Combine metagenomics, culturomics, and whole genome sequencing to discover, isolate, and characterize targeted microbial strains with unique functional potential.
BaseClear’s Strain Discovery service combines advanced culturomics with sequencing technologies to recover, isolate, and characterize microbial strains that are difficult or impossible to identify using conventional cultivation methods. By integrating metagenomic profiling before cultivation with tailored culture strategies and whole genome sequencing, we maximize the likelihood of recovering targeted microorganisms, novel species, and strains with unique physiological or metabolic properties. Every project is designed as a bespoke expert project to address specific scientific or industrial objectives.
This service is intended for researchers and organizations working in the food, biotechnology, environmental, agricultural, pharmaceutical, and clinical sectors that require the isolation of specific microorganisms from complex samples. Typical applications include discovering novel probiotic or industrial strains, identifying microorganisms with unique enzymatic activities, recovering low-abundance species, building microbial culture collections, and isolating strains for downstream functional characterization, product development, or regulatory studies.
Each project starts with a comprehensive assessment of the target organism and sample type. BaseClear designs a customized culturomics workflow using literature research, genomic information, and database mining to define the optimal culture media, enrichment strategies, and environmental conditions. Samples are first characterized using 16S rRNA gene sequencing or shotgun metagenomics to understand microbial composition, followed by selective culturing, isolation of pure colonies, whole genome sequencing, de novo genome assembly, genome annotation, and optional downstream analyses such as phylogenetics, pathway analysis, or targeted gene discovery. This integrated workflow enables efficient recovery and characterization of microorganisms that are often overlooked by traditional microbiological approaches.
Clients receive purified microbial isolates in glycerol stocks together with high-quality whole genome sequencing data, assembled and annotated genomes, taxonomic identification, and comprehensive project documentation. Depending on the project objectives, BaseClear can additionally provide custom genome mining, functional analyses, and identification of genes encoding enzymes, antimicrobial compounds, or other bioactive molecules, delivering a complete foundation for further research, strain development, or industrial application.
We begin with a conversation to make sure we understand your target microorganism or project goal.
We design a tailored culturomics and sequencing plan based on your sample type and desired strain characteristics.
You send us your samples, and we apply selective culturing techniques combined with metagenomic insights.
We isolate the targeted strains and perform whole genome sequencing to fully characterize them.
You receive isolated strains, annotated genome data, and a detailed report outlining your strain’s characteristics and potential applications.
One of our biopharmaceutical clients aimed to isolate a novel probiotic strain from complex gut samples, but conventional culturing methods failed to recover the low-abundance target.
BaseClear applied its tailored culturomics platform. We first conducted metagenomic profiling, then developed a custom enrichment strategy to recover the target organism, and finally sequenced and fully characterized the isolated strain.
As a result, the client successfully incorporated the novel strain into their probiotic pipeline, ultimately launching a new product that showed promising clinical benefits in gut health trials.
Microbial production strains can often be identified directly from commercial products when sufficient DNA is present and recovered successfully from the sample matrix. BaseClear applies optimized DNA extraction, next-generation sequencing, and bioinformatics workflows to detect microbial signatures and compare recovered sequences against reference databases, enabling species-level and, in some cases, strain-level identification.
Recovery of DNA from detergent and fermentation-derived products requires specialized workflows designed to overcome chemical inhibition and extremely low DNA concentrations. BaseClear evaluates matrix-specific extraction strategies, inhibitor removal chemistries, magnetic bead-based purification methods, and optimized library preparation workflows to maximize the recovery of usable sequencing data from challenging industrial samples.
Sequencing data can reveal microbial species, strain-related genetic markers, and genes associated with industrially relevant functions such as enzyme production. Depending on DNA quality and quantity, analyses may provide insights into production organisms, functional genes, and genetic characteristics that help clients understand the biological technologies used within competing products.
Competitive Product Genomics can be applied to a wide range of industrial samples, including enzyme formulations, fermentation-derived materials, detergents, capsules, powders, liquids, and intermediate production products. The analytical strategy is adapted to the sample matrix to address differences in DNA abundance, degradation, and the presence of compounds that may interfere with DNA recovery or sequencing.
A Competitive Product Genomics project delivers sequencing data, microbial identification results, genetic characterization, and expert interpretation tailored to the client’s objectives. Depending on the project scope, deliverables may include raw sequencing data, taxonomic profiles, identification of production organisms, analysis of enzyme-encoding genes, comparative assessments, and a comprehensive report summarizing the key competitive insights generated from the analysis.
Genomic analysis to identify antimicrobial resistance genes and support
Evaluation of biologically active metabolites to assess functional and toxicological risks
Demonstration of absence of viable cells and recombinant DNA in final products for regulatory compliance
Integration of MIC, genomic, and safety data into a submission-ready regulatory dossier
Get expert guidance on MIC testing, interpretation, and regulatory strategy to avoid delays in your submission. Start with a free consultation tailored to your project.
