Natural Health Services

The G.I. Microbial
Assessment Stool Analysis
Microbiology and DNA Analysis

Arkansas Nutrition and Natural Healing

Dr. Roger Trubey, Dr.PH, MPH, and Doctor of Integrative Medicine 362 Unger Trail, Mountain Home, Arkansas 72653

Call 501-538-4944

In the last few decades, DNA analysis has transformed the field of microbiology.   We have sorely needed better assessment techniques because more than ever before, we are now keenly aware of the health benefits or disease risks brought about by the microorganisms that inhabit the human body. You see, culture techniques, previously the standard, left up to 50% of bacterial species virtually invisible.  Anaerobic bacteria that make up a large part of the human microbiome can be opportunistic and cause illness. So our inability to cultivate these organisms left a large blind spot for clinicians when trying to diagnose the source of infection.

The G.I. Microbial Assessment panel is a comprehensive collection of microbial targets as well as immune and digestive markers. It screens for pathogenic bacteria, commensal bacteria, opportunistic pathogens, fungi, viruses, and parasites. It primarily uses multiplex, automated, DNA analysis to give integrative and functional medicine practitioners a better view into the gastrointestinal microbiome.

The G.I. Microbial Assessment measures pathogenic organisms that can cause hospital-acquired infections (HAI) such as C. difficile or norovirus, foodborne illness such as E.coli or Salmonella, and common causes of diarrhea such as Campylobacter, Shigella, and rotavirus A.  This panel measures viral causes of gastroenteritis, unavailable by other common stool tests. It measures parasites such as Cryptosporidium, Giardia, and Entamoeba histolytica. The GI-MAP analyzes Helicobacter pylori and its virulence factors. It can detect opportunistic pathogens such as Pseudomonas aeruginosa, Klebsiella pneumoniae, Yersinia enterocolitica, and Proteus mirabilus, associated with autoimmune molecular mimicry. It includes a panel of single-celled, amebic parasites such as Blastocystis hominis, Dientamoeba fragilis, and Entamoeba coli. Fungal organisms are measured by the GI-MAP such as Candida, Geotrichum, and Microsporidia, with the latter being a new addition to DNA stool analysis. Finally, the GI-MAP measures standard markers of immunity, inflammation and digestion including lactoferrin, secretory immunoglobulin A (sIgA), anti-gliadin antibody, and pancreatic elastase.

Disruption of the gastrointestinal microbiome can cause:

Gastrointestinal symptoms                                              More Gastrointestinal symptoms

  • Abdominal pain                                                          Vomiting
  • Bloating                                                                     Ulcer
  • Constipation                                                               Ulcerative Colitis
  • Crohn’s disease                                                                                
  • Diarrhea                                                                     Autoimmune Conditions
  • Food poisoning                                                           Ankylosing spondylitis
  • Gastric cancer                                                            Reactive and Rheumatoid arthritis
  • Gastritis                                                                     Thyroiditis (Hashimoto’s/Grave’s disease )
  • Gastroenteritis
  • Gastroesophageal reflux                                               Allergic Diseases
  • Irritable bowel syndrome                                              Asthma
  • Small intestinal bacterial overgrowth (SIBO)                   Eczema and Hives

Neurological conditions

  • Parkinson’s disease
  • Alzheimers disease

Diagnostic Solutions Laboratory is using a novel DNA technique to detect a comprehensive list of stool bacteria, viruses, fungi, and parasites. The method and instrument used is FDA-cleared for the detection of 15 of the most common causes of gastroenteritis- bacteria, parasites, and viruses.   This is an automated, multiplex DNA analysis method, allowing for the simultaneous measurement of multiple bacteria, fungi, parasites, and viruses, all from a single sample.
After receiving the stool specimens, nucleic acids are extracted and purified. The samples undergo multiplex polymerase chain reaction (PCR), which amplifies many gene targets.  Amplification can generate thousands to millions of copies of a single target DNA sequence for a much easier identification.

Our Friendly Bacteria
Although they are ubiquitous, pathogenic bacteria do not cause illness in all people. This is because commensal gastrointestinal flora can protect the host from infection. When gut microflora protects the intestines from pathogens and harmful microorganisms it is called, “colonization resistance.”  Animal models show that when normal gut microflora are lacking, the host is more susceptible to GI infections with Salmonella. Similarly, after antibiotic treatment there is increased risk of pathogenic infections.  On the other hand, commensal bacteria such as Lactobacillus and Bifidobacterium can prevent gastrointestinal infection. Colonization resistance explains why most pathogenic bacteria fail to cause disease in healthy subjects.

Commensal bacteria naturally inhabit the human gastrointestinal tract and do not cause disease. Many are beneficial; they produce enzymes, vitamins, short chain fatty acids, and other metabolic products that keep the bowels and the body functioning well. The incredibly complex interaction between human health and the gastrointestinal microbiome is the subject of multiple cutting-edge research studies. Given the metabolic, nutritional, and immune-enhancing roles of these organisms, the microbiome deserves close analysis when treating patients with chronic illness.

Not-so-Friendly Pathogenic Bacteria
Bacterial pathogens are often spread due to contamination of food and water with fecal material containing these pathogens.  And antibiotic therapy is not always recommended because antibiotic resistance can worsen the infection. Hydration, probiotics, and supportive therapies for the gut-immune system can help to remove the pathogen from the GI tract.

The presence of a pathogen does not, by itself, indicate disease.  Results from laboratory tests must be interpreted together with clinical symptoms and history by a qualified health practitioner. With increased awareness of the complexity of the GI environment, a pathogen is likely to cause disease if there are vulnerabilities in the host’s defenses. For example, imbalanced microflora, poor immune defenses, poor diet, toxic exposures, antibiotics, or chronic GI symptoms could make one person more susceptible to harm from a pathogen, while in another person they may have a fecal pathogen but is in good health. In healthy patients, treating pathogens may not be necessary. However, continuing to support a beneficial and diverse microbiota and a strong gut-immune system will further protect the host from infection.

Complete List of Target Analytes Measured on the G.I. Microbial Assessment
Bacterial pathogens:

  • Campylobacter
  • C. diff Toxin A & B
  • E. coli o157
  • Enterotoxigenic E. coli LT & ST (ETEC)
  • Shiga-like Toxin producing E. coli stx1 & stx2 (STEC)**
  • Salmonella
  • Shigella
  • Vibrio cholera
  • Yersinia enterocolitica

Viral pathogens:

  • Adenovirus
  • Norovirus GI & GII
  • Rotavirus A

Parasitic pathogens

  • Cryptosporidium
  • Entamoeba histolytica
  • Giardia

Additional targets

  • Helicobacter pylori and virulence factors, cagA and vacA
  • Enterococcus
  • Lactobacillus
  • Bifidobacter
  • Bacteroides spp.
  • Bacteroides fragilis grp
  • E. coli (total)
  • Citrobacter spp.
  • Citrobacter freundii
  • Proteus spp.
  • Proteus mirabilus
  • Proteus vulgaris
  • Pseudomonas spp.
  • Pseudomonas aeruginosa
  • Morganella spp.
  • Staphylococcus spp. (aureus)
  • Streptococcus spp.
  • Klebsiella spp.
  • Klebsiella pneumoneiae


  • Blastocystis hominis
  • Dientamoeba fragilis
  • Endolimax nana
  • Entamoeba coli
  • Entamoeba hartmanni
  • Chilomastix mesnelli
  • Cyclospora cayetanenensis
  • Pentatrichomonas hominis

LDT fungi/yeast:

  • Microsporidia spp. including Enterocytozoon bieneusi and Encephalitozoon intestinalis **
  • Candida albicans
  • Candida spp.
  • Geotrichum spp.
  • Trichosporon spp.

Other tests:

  • Secretory IgA (sIgA)
  • Anti-gliadin sIgA
  • Pancreatic elastase 1
  • Lactoferrin
  • Occult blood

The G.I. Microbial Assessment can be used in the detection and identification of gastrointestinal microbial nucleic acids and has been clinically validated for the detection of gastrointestinal pathogens that cause infectious colitis or gastroenteritis.   This technology has been used to identify and control pathogen outbreaks because of its rapid turn-around-time.  It measures a substantial list of opportunistic pathogens as well as a list of FDA-cleared pathogens, including novel targets such as viruses, Microsporidia, and pathogenic virulence factors. Chronic gastrointestinal symptoms, intestinal permeability, hormonal imbalance, and food sensitivities may trace their origins to imbalanced gut microbes as a root cause. Further, chronic inflammatory arthritis could have a microbial component that may warrant investigation by stool studies. This stool test offers integrative and functional medicine practitioners superior sensitivity and specificity to help resolve persistent and complex illnesses. Since the immune system, the intestinal barrier, and microbial diversity are intimately interwoven, thorough understanding of our gut microbiome holds promise for new approaches to treat and prevent disease.


Dr. Trubey’s patients with digestive conditions routinely obtain relief from Irritable Bowel Syndrome, Chronic gastritis, and chronic diarrhea. Call for an appointment – 501-538-4944.