Use Case: Calibrated Database for Vaginal and Endometrial Microbiome.
Summary
A reproductive-health diagnostics company wanted to strengthen its position in the fast-growing microbiota analysis market. It already had NGS capacity, trained staff, and an active service line, but needed a more modern bioinformatics system to stay competitive.
To do this, it planned to build an enhanced database of vaginal and endometrial microbiota biomarkers and partnered with BIOINFILE to accelerate development.
As a result, the company achieved measurable improvements across all key performance indicators. The new workflow reduced ambiguous reads by half, increased species detection by 2.5-fold and genera by 4-fold, expanded pathogen coverage with over 1,000 additional clinically relevant organisms, and ensured 100% up-to-date nomenclature. All within a quality controlled ALCOA++ framework for greater diagnostic accuracy, data integrity, and long-term confidence in clinical and research applications.
How did the process work?
1. Planning
The client shared their existing 16S-based metagenomics pipeline, which was outdated, lacked proper QA, and wasn’t adapted to vaginal or endometrial microbiota. Requirements were set to:
Use full-length 16S sequences for relevant bacterial and pathogenic taxa.
Incorporate clinical metadata linked to health/disease states.
Ensure broad pathogen coverage.
Maintain compatibility with external bioinformatic software suites.
2. Preparation
BIOINFILE curated a high-precision database tailored to human vaginal and endometrial samples. This included:
Selecting sequences from trusted INSDC repositories.
Performing strict QC: origin checks, annotation review, trimming, de-replication, calibration, and taxonomic validation.
Standardizing taxonomy using LPSN, SEQCODE, NCBI Taxonomy, and IJSEM, with manual adjustments where needed.
Applying a scoring system to evaluate sequence quality, homology risks, and hypervariable-region coverage.
Ensuring ALCOA++ compliance for traceability and reproducibility.
Running technical evaluations with ARB and BLAST to confirm species-level resolution and document limitations of partial 16S markers.
3. Preview
A formatted database extract was generated so the client could test compatibility in their own pipeline. The structure matched requirements.
4. Delivery and Validation
The final database contained over 5,000 species-level references with accession numbers, NCBI IDs, and internal hashes for full traceability.
BIOINFILE delivered a user manual, QC reports, a test-acceptance document, and a full process-traceability signature.
The client validated the database through comparative analysis on real samples, assessing improvements in accuracy, scalability, and long-term robustness relative to their previous version.
Quantitative Results
BIOINFILE’s database was benchmarked against the client’s earlier solution and consistently outperformed it across every metric:
Broader microbial coverage: It mapped far more reads, cutting unclassified reads by 50% and reducing data loss.
Cleaner classifications: Ambiguous reads were reduced by half, improving assignment accuracy.
Higher taxonomic resolution: The system detected 2.5× more species and 4× more genera, offering a much richer view of the microbiota.
Stronger taxonomic consistency: The database maintained 100% current nomenclature, aligned with international standards and CAP expectations for reliable clinical interpretation.
Expanded pathogen detection: More than 1,000 additional human pathogens were included, enabling detection of organisms previously invisible to the client’s workflow.
Quality Control
Beyond the numerical gains, BIOINFILE’s database was built within an ALCOA++ quality framework, a standard rooted in FDA, EMA, ICH, and GAMP 5 guidelines. ALCOA requires data to be Attributable, Legible, Contemporaneous, Original, and Accurate, while ALCOA++ adds Completeness, Consistency, Durability, Availability, Representativeness, and Traceability. This elevates the database to a standard rarely reached by typical microbiome solutions.
Although these elements aren’t expressed as direct metrics, they provide major value: stronger scientific assurance, higher professional confidence, and a level of regulatory robustness the client previously lacked. In a field where trust and dependability are decisive, this becomes a meaningful competitive edge.
References
Dien Bard J, Sullivan KV, Zhang SX, et al. Navigating Nomenclature in Patient Care: Taxonomy Considerations From the College of American Pathologists' Microbiology Committee. Clin Infect Dis. Published online September 23, 2025. doi:10.1093/cid/ciaf474.
Hoffmann DE, von Rosenvinge EC, Roghmann MC, Palumbo FB, McDonald D, Ravel J. The DTC microbiome testing industry needs more regulation. Science. 2024;383(6688):1176–1179. doi:10.1126/science.adk4271.
