Test Overview of Comprehensive Stool Analysis Panel
The Stool Analysis Panel detects both beneficial and pathogenic microflora in
the GI tract, including yeasts, bacteria, and parasites. It also provides
a number of other markers of gut health.
Test Indications of Comprehensive Stool Analysis Panel
- First-line test for evaluating Autism Spectrum Disorder (ASD), Pervasive Developmental Disorder (PDD), Asperger's Syndrome, Attention-Deficit Hyperactivity Disorder (ADD, ADHD), and learning disability.
- First-line test for evaluating depression, anxiety, and other mood disorders.
- First-line test for evaluating Irritable Bowel Syndrome (IBS), Inflammatory Bowel Disease (IBD), Crohn's Disease, and other intestinal complaints.
- First-line test for evaluating autoimmune disorders, joint pain, and psoriasis.
- First-line test for evaluating Chronic Fatigue Syndrome and Fibromyalgia.
- Environmental toxicity.
- Seizure disorders.
Sample Collection for Comprehensive Stool Analysis Panel
- Your doctor will provide you with the sample collection kit.
- The sample must be sent via overnight FedEx directly to the lab on a Monday through Thursday using the prepaid mailer provided.
- Detailed instructions are in the sample collection kit.
Your doctor or lab may have different instructions that supersede the above.
ICD-9 CODES for Comprehensive Stool Analysis Panel
| ICD-9 Code | Description | Comments |
|---|---|---|
| 112.9 | Yeast infection | |
| 277.9 | Metabolic disorder | |
| 279.9 | Immune system disorder |
Labs Performing Comprehensive Stool Analysis Panel Test
| Name of Lab | Lab Code | Estimated Cost | Processing Time | Comments |
|---|---|---|---|---|
 Great Plains
| $330 | 2-3 weeks | Cash discount and some insurance |
Costs cited are subject to change and may be reduced by insurance or cash discounts and increased by sample collection fees.
Theory of Comprehensive Stool Analysis Panel
Digestion and Absorption
Pancreatic Elastase
Low levels suggest pancreatic insufficiency, which may be associated with pancreatic tumor, chronic pancreatitis, cystic fibrosis, cholelithiasis or diabetes mellitus.
Carbohydrates
Carbohydrates in the stool suggest poor carbohydrate absorption.
Fat Stain (microscopic)
A positive fat stain suggests poor fat absorption (steatorrhea).
Long-chain Fatty Acids
Elevated long-chain fatty acids suggest fat-malabsorption or maldigestion.
Short-chain Fatty Acids (SCFA)
Short-chain fatty acids are necessary nutrients for colonocytes. They are produced in the gut by the fermentation of dietary fiber by beneficial bacteria. Low levels are associated with colonic infammation, low soluble fiber intake, dysbiosis, and colon cancer. The most important markers are total SCFA and butyrate (butyric acid).
The most common SCFA include:
- Acetate (ethanoic acid, 2 carbon)
- Propionate (propanoic acid, 3 carbon)
- Butyrate (butanoic acid, 4 carbon)
- Valerate (pentanoic acid, 5 carbon)
Meat (Muscle) Fibers (microscopic)
Undigested meat fibers in the stool suggest poor digestion due to inadequate stomach acid. Associated symptoms include bloating and flatulence.
Vegetable Fibers (microscopic)
Undigested vegetable fibers in the stool suggest poor digestion or inadequate chewing.
Inflammatory Markers
Lactoferrin
Elevated lactoferrin suggests bowel inflammation (IBD), but is NOT associated with irritable bowel syndrome (IBS).
Calprotectin
Elevated calprotectin suggests bowel inflammation.
Lysozyme
Elevated Lysozyme suggests suggests dysbiosis and bowel inflammation.
Secretory IgA (sIgA)
Elevated sIgA suggests suggests an upreglation of GI immune response to some irritant.
Red Blood Cells (RBC) (microscopic)
Elevated RBC levels are associated with colorectal cancer, inflammatory bowel disease, bacterial dysbiosis, parasites, anal fistulas, and hemorrhoids.
White Blood Cells (WBC) (microscopic)
Elevated WBC levels are associated with inflammatory bowel disease and dysbiosis.
Mucus (microscopic)
Elevated mucus levels are associated with inflammatory bowel disease and dysbiosis.
Other Markers
Stool pH
Elevated stool pH is associated with low SCFA production, and reduced protection against pathogenic gut bacteria.
Occult Blood
The occult (hidden) blood detects hidden bleeding in the GI tract. Although there are many other possible causes, GI bleeding should be considered to be due to cancer until proven otherwise.
β-glucuronidase
Elevated fecal β-glucuronidase may reduce the liver's ability to detoxify the body by encouraging re-absorption of toxins that the liver released into the bile (enterohepatic reabsorption).
Stool Color (macroscopic)
Stool Consistency (macroscopic)
Microbiome Abundance and Diversity Summary (PCR)
A healthy gastroenteric system contains many different beneficial species of bacteria and fungi, that help balance out other unhealthy species of bacteria and fungi. Collectively, all of these different species are called the microflora or gut microbiome. Although normative patterns can be identified, the exact composition of different individual's gut microbiome is nearly as unique as a person's fingerprint.
In general, increased diversity of different species of bacteria and fungi is better. However, proper balance between the different species is equally important. A state of dysbiosis (unhealthy microbiome) occurs when the diversity is reduced, there is an imbalance between the types of species, increased harmful species, or decreased beneficial species.
There are thousands of different species that make up the microbiome; a laboratory technique called Polymerase Chain Reaction (PCR) can identify and measure the DNA of these many different species, and evaluate the diversity and balance.
These thousands of different species (e.g., Escherichia coli) are grouped into genera (e.g., Escherichia), which are in turn grouped into phyla (e.g., Pseudomonadota) etc. For our purposes, we focus on a limited number of important groups, which include (with estimated prevalance reported by the Brave search engine Leo without attribution on 10/23/2025):
- Bacteroidota (Bacteroidetes) (~70–75%) E.g.:
- Bacillota (Firmicutes)
(~20–25%) E.g.:
- Anaerobutyricum hallii
- Agathobacter rectalis
- Bifidobacterium bifidum
- Catenibacterium mitsuokai
- Clostridium methylpentosum
- Coprobacillus cateniformis
- Dialister invisus
- Dorea spp.
- Eubacterium siraeum
- Holdemanella biformis
- Faecalibacterium prausnitzii
- Lachnospiraceae
- Ligilactobacillus ruminis
- Mediterraneibacter gnavus
- Megasphaera micronuciformis
- Pediococcus acidilactici
- Phascolarctobacterium spp.
- Ruminococcus albus
- Ruminococcus bromii
- Streptococcus salivarius ssp thermophilus
- Streptococcus sanguinis
- Streptococcus spp.
- Veillonella spp.
- Actinomycetota (Actinobacteria) (~1–3%) E.g.:
- Pseudomonadota (Proteobacteria) (~1–3%) E.g.:
- Verrucomicrobiota (~0.1–1%) E.g.:
- Mycoplasmatota (<0.1%) E.g.:
Bacterial Culture and Sensitivity
Beneficial Bacteria
We want to see high levels of these in the stool because they help to prevent overgrowth of pathogenic bacteria.
Potentially Pathogenic, Imbalanced, and Dysbiotic Bacteria
Yeast Culture and Sensitivity
Fungal Culture
Fungal Sensitivity
- Suggests which antifungal agents are useful in treating the yeast and fungi isolated.
Parasite Testing
- Searches for evidence of parasites or their eggs (ova).
- Due to the periodic life cycle of parasites, multiple specimens are examined.
ELISA Immunoassays
Immunoassay reveals evidence of pathogen even when not culturable.
Helicobacter pylori
Cryptosporidium
Campylobacter
Giardia lamblia
References regarding Comprehensive Stool Analysis Panel
[GP2008] Great Plains Laboratory, William Shaw, Lori Knowles, Kurt Woeller.
Physician Practitioner Training (Autism) Lecture Notes and Documentation.
Tempe, AZ (8/23/2008 – 8/24/2008). FULL TEXT
FULL TEXT
[Myhill2018] Sarah Myhill.
Sustainable Medicine: Whistle-Blowing on 21st-Century Medical Practice.
White River Junction, VT: Chelsea Green Publishing (2018).
Unless specifically noted above, references used in the construction of this web page include the following:
[FMU] Lecture notes from Functional Medicine University.
[SCNM] Lecture notes from Southwest College of Naturopathic Medicine.
[UT] Lecture notes from the University of Tennessee graduate programs in Chemistry, Microbiology, and Biochemistry.