Comprehensive Stool Analysis

Costs cited are subject to change and may be reduced by insurance or cash discounts and increased by sample collection fees.

	Name of Lab	Lab ID	Estimated Cost	Comments
Show Details	Doctor's Data	DD	$188 +, $321 +, $422	1= Microbiome only; 2=Essentials; 3=GI360; A=Add-on. Note: Mosaic uses/repackages the DD GI360 laboratory platform, and is not included here as an independent lab. Sample Report
Show Details	DiagnosTechs GI Health	DT	$265 +	À-la-carte test selection.
Show Details	Tiny Health Gut Health	Tiny	$249, $379	1=Microbiome only; 2=PRO adds stool chemistry markers. Includes pediatric and adult reference ranges. Sample PRO Report
Show Details	Genova Diagnostics (formerly Great Smokies) GI-Effects	GDX	$370 +, $474, $465	1=Fundamentals; 2=Comprehensive; 3=Microbiomix. Note: Comprehensive and Microbiomix are complementary products with little direct overlap at the assay level; they can be purchased as a bundle at the discounted price of $874. Sample Fundamentals Sample Comprehensive Sample Microbiomix Support Guide
Show Details	Vibrant Wellness Gut Zoomer	Vibrant	$605	Unusually broad, particularly for neuro/GI cases. Sample Report
Show Details	Diagnostic Solutions GI-MAP	DS	$525 +	Optional StoolOMX measures Fatty Acids, Protein Breakdown Products, and Bile Salts. Note: Precision Point Diagnostics uses/repackages the DS GI-MAP laboratory platform, and is not included here as an independent lab. Interpretive Guide
Show Details	BiomeFx	BFx	$435	Whole-genome shotgun metagenomic sequencing. Sample Report Interpretation Guide

How it works:

1. Culture: A portion of the stool sample (which contains many different kinds of biota) is placed in a petri dish containing an appropriate growth medium under conditions designed to support growth and distinguish organisms of interest.
2. Identification: Organisms that grow may be identified by traditional microbiologic methods such as colony characteristics, staining, and biochemical testing, or by newer methods such as MALDI-TOF mass spectrometry.
3. Susceptibility: Organisms of interest can subsequently be exposed to various pharmaceutical antibiotics or natural antimicrobial agents to determine the susceptibility of the patient's isolate to each agent, which can help guide treatment. Some laboratories perform this direct testing on the patient's cultured isolate, whereas other reports may instead provide literature- or database-derived information. Direct testing can be more clinically informative because antimicrobial susceptibility may vary among strains of the same species due to chromosomal differences as well as plasmid-borne resistance genes and other resistance mechanisms. Doctor's Data performs direct isolate testing.

• Demonstrates the presence of living organisms capable of growth under the laboratory conditions used.
• Allows direct antimicrobial susceptibility testing on organisms actually recovered from that patient, which can be particularly useful when treatment of a bacterial or yeast/fungal overgrowth is being considered.

Principal limitations:

• Many intestinal organisms, particularly strict anaerobes, are difficult or impossible to recover under routine culture conditions.
• Some viable biota may fail to grow if their requisite growth requirements were not anticipated and provided by the lab.
• Relative growth on a culture plate does not necessarily accurately represent its abundance in the original microbiome (due to differing growth rates and relative preference for the growth conditions provided).
• Prior antimicrobial treatment, specimen handling, transport conditions, and oxygen exposure can affect recovery.

Best suited for: Identifying viable, potentially treatable bacteria or yeast/fungus when antimicrobial susceptibility information may affect treatment.

How it works: Stool is examined directly under a microscope for organisms or structures that can be visually recognized, including parasite ova, larvae, protozoa, yeast, inflammatory cells, and evidence of incomplete digestion.

Principal advantages:

• Can identify parasites without requiring a predetermined DNA target; Multiple specimens collected on different days can improve detection of parasites that are shed intermittently.
• May identify structures that molecular tests do not specifically test for.
• Can provide direct information about digestion, such as undigested food fibers.

Principal limitations:

• Sensitivity depends heavily upon specimen quality, timing, preservation, and examiner expertise.
• Some organisms are difficult to distinguish morphologically.
• Intermittently shed parasites may be missed in a single sample.
• Microscopy is not an effective method for describing the overall bacterial microbiome.

Best suited for: Suspected parasites, particularly when the organism is not included on a molecular panel, and for selected assessments of digestion.

Some laboratories also use a potassium hydroxide (KOH) preparation as a specialized microscopic technique, particularly when evaluating stool for yeast or fungal elements. KOH helps dissolve or clear much of the surrounding cellular and organic material, making fungal structures easier to visualize microscopically. This is a refinement of microscopy rather than a separate microbiome testing method. GDX offers KOH preparation as an optional add-on.

Some labs also do an add-on macroscopic/direct evaluation for parasites, including GDX.

How it works: Polymerase Chain Reaction (PCR) detects DNA sequences chosen in advance by the laboratory. Short DNA sequences called primers or probes are designed to recognize a particular organism or gene. If that target is present, its DNA is amplified so that very small amounts can be detected.

Principal advantages:

• Highly sensitive and specific for the organisms or genes included in the test.
• Can detect organisms that are difficult or impossible to culture.
• Does not require organisms to remain alive during specimen transport.
• Can simultaneously test for selected bacteria, viruses, fungi, or parasites.
• Particularly useful when the clinical question is whether a specific known pathogen is present.

Principal limitations:

• PCR can detect only organisms or genes for which the laboratory has included a target.
• An organism that is not on the panel will generally not be detected.
• Detection of microbial DNA does not necessarily prove that the organism is alive or metabolically active.
• Very sensitive detection may identify low levels of an organism whose clinical importance is uncertain.
• A targeted PCR panel does not provide a complete survey of the microbiome.
• Results from different laboratories cannot necessarily be compared directly because panels, primers, extraction methods, and reference populations differ.

Best suited for: Highly sensitive detection of selected pathogens or clinically important organisms.

How it works: qPCR is a form of PCR in which amplification is monitored as it occurs. This permits estimation of the amount of DNA corresponding to a selected organism or gene rather than simply reporting whether the target was detected.

Principal advantages:

• Retains the sensitivity and specificity of targeted PCR.
• Provides an estimate of the quantity or concentration of a targeted organism.
• Can help distinguish very small detectable amounts from substantial overrepresentation.
• Particularly useful for monitoring known organisms over time when the same assay is repeated.

Principal limitations:

• Like other targeted PCR methods, it can find only targets selected in advance by the lab.
• DNA quantity is not the same as viable organism count or metabolic activity.
• Quantitative results depend upon specimen weight, DNA extraction efficiency, assay calibration, and laboratory methodology.

Best suited for: Measuring selected organisms when both presence and approximate microbial burden are clinically relevant.

Not all labs using PCR or qPCR report parasites. The ones listed for this section do use one or both of these techniques to detect parasitic organisms or DNA.

Not all laboratories using PCR or qPCR include viral targets. The laboratories listed in this row use molecular methods to detect selected gastrointestinal viruses in stool. A positive finding indicates current or recent viral shedding and therefore generally implies ongoing or recently active viral replication, rather than merely remote past exposure. However, it does not by itself establish clinically significant gastrointestinal infection or disease.

Because these are targeted assays, viruses not specifically included on the laboratory's panel will generally not be detected. For example, Diagnostic Solutions (DS) tests for CMV and EBV.

Some molecular stool tests use quantitative PCR (qPCR) or Shotgun Metagenomics to detect genes in the microbial DNA that are associated with resistance to selected antibiotics. The presence of a resistance gene suggests that microbes in the specimen may carry a genetic mechanism capable of reducing susceptibility to that antibiotic or drug class.

However, detection of a resistance gene does not prove that the gene is being expressed, identify which organisms are carrying it, or establish the actual susceptibility of a particular bacterial isolate. This genotypic approach is therefore different from culture-based susceptibility testing, in which a living organism recovered from the patient is directly exposed to antimicrobial agents.

Diagnostic Solutions includes selected H. pylori resistance genes in the standard DS GI-MAP and offers a broader Universal Antibiotic Resistance Genes Panel as an optional add-on.

BFx bases its microbiome analysis on shotgun metagenomic sequencing and derives resistome information from those sequence data.

How it works: Rather than looking only for predetermined microbial targets or sequencing one marker gene, shotgun metagenomics sequences millions of DNA fragments from essentially all microbial DNA recovered from the specimen. Computer algorithms then compare these sequences with genomic reference databases to identify organisms and microbial genes.

Principal advantages:

• Provides a broad, relatively unbiased survey rather than limiting detection to a predetermined organism list.
• Can identify many bacteria as well as fungi, archaea, viruses, and some parasites, depending upon the laboratory's methods and databases.
• Usually provides substantially better species-level resolution than 16S sequencing and may sometimes distinguish strains.
• Can detect organisms that cannot readily be cultured.
• Particularly useful for assessing microbial diversity, ecological balance, loss of beneficial organisms, and unusual overrepresentation of microbial groups.

Principal limitations:

• Detection of DNA does not establish that an organism is alive.
• Detection of a metabolic gene does not establish that the gene is currently being expressed or that the predicted metabolite is actually being produced in the patient's intestine.
• Results depend substantially upon sequencing depth, DNA extraction methods, the quality of the reference genome database, and the laboratory's bioinformatics algorithms.
• Some findings have strong research associations but uncertain clinical significance.
• Most abundance results are relative abundances.
• If one organism becomes unusually abundant, the reported percentage of another organism can appear to decrease even if its absolute number has not changed.
• Extensive detection can produce findings whose clinical importance is unknown and may therefore require more cautious interpretation than targeted pathogen testing.

Best suited for: Detailed assessment of the entire microbial ecosystem, particularly diversity, beneficial organisms, microbial community structure, and potential metabolic functions.

Enzyme-linked immunosorbent assays (ELISA) and related immunoassays use antibodies to detect specific proteins or other antigens in stool. Depending upon the assay, these may include microbial antigens, host proteins, digestive markers, inflammatory markers, or antibodies produced by the patient.

When used for microbial antigen testing, these assays do not require the organism to remain alive. Unlike PCR, they detect microbial antigen rather than microbial DNA. A positive microbial-antigen result therefore provides evidence that antigen from the target organism is present in the stool, although it does not by itself establish organism viability or quantify the overall microbiome.

Because each assay is designed for a specific target, only antigens or biomarkers specifically included in the laboratory's panel can be detected.

Some gastrointestinal testing programs include saliva-based measurements in addition to stool testing. These assays evaluate a different specimen and may reflect host immune responses or other physiologic processes rather than directly measuring organisms or biomarkers in stool.

Some gastrointestinal testing programs include urine-based measurements in addition to stool testing. In particular, Vibrant's Gut Zoomer also includes timed urine measurements of neurotransmitters, catecholamine metabolites, and related neuroactive metabolites. These assays may measure metabolites or other products related to gastrointestinal or microbial metabolism, but they are not stool measurements and are therefore noted here only as related components of the Gut Zoomer panel.

Short chain fatty acids (SCFAs) are the end product of the bacterial fermentation process of dietary fiber by beneficial flora in the gut and play an important role in the health of the GI as well as protecting against intestinal dysbiosis. They are sometimes named by their un-ionized acid form (e.g., butyric acid [traditional name] or butanoic acid [IUPAC systemic name]), or sometimes by the name of their ionized form (e.g., butyrate).

The most common SCFA include:

• Acetate (acetic/ethanoic acid, 2 carbon) - systemic and microbial roles
• Propionate (propyl/propanoic acid, 3 carbon) - systemic and microbial roles
• Butyrate (butyric/butanoic acid, 4 carbon) - particularly important fuel for colonocytes
• Valerate (valeric/pentanoic acid, 5 carbon)

Diagnostic Solutions offers the optional StoolOMX add-on, which provides a more extensive direct measurement of short-chain fatty acids than most labs.

Low levels are associated with colonic inflammation, low soluble fiber intake, dysbiosis, and colon cancer. The most important markers are total SCFA and butyrate (butyric acid).

SCFAs have numerous roles in the regulation of intestinal health and function.

They also decrease the pH (increase acidity) and make the gut microenvironment more anaerobic, which makes the gut less hospitable to pathogenic bacteria and yeast/fungi.

They provide energy for intestinal cells, and regulate the actions of specialized mucosal cells that produce anti-inflammatory and antimicrobial factors, mucins that constitute the mucus barriers, and gut active peptides that facilitate appetite regulation and euglycemia. They stimulate healing and contribute to normal cell metabolism and differentiation.

Beneficial bacteria (also called commensal bacteria) that ferment non-digestible soluble dietary fiber to produce SCFAs include Lactobacillus spp, Bifidobacterium, Faecalibacterium prausnitzii, Akkermansia muciniphila, Bacteroides fragilis, and some Clostridium spp. Appropriate amounts of these organisms may contribute to a balanced intestinal ecosystem. Optimal abundance varies by organism and host; higher is not necessarily always better.

Food sources of soluble fiber include chick peas, beans, lentils, oat and rice bran, fructo- and galacto- oligosaccharides, and inulin [Doctor's Data]. Intestinal mucus glycans can also be converted to make SCFA.

The measured levels reflect microbial production, consumption by colonocytes and other microbes, as well as transit time and water content of the stool.

Products of Protein Breakdown (PPB, Putrefaction) are bacterial fermentation products of dietary or endogenous protein that reaches the colon without being completely digested or absorbed in the small intestine. Genova's PPB biomarker measures the combined concentration of three short-chain fatty acids: valerate, isobutyrate, and isovalerate. These are sometimes referred to as putrefactive short-chain fatty acids or branched-chain fatty acids.

Increased colonic protein fermentation may contribute to characteristically foul-smelling stool and flatus.

Elevated fecal PPB may reflect increased colonic protein fermentation and can be associated with high protein intake, impaired protein digestion, hypochlorhydria, exocrine pancreatic insufficiency, small intestinal bacterial overgrowth, dysbiosis, gastrointestinal bleeding or protein exudation, and rapid intestinal transit.

Low levels may occur with very low protein intake, antibiotic use, reduced commensal bacterial abundance, or intestinal inflammation.

One of the Phase II liver detoxification pathways consists of glucuronidizing toxins (including many steroid hormone byproducts), and then secreting the resulting conjugation products into the bile for elimination in the stool.

Elevated fecal β-glucuronidase produced by the gut microbiome may undo the liver's glucuronidation process by deconjugating some compounds previously glucuronidated by the liver. This can potentially increase their intestinal reabsorption (enterohepatic recirculation).

Predicts the gut microbiome's genetic potential to produce hexa-LPS; too much of this bacterial product crossing the gut barrier may be pro-inflammatory.

Predicts the gut microbiome's genetic potential to break down gut's protective mucus barrier, which may be pro-inflammatory.

Estimates the gut microbiome's genetic potential to produce hydrogen sulfide, which may be pro-inflammatory.

Secretory IgA (sIgA)

Calprotectin

Lactoferrin

Lysozyme

Alpha 1-antichymotrypsin

Matrix Metalloproteinase-9 (MMP-9)

S100A12

Inflammation-Associated Dysbiosis Score

Beta Defensin 2

Red Blood Cells (RBC) (microscopic)

White Blood Cells (WBC) (microscopic)

Mucus (microscopic)

Eosinophil Protein X (EPX)

Pancreatic Elastase

Chymotrypsin

Fecal Fats Stain (microscopic)

Total Fecal Fat

Steatocrit

Meat (Muscle) Fibers (microscopic)

Vegetable Fibers (microscopic)

Carbohydrates

Zonulin

Fecal Triglycerides

Fecal Cholesterol

Fecal Phospholipids

Long-chain Fatty Acids

Bile Acids

Some stool panels measure antibodies directed against microbial, dietary, or host antigens. These markers reflect mucosal immune reactivity rather than directly measuring microorganisms, inflammation, intestinal permeability, or digestive function.

Fecal Anti-gliadin IgA

Tissue Transglutaminase (tTG) Antibody

Deamidated Gliadin Peptide (DGP) Antibody

Lipopolysaccharide (LPS) Antibody

Actin Antibody

Anti-Saccharomyces cerevisiae Antibody (ASCA)

Occult Blood

Fecal Gluten Peptide

Stool pH

Stool Color (macroscopic)

Stool Consistency (macroscopic)

Host DNA

Oxygen Exposure Index

Yeast (microscopic)

Parasites (microscopic)

Charcot-Leyden Crystals (microscopic)

Pollen (microscopic)

Methane Dysbiosis Score

Beneficial Bacteria

Potentially Pathogenic, Imbalanced, and Dysbiotic Bacteria

Fungal Culture

Fungal Susceptibility

• Searches for evidence of parasites or their eggs (ova).
• Because some parasites may be shed intermittently, examination of multiple specimens collected on different days can improve sensitivity.