Key message
Testing the endometrial microbiome is not a swab taken at home. It requires a sample collected from inside the uterine cavity by a clinician, and a sequencing method designed specifically for the uterus's low-biomass environment. Understanding how the test works, and what it can and cannot tell you, is the foundation for interpreting the result that comes back.
The endometrial microbiome is measurable, but it is not straightforwardly measurable. The uterine cavity contains far fewer bacteria than the gut or any other well-studied body site. That low biomass creates two challenges: getting a clean sample that reflects the endometrium rather than the route taken to reach it, and using a sequencing method sensitive enough to characterise what is present without being overwhelmed by contamination.
This article explains how BioBloom's test is performed, what it measures, and what its limitations are. It is written for patients who want to know what to expect, and for clinicians who need to understand what the test is doing technically.
What the test measures
BioBloom uses 16S rRNA gene sequencing, a DNA-based method that identifies bacteria by reading a specific region of the bacterial genome that varies between species.
The test reports four things:
- Taxonomic composition. Which bacterial taxa are present in the sample, down to species level where the sequencing resolution allows.
- Relative abundance. What proportion of the total bacterial community each taxon makes up.
- Community pattern. Whether the sample is Lactobacillus-dominant, dysbiotic, intermediate, or low biomass.
- Sample quality metrics. Total bacterial signal detected, read depth, and quality indicators that determine how confidently the result can be interpreted.
The test does not measure absolute bacterial counts. 16S sequencing measures proportions, not concentrations. A result of "70% Lactobacillus crispatus" means that, of the bacterial DNA detected, 70% belonged to that species. This distinction matters clinically because two patients with the same proportional profile may have very different total bacterial loads, and clinical interpretation is calibrated against the proportional evidence base.
How the sample is collected
Endometrial microbiome testing requires a sample from inside the uterine cavity. This cannot be done with a vaginal swab, and it cannot be done at home.
The procedure is typically:
- Performed by a fertility consultant or gynaecologist in an outpatient setting
- Scheduled in the secretory phase of the menstrual cycle, though timing varies by clinic
- Collected using a thin, soft catheter passed through the cervix into the uterine cavity, similar in feel to an IUI catheter or embryo transfer
- Completed in a few minutes with minimal discomfort for most patients
- Performed under sterile conditions, with protocols designed to minimise contamination from the vaginal and cervical tract
The sample itself is typically a small volume of endometrial fluid containing cells. It is placed into a transport medium and sent to the laboratory for processing.
The sampling step is the single most important determinant of result quality. Contamination during collection is the most common source of error in endometrial microbiome testing, and it is often why results from different laboratories vary. Validated sampling protocols, not just sequencing methodology, are what distinguish a clinically reliable test from a research-grade one.
What happens in the laboratory
Once the sample reaches the laboratory, the pipeline is:
- DNA extraction. Bacterial DNA is isolated from the sample using protocols optimised for low-biomass material.
- Amplification and sequencing. The 16S rRNA gene region is amplified and sequenced on a next-generation sequencing platform.
- Bioinformatic analysis. Raw sequence data is processed, quality-filtered, and compared against curated reference databases to identify bacterial taxa.
- Contamination control. Sequencing reads corresponding to known reagent or laboratory contaminants are identified through negative-control samples processed in parallel, and are subtracted from the result.
- Report generation. The processed data is summarised into a clinical report structured for both patient and clinician readership.
The contamination-control step is particularly important in endometrial microbiome testing. Because the starting biomass is low, the signal from any given sample can be distorted by background bacterial DNA present in reagents, swabs, or laboratory air. Methods that do not account for this produce inconsistent and sometimes misleading results. This is part of why endometrial microbiome testing is still offered by relatively few laboratories globally, and why laboratory methodology matters as much as clinical sampling.
What the report looks like
A BioBloom report is structured to be read by both patient and clinician. The main components:
Sample quality summary
Confirms that the sample had sufficient bacterial signal for confident interpretation. If bacterial signal is very low, the report flags this as "low biomass" and recommends repeat sampling rather than forcing an interpretation from insufficient data.
Community pattern classification
A high-level categorisation:
- Lactobacillus-dominant
- Intermediate or transitional
- Dysbiotic
- Low biomass or inconclusive
Relative abundance chart
A visual breakdown showing the proportions of the main taxa present, with Lactobacillus species broken out individually where the sequencing data supports it.
Species-level detail
A table listing the specific bacteria detected above a meaningful abundance threshold, with brief notes on their clinical significance and references to the published evidence.
Clinical interpretation
A summary paragraph contextualising the result against published thresholds and, where provided, the patient's clinical history. The report is designed to support a conversation with a fertility consultant, not to replace one. A result alone does not dictate a treatment plan.
What a typical result might show
Three illustrative examples, anonymised and simplified:
Example 1: Lactobacillus-dominant
L. crispatus 78%, L. iners 15%, other taxa 7%. Total Lactobacillus dominance above 90%. This is the pattern associated with favourable reproductive outcomes in the published evidence. No treatment indicated on microbiome grounds.
Example 2: Dysbiotic
L. iners 22%, Gardnerella vaginalis 28%, Atopobium species 14%, Prevotella species 11%, other taxa 25%. Total Lactobacillus well below the 90% threshold, increased diversity, notable presence of dysbiosis-associated taxa. This is the pattern most commonly discussed as a candidate for targeted treatment.
Example 3: Intermediate
L. crispatus 40%, L. iners 35%, Gardnerella 8%, other taxa 17%. Total Lactobacillus above 75% but below 90%, dominated by L. iners rather than L. crispatus. Interpretation depends on the threshold used and the clinical context. An intermediate result in an asymptomatic first-time IVF patient may be interpreted differently from the same result in a patient with three failed transfers.
These examples illustrate why a result is not self-interpreting. Clinical context determines which patterns are acted on and how.
What the test cannot do
Endometrial microbiome testing is a useful addition to the clinical picture, but it has real limitations that matter for interpretation:
- It is a snapshot. The microbial community can shift over weeks. A single sample represents a moment in time.
- It measures proportions, not quantities. A patient with low total bacterial biomass but 90% Lactobacillus shows the same "dominance" as a patient with higher biomass and the same proportion.
- It does not diagnose chronic endometritis. CE is a histological diagnosis requiring plasma-cell staining on a tissue biopsy. Some microbial patterns are associated with CE, but sequencing alone cannot confirm or exclude it.
- It does not identify all microorganisms. 16S sequencing detects bacteria. Fungi, viruses, and archaea are not captured by this method.
- It does not predict whether any specific pregnancy will succeed. It contributes information to a clinical picture that includes embryo quality, endometrial receptivity, hormonal factors, and history.
Honest framing of these limits is part of what distinguishes a clinically serious test from a wellness product. A clinician who knows what the test cannot do is better placed to act on what it can.
When testing is most useful
The clinical situations where endometrial microbiome testing adds the most value are:
- Before a subsequent embryo transfer in a patient with one or more previous failures with good-quality embryos
- As part of the workup for recurrent pregnancy loss, alongside standard investigations
- In unexplained infertility where conventional workup has been unrevealing
- After treatment for chronic endometritis, to confirm that the endometrial environment has been restored before the next transfer
- In planning for a patient's first transfer where the clinical history suggests elevated risk of endometrial disruption, for example prior intrauterine procedures or pelvic inflammatory disease
Testing outside these contexts is usually not clinically necessary, and the result may be harder to act on.
How BioBloom fits in
Where this connects to clinical practice.
BioBloom's test is designed specifically for the low-biomass environment of the endometrium. Our pipeline:
Validated sampling protocols
Developed in collaboration with practising fertility clinics, not adapted from other body sites. Contamination-minimising technique is part of the protocol, not an afterthought.
Contamination controls at every laboratory stage
Negative controls processed in parallel with patient samples, systematic subtraction of known reagent contaminants, and minimum-biomass thresholds below which results are flagged rather than reported.
Species-level resolution where the data supports it
The report distinguishes L. crispatus from L. iners and identifies dysbiosis-associated taxa at genus and species level, supporting more informed treatment decisions.
Clinician-facing reports
Structured to support shared decision-making between patient and specialist. The test is ordered through partner fertility clinics; samples cannot be submitted directly by patients.
Cambridge-based
BioBloom was founded out of Cambridge and works with fertility clinics across the UK. The clinical team supports the partner network with case discussion and interpretation guidance.
Frequently asked questions
Questions, answered.
Next step
Where to go from here.
For patients
If a fertility specialist has suggested endometrial microbiome testing, or if any of the clinical situations described above apply, the next step is to identify a partner clinic that can order the test and interpret the result in the context of your history.
For clinicians
Methodology, sample specifications, and reporting structure are covered in this article and Part 4. Use them as the orientation reference when integrating endometrial microbiome testing into the fertility workup.
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.
- 02Moreno I, Garcia-Grau I, Perez-Villaroya D, et al. Endometrial microbiota composition is associated with reproductive outcome in infertile patients. Microbiome. 2022;10(1):1.
- 03Chen C, Song X, Wei W, et al. The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases. Nat Commun. 2017;8:875.