The benefits of comprehensive stool testing

Disclosure: I have no affiliation with Doctor’s Data, or any stool-testing company, and received no financial incentives to write this article.

Update 9/10/18: In light of recent studies, I am increasingly using a combination of comprehensive stool analysis, PCR-based stool testing, organic acids testing, and SIBO breath testing with my clients to provide a better overall picture of what’s going on in the gut. I still believe comprehensive stool analysis is useful, as it can help screen for potential pathogens, parasites, and yeast, among other important markers; however, I take any bacterial abundance information with a grain of salt and recognize that it is not directly representative of community dynamics in the gut environment. 

Let’s face it, putting a fecal sample in a special container is the last thing you want to do for your doctor. But what if I told you that your doctor’s office is likely only testing about one percent of what they could be testing your gut for? Given how important gut health is, you’d think if you went to all that trouble, they’d at least provide you with some useful information. But here’s a typical stool test result from a basic lab culture:

No visible ova or parasites

Occult blood: negative

Appearance: normal

Give that same person a comprehensive stool analysis, and you’ll often get a very different result.

5 commonly overlooked GI pathologies

Comprehensive stool testing not only assesses for a much wider range of pathogenic bacteria, yeasts, and parasites, but can also provide useful information about the gut environment, digestion, and absorption.

There are five commonly overlooked GI pathologies that can be captured on a comprehensive stool test:

  • Severe gut dysbiosis
  • Parasitic infection
  • Fungal overgrowth
  • Macronutrient malabsorption
  • Immune dysregulation

Who would benefit from a comprehensive stool analysis?

Frankly, everyone could benefit from knowing more about their gut health, but if you have any of the symptoms below, you might particularly benefit from a comprehensive stool test:

  • Digestive issues
  • Gas and bloating
  • Abdominal pain
  • Constipation or diarrhea
  • Rashes or hives
  • Acne
  • Mood disturbances
  • Fatigue
  • Insomnia
  • Brain fog
  • Joint pain
  • Chronic sinus and allergy issues
  • Rapid weight gain or weight loss

Of course, these symptoms can originate from a variety of underlying root causes. However, even if you suspect you don’t have any of the pathologies listed above, I still recommend gut testing to rule out GI pathologies. You’d be surprised how many people have them, even without any overt gut symptoms, and an untreated gut issue will make treating any other body system much more difficult.

Which comprehensive stool testing method is best?

There are many different methods currently used for stool testing and a lot of confusion about which is best. In this section, I’m going to discuss the pros and cons of each method, and which companies are currently using them. If you don’t care about the nitty-gritty details and just want to know which test I recommend, you can skip to the next section.

PCR-based techniques: PCR-based techniques are commonly used in urgent care and emergency rooms, when an acute infection is suspected. PCR requires a specific primer for each microbe that you want to screen for, and involves amplification of a piece of DNA that’s been captured by the primer. It’s much better for asking whether a specific microbe is present, rather than screening someone for any potential overgrowth or infection. PCR-based methods do not provide any information about which treatments (antimicrobials, antibiotics) a pathogen might be susceptible to. Many companies using PCR methods may claim to screen for antibiotic resistance genes, but the mere presence of these genes does not indicate whether they are being expressed.

Popular companies: Genova (GI Effects), Diagnostic Solutions (GI-MAP), and BioHealth

High-complexity stool culture: For decades, culture-based techniques were the only way to study microbes, but they missed many bacteria that only survive in anaerobic conditions. This led to a movement away from stool culture and towards PCR-based and metagenomic techniques. However, improvements in culture techniques and the introduction of special media that favors the growth of anaerobic bacteria has significantly enhanced the utility of stool culture in clinical practice. Stool culture also allows for susceptibility testing, where identified pathogens are exposed to different treatments (antimicrobials, antibiotics) in a petri dish to determine which might be most effective.

Proteomic-based mass spectrometry: This is also called MALDI/TOF, and takes advantage of the fact that each microbe has a unique protein fingerprint. These signature microbial proteins are matched against a database, rapidly identifying over 1,400 species without having to purify or isolate them. Several studies have validated the MALDI/TOF method, and shown that it has 99 percent accuracy in identification of normal gut flora, 100 percent accuracy in identification of common pathogenic species, and high reproducibility across laboratories.1,2 In fact, a 2016 study using high-complexity stool culture coupled with mass spectrometry was able to identify 513 new species in the human gut microbiome.3

Popular companies that combine stool culture with proteomics: Doctor’s Data, BioHealth, Genova (GI Effects)

16S sequencing: This uses conserved and hypervariable regions of the bacterial 16S ribosomal RNA gene to identify which bacteria are present, and in what relative abundance. 16S sequencing does not distinguish between live and dead bacteria, and cannot provide any susceptibility information. It also provides no information about fungi or parasites.

Popular companies: uBiome, American Gut, Thryve, Biohm, DayTwo

Metagenomics: This method provides a very high throughput evaluation of nearly the entire gene content (the meta-genome) of the gut microbiome. Metagenomics can identify microbes that cannot be cultured and provides information about what functional capabilities these microbes have. While metagenomics is excellent for research purposes, we just don’t know enough yet to be able to provide actionable information based on metagenomic outputs in clinical practice.

Metabolomics and meta-transcriptomics: These assess the metabolic output of the gut microbiome and the sum of all of the gene expression of the microbiome, respectively. In the near future, metabolomics and meta-transcriptomics will likely complement culture-based approaches in a way that is accurate, affordable, clinically relevant, and actionable – but for now, they are impractical for clinical use.

Popular companies: Viome

The best commercial stool test available

As someone who regularly tests and recommends treatment for gut conditions, I only use testing companies who employ state-of-the-art methodologies.

Currently, I recommend Doctor’s Data Comprehensive Stool Analysis with Parasitology (CSAP) x3 samples. Doctor’s Data uses a total of ten different anaerobic, aerobic, and microaerophilic culture conditions combined with MALDI-TOF proteomics. This allows for the detection of 1,240 different bacteria and yeast, including 80 different species of Candida.

With Doctor’s Data, any sample that comes back with pathogenic bacteria or yeast automatically undergoes susceptibility testing using both herbal antimicrobials and antibiotics. An example is shown below for Pseudomonas aeruginosa:

Doctor’s Data CSAP also evaluates biomarkers for digestion and absorption, inflammation, immune status, short-chain fatty acids, and overall gut health. This allows for a more complete understanding of what’s going on in the gut environment.

They also look for evidence of parasitic infection. Using three samples increases the chance that any ova or parasites will be detected, as these can often be patchy in their distribution throughout the GI tract.

(While I believe 16S sequencing results are fascinating, and recently shared my own uBiome results, I believe they have little utility in clinical practice, unless used in combination with comprehensive stool analysis and other measures of gut health. I am extremely wary of any company that makes automated diet or supplement recommendations based on the sequencing results of a single stool sample without considering the gut environment or individual symptoms.)

What a comprehensive stool test report looks like: a case study

Here is part of a Doctor’s Data stool test report from a recent client of mine, Katie, who graciously allowed me to share her case. (Katie has a blog at kitchenstewardship.com and is wonderfully transparent about her health journey.) Her major complaints were psoriasis, infrequent bowel movements, and hormone imbalance. When she started working with me, she told me that she had been previously told by a naturopath that she had Candida, and sent me several articles she had written detailing her frequent battles with the Candida rash.

I asked Katie a number of questions, and she admitted that she had never had her Candida diagnosed by a stool test. I explained that the classic symptoms of Candida have quite a bit of overlap with other GI pathologies, and suggested that we order her a Doctor’s Data comprehensive stool test. She enthusiastically agreed, and was shocked when we received the results.

Below is the yeast culture and microscopic yeast analysis, showing that she had no yeast detected at all:

However, she did have Blastocystis hominis, a parasite that is commonly transmitted through contaminated food or water. There is some debate as to whether Blastocystis hominis can be a normal resident of the GI tract, but certain strains can be pathogenic and are known to cause rashes and other symptoms Katie was experiencing. She also had low secretory IgA, and tested positive for methane-predominant SIBO.

In other words, Katie spent the better part of five years believing she had Candida, and fighting tooth and nail to try to get her health back in order. Now, thanks to comprehensive stool testing, we know exactly what she is dealing with, and have designed a targeted botanical protocol that is specific to Blastocystis hominis and methane-predominant SIBO. For the first time, she’s got a more definitive answer as to why she may have been dealing with this ongoing rash, and an evidence-based plan to treat it and prevent it from coming back.

Interested in getting your gut tested? Click here to learn more about working with me and book a free strategy session.

 

Sources:

  1. Tan, K. E. et al. Prospective Evaluation of a Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System in a Hospital Clinical Microbiology Laboratory for Identification of Bacteria and Yeasts: a Bench-by-Bench Study for Assessing the Impact on Time to Identification and Cost-Effectiveness. J. Clin. Microbiol. 50, 3301–3308 (2012).
  2. Samb-Ba, B. et al. MALDI-TOF Identification of the Human Gut Microbiome in People with and without Diarrhea in Senegal. PLoS ONE 9, (2014).
  3. Lagier, J.-C. et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat. Microbiol. 1, 16203 (2016).

The benefits of comprehensive stool testing

Disclosure: I have no affiliation with Doctor’s Data, or any stool-testing company, and received no financial incentives to write this article.

Update 9/10/18: In light of recent studies, I am increasingly using a combination of comprehensive stool analysis, PCR-based stool testing, organic acids testing, and SIBO breath testing with my clients to provide a better overall picture of what’s going on in the gut. I still believe comprehensive stool analysis is useful, as it can help screen for potential pathogens, parasites, and yeast, among other important markers; however, I take any bacterial abundance information with a grain of salt and recognize that it is not directly representative of community dynamics in the gut environment. 

Let’s face it, putting a fecal sample in a special container is the last thing you want to do for your doctor. But what if I told you that your doctor’s office is likely only testing about one percent of what they could be testing your gut for? Given how important gut health is, you’d think if you went to all that trouble, they’d at least provide you with some useful information. But here’s a typical stool test result from a basic lab culture:

No visible ova or parasites

Occult blood: negative

Appearance: normal

Give that same person a comprehensive stool analysis, and you’ll often get a very different result.

5 commonly overlooked GI pathologies

Comprehensive stool testing not only assesses for a much wider range of pathogenic bacteria, yeasts, and parasites, but can also provide useful information about the gut environment, digestion, and absorption.

There are five commonly overlooked GI pathologies that can be captured on a comprehensive stool test:

  • Severe gut dysbiosis
  • Parasitic infection
  • Fungal overgrowth
  • Macronutrient malabsorption
  • Immune dysregulation

Who would benefit from a comprehensive stool analysis?

Frankly, everyone could benefit from knowing more about their gut health, but if you have any of the symptoms below, you might particularly benefit from a comprehensive stool test:

  • Digestive issues
  • Gas and bloating
  • Abdominal pain
  • Constipation or diarrhea
  • Rashes or hives
  • Acne
  • Mood disturbances
  • Fatigue
  • Insomnia
  • Brain fog
  • Joint pain
  • Chronic sinus and allergy issues
  • Rapid weight gain or weight loss

Of course, these symptoms can originate from a variety of underlying root causes. However, even if you suspect you don’t have any of the pathologies listed above, I still recommend gut testing to rule out GI pathologies. You’d be surprised how many people have them, even without any overt gut symptoms, and an untreated gut issue will make treating any other body system much more difficult.

Which comprehensive stool testing method is best?

There are many different methods currently used for stool testing and a lot of confusion about which is best. In this section, I’m going to discuss the pros and cons of each method, and which companies are currently using them. If you don’t care about the nitty-gritty details and just want to know which test I recommend, you can skip to the next section.

PCR-based techniques: PCR-based techniques are commonly used in urgent care and emergency rooms, when an acute infection is suspected. PCR requires a specific primer for each microbe that you want to screen for, and involves amplification of a piece of DNA that’s been captured by the primer. It’s much better for asking whether a specific microbe is present, rather than screening someone for any potential overgrowth or infection. PCR-based methods do not provide any information about which treatments (antimicrobials, antibiotics) a pathogen might be susceptible to. Many companies using PCR methods may claim to screen for antibiotic resistance genes, but the mere presence of these genes does not indicate whether they are being expressed.

Popular companies: Genova (GI Effects), Diagnostic Solutions (GI-MAP), and BioHealth

High-complexity stool culture: For decades, culture-based techniques were the only way to study microbes, but they missed many bacteria that only survive in anaerobic conditions. This led to a movement away from stool culture and towards PCR-based and metagenomic techniques. However, improvements in culture techniques and the introduction of special media that favors the growth of anaerobic bacteria has significantly enhanced the utility of stool culture in clinical practice. Stool culture also allows for susceptibility testing, where identified pathogens are exposed to different treatments (antimicrobials, antibiotics) in a petri dish to determine which might be most effective.

Proteomic-based mass spectrometry: This is also called MALDI/TOF, and takes advantage of the fact that each microbe has a unique protein fingerprint. These signature microbial proteins are matched against a database, rapidly identifying over 1,400 species without having to purify or isolate them. Several studies have validated the MALDI/TOF method, and shown that it has 99 percent accuracy in identification of normal gut flora, 100 percent accuracy in identification of common pathogenic species, and high reproducibility across laboratories.1,2 In fact, a 2016 study using high-complexity stool culture coupled with mass spectrometry was able to identify 513 new species in the human gut microbiome.3

Popular companies that combine stool culture with proteomics: Doctor’s Data, BioHealth, Genova (GI Effects)

16S sequencing: This uses conserved and hypervariable regions of the bacterial 16S ribosomal RNA gene to identify which bacteria are present, and in what relative abundance. 16S sequencing does not distinguish between live and dead bacteria, and cannot provide any susceptibility information. It also provides no information about fungi or parasites.

Popular companies: uBiome, American Gut, Thryve, Biohm, DayTwo

Metagenomics: This method provides a very high throughput evaluation of nearly the entire gene content (the meta-genome) of the gut microbiome. Metagenomics can identify microbes that cannot be cultured and provides information about what functional capabilities these microbes have. While metagenomics is excellent for research purposes, we just don’t know enough yet to be able to provide actionable information based on metagenomic outputs in clinical practice.

Metabolomics and meta-transcriptomics: These assess the metabolic output of the gut microbiome and the sum of all of the gene expression of the microbiome, respectively. In the near future, metabolomics and meta-transcriptomics will likely complement culture-based approaches in a way that is accurate, affordable, clinically relevant, and actionable – but for now, they are impractical for clinical use.

Popular companies: Viome

The best commercial stool test available

As someone who regularly tests and recommends treatment for gut conditions, I only use testing companies who employ state-of-the-art methodologies.

Currently, I recommend Doctor’s Data Comprehensive Stool Analysis with Parasitology (CSAP) x3 samples. Doctor’s Data uses a total of ten different anaerobic, aerobic, and microaerophilic culture conditions combined with MALDI-TOF proteomics. This allows for the detection of 1,240 different bacteria and yeast, including 80 different species of Candida.

With Doctor’s Data, any sample that comes back with pathogenic bacteria or yeast automatically undergoes susceptibility testing using both herbal antimicrobials and antibiotics. An example is shown below for Pseudomonas aeruginosa:

Doctor’s Data CSAP also evaluates biomarkers for digestion and absorption, inflammation, immune status, short-chain fatty acids, and overall gut health. This allows for a more complete understanding of what’s going on in the gut environment.

They also look for evidence of parasitic infection. Using three samples increases the chance that any ova or parasites will be detected, as these can often be patchy in their distribution throughout the GI tract.

(While I believe 16S sequencing results are fascinating, and recently shared my own uBiome results, I believe they have little utility in clinical practice, unless used in combination with comprehensive stool analysis and other measures of gut health. I am extremely wary of any company that makes automated diet or supplement recommendations based on the sequencing results of a single stool sample without considering the gut environment or individual symptoms.)

What a comprehensive stool test report looks like: a case study

Here is part of a Doctor’s Data stool test report from a recent client of mine, Katie, who graciously allowed me to share her case. (Katie has a blog at kitchenstewardship.com and is wonderfully transparent about her health journey.) Her major complaints were psoriasis, infrequent bowel movements, and hormone imbalance. When she started working with me, she told me that she had been previously told by a naturopath that she had Candida, and sent me several articles she had written detailing her frequent battles with the Candida rash.

I asked Katie a number of questions, and she admitted that she had never had her Candida diagnosed by a stool test. I explained that the classic symptoms of Candida have quite a bit of overlap with other GI pathologies, and suggested that we order her a Doctor’s Data comprehensive stool test. She enthusiastically agreed, and was shocked when we received the results.

Below is the yeast culture and microscopic yeast analysis, showing that she had no yeast detected at all:

However, she did have Blastocystis hominis, a parasite that is commonly transmitted through contaminated food or water. There is some debate as to whether Blastocystis hominis can be a normal resident of the GI tract, but certain strains can be pathogenic and are known to cause rashes and other symptoms Katie was experiencing. She also had low secretory IgA, and tested positive for methane-predominant SIBO.

In other words, Katie spent the better part of five years believing she had Candida, and fighting tooth and nail to try to get her health back in order. Now, thanks to comprehensive stool testing, we know exactly what she is dealing with, and have designed a targeted botanical protocol that is specific to Blastocystis hominis and methane-predominant SIBO. For the first time, she’s got a more definitive answer as to why she may have been dealing with this ongoing rash, and an evidence-based plan to treat it and prevent it from coming back.

Interested in getting your gut tested? Click here to learn more about working with me and book a free strategy session.

 

Sources:

  1. Tan, K. E. et al. Prospective Evaluation of a Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System in a Hospital Clinical Microbiology Laboratory for Identification of Bacteria and Yeasts: a Bench-by-Bench Study for Assessing the Impact on Time to Identification and Cost-Effectiveness. J. Clin. Microbiol. 50, 3301–3308 (2012).
  2. Samb-Ba, B. et al. MALDI-TOF Identification of the Human Gut Microbiome in People with and without Diarrhea in Senegal. PLoS ONE 9, (2014).
  3. Lagier, J.-C. et al. Culture of previously uncultured members of the human gut microbiota by culturomics. Nat. Microbiol. 1, 16203 (2016).
By |2018-09-10T22:18:13+00:00June 17th, 2018|