Stool testing 101 and how your gut impacts how you feel.

Danh NgoFibromyalgia + Chronic Pain, Gut Health, Holistic Medicine Division, Pain Relief Division

Your digestive health is an important and under-treated aspect of your quest to improving mobility, strength, alignment, and being pain-free. There is undeniable and growing research that is linking the health of how your body feels through pain and emotions. The gut’s impact on the following systems: bone, muscles, joints, brain, nerves, hormones, skin, and immune system.

This article cannot go into an extensive explanation of how your digestive system work or what is troubling your gut. We will explain when, why, and what will you gain when you get a stool test. There are many types of stool tests out there that can make consumers like you confused or spend money with little value afterward.

We use stool testing with the interest in learning how your digestive system is functioning. Stool tests are to be used to help you to learn more about your digestive system can be impacting your mood, pain, and health. A big misconception is to use stool testing as the primary or only source of information for your health. The science is still too early for this purpose.

Here are known “functional” terminology that you will want to know about your digestive health.

  • Gut Dysbiosis
  • Insufficiency dysbiosis
  • Malabsorption
  • Fungal overgrowth

There is a specific digestive “functional” disorder called gut dysbiosis that we are going to write about. Dysbiosis is an imbalance of your microbiome or the environment within that region. Gut dysbiosis is an imbalance of the microflora within your digestive system. The goal is to have more “good” and “less” bad microbes species.

Gut dysbiosis tends to refer to more “bad” species over dominating the beneficial gut flora. Insufficiency dysbiosis is the opposite. You have less of the beneficial gut flora.

Microbes exist within your digestive systems to help make sense of the food you eat. Microbes consist of numerous species of bacterias, fungi, and yeast. The amount of energy you get from your food is largely impacted by the types and diversity of these microbes. The specific functions of your gut microflora include making vitamins, fermenting fibers, digesting proteins and carbohydrates, and propagating anti-tumor and anti-inflammatory factors.

Everyone has a special mix of microbes within their small and large intestines. You can say that your gut microbiota is like a “fingerprint” or “DNA”.

There are known microbial species that have been linked to certain symptoms and diagnosis. The vast majority of microbial species are beneficial when they are populated in the appropriate amount. We will explain later in this article, but a classic example is that E. Coli is a beneficial species to our health.

Fun fact: There are numerous types of microbiomes within your body, such as your eyes, nose cavity, mouth, skin, reproductive region, respiratory, and ears. When there is a disruption of your gut microbiota, you can find a disruption to one or multiple microbiomes listed earlier too!

Before we dive into the nitty-gritty details of the sexy topic of stool testing, we would like to emphasize that you can have absolutely no digestive symptoms and still could have an underlying digestive weakness and imbalance! For this reason, we find the value that stool testing provides is CLARITY and clear intention of results.

A disruption of your gut microbiome can present for someone as bloating, constipation, depression, and chronic nerve sensitivity and pain. For another person, the only symptoms are asthma, allergy, and tiredness at the end of the workday. This can be brushed as normal aging “feelings”.

As they feel tired, they may feel occasional muscle tightness and discomfort that goes away with stretching. The problem is that they have to stretch all the time. As a Specialist in Orthopedic and Sports Medicine Physical Therapy, our philosophy is that 3 weeks of stretching (this includes foam rolling or massages) protocol is supposed to help you to not feel tight anymore.

Recurrent tightness is a cause to pause and reflect on “WHY am I continuing to feel tight? WHY can I not shake this off?”.

Due to the mentioned statement, many find it helpful to understand the many variables of why they cannot shake off symptoms like muscle tightness, joint discomfort, cramps, and nerve pain. We know that it is better to be clear and have a solid plan of attack, then based it on best clinical judgment.

ReVITALize Rehab Club has the holistic philosophy that your internal health plays a role in how you feel muscle, joint, and/or nerve-related discomfort. How is pain related to your heart, gut, renal, hormonal, lymphatic system, and such? The answer is that your internal health impacts how you recover and regenerate.

You cannot “out-do” poor recovery with “just a little bit more” exercise, stretch, foam roll, and/or massage. You need the energy to waste energy.

But, I do not have any digestive problems? Why should I get tested?

Aaahhhh… There are many misconceptions about stool testing that we hope you will want to get your stool tested if you desire to stay active and healthy.

We will follow-up this article with Dr. Danh Ngo’s own stool testing so you can see how to allow what you learn in this article and make it more practical.

Here is the order of this article.

Three primary methods of stool testing:

  • The three main types of stool testing.
  • Pitfalls of stool testing.
  • Gut Microbiome: Bacteria diversity and Samples of common microbial species.
  • What else can a comprehensive stool test tell you?

The three main types of stool testing.

The three types of stool testing are PCR-based technology, high-complexity stool culture, and proteomic based mass spectrology (MALFI-TOF).

PCR-based technology’s primary benefit is the test is good in detecting for foodborne diseases and common infections like Campylobacter, Salmonella, Yersinia, Shigella, and C. Diff.

PCR-based technology requires a specific primer for each microorganism. Primer is a molecule that serves as a starting material for a polymerization process. This can be costly, and limited in assessment, as there are limited slots for testing. These reasons make this stool testing ideal for hospitals and immediate situations.

High-complexity stool culture is helpful in the identification of living organisms. Stool culture is considered the gold standard. The test is the most sensitive, which means that the test detects microorganisms the best.

The third method is proteomic-based mass spectrology, it’s also known as MALDI-TOF. MALDI-TOF stands for Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectronomy.

Proteomics looks to examine and identify based on the characteristics of the proteins in cells, tissues, or organisms. A simple way of looking at MALDI-TOF is comparing it to fingerprint analysis. Each microorganism has a unique ribosomal fingerprint. These proteins are quickly matched with a huge database.

Speed and accuracy make this testing very appealing for hospital and Functional Medicine clinics, like us, to shift its focus towards.

Gut Microbiome: Bacteria diversity

There are over trillions of bacteria and yeast organisms in our digestive system. We cannot dive into every single bacteria micro-organism and how they relate to your health. There are pieces of evidence that demonstrate that your health and how you feel is more complicated to judge based on what species are in your digestive system and stool results.

What we mean to imply is the misconception that certain species are good or bad for your health. Many people are familiar with the two publicly infamous infections called E. Coli and C. Diff. E Coli (known as Escherichia coli) and C Diff (known as Clostridium difficile). You might be surprised to know that these two species are important to keep us healthy!

E coli and C diff are needed to kept you healthy.

We can make reasonable clinical judgments if there is a lack of certain beneficial bacterial species. There two main bacteria species that makeup 30% of 100 trillions of micro-organisms in the gut.

Bifidobacterium spp. and Lactobacillus spp. accounts for 1/3 of your gut microbiota. This is crucial to understand and a quick thing to fix. When you have low counts of Bifidobacterium and Lactobacillus spp, this is called insufficiency dysbiosis. The plan is to have a lot of good and less bad.

Another important species that help to make up a healthy gut flora is Clostridium.

Before we go into bacterial, yeast, fungi, and parasites that are “bad” when overpopulated, alongside, low amount of “good” microbial, we would add Candida species to the discussion necessary for good health.

What are commensal or dysbiotic strains that you should know about?

Klebsiella is the first that comes to our mind. Klebsiella is a strain of bacteria that has been associated with joint pain. The theory is that your possible joint pain is coming from the immune system reacting and forming antibodies against Klebsiella.

The next species is the infamous Helicobacter pylori, also known as H. Pylori. The is evidence linking H. Pylori to ulcers to the stomach and duodenum and gastric cancer. Before we make H. Pylori into a scary monster, Dr Martin Blaser’s research shows how H. Pylori can be protective and beneficial in children. The earlier you get H. Pylori, the chances you will not suffer from asthma and allergies. If you get H. Pylori later in life, there is more connection to inflammation within your body. When you have less of the beneficial bacterias and yeast, the H. Pylori can put you at risk of gastric cancer.

Giardia is the next on this list of possible microbial to cause a long list of symptoms. The list includes muscle and joint pain, cancer, fatigue, allergies, and do not absorb nutrients well. We chose Giardia because of the non-controversial agreement to manage when detected. The only trouble is that it can be evasive when using stool testing, so other tests are better for Giardia.

The last microbial we are going to highlight is the parasite, Blastocystis species. You may find this in your stool testing result for good reason. It is the most common parasite in North America. This species follows the same interpretation as the other species. Blastocystis is to be taken seriously in management when there are too many of them, in conjunction with a low population of beneficial bacteria. The healthier you are, the less you have to worry.

What else can a comprehensive stool test tell you?

The other notable information stool testing can show include how well you are digesting certain materials, the amount of possible inflammation in your digestive systems, and the amount of short-chain fatty acids. Let us breakdown each one of these.

Inflammation is necessary for survival. It is the time when your body is trying to heal and feel better. The problem is when you have a low grade and undetected inflammation by medical standards of swelling and fever. Your body may present with muscle achiness and stiffness instead. If you have been following us, we have written about how pain is a way for our body to let us know that there is a possible danger.

A comprehensive stool test by Doctor’s Data looks at markers for certain patterns of inflammation such as Lactoferrin, Calprotectin, lysozyme, and secretory IgA.

Lactoferrin, Calprotectin, and lysozymes level can help identify possible IBD, inflammatory bowel diseases, such as Crohn’s disease. Lysozyme is an enzyme that is produced at the site of inflammation. Lactoferrin and Calprotectin are digestive specific inflammation markers or tags. You will still have to get further testing to confirm, and work with a Gasteroentologist for medical diagnosing.

Secretory IgA is produced by your gut wall’s mucosal tissues. The mucous produces these as your body’s first line of defense against gut toxins and “bad” pathogenic organisms from the lower digestive tract (colon). We use it to help monitor treatment and if it will last. The tricky part of getting well is that these pathogenic organisms can reoccur and overpopulate when our body is not healthy. Secretory IgA indicates if your gut wall line of defense is built and ready to defend.

Short-chain fatty acids (SCFA) are produced by beneficial bacteria in the digestive system. Fermentation is the process of producing energy without oxygen. The fermented bacteria use fermented carbohydrates as a source of sugar to help make the digestive system more acidic or a lower pH. This helps to make bacteria, yeast, fungus, and parasites to not thrive.

SCFA are very important in regulating inflammation and enhance your immune system. Examples of SCFA are Butyrate and Propionate. These help to repair and grow the cell lining of the Gastrointestinal tract.


We hope to have cleared up the importance of testing your gut. Your gut microbiome is important for mood, cognitive brain function, muscle, tendon, bone, and joint health. The tricky part is that many come in without digestive problems that appears “serious” enough to be taken seriously.

Stool testing helps you to know more about how your digestive system are working. You cannot make medical assumptions with stool testing alone. The test is part of an assessment with you in the middle of the discussion.

You need to do multiple samples to get accurate insights of microflora, inflammation status, and absorption capacity.

If you are dealing with a mobility problem, improve on your health with an auto-immune disorder, or trying to avoid surgery because of an arthritis problem, we are here to bring clarity through a comprehensive approach.

Click on the button below to schedule your COMPLIMENTARY chat with Dr Ngo and we will determine what is your next best step towards a fuller and active lifestyle.


Danh Ngo PT, DPT, OCS, SCS, ADAPT trained practitioner

Doctor of Physical Therapy

Board Certified Specialist in Orthopedic and Sports Medicine

Mind Body Health Results Coach

Long Beach’s Functional Sports Medicine Clinic