Gut Testing: Complete Digestive Stool Analysis Guide

gi map testing australia complete guide byron bay herbalist naturopath gut health specialist

Today we’ll be covering one option to test your gut for infections called the CDSA (comprehensive digestive stool analysis) test and why I recommend getting the add on PCR stool test as well. The CDSA is offered by a number of different lab companies throughout the world so depending on where you live yours might look a bit different. Here in Australia the lab company most commonly used is Nutripath.

This article will cover the cost of the comprehensive digestive stool analysis (CDSA) and what gut markers the report provides including markers for

  • gut infections like parasites, bacterial infections and fungal infections
  • markers on inflammation in your gut
  • markers on the beneficial bacteria found in your gut.

Not all of these markers are accurate so read on to learn the benefits and shortcomings of the CDSA test.


Why Use Gut Testing?

Gut testing can be a great way to get to the bottom of your chronic digestive health issues. It can be helpful in ruling out parasite, bacterial and fungal infections.

But is it always necessary?

This very much depends on where you are at in your health journey. There isn’t one answer for everyone.

Have you only recently been experiencing different gut health symptoms like constipation, loose bowel movements or even abdominal pain? How serious are the symptoms? If the symptoms are mild and you have just recently started experiencing them then maybe the CDSA stool test is overkill. A simple change in diet, some herbal medicines, maybe a selection of prebiotics and probiotics can all go a long way in bringing your gut health back into balance.

If on the other hand your have been struggling with years and years of poor gut health with serious or ongoing symptoms then gut testing is 100% necessary to get to find the root cause of you gut health issues.

As with many other health care students and practitioners my interest in herbal medicine and nutrition came about from a personal illness. After suffering for two years with a GI infection (eventually found with a CDSA stool test and PCR test) that modern medicine had little solutions for I became seriously motivated!

Instead of going the standard of care route I decided to shell out the cash for a full comprehensive stool analysis (aka a CDSA) plus a PCR test. The thinking behind that was to be 100% sure of what I was dealing with and be able to work with a functional medicine practitioner to customise a specific protocol.

blastocystis hominis gut testing and option byron bay herbalist australian naturopath


Gut Testing Options

There is a whole range of gut testing on the market. If you are confused I totally get it. Each gut testing company is telling you that their test is the best and that you won’t be healthy until you fork out the cash and run theirs. As the gut ecosystem is so damn complex it shouldn’t come as a surprise that there isn’t one test that covers everything.

Update: Since publishing this article a new gut test has been made available here in Australia. It is incredibly detailed and gives a ton more information than any test previously available.


Today we will be covering the CDSA markers and why it is recommended to run another test called a PCR alongside the CDSA if that is the route you choose to take.

But first a little comment on the stool test your GP will offer you.


Standard of care Stool Test

Many people opt for the stool test recommended by their doctor. If you decide to head in that direction then keep the following in mind.

  • Be sure that the stool test is a PCR (polymerase chain reaction) test that assesses the DNA of different pathogens. Here in Australia we have moved towards this test thankfully. Other areas of the world may not use this test yet.
  • Be aware that this test, at least here in Australia, will only screen for the top 5-10 pathogens. Generally this will include nasties like Blastocystis spp., Giardia, Entamoeba histolytica and a handful of others. It almost 100% won’t include many of the others including Klebsiella and Citrobacter. It probably won’t screen for Helicobacter pylori either. Some doctors are onto this one but it is an extra test that needs to be included if suspected.
  • The test won’t provide you with any extra information. This includes what the different bugs are susceptible to which helps with the treatment plan. It won’t tell you if there is blood in the stool which is helpful if you are concerned about ulcers or even inflammatory bowel disease (that is an add on test)
  • The stool test offered by your doctor will not generally screen for fungal overgrowth. As this could be the root cause of your digestive issues this is a big oversight that can be addressed with the tests below.

With all this in mind lets move onto the CDSA stool testing.

CDSA Stool Test – Cost

First off let’s cover the cost of the CDSA stool test. Nutripath offers a number of ‘levels’ of testing. Each levels provides more information on what is happening in your gut.

Level 1 (the most basic) costs $130.

This level will screen for parasites, fungi and bacterial overgrowths.

As you go up, levels 1-4, the testing becomes more expensive. Level 4+ CDSA costs $450. It provides a ton of information including metabolic and inflammatory markers as well as tumour markers.

In many cases I feel that this is way overkill. There are cases when this could be indicated but generally levels 1 and 2 are where we hit the sweet spot of money for value.

CDSA Stool Test – The Information It Gives You

A stool sample is collected in different collection tubes and sent via post to the functional pathology lab. At the lab they physically culture the stool sample on agar plates and analyse the microbes that grow.

Many different parasites can be evaluated and identified this way. Be sure to check in on the specifics of the test available to you. Unfortunately you need to have your health care provider (GP, Acupuncturist, Naturopath, Herbalist) order the labs for you.

Many functional labs offer a range of CDSA options. There is the most basic that screens for pathogens, yeasts and beneficial bacteria all the way up to the most comprehensive CDSA that analysis fat, carb and protein digestion among many other things. It is all a choice that comes down to benefit vs cost.  

The basic CDSA that I have personally run gives the following information

  • A macroscopic description of the stool (blood, mucous, formation and colour) that indicates different things – as noted on the test
  • Microscopic description of stool (RBC, WBC, food remenants)

GI pathogen stool test CDSA blastocystis parasite infection and bacterial infections

  • Basic digestive and metabolic markers – The more expensive CDSA tests will give you much more information here but it will cost

GI pathogen stool test CDSA

  • Beneficial Bacteria – Even a most basic CDSA should screen for the top beneficial bacteria (bifidobacteria, lactobacteria, escherichia coli, enterococci)
  • Other bacteria – This is a very important part of the picture that a CDSA can give you. Many ‘other’ bacteria are actually quite nasty guys. The example below shows Klebsiella spp. in the ‘other’ section. Many clinicians regard an overgrowth of klebsiella an issue and will treat accordingly.

Continuing on the CDSA readout

  • YeastMany yeasts are screened for here. The most common results would be Candida spp.
  • Parasites – This is what we signed up and shelled out the cash for. The list of parasites will differ depending on the lab. The one that Nutripath Labs screen for include Cryptosporidium, Giardia, Entamoeba, Blastocystis and other parasites.

GI pathogen stool test CDSA

It is VERY important to note that both Helicobacter pylori and Clostridium difficile two common parasites need to be added onto the CDSA as a separate (but affordable) screening test for some labs, including Nutripath.

Microorganism Summary – CDSA Results 

A quality CDSA will give you a break down on the microorganisms present. If there are any problematic organisms present it will give you a readout on the different conventional antibiotics as well as the popular antimicrobial herbs that the specific strain found IS or IS NOT susceptible to. This is incredible information to have when working out a protocol and I am amazed and impressed that many CDSA results provide this. The screening alone of each antibiotic/herb would take a decent amount of time and effort.

Seagate Crystal Reports - Pathl

The last section of a standard, quality CDSA will give you a readout on the ‘other bacteria present.’ A breakdown on the specifics and the quantity is extremely valuable information. The test example below shows two different form of Streptococcus, Bacillus and the specific Klebsiella spp (in this case pneumoniae.) A skilled functional medicine clinician will know which are issues, which are actually non-pathogenic and the best approach to a tailored protocol to pursue.

GI pathogen stool test CDSA

PCR – The Second and Possibly More Necessary Test

A PCR test, standing for polymerase chain reaction, works as an amplifier on any DNA strands that may be found in the stool sample. 

It is wise to combine the CDSA (described above) with the PCR test. It is much more accurate!

Nutripath offers a discount on the PCR when you order it alongside the CDSA.

  • The PCR costs $50 dollars on top of the CDSA cost
  • If you order it alone it costs $90

It doesn’t cost much (when combined with a CDSA) and it doesn’t give you much info but the info it does give you is reliable and valuable. Basically that you do or do not have a parasite.

That being said a PCR test can and does still miss parasites present from time to time.

PCR is now recommended with all CDSA tests.

The one that from Nutripath screens for Giardia intestinalis, Cryptosporidium species, Dientamoeba fragilis, Blastocystis species, Campylobacter species, Salmonella species, Shigella species, Yersinia enterocolitica and Aeromonas species.

An example of a clean PCR test

GI stool test PCR pathogen

An example of a PCR that detected two parasites

GI stool test PCR pathogen

Where These Tests Fall Short

A few important points to mention revolve around the shortcomings of these tests.

There are a few and it is important to understand the limitations of these tests or any others that you might be relying on to find the root cause of your illness.

1. The first point is the beneficial bacterial count that is marked by plus or minus signs. A number of people have been in touch or commented that their beneficial bacterial count has come back quite low. Obviously they were concerned. The CDSA test recommended above (the one that has a measurement for your beneficial bacteria) has been shown to be less than accurate in that particular reading. It makes sense when you think about the travel time that your stool sample makes from your house to the lab. If you are concerned about the status of your whole microbiome (including your beneficial bacteria) then a complete microbiome test might be an option.

2. There is the possibility of a false negative as mentioned above. This is when the test comes back clean but has actually missed the infection. There is little you can do to guard against this but if you get a clean test result and it doesn’t feel right then it might be a good idea to cough up the cash and test again.


Microbiome Gut Testing

This article has covered the testing that I have used to find and track the treatment of my intestinal parasites (Blastocystis and Dientamoeba fragilis).

Now this is only to rule in or rule out pathogenic infections including fungi, parasites and bacteria. If your Nutripath testing has come back clean but you still suspect an imbalanced gut microbiome another approach would be to get a picture of the whole bacterial microbiome.

As the microbiome is becoming a hot topic there are new tests coming to the market each year. It can be hard to keep up. While I have not looked at depth into these testing I will rely on Dr. Jason Hawrelak’s recommendation of the Ubiome explorer. It is affordable (but does take time to get the results) and gives you a birds eye view of the state of your microbiome.

Just a word of caution. This test can be overwhelming to read and very difficult to interpret so it is best to find a microbiome savvy clinician to interpret them.


A Few Points To Close On

A standard stool test, ordered from your conventional doctor will not provide the extra relevant information that a CDSA combined with a PCR test will.

Personally I have experienced this (my standard stool test came back positive with Blastocystis hominis but missed Dientamoeba fragilis.

Another prime example – the person’s standard stool test came back clear and free. The PCR test came back free and clear. The CDSA on the other hand (used as examples above) showed a very different story. It flagged a number of different possible microorganisms that can be issues including a Candida spp, Klebsiella spp, and numerous different Streptococcus strains.

A very different story compared to the standard of care stool test that conventional doctors rely on. These can be helpful to rule out the top pathogenic microorganisms, but they definitely won’t give you the full picture.

If you have read this far chances are you are struggling with a gut issue or know someone else who is. Leave a comment below if you have anything to add to the conversation.


References and Resources

  2. Nutripath Lab Testing
Legal and Affiliate Disclosures: This post may contain affiliate links. That means if you decide to make a purchase through one of these links, I may earn a small commission at no extra cost to you. Learn more here

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  1. Hi Todd,

    I just came across your insightful website and was wondering if you offer one on one support? I have decided to do a comprehensive stool test to find out exactly what is going on inside my gut and would like to talk to someone to know which lab would be the best one to use.I will also need support to help me read the results and decide what to do in term of treatments.
    Thank you,

    1. sorry murielle, I missed your comment somehow. Currently I am still a student so can’t offer support. Wish I could help more! Let me know how you go with your digestive issues.

  2. Hi Todd,

    What do you think about ?

    I have Crohn’s and want to find out as much detail as I can, and I want to do the correct test.

    A GP gave me prescription for Bioscreen FMA, but I heard it is not as good as others around (old technology).

    It’s all a lot of money, and I just want what will show me as much as possible.

    Thank you!

    1. I haven’t come across either test. I tried to dig a bit deeper on the bioscreen but their website is down. Also can’t find a test example from the microbiota website. In my opinion there are two ways to go (probably need to update this article) first you want to screen for known pathogenic microbes (fungi, parasites and bacterial infections) Here in Australia Nutripath is the one I have seen ordered most often and is quite reliable from experience (have to use the CDSA combined with the PCR as mentioned in the article). If you have been through this process with no hint as to the root cause of your IBD then digging deeper into the full microbiome composition might be advisable. The test that is most recommended by the expert clinicians is (the explorer is the only one that ships to Australia at the moment, hopefully that will change). One point on that is you definitely someone to help interpret the information as it is incredibly overwhelming. Hope that helps. I’ll look deeper into the tests you mentioned and post up here when I have more info.

  3. Hi Todd
    I’m a Clinical Nutritionist wanting to learn more about testing. I stumbled across your website and this blog on Google. I found it easy to understand and informative. As you say, there are so many tests and it can be confusing. Just one thing, Nutritionists also do testing.
    Thanks again.

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