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Microbiome testing
For most patients, having a routine cycle of proven fertility treatment is effective without using any treatment add-ons.
Our ratings indicate whether the evidence from studies shows that a treatment add-on is effective at improving treatment outcomes for someone undergoing fertility treatment. Our rating does not tell you how much that treatment add-on improves your chances of having a baby – please discuss this with your clinic.
What is microbiome testing?
The microbiome refers to the community of microorganisms (tiny living organisms) that live in various parts of the human body, such as, the gut, skin, and reproductive tract which includes the uterus (endometrium) and vagina. Microorganisms primarily include bacteria, but also fungi and viruses.
Not all bacteria are harmful. Many bacteria are a normal and important part of a healthy body.
In fertility treatment, microbiome testing usually involves looking at a sample from the vagina or uterus (endometrium). Some clinics may also offer testing of the gut microbiome.
Why test the microbiome?
Some clinics may offer microbiome testing to identify the presence of different types of bacteria and other microorganisms. The test is used to assess whether the balance of microorganisms or the types of bacteria found in the vagina, uterus (endometrium) or gut may be associated with fertility or the chances of a successful pregnancy.
For example, some tests look for bacteria that have been linked to long-term inflammation of the lining of the uterus (endometrium), known as chronic endometritis.
What tests are used?
Several different tests might be used by your clinic to look at the vaginal, uterine (endometrial) or gut microbiome. The results of the microbiome test are unlikely to impact on the management of your treatment.
Different tests look for different things. For example, some tests may look at the bacterial composition of an endometrial sample, and others may look for particular types of bacteria reported to be associated with chronic endometritis. Other tests look at the bacteria in the vaginal microbiome or gut microbiome.
Some clinics may also offer endometrial receptivity testing alongside microbiome testing. Endometrial receptivity testing is a separate test and is not a microbiome test.
Who may be offered microbiome testing?
Microbiome testing may be offered to patients with:
- recurrent implantation failure (RIF); or
- suspected chronic (long-term) endometritis.
Some clinics may also offer it more generally before starting fertility treatment, as part of what may be described as “fertility optimisation” investigations.
What happens after microbiome testing?
If the test suggests that there may be a difference in the types of bacteria present or for example, the presence of certain bacteria associated with chronic endometritis, the patient may then be advised to have one of the following interventions:
- To take antibiotics for a period of time before undergoing IVF.
- To take probiotics for a period of time before undergoing IVF.
- To take a combination of antibiotics with probiotics for a period of time before undergoing IVF.
These treatments intend to change the types or amounts of bacteria present with the aim of improving the chances of a successful pregnancy.
Are there any issues with microbiome testing?
There are many different tests available to look at the microbiome, but there is currently no agreed best way to carry out the test or understand the results. This can result in the same patient having very different test results and being advised to undergo different treatments due to the way the tests are undertaken by different laboratories and interpreted.
This review assigns a rating to the interventions advised following microbiome testing. The review does not assess the tests themselves.
| Rated outcomes for microbiome testing | |
|---|---|
| Rated grey for increasing the chances of having a baby for most fertility patients.
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The use of probiotics, probiotics with antibiotics, and antibiotics following microbiome testing is rated GREY for improving the chances of having a baby for most fertility patients. This is because there is insufficient moderate/high-quality evidence investigating the effectiveness of the use of these treatments following microbiome testing in most fertility patients. |
| Rated grey for increasing the chances of having a baby for patients with recurrent implantation failure (RIF).
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The use of probiotics, probiotics with antibiotics, and antibiotics following microbiome testing is rated GREY for improving the chances of having a baby for patients with recurrent implantation failure. This is because there is insufficient moderate/high-quality evidence investigating the effectiveness of the use of these treatments following microbiome testing in patients with recurrent implantation failure. |
| Rated grey for increasing the chances of having a baby and reducing the chances of miscarriage for patients with chronic endometritis.
Grey traffic light
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The use of antibiotics and antibiotics with probiotics following microbiome testing is rated GREY for improving the chances of having a baby and reducing the chances of miscarriage for patients with chronic endometritis. This is because there is insufficient moderate/high-quality evidence investigating the effectiveness of the use of these treatments following microbiome testing in patients with chronic endometritis. |
Specific safety concerns about a treatment add-on, including those discussed above, are included under the dedicated section titled Is this treatment add-on safe?.
What do ratings mean?
There are five ratings that indicate whether a treatment add-on is effective at improving treatment outcomes for someone undergoing fertility treatment, according to the evidence from studies. To make it easier to understand the scientific evidence for each treatment add-on, we have a range of symbols and colours for each rated add-on below.
Green traffic light
On balance, findings from high quality evidence shows this add-on is effective at improving the treatment outcome.
Yellow traffic light
On balance, it is not clear whether this add-on is effective at improving the treatment outcome. This is because there is conflicting moderate/high quality evidence – in some studies the add-on has been found to be effective, but in other studies it has not.
Grey traffic light
We cannot rate the effectiveness of this add-on at improving the treatment outcome as there is insufficient moderate/high quality evidence.
Black traffic light
On balance, the findings from moderate/high quality evidence shows that this add-on has no effect on the treatment outcome.
Red traffic light
There are potential safety concerns and/or, on balance, findings from moderate/high quality evidence shows that this add-on may reduce treatment effectiveness.
All treatment add-ons on our list will have a rating to indicate whether the evidence shows that the treatment add-on is effective at improving the chances of having a baby for most fertility patients. Some treatment add-ons on our list may also have additional ratings for specific treatment outcomes. For example, whether the evidence shows that the treatment add-on reduces miscarriage. There may also be further ratings for specific patient groups, for example whether the evidence shows that the treatment add-on is effective for those who are aged over 40. Please see the individual webpages for each treatment add-on for their ratings.
An agreement between the HFEA and other professional and patient bodies (the 19th October 2023 consensus statement) states that treatments that have no strong evidence of their safety and/or effectiveness should only be offered in a research setting. Patients should not be charged extra to take part in research, including clinical trials.
What’s the evidence for microbiome testing?
Overall, there is insufficient moderate/high-quality evidence to determine whether microbiome testing followed by various treatments improves the chance of having a baby.
For most fertility patients
Some studies suggested that probiotics may increase the chances of having a baby. However, the studies had some limitations and included only a small number of patients. Results are inconsistent across studies investigating the use of antibiotics and taken together do not show any benefit.
For patients with recurrent implantation failure
Some studies suggested that probiotics, either alone or combined with antibiotics, may improve the chances of having a baby. However, the evidence came from low-quality studies with a small number of patients. Studies also found no clear improvement in other outcomes such as, ongoing pregnancy or miscarriage rates.
For patients with chronic endometritis
Studies investigating antibiotics, with or without probiotics, generally found no clear improvement in increasing the chances of having a baby or reducing miscarriage. Overall, most studies were of low quality and showed no clear benefit.
Important points to note:
Although a large randomised controlled trial (Chronic Endometritis and Recurrent Miscarriage; CERM trial) has been completed, its full results have not yet been published and therefore were not included in the HFEA's assessment.
At the June 2026 meeting, the Scientific and Clinical Advances Advisory Committee (SCAAC) evaluated the evidence for microbiome testing. Details of the evidence considered, and the Committee’s discussions can be found here: SCAAC papers June 2026 (pages 17-33) and SCAAC minutes June 2026 (pages 8-9).
Is this treatment add-on safe?
Most studies looking at the use of microbiome testing and associated treatments in fertility treatment have not addressed safety in great detail.
Safety of microbiome testing
Vaginal and endometrial microbiome testing are generally considered to be low risk, but the risks can vary depending on how the sample is collected.
Depending on the type of test, it may involve collecting a vaginal swab or taking a sample from the lining of the uterus (endometrium). A vaginal swab can cause some mild discomfort, cramping or some light bleeding or spotting. Taking a sample from the endometrium can also cause discomfort, cramping, light vaginal bleeding or spotting, and carries a small risk of infection.
Safety of treatments following microbiome testing
The safety of any treatment recommended following microbiome testing will depend on the type used.
Some clinics may prescribe antibiotics if the microbiome test has suggested an imbalance in the presence of bacteria. While antibiotics can be appropriate in some circumstances, unnecessary or repeated use may contribute to antibacterial resistance. Antibiotics can also be associated with some side effects such as feeling sick or diarrhoea. Further information can be found here: Antibiotics - NHS.
Other treatments, such as probiotics, may also be associated with some minor side effects such as bloating. Further information here: Probiotics - NHS.
If you have any questions about the safety and risks of this treatment add-on, your clinic will be able to discuss the use of a treatment add-on with you, taking into account your specific medical history and circumstances.
Studies reviewed for this treatment add-on
The SCAAC have reviewed the following studies for Microbiome testing:
| Intervention | Study | DOI/Reference |
|---|---|---|
| Probiotic | Di Pierro 2023 | 10.3390/microorganisms11112796 |
| Hanaoka 2025 | 10.1007/s10815-025-03759-0 | |
| Irollo 2017 | 10.4081/jsas.2017.7883 | |
| Jafarabadi 2024 | 10.18502/ijrm.v22i5.16435 | |
| Kamrani 2025 | 10.1016/j.humimm.2024.111220 | |
| Raimondo 2025 | 10.3390/nu17030410 | |
| Tanha 2023 | 10.1007/s00404-023-07147-w | |
| Thanaboonyawat 2023 | 10.1038/s41598-023-39078-6 | |
| Wei 2024 | 10.1007/s10815-024-03066-0 | |
| Probiotic with/without antibiotics | Iwami 2022 | 10.1007/s10815-022-02688-6 |
| Iwami 2025 | 10.1002/rmb2.12634 | |
| Haahr 2025 | 10.1038/s41467-025-60205-6 | |
| Hu 2024 | 10.3389/fcimb.2024.1494931 | |
| Antibiotics | Cicinelli 2015 | 10.1093/humrep/deu292 |
| Eskew 2021 | 10.1016/j.xfss.2021.01.002 | |
| Hanaoka 2025 | 10.1007/s10815-025-03759-0 | |
| Kitaya 2017 | 10.1111/aji.12719 | |
| Liu 2022 | 10.1111/aji.13669 | |
| Xiong 2021 | 10.1016/j.fertnstert.2021.03.036 | |
| Zou 2023 | 10.1016/j.jri.2022.103782 |
Other reviews include:
| NICE | NICE 2026 (NG 257) | Fertility problems: assessment and treatment |
| EAU guidelines on sexual and reproductive health | NICE 2026 (NG 257) | EAU Guidelines on Sexual and Reproductive Health 2026 |
What are treatment add-ons?
In vitro fertilisation (IVF) and intrauterine insemination (IUI) are established treatments that have been proven effective for most patients. Treatment add-ons are optional non-essential treatments or tests that may be offered in addition to such proven fertility treatment. Treatment add-ons are:
- Additional treatments (to the core treatment e.g. IVF or IUI) or tests that are being offered to the general patient population in licensed fertility clinics in the UK,
- where there is published scientific literature which claims to demonstrate that the add-on improves live birth rates or other treatment outcomes rated by the HFEA; but
- where evidence of effectiveness for the use of the treatment or test in a clinical setting is lacking or absent; and
- where patients need unbiased information about the effectiveness and risks of this treatment or test
It is important to keep in mind that for most patients, having routine cycles of proven fertility treatment are effective without using any treatment add-ons. If you are paying for your own treatment, you may want to think about whether it might be better to pay for multiple cycles of IVF or IUI, rather than spending large sums of money on a single treatment cycle with treatment add-ons that haven’t been proven to be effective.
We aim to publish clear and reliable information about some of the treatment add-ons that don’t have enough evidence to show that they improve your chances of having a baby and other relevant treatment outcomes. This provides useful information to patients and allows them to question the use of add-ons.
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