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At Home Stool Test vs Comprehensive Stool Test: A Comparison

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At Home Stool Test vs Comprehensive Stool Test: A Comparison

Gastrointestinal (GI) complaints are quite common. In a study of over 70,000 people, 61% reported having one or more GI symptoms in the week before the survey.

Stool testing can provide valuable insight into the root cause of GI symptoms, as they can evaluate infections, allergies, digestive problems, inflammation, and more. At-home tests provide the convenience of completing the test in a comfortable environment. There is, however, a difference between the standard at-home bowel health tests and comprehensive-functional medicine GI testing. First, let's assess what exactly stool tests are.    


What are Stool Tests?

Stool testing is often done in the comfort of the patient's home, with a small sample being put in a preservative solution and shipped to the respective lab. Laboratories have many different ways to evaluate stool testing, the most common being:

  • Microscopy: a sample is assessed under a microscope
  • PCR: DNA frequency is used to detect various organisms
  • Culture: a stool sample is placed in an incubator for up to 72 hours and then checked for growth. Depending on which organism is being assessed, different additives may be added to aid in growth.

What Patients Would Benefit From a Stool Test?

There are many reasons why someone may consider a stool test. The most common GI complaints that would indicate testing are:

  • Diarrhea
  • Constipation
  • Nausea
  • Vomiting
  • Acid Reflux
  • Burping
  • Flatulence
  • Bloating
  • Flatulence
  • Blood or mucus in stool

However, we also know that the microbiome, a collection of microbes located within our large intestine, influences many other systems in the body. The following conditions may be related to our microbiome, and thus testing may be warranted:

  • Acne
  • Rashes
  • Menstrual irregularities, including abnormal cycles as well as heavy and painful cycles
  • Autoimmune conditions
  • Metabolic disease
  • Cancers
  • Neurodegenerative Disorders
  • Cardiovascular disease

At-Home Bowel Health Stool Test Overview

There are two common types of at-home bowel health test:

Direct to Patient At Home Bowel Health Testing:

These tests can be ordered online by anyone and commonly only look at the bacteria overview. The  results  are easy to read and let the patients know which foods they should incorporate in their diet to encourage healthy bacteria to thrive alongside foods to eliminate.

Practitioner Ordered At Home Stool Testing:

This type of stool testing has traditionally been used to evaluate common pathogenic or "bad" bacteria, rule out parasites, check for occult blood (blood that is not present to the naked eye), mucus (an indicator of gastrointestinal disease), and calprotectin (the gold standard GI inflammatory marker).  

The results are reviewed and a treatment plan is established based on the above markers.

Comprehensive Stool Test Overview

Comprehensive stool testing is usually done over 1-3 days and looks deeper into the gastrointestinal microbiome. These test look at the following markers:

  • Infections due to pathogenic or bad bacteria, viruses, and parasites
  • Commensal: normal, healthy microbes
  • Opportunistic: microbes that in small amounts may be OK, but when presented with an opportunity, such as a weakened immune system, will flourish and cause problems
  • Pathogenic: microbes that can induce disease
  • Fat, Protein, and Carbohydrate Absorption
  • Estrogen Metabolism
  • Leaky Gut Markers
  • Immune Response
  • IBD and IBS Markers
  • Inflammatory Markers

These tests are commonly used for patients suffering from autoimmune disease, hormone imbalances, IBS, IBD, dermatological disorders, mental health disorders, and fatigue (just to name a few). The results from these tests help practitioners individualize treatment plans with nutrition and supplements to help support the microbiome, immune system, and digestion. Results may also guide practitioners towards other testing based on patients symptoms (i.e. hormone panels, neurotransmitters, micronutrient testing etc). Retesting at the 4 month mark is common so practitioners can see how the above markers have changed over time and adjust the treatment plan as necessary.

Rupa Health's Top 4 Comprehensive Stool Tests

GI Map

GI Map, by Diagnostic Solutions, is a stool test that uses DNA via qualitative polymerase chain reaction (qPCR) to detect the DNA of various microbes and markers of gastrointestinal health. The lab provides at-home collection kits with shipping materials included, and the average turnaround time for results is ten business days.

Test Breakdown:

  • Microbes: Pathogens (bacterial, parasitic, and viral), H.pylori, normal bacteria flora, opportunistic/potentially harmful microbes, inflammatory and autoimmune related bacteria, fungi and yeasts, viruses, parasites including worms
  • Intestinal Health: markers for digestion, estrogen metabolism, gluten sensitivity, immune response, and inflammation

What Makes This Test Stand Out?

Helicobacter pylori (H. pylori) virulence factors: H. pylori is a bacteria commonly found in small amounts in the stomach. However, H. pylori in large quantities can lead to abnormal stomach acid levels, stomach ulcers, and certain types of stomach cancer.

Virulence factors are what help bacteria to adhere to and damage their host. H. pylori's virulence factors can be separated into three different categories: colonization (how H. pylori can survive in the host), immune escape (how H. pylori fights the host's immune system), and disease induction (peptic or duodenal ulcers, gastric carcinoma, or gastritis). Knowing if any virulence factors are present with an H.pylori infection allows risk to be better assessed and for a more specific treatment plan that will hopefully aid in complete eradication.  

GI Effects Comprehensive Profile

The GI Effects Comprehensive Profile, by Genova Diagnostics, uses PCR, culture, and microscopic evaluation to assess microbes within a stool sample. This test is a single-day collection. The average processing time is 17 business days.

Test Breakdown:

  • Microbes: commensal bacteria, pathogenic bacteria, yeast, parasites
  • Intestinal health: occult blood, zonulin (a marker of intestinal permeability), white blood cells and Charcot-Leyden Crystals (indicates parasites), digestion markers, inflammatory markers, and metabolic markers

What Makes This Test Stand Out?

GI Effects begins by giving Functional Imbalanace Scores. These scores use a zero to ten scale, rating the need for support in the following categories: maldigestion, inflammation, dysbiosis, metabolic imbalance, and infection. These scores make the test easy to read and understand. This test also shows the type and amount of short-chain fatty acids (SCFA), a byproduct of microbial digestion of prebiotics. SCFAs are important for health as they enter into the circulation and can affect various body systems.  

Comprehensive Stool Analysis + Parasitology - 3 Day

The Comprehensive Stool Analysis + Parasitology (CSAP)- 3 Day by Doctors Data is a three-day collection stool test that uses culture, PCR, microscopy, and other methods to assess for various microbes and intestinal health. Samples should be collected on consecutive days, and certain medications should be avoided before completing the test. The average turnaround time for results is eight business days, and there is an additional shipping fee.

Test Breakdown:

  • Microbes: bacteria including beneficial, opportunistic and parasitic, yeast including beneficial and opportunistic, viruses, and parasites
  • Intestinal Health: digestion and absorption markers, inflammation, immune markers

What Makes This Test Stand Out?

Doctor's Data will test the positive microbes found in the stool samples against natural antimicrobials such as berberine, black walnut, and oregano, and prescriptive agents including ciprofloxacin, nystatin, and amoxicillin-clavulanic acid. This analysis gives the practitioner an advantage, as they know with high certainty what will work while also reassuring the patient that what they will be using for treatment should have a high success rate.

GI 360

GI 360, by Doctor's Data using PCR, microscopy, cultures, and more to assess 116 biomarkers, including microbes. GI 360 is similar to Doctor's Data Comprehensive Stool Analysis + Parasitology (CSAP) discussed above but has additional microbes. This test is a three-day stool collection test with a turnaround of, on average, eight days, and there is an additional shipping fee.

Test Breakdown:

  • Microbes: Pathogens (viruses, bacterial, parasites), normal bacteria flora microbes
  • Intestinal Health: digestion and absorption markers, inflammatory markers, pH, immune markers, occult blood, estrogen recycling markers

What Makes This Test Stand Out?

The test begins with a Microbiome Abundance and Diversity summary and a Dysbiosis score. These scores provide a quick overview of the test with easy-to-read visuals. Like the CSAP, it also shows positive microbe susceptibility to natural and prescriptive agents. It could be said that this test is a more comprehensive version of the CSAP.

Here is a complete comparison of the five tests, including a list of all microbes.


With gastrointestinal complaints being so common, the availability of GI testing can be beneficial for many people. In addition, it seems the more research is done on the microbiome, the more we realize its critical impact on health. Thus, knowing what our microbiome is comprised of can be a valuable tool in treating many disorders.

Figuring out what GI test to order can be overwhelming and confusing. This guide can be a reference when assessing what test is appropriate for what patient or yourself.  

The information provided is not intended to be a substitute for professional medical advice. Always consult with your doctor or other qualified healthcare provider before taking any dietary supplement or making any changes to your diet or exercise routine.
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