​Gut Microbiome Test NZ: How To Choose The Best Test

Not all gut microbiome tests are created equal, and choosing the right microbiome test for you can feel overwhelming.

Based on my experience as a Naturopath, I've seen how gut microbiome testing can uncover underlying issues in digestive health. The tests decode your intestines' hidden microbial world and show imbalances that could lead to bloating, fatigue, skin problems, and mood changes. 

The testing options available in New Zealand range from $264 to over $1,000, with varying reliability, comprehensiveness and testing methodology.  So, choosing the best gut microbiome test needs careful consideration before investing in your health.

What is the gut microbiome and why it matters

For every one of your own cells, nearly 1,000 bacterial cells live in your gut. Your body is home to this incredible microscopic universe known as the gut microbiome, made up of trillions of organisms including bacteria, viruses, fungi, and more. With over a thousand different types of microbes, it plays a crucial role in our overall wellbeing.

The role of gut bacteria in digestion and immunity

You and your gut microbiome share a true partnership. You give these microbes a home and food, and they help keep you healthy in return.

These microscopic allies do what your digestive system alone can not.  They break down complex carbohydrates and dietary fibre through fermentation, producing beneficial compounds called short-chain fatty acids that nourish the cells lining your gut.

The gut microbiome also plays a key role in immune health, acting as your largest immune organ and housing up to 80% of your immune cells. Beneficial bacteria help train your immune system to distinguish between harmful invaders and harmless substances.
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They also help maintain a strong gut barrier, preventing unwanted substances from leaking into the bloodstream, and even produce essential vitamins such as B1, B9, B12, and K.

How gut health affects mood, weight, and energy

There is a strong two-way connection between your gut and brain called the gut-brain axis. This is why stomach issues often come with mood dysregulation.

Over 90% of your body's serotonin is produced in your gut, not your brain. Serotonin affects many aspects of your gut function, including:
  • how fast food moves through your system (motility)
  • how much fluid, such as mucus, is secreted in your intestines
  • how sensitive your intestines are to sensations like pain and fullness from eating

Your gut bacteria also influence metabolism and body weight. Research has shown that specific combinations of gut microbes can impact how your body processes food, stores fat, and regulates appetite.​


Common symptoms linked to gut imbalance

Your body shows gut microbiome imbalance (dysbiosis) in many ways. The signs go well beyond digestive issues and can affect multiple body systems. Watch out for these symptoms:
  • Digestive disturbances: bloating, gas, constipation, diarrhea, or heartburn 
  • Unexplained weight changes 
  • Persistent fatigue or low energy levels
  • Skin irritations like eczema, psoriasis, or acne
  • Mood disorders, anxiety, or depression
  • Sleep disturbances or insomnia 
  • Food intolerances or sensitivities you never had before 

What is a gut microbiome test and how does it work?

The test works by analyzing a stool sample to identify the types and amounts of bacteria, fungi, and other microbes in your digestive tract.

How do I test my gut microbiome?

Once you have determined the right test for you, the rest is pretty simple. The process involves these basic steps:
  1. Understand the tests available and decide what is best for you.
  2. Order a test kit online or your naturopathic provider will send you a link to order.
  3. Collect small stool sample/s following the kit's instructions.
  4. Send your sample to the laboratory in the prepaid package provided
  5. Wait for your results (up to 4 weeks).
You'll find the collection process quick and clean. No labs in New Zealand currently do this type of comprehensive testing, so the samples need to be sent to overseas labs.  At SmartGENES Naturopathic, we use Nutripath in Australia.  Due to the necessity of speed, you will likely find specific instructions provided as to the day to take the sample/s and when to have it on the courier. 

Who should consider a gut health test in NZ

Should you invest in a gut microbiome test? That is a very good question.  Understanding whether you actually need to spend money on this test is important.   At SmartGENES we have helped countless patients decide if microbiome testing suits their needs.  To make this decision we need to understand your symptom picture, your financial constraints, the limitations of the testing, and whether the testing is likely to change the future course of action.  We can only know this once we have sat down and spent time in a consultation.  Sometime the answer is YES, sometimes it is NO.  

Chronic conditions that may benefit from testing

A gut health test proves especially valuable information for people diagnosed with certain chronic conditions. Clients will often see  improvements after they fix their gut imbalances:
  • Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD)
  • Small Intestinal Bacterial Overgrowth (SIBO)
  • Autoimmune conditions like rheumatoid arthritis
  • Type 1 diabetes and metabolic disorders
  • Atopic conditions like eczema and asthma
  • Chronic kidney disease

Preventative health and biohacking

Some New Zealanders choose gut microbiome testing as part of their proactive health strategy, even without obvious symptoms.  As our beneficial gut bacteria naturally decline with age, regular monitoring of these populations helps maintain optimal health. Your gut houses 80% of your immune cells, and knowing your microbiome's makeup helps enhance immune function, mental clarity, and energy levels.

How to choose the best gut microbiome test NZ

When choosing the best gut microbiome test available in New Zealand, it's important to carefully consider several key factors. Making a well-informed decision ensures you get the best value and the most relevant insights for your investment.

What makes a test reliable?

A gut health test's reliability is based on its analysis methodology, and gut microbiome testing technology has improved a lot. The gold standard in technology is Shotgun metagenomic sequencing which analyzes all DNA in your sample. This complete approach identifies specific bacterial species, fungi, and viruses.  It does however, come in at the high end of costings.

Practitioner-guided vs. self ordered tests

To determine how you proceed, I suggest you ask yourself  a series of questions:
  • Do you know which test is the best option for you? 
  • Do you know what to do with the results?  If not, you will want to have access to someone who can help with interpretation.
  • Can you access quality products to address any potential problems or imbalances?  The problems in the retail supplement market are vast, resulting in a minefield of poor quality, sub-therapeutic products.  Read our rundown of the current issues . . .

Cost, turnaround time, and ease of use

At-home microbiome testing kits available in New Zealand vary widely in cost, depending on the testing method used and the depth of analysis provided.  We recommend you compare test prices online for the specific test you are looking to purchase.  Some of the big testing sites can charge hundreds of dollars more for the same test you can get through a naturopath.

Because all comprehensive microbiome testing must be processed overseas, reliable and expedited shipping is essential to maintain the viability of the sample. Most results are returned within four weeks of the lab receiving your sample.
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The collection process is straightforward and hygienic, with all necessary materials included in the kit. Instructions are detailed and may specify the exact day for sample collection and courier drop-off, to ensure timing aligns with lab requirements. A prepaid return courier envelope is included, although you may need to personally drop it off to ensure the sample reaches the lab quickly and in optimal condition.

The value of experienced interpretation

The interpretation forms the core value of gut microbiome testing. Over the years we have had numerous clients come in with recent or old microbiome tests that they have not understood. The test only has value if you understand the results and understand how to address any potential problems or imbalances.

Self-ordered tests will often give you general recommendations, but this is not always helpful.  Understanding the nuances of prescribing specific products, at the correct dose, for the correct period of time, and in the right sequence, takes experience.  It also avoids the minefield of retail products. Ordering through a naturopathic practitioner not only gives you the information to decide whether, and what test is useful, it also gives you access to someone who can guide your next steps.

Overview of top gut microbiome tests in NZ

Let's look at gut microbiome test options you can get in New Zealand. 
(all prices are correct at time of writing 07/2025)

CDSA Level 1 – Simple digestive health insights
This starter test gives you a detailed picture of your gut's microbiological environment.  It is best used to check for a gut infection or confirmation of dysbiosis. The test checks for beneficial bacteria, yeasts, and parasites. It uses Macroscopy, Microscopy, Bacteriology, Mycology and Parasitology - NZD264.00

CDSA Level 1 with PCR – Adds pathogen detection
This version enhances the Level 1 test with PCR technology. The addition helps find hard-to-spot pathogens like Dientamoeba fragilis and Giardia more effectively so should be added on if suspected - NZD336.00

CDSA Level 2 with PCR – Broader microbial analysis
This test gives you Level 1 results plus biochemical markers. These markers include digestive absorption and metabolic markers. Through these you'll learn more about your digestive function beyond just what microbes are present. It also provides information on the sensitivity of out of balance microbes to natural or prescriptive interventions - NZD447.00

CDSA Level 3+ – Inflammation and immune markers
Level 3+  adds onto Level 2 with advanced biomarkers that show inflammation levels. These include Transglutaminase IgA, Eosinophil Protein X, and Calprotectin, M2-PK, and H.Pylori . It does not contain PCR testing but can be added on - NZD541.00
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CDSA Level 4+ with PCR – Detailed gut health panel
This top-tier CDSA test is the most comprehensive of all the CDSA panels - NZD708.00
Complete Microbiome Mapping (CMM) – Functional and species-level data
CMM is a comprehensive panel of microbial targets as well as immune and digestive markers.  It screens for pathogenic bacteria, commensal bacteria, opportunistic pathogens, fungi, viruses and parasites.  Testing methods include:  qPCR-Quantitative PCR, ELISA, GC/MS- NZD662.00

Microbiome Basic (CMM) – A follow up profile to CMM (above)
The Microbiome Basic Test is designed as a follow up test to the standard CMM above  - NZD575.00
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Advanced CMM – High-resolution mapping with functional markers
This test stands as New Zealand's most detailed CMM option. The panel is a comprehensive collection of microbial targets as well as immune and digestive markers.  It screens for pathogenic bacteria, commensal bacteria, opportunistic pathogens, fungi, viruses, and parasites.  Testing methods include: In duplicate via: qPCR-Quantitative PCR and Culture via MALDI-TOF; ELISA, GC/MS - NZD805.00
Microbiomix Metagenomic Mapping (MMM) – Deep sequencing and metabolic profiling
This test stands at the forefront of gut microbiome testing technology. This analysis uses metagenomic shotgun sequencing, the gold standard method to study gut microbiota. The term shotgun refers to the random and unbiased sequencing of all the genetic material in the sample, including DNA from bacteria, viruses, fungi and other microorganisms. MMM scans all genetic material randomly, unlike other tests that target specific genes or organisms. This creates a detailed picture of your entire microbial community.  It also analyses biochemical markers linked to digestion and inflammation - NZD828.00

Key Takeaways

  • Having a healthy diverse gut microbiome is essential for good health. These trillions of microorganisms influence digestion, immunity, mood, weight regulation, and energy levels.
  • Stool-based microbiome tests identify bacterial imbalances that may contribute to symptoms like bloating, fatigue, skin issues, and mood disturbances.
  • Before purchasing a gut microbiome test in New Zealand, we advise having a consultation with a qualified naturopath. We are not here to sell you a test, rather we want to help you identify the next best step for you.
  • Professional input can help identify the most appropriate test for your health needs, symptoms, and budget, ensuring you get meaningful, clinically relevant results. From basic CDSA Level 1 (NZD 264) for foundational insights to the advanced MMM test (NZD 828) for detailed species identification and deeper analysis.
  • It is worth your time to compare prices (ie, Complete Microbiome Mapping CMM). Some sites charge hundreds of dollars more for the same test.
  • Interpretation is key: experienced analysis transforms raw test data into personalized strategies that support long-term, sustainable health improvements.
  • The right test is only the beginning. Lasting changes to your health depends on how the results are used. Working with a naturopath ensures a tailored plan and access to high-quality products that align with your unique microbiome profile.
  • Testing can be especially valuable for those with chronic digestive symptoms, autoimmune conditions, or vague, unresolved health issues affecting multiple systems.
  • Investing in gut microbiome testing, supported by professional advice, often yields lasting benefits: resolving persistent symptoms, restoring function, and helping to prevent chronic disease through targeted, evidence-informed care.