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Comprehensive Stool Analysis

One of the most common complaints of our time is gastrointestinal issues. While it is quite easy to ignore the slightest discomfort, it could be a sign of serious impairments such as gastrointestinal malfunction or mucosal issues. These issues can easily lead to systemic illnesses, toxic overload, autoimmune diseases, and food allergies among other problems.

Did you know that your gastrointestinal tract has more than 1000 species of microbial organisms? These organisms, collectively referred to as microbiome, are mostly bacteria – good and bad. Microbiome biomarkers show how well the shared metabolic functions are with their host – the human. A comprehensive stool analysis test helps to determine the exact cause of any systemic and gut condition. The test can be Stool Culture based on PCR, depending on your preferred results.

The tests come with 6 actionable panel areas. Here is a brief breakdown of these areas and what they indicate.

1. Inflammation

2. Microbiome

3. Digestion

4. Intestinal health markers

5. Infection

Pathogenic aerobic and anaerobic bacteria, yeast, parasites and ova that can potentially cause disease or damage tract

6. Antimicrobial susceptibility is a test done using natural agents and prescription medication to identify the sensibility and/or resistance of pathogens to selected remedies

Culture Based VS Microbial Testing; Which Is Best?

Stool testing can be done in many different fashions, the most common ones being culture based and microbial. Each of these methods has their pros and cons. The preference for each of these testing methods differs from one person to the other depending on perceived and actual accuracy. Let’s look at what each method entails.

Culture Based Stool Testing

One of the most ancient methods of testing for microbes involves culturing, staining and using a microscope. While this method works wonders with aerobic microbes, the growth media does not favor the anaerobic microbes, making them less effectively cultured.

Microbiology significantly changed with the arrival of DNA sequencing. This is an approach that allows parallel assessment of microbes in a single sample without the need to use growth media. This led to the need to improve culture based testing. One of the significant changes is using growth media that favors even the anaerobic microbes. This, combined with MALDI – TOF, has allowed rapid identification of more than 1,400 microbe species without the need to isolate and purify.

Studies have shown that the MALDI – TOF (usually termed as proteomic based mass spectrometry) has up to 99% accuracy when identifying normal flora in the gut and 100% for common pathogens. Additionally, it is highly reproducible across labs. The thing is, the microbes have to be cultured successfully first before identification of the microbes is done.

Cons of Culture Based Stool Testing

  1. Restricted microbe identification

Culturing can use up to 70 different conditions to accurately identify a good number of species. MALDI – TOF uses only up to 5 conditions. This significantly reduces the number of microbes that can be identified.

  1. Lack of concrete quantification

Culture based test results do not indicate the relative abundance of microbes in a substance. For example, a microbe can be only 0.0001% abundant in a sample, but grows rapidly when exposed to a growth media. This results into a misleading report of an overgrowth of the microbe, which may in turn result into poorly informed treatment choices.

Here is the thing, culturing only identifies a small amount of microbes present in the gut. The amount of microbes identified is usually dependent on the number of culturing conditions used, in which case, only a few are used. Additionally, the quantities of the microbes present can be misleading. The fact that culturing involves using a growth media which may cause one microbe to thrive over others can give false abundant results leading to misdiagnosis.

Molecular Stool Testing

One of the most preferred methods of comprehensive stool testing is the molecular technique. It gives a more accurate presentation of the gut ecosystem. Molecular testing can be done in a variety of approaches in commercial and Clinical Research laboratory settings. Let’s look at some of the most common approaches.

Targeted PCR

Polymerase Chain Reaction is a procedure that involves amplification of a DNA. The process involves using a unique primer for every microbe that is to be tested. The primer then captures and amplifies the DNA of the microbe. This method tests the presence of and accurately identifies the microbes present in a stool sample.

Here is the thing; the identification process is dependent on the primer used. Therefore, if you want the result to show the overall health of the gut ecosystem, you may need to carefully choose the primers to be used. The best option is to use primers that maximize the number of the most abundant microbes and pathogens identifiable.

16s rRNA Gene Sequencing

Ribosomal RNA gene sequencing can be used to identify a number of microbes, thanks to its unique characteristics. This gene, which is present across all bacteria species, has two definite sides; conserved and hyper variable regions. The conserved region evolves slowly while the hyper variable evolves rapidly. These regions differ greatly in each species. The conserved regions are instrumental in designing primers that allow sequencing and amplification of the hyper variable regions. The resultant sequences are then classified accordingly after comparing them to the database of fully sequenced rRNA genes.

The good thing about this sequencing is that it is accurate in identifying the species of bacteria present as well as indicating their specific quantities in a sample. While this approach is susceptible to primer bias, it is one of the most accurate and cost effective stool testing options.

It is important to note that this approach is quite thorough with bacteria, parasites and fungi. As such, it can be used on its own to provide comprehensive stool analysis results. If the disease causing microbes fall outside the bacteria group, they may not be easily picked up.

Quantitative Polymerase Chain Reaction

While this approach is similar to targeted PCR, it amplifies the sequenced microbes in real time. This makes the approach significantly faster, more accurate and extremely sensitive. This approach detects as little change as two fold, while targeted PCR detects ten-fold change solutions. This approach to stool testing is also as popular as targeted PCR as it is faster and equally accurate and more affordable.


This approach to stool testing identifies microbes by assessing their entire gene content and determines relative abundance in a sample. Additionally, metagenomics identifies the functional capabilities of the microbes present in the gut. This stool testing technique is considered more accurate than gene sequencing.

The downside to metagenomics is that it is pricey, and may not always be as readily available as other options. It is not yet adequately developed as it is yet to provide sufficient actionable information to clinical users. There are a few cases where you can opt for metagenomcs over gene sequencing.


Meta-transcriptomics, in addition to metabolomics, are high output techniques that give information of the entire gene expression of the gut microbiome. This technique is so thorough that it is mostly used in research settings in a bid to increase understanding of the gut microbiome. There are plans to use meta-transcriptomics alongside other accurate, affordable, and actionable clinical options for better diagnosis of gastrointestinal tract issues.

This technique accurately shows the rate of metabolism of gastrointestinal microbiome. As such, it is important to note that this technique, when used by itself, cannot accurately estimate microbiome abundance. This is because the rate of metabolism of any microorganism doesn’t necessarily represent its abundance. Therefore, there is a need to use this technique with another clinically relevant option in order to produce accurate test results and a well-informed treatment plan.


It is extremely essential to get the best testing option, especially if you deal with giving relief for gastrointestinal issues. Each stool testing option has its pros and cons, and none is 100% comprehensive on its own. As such, it is advisable to use a combination of techniques based on what your need is. Here is a summary of the most essential categories of stool analysis testing factors.

Different tools can be used simultaneously in order to accurately detect the factors aforementioned. Depending on what one is testing, and the superiority of the results needed, one can easily pick out the relevant techniques.

Is There a Difference between Fecal and Gut Microbiome

Recent studies have suggested that fecal samples do not accurately reflect mucosal gut microbiome. Well, the truth is that stool samples tend to under or over-represent various genera from the most distal colon parts. While this may be true, majority of the published gut microbiome studies have used fecal samples in their tests. Therefore, since there are no studies on gut mucosa, stool samples are deemed more clinically useful compared to an invasive option such as mucosal biopsy.

Natural Treatment Options for Gastrointestinal Complaints

We offer a UK based PCR Comprehensive Stool Analysis which is an alternative to Genova Giagnostics Labatories (GDX) who are an overseas provider, and as such entail less difficult logistical challenges.

Naturopathy refers to the process by which an ailment is treated without the use of conventional use of drugs. In most cases, naturopathy involves using techniques such as controlled diet and exercise as well as massage and other natural non-invasive self-healing practices. It has been adopted as one of the common treatment options for conditions arising from any sort of imbalances in the gut.

Naturopathic treatments are highly personalized. Some important elements of a natural treatment plan include the following.

Naturopathy also involves other approaches such as integrative medicine and naturally healing related conditions that maybe affecting the gut’s function. Such conditions that affect the digestive tract system include fatigue, mental-emotional fog, auto-immune diseases, headaches, migraines, weight fluctuations, joint conditions as well as allergies among others.

Naturopathy focuses on the general wellness and health of the body as a way to treat conditions and prevent recurrence of common gut issues.

It is important to note that as natural as the remedies are, it is vital that the appropriate tests are done. A comprehensive health history is necessary before any treatment plans and dietary recommendations are given. The naturopathic doctor takes time to gather information about emotional, mental, physical, social and environmental factors that may be influencing gut problems. This information also includes a history of food choices, surgical procedures, as well as any other detail related to onset of symptoms of the gut problem.

Once the history is clear, targeted tests are carried out to evaluate the causative issues. You may need a comprehensive stool analysis test in addition to specific blood tests so as to pin down the problem and recommend a well-informed healing plan.

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