell counts may respond favorably to antifungal treatment. Patients with psychotic behavior may have gastrointestinal overgrowth of both yeast and Clostridia.

We were very interested in a possible role in the mechanism for autism for HPHPA because it is related structurally to the neurotransmitters dopamine and norepinephrine, because similar compounds are inhibitors of dopamine decarboxylase, the enzyme responsible for the conversion of dihydroxyphenylalanine (DOPA) to dopamine, and because of the possibility of the formation of false neurotransmitters from abnormal microbial products of phenylalanine such as 3-hydroxyphenylalanine and 2-hydroxyphenylalanine. Both of these products are isomers of tyrosine that would form false neurotransmitters when transported into the neurons.

High DHPPA (3,4 dihydroxyphenylpropionic acid), a unique but similar compound, indicates excessive intake of chlorogenic acid, a common substance found in beverages and in many fruits and vegetables, including apples, pears, tea, coffee, sunflower seeds, carrots, blueberries, cherries, potatoes, tomatoes, eggplant, sweet potatoes, and peaches. Harmless or beneficial bacteria such as Lactobacilli, Bifidobacteria, and E. coli mediate the breakdown of chlorogenic acid to 3,4-dihydroxyphenylpropionic acid (DHPPA), and high values may indicate increased amounts of these species in the GI tract. In addition, one Clostridia species, C. orbiscindens, can convert the flavanoids luteolin and eriodictyol, occurring only in a relatively small food group that includes parsley, thyme, celery, and sweet red pepper to 3,4-dihydroxyphenylpropionic acid. The quantity of Clostridia orbiscindens in the GI tract is negligible (approximately 0.1% of the total bacteria) compared to the predominant flora of Lactobacilli, Bifidobacteria, and E. coli. Consequently, this marker is essentially useless as a general Clostridia marker but may be a good indicator of the presence of beneficial flora.

High HPHPA is associated with behavioral, gastrointestinal, and/or neuropsychiatric effects. Gastrointestinal symptoms may include diarrhea or constipation. Neuropsychiatric effects are more common when values exceed 500 mmol/mol creatinine. HPHPA is an abnormal phenylalanine metabolite produced by gastrointestinal bacteria of Clostridia species, including, C. sporogenes, C. botulinum, C. caloritolerans, C. mangenoti, C. ghoni, C. bifermentans, C. difficile, and C. sordelli. In most cases, Clostridia overgrowth can be controlled by supplementation, with 30 billion cells per day of Lactobacillus rhamnosus GG (Culturelle) and/or 2-6 billion cfu's of Saccharomyces boulardii.


Products of gastrointestinal microorganisms that have been largely ignored in the past appear to play major roles in human metabolism, development, aging, and disease. Abnormal bacterial products of the amino acid tyrosine are elevated in psychosis, depression, autism, seizures, as well as gastrointestinal disorders like colitis. Treatment of this overgrowth of bacteria that appear to be largely of the Clostridia species has resulted in significant clinical improvement or complete remission of symptoms in a number of cases.

What Tests are Recommended for this Condition?

The Comprehensive Stool Analysis helps detect the presence of pathogenic yeast, parasites, and bacteria, which could be contributing to chronic illness and neurological dysfunction. It provides helpful information about prescription and natural products effective against specific microorganism strains detected in the sample. The test also evaluates beneficial bacteria levels, intestinal immune function, overall intestinal health (presence of occult blood, short chain fatty acids analysis, pH, mucus, and other criteria), and inflammation markers.

The Organic Acid Test (OAT) Profile can detect 65 metabolites that relate to yeast, bacteria, Clostridia, water soluble vitamins, oxalates, neurotransmitters, mitochondrial function, and other metabolic pathways which can affect the function of the gastrointestinal tract. This test can identify invasive intestinal pathogens that are difficult to detect and are often not found using other methods. Some of the metabolites tested using our analysis are patented and only available through The Great Plains Laboratory, Inc.

Click here to read about the role of abnormal levels of gastrointestinal microorganisms in bowel disorders and chronic diseases. Read an Interview with Dr. Shaw to find out more about Dr. Shaw's important work and what it means to you. Click here to read scholarly journals related to digestive disorders.

Forward this page to a friend

Please complete the information below to send this page as a link to a friend :

Your email address:

Your friend's email address:




Please type what you see in the box below :
The CAPTCHA image

Back to Top

Contact Us

11813 W. 77th St., Lenexa, KS 66214 USA | Phone: 913-341-8949 | Fax: 913-341-6207
© Great Plains Laboratory, Inc. 2014 GPeLephant