Australian GI MAP: Complete Test Guide

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

Welcome to the Australian guide to the Complete Microbiome Mapping gut testing.

This guide will be covering a new test on the Australian market that gives you an incredible amount of insight when it comes to digestive health and gut issues. This test almost does it all. It screens for important markers of gut inflammation, leaky gut and digestive enzymes, it looks for parasites including protozoan bugs and worms. It screens for bacterial and fungal infections and it even screens for active viral infections. Finally the gut test looks at some beneficial bacterial markers.

In The Australian Guide to the Complete Microbiome Mapping we will cover each and every one of these areas that the Complete Microbiome Mapping stool test covers, giving examples of when to use this test and what some results may mean for you and your digestive health.

Introduction to the Australian GI MAP

When evaluating and assessing someone with a case of chronic gut complaints it can feel like looking for a needle in a pile of needles. All testing, general pathology and functional testing, have their inherent flaws. The good tests can give you a piece to the puzzle.

The Complete Microbiome Mapping test offered by Nutripath, a functional pathology provider here in Australia, is the gut test that Australia has been waiting for…begging for….desperate for.

In the not-too-distant past stool tests (aka poop tests) were assessed by culturing the stool and microscopy. Needless to say it is incredibly hard to find different bugs hiding out in the stool sample. Because of this the instances of what are known as a ‘false negative’ were sky high.

Picture this scenario.

You go to your herbalist, naturopath or nutritionist.

No, unfortunately not your doctor (generally they will only run the basic PCR stool test. While this is a good test it only screens for the top pathogenic parasites and bacteria. It won’t test for opportunistic bacterial overgrowths or fungi and it definitely won’t help to tell you if you are suffering from leaky gut).

Ok. Back to the scenario. You and your herbalist/naturopath/nutritionist decide, based on your signs, symptoms and case history to run the old fashioned culture and microscopy test. It comes back clean and clear when in fact the testing missed the gut infection. You move onto other theories to help explain your gut symptoms.

This is a classic ‘false negative’ scenario. Not the best outcome.

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New School Gut Testing – DNA

The new form of testing makes culture and microscopy look like the dark ages.

It focuses on finding DNA fragments of dozens of different bugs. For the past few years companies in the United States have been coming out with incredible testing based on DNA.

While you can still work with these US companies from Australia, it does present some challenges (like shipping the sample express through an expensive courier company). The price tag isn’t cheap.

There are a few other DNA gut tests in the States that are more affordable. They provide a great snapshot of the gut microbiome, which really comes in handy. Unfortunately they miss the parasites and fungi that could be causing all of your gut symptoms. An example of this testing would be the UBiome testing, particularly the explorer.

For the longest time I have been jealousy following these testing options coming out in the States.

Now, and thankfully, the Complete Microbiome Mapping gut testing is a comparable stool test that is available in Australia.

Drum roll please…

Complete Microbiome Mapping In Australia GI MAP – Overview

Recently I stumbled on this test (thanks to a fellow student who was sharing her results).

It is exactly what we have been waiting for all these years.

The Nutripath Complete Microbiome Mapping test has every marker that you could ever want and more. Using the DNA based testing it screens for

  • Opportunistic bacteria
  • Fungal overgrowths
  • Parasites including protozoan bugs and even worms
  • Beneficial bacteria
  • Beneficial bacterial balance
  • Viral pathogens

This test is so comprehensive it even gives you some very important digestive markers such as calprotectin, elastase, secretory IgA, Zonulin and beta glucuronidase.

If you are scratching your head at a few of these markers don’t worry, we will cover them one at a time, in depth.

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First off the Price Tag

First off let’s get one thing out of the way. How much does the Complete Microbiome Mapping from Nutripath cost? It is an important question. Especially if you have an idea on what some of these functional tests can cost.

One gut health specialist was recommending a gut test that cost over $700! Sounds pretty extreme right?

Surprisingly the Complete Microbiome Mapping isn’t overly expensive.

For a total cost of $360 this incredibly comprehensive and reliable stool test comes in well under many tests of the same calibre.

Now that might still sound like a fair amount of cash but before you stop reading let’s explore what information this test can provide and how it can help if you.If you are suffering from chronic gut symptoms and haven’t been able to find any solutions then read on.

From here on we are going to dive into each section of the test, exploring the different gut markers in a bit more detail giving examples of some test results that are common and what that may mean for you.  I think it is important for you to know what you are looking at and looking for.

Section 1 – General Macroscopic Description Section

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

Below is an image taken from the Complete Microbiome Mapping Gut Test.

complete microbiome mapping general description

Under the heading General Microscopic Description It shows some markers that describe the composition of the stool. This is a common marker section on many stool tests. For anyone that has ordered a Complete Digestive Stool Analysis before this should look fairly familiar.

It’s nothing to write home about and the markers are reasonably self explanatory so we won’t spend long on them but it is important to note that this section does provide information on how your digestive function is working.

The marker on Mucous is important to note. It provides information on whether you are experiencing inflammation, an infection or even possible malignancy (cancer in the gastrointestinal tract).

A positive marker for mucous in the stool can also indicate inflammatory bowel disease, particularly ulcerative colitis, as can blood in the stool found in the marker called Faecal occult blood (1). IBD isn’t a sure thing when these markers come back flagged but it raises follow up questions and investigations.

The next section has another maker than could possibly indicate inflammatory bowel disease.  

Further Reading –

Section 2 – Gastrointestinal Markers

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

Now we move onto some more advanced markers.

complete microbiome mapping gastrointestinal markers australia

I’m incredibly excited that Nutripath have chose to include these in their Complete Microbiome Mapping Gut Test. It saves the clinician ordering follow up tests if they think that a particular issue may be causing the patient’s symptoms.

More on that below.

Calprotectin.

First off we see the marker Calprotectin. This marker is incredibly helpful for determining the state of inflammation in the gastrointestinal tract. It is released from the neutrophil white blood cells. Elevated levels signify acute inflammation (2).

High levels of Calprotectin cannot be used as a stand alone marker for inflammatory bowel disease but the thinking is that the possibility of IBD should be investigated by your doctor and possibly a medical specialist.

Calprotectin is used to screen people with suspected inflammatory bowel disease with follow up endoscopic investigations needed to confirm or deny the disease (3).

Interestingly one review found low faecal calprotectin to be a good way to rule out inflammatory bowel disease (4).

Pancreatic Elastase

This marker is looking at the function of the pancreas organ. Along with the production of insulin and glucagon (which help to regulate blood sugar levels) this particular organ is responsible for many of the digestive enzymes that help to break down food into absorbable molecules. The marker pancreatic elastase helps to determine how the pancreas is functioning.

This particular enzyme, secreted by the pancreas, remains unchanged and can be measured in the stool when looking for pancreatic insufficiency. This marker is helpful in establishing how well the pancreas is functioning and correlates well with other digestive enzymes, produced by the pancreas, including amylase (to digest starch), lipase (for fat digestion) and finally trypsin (for protein digestion) (5).

This marker can help to explain symptoms such as diarrhea and abdominal pain with the absence of infections..

IMPORTANT NOTE – If low levels are found on the Complete Microbiome Mapping test then it should really be followed up with a visit to your doctor as there is the possibility of issues such as pancreatitis which needs to be ruled out by more investigations, including imaging (6).

Secretory IgA

An incredibly important marker, secretory immunoglobulin A (sIgA) is a key part of the gut defence system. This particular antibody, secreted in the gut, is responsible for reducing the adherence of bacteria to the gut wall and minimising the passage of different antigens (undigested food, microbes, etc) from passing into the bloodstream (7).

Interestingly, certain parasites, including Blastocystis hominis and Entamoeba histolytica, secrete certain enzymes that break the defensive secretory IgA down. This helps these bugs adhere to the gut wall and protects them from our immune systems attack (8).

intestinal permeability leaky gut GI map australia gut health parasite infections

 

Image taken from Cross-Talk between Probiotic Bacteria and the Host Immune System.

Here we can see a healthy gut wall at work including maintenance of proper gut permeability (remember there needs to be some permeability otherwise properly digested foods and nutrients wouldn’t be able to pass. Also we can see secretory Iga controlling the growth of bacterial populations in the gut environment.

Zonulin

Moving the next marker in the gastrointestinal marker section we turn to zonulin. If this marker is unfamiliar to you don’t worry you aren’t alone.

Before we dive into what exactly zonulin is and why it is important fist we need to make a quick mention of a brilliant Italian doctor and researcher Alessio Fasano. He is at the cutting edge, no the bleeding edge, of research into autoimmune diseases, particularly coeliac disease and intestinal permeability (aka leaky gut).

Recommended reading:

Fasano, along with his research team, discovered zonulin back in 1998 (10).

Zonulin is a protein that has been shown to regulate the tight junctions which allow certain things across the membrane that separates the gut from the rest of the body (11). So a quick interpretation here. The more zonulin the more that is allowed to pass the gut wall. Following this thinking an elevation of zonulin would equal leaky gut.

Fasano has been working on the connection between leaky gut and different disease states and lists a number that involve increased intestinal permeability including (12).

  • Type 1 diabetes
  • Multiple sclerosis
  • Rheumatoid arthritis

But, and this is a big but…is zonulin a reliable marker for intestinal permeability?

In a recent article over at the Kresser Institute, Chris Kresser breaks down some important points on why zonulin may not be the best marker for assessing leaky gut.

Have a read here.

If you’re short on time the takeaway points include

  1. Not everyone with the diseases listed above have high levels of zonulin
  2. When zonulin is compared to the gold standard tests for leaky gut there is only a very weak correlation (ie they don’t match up).
  3. In many people the levels of zonulin fluctuate from day to day

From these points it’s clear, at least currently, that zonulin isn’t the best marker for assessing leaky gut.

B-glucuronidase

Beta glucuronidase is an enzyme that is produced by certain gut bacteria. This particular enzyme has the ability to reverse the effects one unique phase 2 detoxification pathway that happens in the liver known as glucuronidation (13). 

On the sample given we can see high normal b-glucuronidase activity in the gut but what does this mean?

In simple terms it means that your detoxification process has been reversed and has to work double time to keep up. Most of the time we will look to the gut and work on balancing this complex ecosystem to fix this issue of re-toxification. Things like prebiotics and probiotics are very helpful here (14).

complete microbiome mapping gastrointestinal markers australia

Section 3 – Microbiome Mapping Summary

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

complete microbiome mapping gi map australia pathogen screening do i have a parasite gut health byron bay australia

Here we can see the pathogen screening area of the test including the parasites and worms, bacteria and viruses and fungi and yeasts. To date this is the most comprehensive list of pathogens and opportunistic microbes that we can screen for in one test.

Let me tell you why I am so excited that this comes in a all-in-one package. Before the GI-MAP was available in Australia we had one of three options

  1. We could order the test from overseas and ship the stool sample back. That was pretty expensive and not the best option
  2. We could hack together a collection of testing from different companies and work at making the results fit with the person presenting with the health concern (all the while hoping we didn’t miss anything)
  3. Most clinicians make educated guesses and choose the most appropriate test as a way of keeping the cost down for the patient and to streamline the process.

None of these options were ideal.

Finally we can order one test that will tell us most of what is going on in the gut. At the end of this article we can cover what this test misses out on but for now let’s focus on this section of the GI-MAP.

Many gut issues including the list below can be traced back to different gut infections.

  • Constipation
  • Loose stools
  • Gut pain
  • Bloating and distention
  • Difficulty digesting foods
  • Blood in the stool
  • Mucus in the stool

The Australian GI-MAP screens for many of these top offenders that can cause gut symptoms and more. Pretty exciting.

Up until the release of this test on the Australian market the best option was to combine a Comprehensive Digestive Stool Analysis and a PCR test together. However, there were problems with this combination. The PCR test was quite an accurate test but didn’t screen for fungal infections, worms, or even opportunistic bacterial overgrowths like Klebsiella. Adding on the CDSA test helped to screen for these additional possible infections but this test was pretty darn poor at finding them (ie the sensitivity was quite low).

The GI-MAP uses the more advanced methods of screening for the pathogens and is much more reliable and dependable. It also helps us to widen the scope to include more possible infections meaning we miss less.

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Section 4 – Parasites and Worms

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

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Getting into the specifics of each of these pathogen screening sections of the test we can see the top parasites including the protozoans like

The other incredibly helpful part of this section is the screening for the different worms (helminths) that can be causing issues. The GI-MAP uses the DNA based testing  (PCR) to look for these worms so it would be considered very specific and sensitive.

Section 5 – Opportunistic Bacterial Overgrowth

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

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The bacteria overgrowth section helps us look at what is happening in the bacterial world of the large intestine. Unfortunately we can’t use this data to see what it happening in the small intestine so testing for SIBO may still be needed. Unfortunate I know but this is where we are at currently. It would be great to see a test in the future that combined everything but I think that is a ways off still.

Most of the bacterial species seen above would be considered opportunistic. If we see an overgrowth of them we can suspect an imbalance in the large intestinal ecosystem. This is a major focus of what we cover here and a significant interest of mine

Here’s some further reading on the subject of bacterial overgrowths

Section 6 – Fungi and Yeast

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

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Moving onto the fungal infections we can see some classic fungal infection markers like Candida and then some other less well known ones like Geotrichum and Rhodotorula.

I must be starting to sound like a broken record by now but these makers are showing us an imbalance in the gut. I think we are starting to move away from the one infection = gut symptoms picture (well at least I am) and are starting to look at the gut as a very complicated ecosystem. In the readout above we can see an overgrowth of one of the Geotrichum species of fungi. In regards to treating this issue we can definitely focus on the antifungal herbal medicines but at the same time it is key to rebalance the gut. If we don’t do that then it is almost certain that the imbalance will happen again. This is one of the reasons why people end up feeling better during the treatment phase, maybe continue to feel better for a few months and then start to feel worse again. Rebalancing the gut is key!

Section 7 – Bacterial Pathogens

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

bacterial infection gut health gi map australia micrbiome health and disease byron bay australian naturopath herbalist

The bacterial pathogen list is pretty darn impressive. Not only does it screen for the major bacterial pathogens that are starting to become real problems for many people (I’m talking to you Clostridium difficile!) it also shows whether these bacterial infections are the particular strains that produce the toxins that cause the major issues in people’s gut.

Let me explain. Different bacterial infections like Helicobacter pylori, Clostridium difficile and Shigella can secrete very toxic by products. Above you can see a whole list of Helicobacter pylori virulence factors. Now here’s the key bit. Not every H. pylori strain secretes these toxins. The same goes for Clostridium difficile. Previously we could screen for these infections but it wasn’t clear whether they were causing the gut symptoms. Now we can see very clearly whether they are (check out the Clostridium markers below).

Section 8 – Viral Pathogens

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

virus infection gut health byron bay australian herbalist naturopath parasite specialist

Finally in the pathogen section we can see viral infections. Again we could order all of these as separate tests from standard pathology labs and they aren’t incredibly expensive. It is just very nice to see it all together under one testing option. Cytomegalovirus and Epstein Barr virus are commonly screened for. These can become chronic viral infections that almost burn away in the background.

Epstein Barr and Cytomegalovirus specifically can contribute to a number of different disease states.

gi map australia ebstein barr and autoimmune diseases herbalist natural treatments

Image taken from: Epstein-Barr virus and cytomegalovirus in autoimmune diseases: are they truly notorious? A preliminary report.

In the table above we can see elevated Epstein Barr antibodies to a whole range of autoimmune conditions including some common ones like multiple sclerosis, hashimotos (autoimmune hypothyroid), SLE and rheumatoid arthritis.  

Then moving onto cytomegalovirus issues we can see the following table

cytomegalovirus gi map australia virus gut health byron bay australian herbalist

Image taken from: Epstein-Barr virus and cytomegalovirus in autoimmune diseases: are they truly notorious? A preliminary report.

We can see that elevated antibodies to cytomegalovirus (CMV) is related to some common autoimmune diseases like SLE.

Section 9 – Normal Bacterial Gut Flora

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

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Finally, we move onto the ‘normal’ bacterial gut flora, what we might consider the beneficial bugs.

This section may be the weakest part of the GI-MAP test. It gives us a very preliminary view of only a few beneficial bacterial species in the large intestine. Still this section does help to paint the picture on what is happening and shows some of our popular Bifidobacterium and Lactobacillus genus readouts as well as a very brief readout on the two dominant phyla in the gut Bacteroidetes and Firmicutes.

A better test would be a complete bacterial gut test like the Ubiome test that gives us a much better readout on what the balance of the gut is like. I would like to see more on the Proteobacteria phylum (overgrowths here can be problematic) although we can see this in select species in the opportunistic panel above (section 5).

Section 10 – Conclusion and Comments on the findings

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

This section is commonly found on different lab tests. The lab company will provide a quick summary of the findings along with some (hopefully) evidence based interpretation on pathogenic nature, conventional treatment and even some herbal treatment options.

This is where your practitioner can step in and provide a few more details. Here we can start to connect your symptoms to some of the lab findings. For the most part a skilled clinician can skip this section and make their own judgments on what is happening in the gut and what the best approach is to getting you feeling better and back on track. That said this section can be helpful for you, the patient, to get a grip on some of the more important aspects of your gut testing results.

Final Thoughts on the Australian GI MAP

The Australian Guide to the Complete Microbiome Mapping GI MAP Gut Testing

There are some practitioners, specialists in gut health, that insist that each and every new patient of theirs runs a comprehensive stool analysis. Frequently they come back with infections that, once addressed, help to move the patient towards health.

Acting as a health detective we need to determine whether a comprehensive stool analysis such as the Complete Microbiome Mapping is warranted. Thankfully the price tag isn’t astronomically high, especially in the face of chronic gut symptoms and ill health.

There are times when a simple (and free if you live in Australia) PCR test from the doctor is indicated. Especially if money is tight.

On the other hand if you are struggling with chronic gut symptoms, an autoimmune disease, chronic fatigue syndrome or another health concern that is bringing your quality of life down (I’ve been there too, it isn’t fun!) the Complete Microbiome Mapping test (aka the GI-MAP) is now available through your healthcare practitioner here in Australia

Hopefully this article has helped to explain some of the more complicated aspects of this advanced gut test to you and has answered any questions that you might have had. If I have missed anything then be sure to leave a comment below, I answer each and every one of them! I can include it in future updates to this article so that we have more complete answer to the gut health questions you have.

References and Resources

  1. Inflammatory Bowel Disease
  2. Inflammatory Bowel Disease – Atlas of Investigation and Management
  3. Faecal calprotectin for screening of patients with suspected inflammatory bowel disease: diagnostic meta-analysis
  4. Faecal calprotectin testing for differentiating amongst inflammatory and non-inflammatory bowel diseases: systematic review and economic evaluation.
  5. Potential for Screening for Pancreatic Exocrine Insufficiency Using the Fecal Elastase-1 Test
  6. Fecal pancreatic elastase: a reproducible marker for severe exocrine pancreatic insufficiency
  7. The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases.
  8. Degradation of human secretory immunoglobulin A by Blastocystis.
  9. Cross-Talk between Probiotic Bacteria and the Host Immune System.
  10. Isolation and functional characterization of zonulin, a physiologic modulator of tight junctions
  11. Zonulin, regulation of tight junctions, and autoimmune diseases
  12. Zonulin and its regulation of intestinal barrier function: the biological door to inflammation, autoimmunity, and cancer.
  13. Distribution of b-glucosidase and b-glucuronidase activity and of b-glucuronidase genegus in human colonic bacteria
  14. Effect of dietary intervention with different pre- and probiotics on intestinal bacterial enzyme activities
  15. Epstein-Barr virus and cytomegalovirus in autoimmune diseases: are they truly notorious? A preliminary report.
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4 comments

  1. Hi Todd
    Thanks for your insights 🙂 You didn’t comment on the “Genomic Assessments” Steatocrit and Anti-Gliadin IgA and I realise these may be new additions to the test. Do you have further input as to their relevance?

    1. yes indeed they have been adding new marker to the GI map all the time. It is good to see, and happy that they aren’t increasing the cost of the test too!

      I think we still need to be questioning what each of the markers indicate (example zonulin, as outlined in the article, may not be the best marker for intestinal permeability). On the same note Anti-gliadin IgA (the new marker added) is pointing us towards gluten sensitivity and/or coeliac disease but is not 100% reliable for the coeliac disease diagnosis (more on that here https://www.ncbi.nlm.nih.gov/pubmed/20442390). It would be unfortunate to see someone wrongly diagnosed with coeliac disease using that marker. Still I think they are useful markers and am happy they have included them!

      (Steatocrit is useful to paint the picture of fat malabsorption but a good history on intake would probably get you there too)

      Thanks for the comment and apologies on the long reply!

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