Comprehensive Stool Analysis

Comprehensive Stool Analysis

The Key to Optimal Health

Imbalances in gastrointestinal function can lead to both local and systemic health issues, with the gut microbiome playing a vital role in supporting overall health. Our Comprehensive Stool Analysis profile helps identify the underlying causes of acute and chronic symptoms, enabling providers to create personalized treatment plans.

The Comprehensive Stool Analysis measures key markers of digestion, absorption, and intestinal function, including a comprehensive bacteriology and yeast culture to detect beneficial, imbalanced, and dysbiotic flora. We use gold standard methods, such as PCR, to identify infectious pathogens and parasites, and perform antimicrobial susceptibility testing on cultured bacterial and fungal species to recommend prescriptive and natural agents.

Turnaround Time: 1-2 weeks

Turnaround times are estimates. Detailed order tracking is available in the MosaicDX Portal.

Comprehensive Stool Analysis

What Patients Might Benefit from the Comprehensive Stool Analysis

The Comprehensive Stool Analysis is indicated for all chronic GI problems, for acute bowel pattern changes, and for many systemic diseases.

  • Allergies
  • Autoimmune Disorders
  • Cardiovascular Disease
  • Celiac Disease
  • Diabetes
  • Diarrhea, Constipation, Abdominal Distension
  • Food Sensitivities
  • Gastrointestinal Symptoms
  • IBD
  • IBS
  • Immune System Imbalances
  • Inflammation
  • Joint Pain
  • Leaky Gut
  • Malnutrition
  • Mood Disorders
  • Neurological Disorders
  • Weight Concerns


Why Conduct a Comprehensive Stool Analysis?

The Comprehensive Stool Analysis + Parasitology (CSAP) is an essential diagnostic tool that enables practitioners to assess the status of beneficial and imbalanced commensal bacteria, pathogenic bacteria, yeast/fungus, and parasites. The identification of pathogenic species and susceptibility testing assists in the selection of the most suitable pharmaceutical or natural treatment agents.

Our Comprehensive Stool Analysis test measures:

  • Digestion and absorption of nutrients (Pancreatic Elastase, Muscle Fibers, and Vegetable Fibers)
  • Elimination efficiency of undigested food residues and toxins
  • Assessment of the gut microbiome, measuring levels of healthy bacterial flora versus potentially pathogenic bacteria species, yeast, and parasites
  • Culture and sensitivities of pathogenic yeast and bacteria
  • Infectious pathogens (EIA evaluation for Campylobacter, Enterohemorrhagic E. coli cytotoxin, Giardia lamblia, and Cryptosporidium)
  • Indices and markers of intestinal immune function (Secretory IgA)
  • Indices and markers of inflammation (Calprotectin, Lactoferrin, and Lysozyme)
  • Indices and markers of intestinal physiology and of intestinal health (Presence of RBC, WBC, Mucus, Occult Blood, Fecal pH, and Short Chain Fatty Acids)

Efficient remediation of GI dysfunctions involves a comprehensive approach that includes elimination of pathogens and irritants, supplementation of hydrochloric acid, pancreatic enzymes, and pre- and probiotics, and repair of the mucosal barrier.

Learn More About Comprehensive Stool Analysis: Explore FAQs


The Comprehensive Stool Analysis measures key markers of digestion, absorption, and intestinal function, including a comprehensive bacteriology and yeast culture, GI pathogens, parasitology, macroscopic appearance, stool chemistries, bacterial susceptibilities and yeast/susceptibilities.

See detailed list of markers below organized by clinically important groups:

  • 73 possible species of imbalanced and dysbiotic bacteria
  • 4 species of beneficial bacteria
  • 48 possible yeast and fungal species
  • Yeast


  • Adenovirus F40/41
  • Norovirus GI/GII
  • Rotavirus A

Pathogenic Bacteria:

  • Campylobacter (C. jejuni, C. coli and C. lari)
  • Clostridioides difficile (Toxin A/B)
  • Escherichia coli O157
  • Enterotoxigenic Escherichia coli (ETEC) lt/st
  • Salmonella spp.
  • Shiga-like toxin-producing Escherichia coli (STEC) stx1/stx2
  • Shigella (S. boydii, S. sonnei, S. flexneri & S. dysenteriae)
  • Vibrio cholerae


  • Cryptosporidium (C. parvum and C. hominis)
  • Entamoeba histolytica
  • Giardia duodenalis (intestinalis & lamblia)


  • Balantidium coli
  • Blastocystis spp.
  • Chilomastix mesnili
  • Dientamoeba fragilis
  • Endolimax nana
  • Entamoeba coli
  • Entamoeba hartmanni
  • Entamoeba polecki
  • Enteromonas hominis
  • Giardia duodenalis
  • Iodamoeba bütschlii
  • Isospora belli
  • Pentatrichomonas hominis
  • Retortamonas intestinalis

Nematodes – Roundworms:

  • Ascaris lumbricoides
  • Capillaria hepatica
  • Capillaria philippinensis
  • Enterobius vermicularis
  • Strongyloides stercoralis
  • Trichuris trichiura
  • Hookworm

Cestodes – Tapeworms:

  • Diphyllobothrium latum
  • Dipylidium caninum
  • Hymenolepis diminuta
  • Hymenolepis nana
  • Taenia

Trematodes – Flukes:

  • Clonorchis sinensis
  • Fasciola hepatica/Fasciolopsis buski
  • Heterophyes heterophyes
  • Paragonimus westermani
  • Yeast
  • RBC
  • WBC
  • Muscle fibers
  • Vegetable fibers
  • Charcot-Leyden Crystals
  • Pollen
  • Mucus


  • Elastase
  • Fat Stain
  • Carbohydrates


  • Lactoferrin
  • Calprotectin
  • Lysozyme


  • Secretory IgA

Short Chain Fatty Acids:

  • % Acetate
  • % Propionate
  • % Butyrate
  • % Valerate
  • Butyrate
  • Total SCFA’s

Intestinal Health Markers:

  • pH
  • Occult Blood

Macroscopic Appearance:

  • Color
  • Consistency

Natural Antibacterials:

  • Berberine
  • Black Walnut
  • Caprylic Acid
  • Uva Ursi
  • Oregano
  • Grapefruit Seed Extract
  • Silver

Prescriptive Agents:

  • Amoxicillin-Clavulanic Acid
  • Ampicillin
  • Cefazolin
  • Ceftazidime
  • Ciprofloxacin
  • Sulfamethoxazole / Trimethoprim

Natural Antibacterials:

  • Berberine
  • Caprylic Acid
  • Uva Ursi
  • Plant Tannins
  • Oregano
  • Undecylenic Acid
  • Grapefruit Seed Extract

Non-Absorbed Antifungals:

  • Nystatin

Prescriptive Agents:

  • Fluconazole
  • Itraconazole
  • Ketoconazole

Sample Reports

The Comprehensive Stool Analysis test report is a useful resource for practitioner who want to uncover potential causes of gastrointestinal symptoms and chronic systemic conditions.

This test report groups the markers on the Comprehensive Stool Analysis into the following clinically important groups:

  • GI Pathogen Profile, Multiplex PCR; stool
  • Parasitology; Microscopy
  • Stool Chemistries
  • Bacterial Susceptibilities to Natural Antibacterials & Prescriptive Agents

Test Prep and Instructions

MosaicDX offers patient-friendly sample collection kits that simplify testing. Our kits include visual, step-by-step instructions for test preparation and sample collection, personalized shipping cards, and pediatric collection bags if needed. With MosaicDX, patients can easily collect samples for testing with confidence and accuracy.

Importance of Digestive Testing: Expert Insight from Kurt Woeller, DO

“It’s a common mistake to think that if a patient has no digestive symptoms, testing is unnecessary. It’s important to note, even without visible signs of digestive issues, underlying infections or indicators of inflammation could still exist.” – Kurt Woeller, DO

OAT Organic Acids Test logo

Frequently Asked Questions

The ordering process for MosaicDX tests starts with your healthcare practitioner assessing your symptoms and recommending the most appropriate test.

Once a test has been recommended, collection kits can be conveniently ordered and delivered straight to your doorstep. If you already have a collection kit, you can register your test and begin the process at your convenience.

It is important to carefully follow the collection instructions and include all required information about yourself and your specimens when registering your test. When your specimens are collected, you can use the prepaid shipping materials provided in your kit to ship them to MosaicDX. Your results will be accessible online via the MosaicDX portal. We recommend scheduling an appointment with your healthcare practitioner to discuss your results and develop a plan for your healthcare

If you are located outside of the U.S., our customer service team can assist you in finding a distributor in your country. In countries where a distributor is not required, you can place an order through our international patient ordering site. Please note that all international shipping costs must be paid prior to shipping the kit.  

Stool samples should be shipped only on Mondays, Tuesdays, or Wednesdays. It is important to collect samples on two separate days, with a minimum gap of 12 hours between collections using yellow-topped vials. All four stool specimens should be shipped together within five days of the first collection. 

Different states have regulations that define the scope of practice for practitioners. It is the practitioner’s responsibility to abide by these rules. Check with your state board of health to determine any restrictions related to laboratory testing. Please note, Mosaic Diagnostics does not offer testing in New York. 

Once you have opened your account, you have the options of ordering kits to stock in your office or drop-ship kits directly to your patients through your MosaicDX portal.   

Watch our short tutorial videos on how to conveniently  

Already have a kit? Watch this video on how to place an order for your patient using a kit from your inventory.   

Please refer to your test’s specific Test Preparation and Instructions for more information regarding the potential effects of medications, foods, and supplements on this test. 

You make also consult your healthcare provider prior to making any changes to your medications.

Visit the payment information page for an overview of payment options and procedures along with insurance coverage overview.

NOTE: Insurance coverage for testing is based on several factors such as the type of procedure, diagnosis, and insurance policy guidelines. Patients are encouraged to contact their insurance company to check for coverage and to provide the procedure codes (CPT codes) and diagnostic codes (ICD-10 codes). The CPT codes can be found on the billing information page, while ICD-10 codes are provided by the practitioner.

Mosaic Diagnostics offers written interpretations within test reports and complimentary consultations with our clinical educators for qualified practitioners. To schedule a consultation, simply sign in to your MosaicDX account and book a consultation online. 

We encourage all patients to discuss results with your practitioner.

Our Resources tab also contains educational materials that you may find useful, we also offer MosaicEDGE workshops for qualified practitioners to better understand the fundamentals of lab testing.

Have a question? We've got answers.

Our team of experts can help you find exactly what you need. Contact us now and let's get started.

Clinical References