Key message
An endometrial microbiome result is not a verdict. It is one piece of information, added to the clinical picture a fertility consultant is already building. How that information is used, whether to treat, when to retest, and whether to adjust the timing of embryo transfer, depends on the full context of care. This article describes the clinical pathways most commonly followed after each type of result, and the evidence behind them.
Receiving a microbiome test result can be unsettling, particularly if the result is unexpected or the terminology is unfamiliar. The most important thing to understand is that the result is the start of a conversation, not the end of one. What happens next should be decided with a fertility specialist who knows your history.
For clinicians, the article is a reference for the clinical pathways the evidence currently supports and the situations where practice varies. It covers the three broad categories of result, the treatment options associated with each, the evidence base, and the role of retesting.
Important note. This article describes the clinical approaches most commonly used after endometrial microbiome testing. Specific treatment decisions are made by your fertility consultant based on your individual clinical picture. BioBloom does not provide treatment recommendations.
If the result is Lactobacillus-dominant
A Lactobacillus-dominant endometrial microbiome is the pattern associated with better reproductive outcomes in the published evidence. For most patients, this is a reassuring result.
What it means in practice:
- No treatment is indicated specifically for the microbiome
- Existing plans for embryo transfer, investigations of other factors, or ongoing fertility treatment continue as planned
- The microbiome can still shift over time, particularly after antibiotics, intrauterine procedures, or significant gaps between cycles. Retesting may be considered before a subsequent transfer if there have been intervening events that could have disrupted the community
A Lactobacillus-dominant result does not guarantee a successful pregnancy. Fertility outcomes depend on many factors, and the microbiome is one variable among several. What the result does is remove one potential contributor to implantation failure, letting clinical attention focus on the other parts of the picture.
If the result is dysbiotic
A dysbiotic result, meaning Lactobacillus below the dominance threshold, with increased diversity and elevated dysbiosis-associated taxa, is the result most likely to prompt treatment.
The evidence-based treatment approach has two components:
Targeted antibiotic therapy
The specific antibiotic depends on which taxa are dominant in the dysbiotic pattern. Protocols commonly involve oral antibiotics active against the relevant bacteria, for example metronidazole for anaerobes including Gardnerella, or broader-spectrum regimens where mixed flora are present. Typical duration is one to two weeks.
Probiotic or Lactobacillus supplementation
Following antibiotic treatment, Lactobacillus supplementation, oral, vaginal, or both, is used to support re-establishment of dominance. Vaginal formulations designed for reproductive-tract use have the strongest mechanistic rationale.
The evidence supporting this approach comes from several studies. Kyono et al., 2019 (Reprod Med Biol) reported that around half of treated patients converted from a dysbiotic to a Lactobacillus-dominant profile following combined antibiotic and probiotic therapy. Larger subsequent cohorts have reported higher conversion rates with extended protocols. Cicinelli et al., 2015 (Hum Reprod) demonstrated that antibiotic treatment for chronic endometritis, a related but distinct condition, significantly improved subsequent IVF outcomes. Hiratsuka et al., 2025 (Sci Rep) reported that dysbiotic patients who received targeted treatment achieved significantly higher clinical pregnancy rates in the subsequent cycle.
What the evidence does not yet include is a large randomised controlled trial specifically comparing treated versus untreated dysbiosis on live birth outcomes. The decision to treat is therefore based on the strong observational evidence of improved outcomes, the treatability of the condition, and the relatively low risk of a short course of targeted antibiotics in this clinical setting. That decision is made between patient and consultant.
If the result is intermediate or inconclusive
An intermediate result, meaning Lactobacillus present but not dominant, without clear dysbiosis, is the hardest to act on. The published evidence is less clear on whether these patients benefit from treatment, and practice varies between clinics.
Common clinical approaches include:
- Watchful monitoring, with retesting before the next embryo transfer
- Probiotic supplementation alone, without antibiotics, to see whether dominance can be re-established
- Reviewing recent events that might explain the intermediate state, including recent antibiotics, intrauterine procedures, or cycle timing of the sample, and retesting once those factors have resolved
A low-biomass or inconclusive result is different. It usually means the sample did not contain enough bacterial signal to interpret confidently. The standard response is to repeat the sample, often at a different point in the cycle. It does not indicate a clinical problem with the endometrium.
Retesting after treatment
If treatment is undertaken, retesting is often recommended to confirm that Lactobacillus dominance has been restored before the next embryo transfer. This step matters clinically. It confirms the treatment worked and that the endometrial environment is as favourable as possible when the transfer happens.
Timing of retesting is typically:
- Four to six weeks after completing treatment, allowing time for the community to stabilise
- In the same phase of the menstrual cycle as the original test, to make results directly comparable
- Before any planned embryo transfer, not after
The clinical logic is straightforward. If the first test identified a modifiable factor, the second test confirms whether the modification worked. Proceeding to transfer without confirming restoration means transferring without knowing whether the original finding has been addressed.
How results fit into a fertility care plan
Microbiome results are one input into a clinical picture that includes many others: age, embryo quality, endometrial receptivity, hormonal factors, anatomy, and treatment history. A good fertility consultant will integrate the microbiome result with these other factors rather than treating it in isolation.
In practice, this often means:
- For patients with recurrent implantation failure, a dysbiotic result may be the first clearly modifiable finding and often prompts treatment before the next transfer
- For patients with recurrent pregnancy loss, a dysbiotic result is usually considered alongside investigations for autoimmune, endocrine, and anatomical causes
- For patients with unexplained infertility, a dysbiotic result may shift the clinical approach toward addressing the microbiome before proceeding with further cycles
- For patients with a Lactobacillus-dominant result, clinical attention moves to other factors while monitoring for any changes that might warrant retesting
The principle underlying all of these: a test result should change what happens next. If a Lactobacillus-dominant result confirms existing plans, or a dysbiotic result prompts a targeted intervention, the test has done its job. If a result is received, filed, and never acted on, something has gone wrong in the clinical pathway.
Questions to ask your consultant
A short checklist for the conversation after receiving a result:
- What does this specific result mean in the context of my history?
- Are you recommending treatment, and if so, what does it involve?
- How long will the treatment take, and when can I resume planned fertility treatment?
- Should I retest after treatment? If so, when?
- Are there other investigations you want to do alongside this?
- How does this result fit with my planned embryo transfer timing?
Bringing the result and this list to an appointment tends to produce a more useful conversation than arriving with the result alone.
What not to do
A few common mistakes worth avoiding:
- Do not self-treat. Antibiotics are prescription medications for good reasons. Self-medicating with leftover antibiotics or non-prescribed regimens can worsen dysbiosis, encourage resistance, and complicate future clinical decisions.
- Do not rely on over-the-counter probiotics as a substitute for clinical treatment. Most commercial probiotics are not formulated for the reproductive tract, and the evidence that they restore endometrial Lactobacillus dominance as monotherapy is limited.
- Do not make major lifestyle changes on the basis of a microbiome result alone. The evidence that diet, supplements, or wellness products meaningfully alter the endometrial microbiome is limited. The interventions with the strongest evidence are clinician-led.
- Do not assume a single result tells the whole story. The microbiome is dynamic, and a result reflects a moment in time. Retesting and clinical context matter.
How BioBloom fits in
Where this connects to clinical practice.
BioBloom's role does not end when the report is delivered. Our test is designed to support the clinical pathway that follows:
Reports built for clinical decision-making
Species-level detail where the data supports it, structured to inform targeted treatment selection rather than leaving interpretation to the reader.
Integrated retesting pathway
Retesting after treatment is ordered through the same clinical pathway as initial testing, with sample comparability designed into the reporting structure.
Experienced clinical network
Our partner fertility clinics include specialists experienced in interpreting and acting on microbiome-guided care. If a patient has received a BioBloom result and their current clinician is unfamiliar with this area, a specialist fertility clinic in the BioBloom network can provide the clinical context needed to act on the result.
Cambridge-based clinical team
A UK-based clinical and scientific team supports the partner network with case discussion, methodology questions, and interpretation guidance.
Frequently asked questions
Questions, answered.
Next step
Where to go from here.
For patients
If you have received a BioBloom result and want to discuss what it means, the next step is a conversation with a fertility specialist familiar with microbiome-guided care. Our partner clinic network covers most of the UK.
For clinicians
Clinical pathway guidance, evidence summaries, and treatment workflow are covered across this four-part series. Parts 3 and 4 give the practical reference for integrating testing and acting on a result.
References
Citations & further reading
- 01Moreno I, Codoñer FM, Vilella F, et al. Evidence that the endometrial microbiota has an effect on implantation success or failure. Am J Obstet Gynecol. 2016;215(6):684-703.
- 02Kyono K, Hashimoto T, Kikuchi S, Nagai Y, Sakuraba Y. A pilot study and case reports on endometrial microbiota and pregnancy outcome: an analysis using 16S rRNA gene sequencing among IVF patients, and trial therapeutic intervention for dysbiotic endometrium. Reprod Med Biol. 2019;18(1):72-82.
- 03Cicinelli E, Matteo M, Tinelli R, et al. Prevalence of chronic endometritis in repeated unexplained implantation failure and the IVF success rate after antibiotic therapy. Hum Reprod. 2015;30(2):323-330.
- 04Hiratsuka D, Matsuo M, Kashiwabara K, et al. Comparison of diagnostic tests for chronic endometritis and endometrial dysbiosis in recurrent implantation failure: impact on pregnancy outcomes. Sci Rep. 2025;15:8272.
- 05Vitagliano A, Saccardi C, Noventa M, et al. Effects of chronic endometritis therapy on in vitro fertilization outcome in women with repeated implantation failure: a systematic review and meta-analysis. Fertil Steril. 2018;110(1):103-112.