GxP-aligned and GCP-supportive fecal sample microbiome sequencing for clinical trials, cohort studies, probiotic studies, and regulated microbiome research.
BaseClear provides clinical microbiome sequencing services for regulated studies. The service can cover the full workflow from sample collection advice and reliable fecal sample receipt through DNA extraction, library preparation, high-throughput sequencing, documented quality control, technical reporting, and data package release.
This service is designed for clinical trial sponsors, CROs, probiotic and live biotherapeutic companies, microbiome-focused biotech companies, nutrition and infant health companies, academic clinical research groups, and hospital-led cohort studies. It solves common challenges in clinical microbiome projects, including large sample numbers, batch consistency, sample traceability, control strategy, documentation requirements, cross-site fecal sample collection, and the need for reproducible sequencing data that can support downstream clinical and statistical analysis.
BaseClear uses standardized and controlled workflows for human specimen DNA extraction, DNA QC, Illumina library preparation, library QC, high-throughput sequencing, and sequencing run review. For large studies, automated extraction and library preparation can support consistent processing across batches. Clinical microbiome studies can include whole-cell microbial controls, extraction controls, library controls, and sequencing controls to monitor workflow performance and support downstream quantitative or comparative interpretation.
Clients receive sequencing data packages, documented DNA and library QC results, sequencing run metrics, technical reports, batch and control information, and secure data transfer to the agreed client environment. Documentation can be prepared in a GxP-aligned and GCP-supportive format, with traceable sample handling, controlled workflow records, deviation notes where applicable, and technical reporting suitable for regulated clinical research environments.
We review your study design, sample type, expected sample numbers, collection format, sequencing objective, control strategy, and reporting needs. BaseClear then defines the sequencing approach, documentation level, data delivery format, and project timeline.
Your team collects fecal samples using the agreed collection and stabilization format, such as Zymo Shield Fecal tubes where appropriate. BaseClear can advise on collection logistics, batch planning, and sample submission requirements for multi-site clinical studies.
BaseClear receives and tracks the samples, performs fecal sample DNA extraction, DNA QC, library preparation, library QC, high-throughput Illumina sequencing, and sequencing run review. Controls can be included across extraction, library preparation, and sequencing batches.
We compare treated and control cohorts using alpha diversity, beta diversity, taxonomic composition, and microbiome stability metrics. Statistical analyses identify significant differences and assess their biological relevance in the context of treatment-associated microbiome changes.
Sample clinical trial scale supported in project scoping
Illumina paired-end sequencing option for shotgun metagenomics
Controlled documentation and traceable workflow records
Information security standard for data handling
A clinical trial sponsor needed a scalable workflow for fecal sample microbiome sequencing across approximately 1,000 patients in the Nordics. The project required controlled sample handling, consistent fecal sample DNA extraction, sequencing batch controls, documented QC, and secure data release suitable for clinical research documentation.
BaseClear proposed a GxP-aligned and GCP-supportive workflow covering Zymo-based fecal sample collection options, automated DNA extraction, DNA QC, Illumina library preparation, library QC, NextSeq sequencing, whole-cell controls, technical reporting, and secure upload of data packages to the client-designated environment.
The proposed workflow gave the sponsor a clear path from sample collection to technical reporting, including batch-level controls, QC documentation, and optional add-ons such as BioIT analysis, dPCR-based target quantification, and metabolomics for residual antibiotics or microbiome-linked metabolites.
BaseClear can process fecal samples for clinical microbiome sequencing when the collection format, stabilization chemistry, and storage conditions are aligned before study start. Fecal samples can be collected using validated stabilization products, including Zymo Shield Fecal tubes where appropriate. Early alignment on collection logistics helps reduce site-to-site variability and supports consistent processing across large clinical studies.
BaseClear can provide GxP-aligned and GCP-supportive documentation for clinical microbiome sequencing studies. This includes traceable sample handling, documented QC steps, controlled workflow records, technical reporting, and secure data release. The exact documentation package should be agreed during project scoping so it matches the sponsor, CRO, or clinical study requirements.
Clinical microbiome studies can use shotgun metagenomic sequencing or targeted amplicon sequencing depending on the study question. Shotgun metagenomics is useful when the study needs species-level or functional insight, while targeted approaches such as 16S or ITS can support broader community profiling at lower complexity. BaseClear can align the sequencing strategy with sample number, required depth, budget, and downstream analysis plan.
Clinical microbiome sequencing projects can include whole-cell microbial controls, extraction controls, library preparation controls, sequencing controls, and negative controls. These controls help assess workflow performance, batch consistency, contamination risk, and sequencing quality. The control strategy should be defined before study start and kept consistent across batches.
The technical report can include DNA concentration, DNA quality, library concentration, fragment size, sequencing yield, Q30 scores, cluster density, lane balance, sample-level performance, control performance, and an overall run assessment. Deviation notes can be included where relevant. The report gives the clinical team a traceable technical record from sample processing to final data release.
BaseClear can provide BioIT analysis, dPCR assays, and metabolomics as add-on services for clinical microbiome projects. BioIT can include taxonomic profiling, functional profiling, diversity analysis, strain-level analysis, and custom reporting. dPCR can support targeted quantification or strain tracking, while metabolomics can support analysis of residual antibiotics, short-chain fatty acids, bile acids, and other relevant metabolites.
SERVICES
Phenotypic assessment of antimicrobial resistance aligned with EFSA guidelines
SERVICES
Phenotypic assessment of antimicrobial and cytotoxic production
Book a scoping call with BaseClear to align your study design, sample collection strategy, sequencing approach, QC requirements, and reporting needs. You will get practical input on the workflow before committing to a project.
