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Microbiome testing NZ

Microbiome testing is a test that is becoming increasingly popular and accessible in NZ. But is it really useful?

Personally, I was very sceptical and did not recommend it when I started my career over 8 years ago.

However, over the years of practice and research, I’ve started using this test and I always found great information for my patients.

Here is an article that explains what intestinal microbiome analysis is, its benefits, and what it measures. I also share my opinion.

What is the microbiome?

The gut microbiome refers to the complex community of microorganisms, including bacteria, viruses, fungi, and archaea, that inhabit the gastrointestinal tract, particularly the intestines.

These microorganisms play a crucial role in various bodily functions, including digestion, metabolism, immune system regulation, and protection against pathogens.

Key Points About the Gut Microbiome:

  1. Diversity: The gut microbiome is highly diverse, containing trillions of microorganisms from hundreds of different species. This diversity is essential for a healthy and balanced microbiome.
  2. Functions:
    • Digestion: Helps break down complex carbohydrates, proteins, and fats.
    • Nutrient Absorption: Aids in the absorption of essential nutrients and the production of certain vitamins (e.g., vitamin K and B vitamins).
    • Immune System: Regulates immune responses and helps protect against infections.
    • Metabolism: Influences metabolic processes and can impact body weight and energy balance.
    • Barrier Function: Maintains the integrity of the gut barrier, preventing harmful substances from entering the bloodstream.
  3. Health Implications: An imbalance in the gut microbiome, known as dysbiosis, is associated with various health conditions, including gastrointestinal disorders (e.g., irritable bowel syndrome), metabolic diseases (e.g., obesity, diabetes), autoimmune diseases, and even mental health issues (e.g., depression, anxiety).

Understanding and maintaining a healthy gut microbiome is crucial for overall health and well-being.

The Importance of Knowing Your Microbiome

Why is it interesting to know more about the composition of one’s gut microbiome?

While the link between the microbiome and digestive disorders is fairly quick to establish, it is less so for other pathologies.

However, we now know and are discovering that many diseases are linked to dysbiosis (an imbalance of the gut microbiome):

  • Endometriosis. A study was conducted on mice. Researchers took two mice with endometriosis and cured one of them. By performing a fecal transplant from the mouse still suffering from endometriosis to the cured mouse, the latter redeveloped endometriosis (Jiang et al., 2021). This is just one example, and the link between dysbiosis and endometriosis is known today (Jeffery et al., 2012; Laschke & Menger, 2016).
  • PCOS (Polycystic Ovary Syndrome). Research shows that dysbiosis is found in women with PCOS, and modulating the microbiome is one of the management strategies for PCOS (Wang et al., 2021).
  • Diabetes (Bielka et al., 2022)
  • Overweight, obesity (Carding et al., 2015)
  • Autoimmune diseases (Mousa et al., 2022)
  • Coeliac disease (Akobeng et al., 2020)
  • Inflammatory Bowel Diseases (IBD) (Carding et al., 2015)

In short, knowing more about your microbiome to modulate it can greatly help!

Analysis of the Microbiome: What We Measure

Microbiome analysis is not just a simple counting of bacteria, which would not be relevant. Indeed, many species are anaerobic, meaning they die in the presence of oxygen.

The metagenomic analysis of the gut microbiome involves sequencing the genetic material of the microorganisms contained in a stool sample.

What Information Does Metagenomic Microbiome Analysis Provide?

The analysis of the microbiome provides us with a wealth of information.

The Diversity of the Microbiome

First and foremost, we look at the overall diversity of the microbiome.

There is no “perfect” microbiome, but diversity is one of the factors indicating a quality microbiome. The diversity index, known as the Shannon index, provides a global overview.

Next, we zoom in on the phyla.

Global View on the Distribution of Phyla

Phyla are the major categories of bacteria. The main phylum is Firmicutes, which includes bacteria of the genus Lactobacillus, well-known in probiotics. This is followed by Bacteroidetes, Actinobacteria (which includes Bifidobacterium), Proteobacteria, and Verrucomicrobia, with Akkermansia muciniphila being the predominant species.

Additionally, there are Euryarchaeota, which are not actually bacteria but archaea, with Methanobrevibacter being well-known in cases of intestinal methanogen overgrowth (IMO).

Microbiome analysis allows us to highlight the proportion of these phyla in our microbiome.

Main phyla of bacteria in Human gut microbiome

Main phyla of bacteria’s in Human gut microbiome

Focus on bacteria’s genus within Phyla

Each phylum comprises several bacterial genus that are measured qualitatively and quantitatively. While some bacterial genus are beneficial, others are opportunistic and can become problematic if they proliferate excessively.

In essence, each phylum contains both “friendly” and “less friendly” bacteria, much like families !

Microbiome analysis also highlights the presence of archaea, methane-producing microorganisms, and other bacteria that produce gases harmful to health (e.g. hydrogen sulfur).

Estimation of Short-Chain Fatty Acid Production

This analysis allows us to indirectly evaluate the production of short-chain fatty acids (SCFAs), such as butyrate, which is a favorite food for our colon cells.

In summary, microbiome testing :

  • Informs about the diversity of the microbiome.
  • Provides a global view of the distribution of phyla, the major families of bacteria.
  • Gives a more detailed indication of the presence of beneficial and potentially pathogenic bacterial species (pathobionts), and their quantities.
  • Allows for the indirect evaluation of the production of SCFAs including butyrate.
  • Highlights the presence of archaea (Methanobrevibacter).
  • Highlights the presence of bacteria producing gases harmful to health.

Additionally, with experience and depending on the context, one can also “read between the lines” and identify risks of intestinal hyperpermeability (i.e. “leaky gut”), inflammation, or SIBO/IMO.

Microbiome testing : warnings

As with any analysis, it is essential to interpret the results within the context.

Contrary to what one might think, the use of probiotics does not repopulate the microbiome with the present strains.

Therefore, depending on the need, one should use diet, specific prebiotic fibers, and micronutrients.

The main reason I previously found microbiome testing not useful was that the conclusions often seemed similar: favor certain types of fibers over others.

And how to get someone who is already bloated to consume more fiber?

Well, by simply choosing the appropriate type and dosage!

Not to mention that fibers are not the only elements capable of modulating the microbiome! Omega-3 fatty acids, polyphenols, and other compounds significantly influence it.

With hindsight and a better understanding of these analyses, it is possible to further personalize recommendations based on the results.

Drawbacks of microbiome testing

The metagenomic analysis of the microbiome remains a recent test. The gut microbiome still holds many surprises, and research is constantly evolving.

We currently have a wealth of information on microbial species, their beneficial effects, or their potential risks. However, even though we know that certain bacteria promote or inhibit the growth of others, it remains difficult to precisely determine how all these species interact with each other.

We must also remember that we mainly present bacterial species, but we also host viruses, yeasts, and other microbes that are not measured in all microbiome tests.

Another disadvantage can be the cost. However, this analysis is becoming increasingly accessible.

Situations where microbiome testing can be useful

In my opinion, several scenarios apply:

  • Out of curiosity, for prevention. If low diversity or the presence of potentially pathogenic opportunistic bacteria is detected, action can be taken before digestive disorders (or other pathologies) occur.
  • In cases of unresolved digestive issues despite previously implemented strategies.
  • In cases of personal or family history of diseases such as gastrointestinal cancer, IBD, or coeliac disease.
  • Post-cancer (chemotherapy is a “weapon of mass destruction for the microbiome”) or after repeated antibiotic use for one or various conditions.
  • In cases of difficulty losing weight when common strategies have been ruled out.

Microbiome testing in NZ

Microbiome testing is available in NZ. I use the Advanced Complete Microbiome Mapping which is very similar to the GiMaps you may heard about before, or the GiMaps itself.


The metagenomic analysis of the microbiome provides valuable information that must be considered within the context of why the analysis was requested. It is by no means a test that will revolutionize your health on its own.

The main strength of this test, in my opinion, is its ability to highlight the presence of potentially pathogenic bacteria, allowing for preventive action.

This test also helps identify the lack of certain important strains, such as those producing GABA, a “relaxing” neurotransmitter that plays a crucial role in visceral sensitivity and stress response.

Moreover, it is an excellent visual tool to show how current diet and lifestyle impact microbial diversity and distribution. By making concrete dietary and micronutritional changes, one can quickly see improvements.

However, many other analyses can sometimes be more relevant or can complement the analysis of the gut microbiome. The choice will depend on your situation, but examples include measurements of LBP (LPS-binding protein) and fecal zonulin, which reflect intestinal permeability.

Of course, micronutritional analyses remain, in my opinion, the first ones to perform.

You’re interested in microbiome testing in NZ ?

Contact me to talk about it !


  • Akobeng, A. K., Singh, P., Kumar, M., & Al Khodor, S. (2020). Role of the gut microbiota in the pathogenesis of coeliac disease and potential therapeutic implications. European journal of nutrition, 59, 3369-3390.
  • Al-Yami, A. M., Al-Mousa, A. T., Al-Otaibi, S. A., & Khalifa, A. Y. (2022). Lactobacillus species as probiotics: isolation sources and health benefits. J. Pure Appl. Microbiol, 16, 2270-2291.
  • Bielka, W., Przezak, A., & Pawlik, A. (2022). The role of the gut microbiota in the pathogenesis of diabetes. International journal of molecular sciences, 23(1), 480.
  • Carding, S., Verbeke, K., Vipond, D. T., Corfe, B. M., & Owen, L. J. (2015). Dysbiosis of the gut microbiota in disease. Microbial Ecology in Health and Disease, 26(1), 26191.
  • Jeffery, I. B., O’toole, P. W., Öhman, L., Claesson, M. J., Deane, J., Quigley, E. M., & Simrén, M. (2012). An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut, 61(7), 997-1006.
  • Jiang, I., Yong, P. J., Allaire, C., & Bedaiwy, M. A. (2021). Intricate connections between the microbiota and endometriosis. International journal of molecular sciences, 22(11), 5644.
  • Laschke, M. W., & Menger, M. D. (2016). The gut microbiota: a puppet master in the pathogenesis of endometriosis? American journal of obstetrics and gynecology, 215(1), 68. e61-68. e64.
  • Mousa, W. K., Chehadeh, F., & Husband, S. (2022). Microbial dysbiosis in the gut drives systemic autoimmune diseases. Frontiers in immunology, 13, 906258.
  • Wang, L., Zhou, J., Gober, H.-J., Leung, W. T., Huang, Z., Pan, X., Li, C., Zhang, N., & Wang, L. (2021). Alterations in the intestinal microbiome associated with PCOS affect the clinical phenotype. Biomedicine & Pharmacotherapy, 133, 110958.

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