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Gut health check-up: should you use a microbiome test kit?

We trial at-home microbiome tests from Microba and i-Screen.

Last updated: 22 October 2020


Checked for accuracy by our qualified fact-checkers and verifiers. Find out more about fact-checking at CHOICE.

There are trillions of microbes inside your gut including bacteria, fungi and viruses, making up what's known as your gut microbiome (or gut flora). 

Books such as Giulia Enders "Gut" and Michael Mosley's "Clever Guts" have sparked interest in this invisible part of our body and the complex and essential role it plays in overall health and wellbeing. 

But just how useful is it for the average person to get to know their gut microbiome? 

We try two direct-to-consumer (DTC) gut microbiome tests and speak with the experts about whether these products are worth the investment.

Our verdict

If you're curious about your gut health and would like to learn more about your bacterial inhabitants, investing in a gut microbiome test will prove to be an interesting experiment, if nothing else.

But if you're suffering from gastrointestinal symptoms caused by common pathogens, routine clinical testing would detect these, so visiting your healthcare provider is still the best option. 

Experts are cautious about over-interpretation or applying any serious changes to your diet based on the results of home gut microbiome tests. Microba, i-Screen, and the experts we spoke to advise that people seek further advice from qualified healthcare professionals before making any big changes to their diet based on their results. 

And remember, these tests may be fascinating but they're not to be used as a diagnostic tool. Well, not yet anyway. 

Why test your gut microbiome?

Our relationship with our gut bacteria is mutually beneficial – we feed them and help them thrive in our large intestines and in return they help keep us alive. 

Recent scientific studies even suggest your gut microbiome plays a significant role in preventing disease and may even influence your mental health. 

As scientists continue to unravel the secrets of the human gut, many are fascinated by the possibilities these discoveries may offer. 

Understanding our own unique gut microbiome and how we can optimise it to potentially prevent disease, improve health and enhance our quality of life is certainly a compelling prospect. 

Gut flora plays a significant role in preventing disease and may even influence your mental health

Is that a good enough reason for you to get to know your gut microbiome? A handful of private Australian companies seem to think so, tapping into the rising mainstream fascination into gut health by offering personal gut microbiome testing direct to consumers (DTC). 

Using similar business models to DTC DNA and ancestry testing, for just a few hundred dollars you can now go online and, with the click of a button and credit card, order a gut microbiome testing kit to do at home.

So how much information can you get from a gut microbiome test and, for those of us not scientifically minded, how do you decipher the results and use them to your advantage? 

To find out, we trialled two of the most popular gut microbiome tests on the Australian market. Writer Kylie Matthews tested the microbiome at-home test kits, while Rachel Clemons provided additional research and words. 

Microba Microbiome Sample Kit

The Microba Insight Sampling Kit.

Microba Insight™ Sampling Kit

Price: $349

In 2018, Microba was the first company to offer DTC metagenomic testing in Australia and claims to have "the most comprehensive microbiome test available". 

The company was founded by University of Queensland researchers Professor Philip Hugenholtz and Professor Gene Tyson, and boasts having Professor Ian Frazer as a director, co-inventor of the technology enabling HPV vaccines.  

How it works

My Microba Insight™ Sampling Kit came swiftly via post, and contained a sterile swab for faecal collection, simple instructions and a return prepaid satchel. Only a small faecal sample was required and collection was quick and easy to complete; in fact, the accompanying online questionnaire about diet, lifestyle and background was far more time consuming. 

Deciphering the results

Three weeks later, the results were ready. It presented a comprehensive list of the bacterial species in my gut microbiome, detailing the functions they perform and making suggestions on how they can contribute to my health and beneficial changes to my specific diet. 

The sheer amount of information provided ... made it relatively difficult to get an overall understanding of what my test results actually mean 

There's just so much complex scientific information on this report, and Microba's challenge is to ensure the report is easy to understand. 

Did Microba achieve this? Yes, to a point. The sheer amount of information provided meant the details needed to be brief, which made it relatively difficult to get an overall understanding of what my personal test results actually mean. 

The report reveals that my gut has high levels of a bacterial species known as Bacteroides _A plebeius _A, when compared with the company's comparison group. Is it a good thing, or should I be worried? 

What the Microbiome Coach said 

Thankfully, the cost of the test also includes a 10-minute phone consultation with a "Microbiome Coach" to help people better understand their results. 

My coach was very helpful, offering suggestions on ways I could change my diet to optimise my gut microbiome and answering my myriad questions. She assured me that Bacteroides _A plebeius _A was a perfectly good and friendly bacteria to be colonised by. 

She also reinforced the point that gut health is an 'emerging science', that there are limitations in the small control group sample my results have been compared to, and gently suggested I avoid over-interpreting the results. 

iscreen testing kit in box

The i-Screen Microbiome Check kit.

i-Screen Microbiome Check

Price: $199

Launched in 2017, i-Screen is a 'healthtech' startup that offers numerous medical tests directly to consumers. The i-Screen Microbiome Check promises to measure and quantify the bacteria and fungi in your gut, and shows if you have an undergrowth or overgrowth in specific categories of gut microbe.

How it works

I bought my i-Screen Microbiome Check online and received the test in the post a few days later. Inside were four plastic test tubes with different coloured lids – one containing preserving liquid, along with a thin latex glove, a small plastic scoop, a set of directions and a prepaid return envelope.

Their sample retrieval process is a lot more complex and hands on

i-Screen doesn't require you to fill out as comprehensive a questionnaire as Microba, but their sample retrieval process is a lot more complex and hands on. All four test tubes have to be filled to a designated line with faeces – and the test tube with the liquid has to be mixed with the scoop. 

Unfortunately, my latex glove had a hole in it, making things all the more ... gag-inducing. I also had to fill out my own information in pen on the test tubes and worried the whole time about contamination and writing incorrect information.

Deciphering the results

The results arrived four weeks later and, compared to the wealth of information provided by the Microba report, I was underwhelmed by the lack of detail provided by i-Screen. 

But, to be fair, it was impossible to compare the results from the two tests as they used different testing methods and presented very different reports. 

While Microba uses metagenomic testing methodology, which measures the amount of DNA of the bacteria in the sample, i-Screen cultures the bacteria and measures the growth of these bacteria visually.

On opening my i-Screen report, I was immediately alarmed by the notification, highlighted in red, that I had an abnormal result. 

Apparently I harbour slightly "lower-than-normal" levels of lactobacilli, a beneficial bacteria required to break down foods, take in nutrients and prevent the overgrowth of "bad" pathogenic bacteria in the gut. 

Well, that explains my irritable bowel symptoms … or does it? 

"Possible causes are varied and can include antibiotics use, chlorinated water, food allergy or sensitivity, irritable bowel syndrome, inflammatory bowel disease, inadequate dietary fibre or water, maldigestion, nonsteroidal anti-inflammatory drugs (NSAIDs) such as aspirin, nutritional deficiencies, parasite infection and slow transit time," the i-Screen report reads.

Well, that explains my irritable bowel symptoms … or does it? Should I be drinking filtered water instead of water from the tap? Could I have inflammatory bowel disease or nutritional deficiencies? 

The other important friendly bacteria necessary for a healthy gut is bifidobacteria, which my report says is "adequate" – does this counteract the lower levels of its good mate lactobacilli? How do I improve my lactobacilli bacteria levels?

i-Screen's support options

The report included suggestions to increase my beneficial bacteria, such as "use nutraceutical agents to help heal the gastrointestinal lining". 

While I don't have the scientific or nutritional know-how to successfully prescribe to this action plan on my own, thankfully i-Screen does provide additional support options.

The first welcomes you to email brief questions about your test results, which they answer at no extra cost. I opted to do this and emailed a few queries across to i-Screen and received clarifications and (limited) suggestions a few hours later.

I emailed a few queries across and received clarifications and (limited) suggestions a few hours later

The second option promises a more in-depth discussion of your test results, but you'll pay extra for the privilege. Buy an i-Screen Nutrition Assessment ($49) and the company's online nutritionist will help you interpret your results and identify key dietary and lifestyle adjustments and supplemental support to improve your health and wellbeing. 

The third, and most expensive, option is a Nutrition Teleconsult ($185), offering a comprehensive consultation with the company's online nutritionist to review, interpret and discuss your test results and work with you to develop a bespoke treatment plan to improve your specific health concerns through a variety of food and lifestyle changes. 

What the experts say about at-home microbiome test kits

Dr Sam Forster, group leader at the Microbiota and Systems Biology Laboratory, Centre for Innate Immunity and Infectious Diseases at the Hudson Institute of Medical Research, looked at both test results and was impressed with how they were interpreted and presented.

"I think they're actually quite good at presenting the data in a way that's at least interpretable, compared to what [scientists] would be used to looking at," he says. 

"But I think there's a danger of people over-interpreting their results and making major diet and lifestyle changes based on an association with a particular bacteria that may be detrimental for some people but beneficial for others.

"It should be seen as a component of a wider evaluation of your health." 

There's a danger of people over-interpreting their results and making major diet and lifestyle changes … that may be detrimental for some people but beneficial for others

Dr Sam Forster, group leader at the Microbiota and Systems Laboratory, Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research

While scientific knowledge of the gut microbiome has come a long way in a short space of time, Forster says it's important to be mindful that we still have a great deal to learn. 

"I do see the weaknesses at the moment, and it's our lack of knowledge. We aren't yet able to say that for you, at this time of your life, with your genetics, with your lifestyle, that this bacteria is absolutely going to be positive or negative," he says. 

Nicole Dynan is an accredited practising dietitian, spokesperson for Dietitians Australia and a Microba-certified dietitian who has completed training on interpreting Microba's technology and reports. 

She says these tests are a wonderful resource for curious people, but that they're not yet ready to be used as a diagnostic tool. 

"The reason to take that test is really from the point of view of being interested in the information it provides. These tests aren't necessarily diagnostic at this stage but they certainly can give you some insight," she says. 

Forster also believes the test results will be more helpful when they can be compared with future tests. 

"Having testing every few years, you'll be able to see how your microbiome community changes, which would give you a baseline where if you're feeling healthy now and you're feeling less healthy in the future, you can start to say, well, what was different in my microbiome? What's changed in my life? And some of these things might be clues."

If you have any concerns about the results you should definitely talk to a health professional

Nicole Dynan, accredited practising dietitian at Dietitians Australia

Forster adds that, while interesting, no action should be taken on the results of these tests without the advice and supervision of a medical specialist or dietitian who is able to interpret the results. 

"I don't think it will ever be a scenario where you'd be interpreting the results on your own. I mean, it's equivalent to someone getting a detailed blood chemistry result and trying to interpret it," he says. 

Dynan agrees. "It's definitely worth speaking with somebody that's had some training in these test interpretations, to make sure you're reading it correctly. 

"You should be aware of the limitations of these results and if you have any concerns you should definitely talk to your health professional about it." 

How to improve gut health

There are many things you can do to improve your gut health, including:

  • Eat more high fibre foods. Soluble fibre – such as that found in oats and vegetables – helps to hold fluids in the digestive tract, which ensures your poo is soft and passes easily. Insoluble fibre – the type in bran and wholegrains – helps food move through the digestive tract more easily. Both types of fibre provide food for the good bacteria in your large bowel, which is good for your overall bowel health.
  • Drink plenty of water so that the food you eat moves smoothly through the gastrointestinal system.
  • Eat foods high in probiotics and prebiotics. Probiotics are beneficial bacteria found in yoghurts and fermented foods such as sauerkraut and kimchi. Prebiotics – found naturally in certain foods including lentils, oats and barley – 'feed' the good bacteria in your gut, allowing them to thrive and grow.
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