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Six easy steps for microbiome stool testing

At The Microbiome Group, we use cutting-edge microbiome stool testing. These tests identify genetic material from the bacteria, so they give us details on all the bacteria in your gut. In contrast, standard tests only identify bacteria that grow under lab conditions. The test kits are easy to use – and there‘s usually no need to catch a sample before it disappears around the bend!

Here are the 6 easy steps, in stool-free pictures and descriptions, for the test we most commonly use. We've also included top tips for getting a great sample, together with more detail about the test and when to do it.

1️⃣ Swab used toilet paper. Collect a sample the size of a grain of rice, or fully colour the swab. Too much or too little sample will result in processing errors at the lab. Most people have enough sample on their used toilet paper. However, if your toilet paper is clean, you will need to collect a stool to swab. You may find it easiest to catch a sample in toilet paper or using a clean freezer bag. Alternatively, contact your practitioner for further guidance. It's a good idea to swab the stool in several locations if you can.

2️⃣ Stir the swab in the small sample tube for 30 seconds, to mix it in the preserving solution.

3️⃣ Shake: Screw the cap on securely and shake vigorously for 10 seconds.

4️⃣ Register the sample online, using the code on the sample tube — no personal details are included with the sample. Make sure you grant access to your practitioner, under the Practitioners tab, so your practitioner is notified when your results are ready.

5️⃣ Seal the tube in the little plastic specimen bag, then remove the cover strip on the lip of the box to seal the box firmly.

6️⃣ Post: Drop in your nearest post box — postage is prepaid in the UK and US. In other countries you will need to affix postage and a customs label. You can find guidance here, for postage, lab address and customs outside the UK.

Once collected, samples are shelf stable for several weeks. However, please make sure you have left plenty of time from posting your sample, to allow for mailing time, lab processing and our analysis, before your results session. (We usually recommend at least one month.) Please contact your practitioner as soon as possible if you think your results may be delayed.


To avoid contaminating your sample:

✅ Get everything ready to hand so you can collect your sample from the toilet paper straight away.

✅ Wipe carefully to avoid collecting vaginal or skin bacteria on the toilet paper — as best you can!

✅ Do not allow the sterile swab or toilet paper to touch another surface, until you’ve finished.

✅ If you are taking a sample from a nappy, the stool sample must be really fresh (ideally within 1 minute of soiling) otherwise the bacterial profile will reflect the bacterial populations that thrive in used nappies, rather than the child's gut.

Why we use Biomesight tests for Microbiome Analysis

We’ve found Biomesight to be the most clinically useful and reliable of all available tests, while giving a good level of detail in the raw data that we use for analysis. The kit is also among the easiest to use at home. The swab and its wrapper can safely be disposed of in bathroom (household) waste.

Another reason we choose Biomesight is because you retain full control of your microbiome data to explore yourself. You can grant access to your practitioner, and can revoke it at any time, while still retaining your full data and the automated analysis provided by Biomesight.

Biomesight gives our clients a £25 discount (making the price £125), and has supported our research, including providing free tests to Viola Sampson's Long Covid case study programme as well as testing the bacterial profile of sauerkraut!

Stool tests are ordered directly from Biomesight, singly (Snapshot) or in packs of three (Time-lapse) for those who wish to do follow-up testing.

When should you take a test?

For most people, we recommend microbiome stool testing at the start of our work together, as these guide our treatment recommendations.

We may suggest testing part-way through your treatment plan (usually after at least two or three months) and some people like to test at the conclusion of treatment and receive a full written progress report. Some like to test six months to a year after completing treatment, to ensure microbiome balance has been maintained. As you retain access to all your results, follow-up testing can be done in consultation with a practitioner, or independently, as preferred.

It's usually best to discuss the timing of your initial test with us in your first consultation, as there are several factors we may want to consider, such as any recent antibiotic use. We can discuss follow-up testing at any time in your microbiome journey.

The Microbiome Group offers treatment plans tailored to your unique profile of gut bacteria, with detailed microbiome analysis by registered practitioners. You can book a consultation, or get in touch to find out more.

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