Tailored culturomics with environmental sourcing and genome mining to uncover novel strains and their valuable functions.
Nature is a rich source of microbial diversity, providing genes, enzymes, metabolites, and other biomolecules with potential applications across food processing, enzymatic innovations, pharmaceuticals, and biofuels. While metagenomic analysis reveals vast microbial communities, only a fraction of these microorganisms can currently be cultured and studied in the lab. BaseClear’s advanced culturomics approaches are designed to access this “microbial dark matter,” expanding the pool of not yet cultured or difficult-to-culture microorganisms.
Genomics and culturomics strengthen each other by combining high-quality genome data with robust microbial cultivation. Culturomics generates large numbers of pure isolates for accurate genomic analysis, while genomics helps unlock previously uncultivable microbes by predicting their nutritional and environmental growth requirements.
Together, these approaches—enhanced by AI—accelerate the discovery, cultivation, and functional characterization of microbial diversity.
BaseClear offers a comprehensive strain discovery workflow to culture and identify novel microbial isolates. Our platform is used for culturing of microorganism from environmentally sourced samples with identification and whole genome sequencing to discover strains with valuable functional properties, supporting applications in food fermentation, probiotics, agriculture, industrial biotechnology, and pharmaceuticals. High-throughput culturing and rapid genomic analysis significantly accelerate the discovery process, enabling the development of proprietary microbial collections and unique strains with distinctive physiological and metabolic capabilities.
From sample collection and nucleic acid extraction to sequencing, bioinformatics, and interpretation, BaseClear performs the complete microbiome workflow in-house. This minimizes handoffs, improves data consistency, and provides clients with a single accountable partner throughout their project.
BaseClear offers a broad portfolio of microbiome services, including taxonomic profiling, functional metagenomics, transcriptomics, biomarker discovery, and microbiome-friendly testing. This allows clients to select the most appropriate analytical approach for their scientific, clinical, or product development objectives.
Our team of scientists and bioinformaticians applies validated analysis pipelines, machine learning, and statistical modeling to transform complex sequencing data into actionable biological insights. Clients benefit from robust taxonomic classification, functional pathway analysis, biomarker identification, and intuitive reporting.
Using both amplicon sequencing and deep shotgun metagenomics, BaseClear delivers species- and strain-level microbial characterization across bacteria, archaea, fungi, viruses, and other eukaryotes. This provides a comprehensive and unbiased view of microbial communities that supports research, product development, and clinical studies.
ISO17025
Publications
[Metric label]
[Metric label]
BaseClear offers microbiome analysis services including taxonomic profiling, functional metagenomics, transcriptomics (RNA-seq and metatranscriptomics), microbial biomarker discovery, and microbiome-friendly testing. Depending on the research question, we can apply amplicon sequencing, shotgun metagenomics, or transcriptomics workflows combined with advanced bioinformatics analysis to generate actionable biological insights.
Amplicon sequencing targets specific genetic markers such as the 16S rRNA gene or ITS regions, while shotgun metagenomics sequences all DNA present in a sample. Amplicon sequencing is a cost-effective method for profiling microbial composition, whereas shotgun metagenomics provides higher taxonomic resolution and enables functional analysis of bacteria, archaea, fungi, viruses, and other microorganisms in a single dataset.
BaseClear uses validated bioinformatics workflows and machine learning approaches to identify microbial biomarkers associated with health, disease, treatment response, or product performance. By combining statistical analysis with microbiome sequencing data and metadata, we help researchers uncover microbial signatures that can support patient stratification, product claims, and scientific discovery.
BaseClear performs the complete microbiome workflow in-house, from sample processing and sequencing to bioinformatics and reporting. This integrated approach, combined with laboratory automation, standardized quality controls, secure data management, and experienced scientists and bioinformaticians, ensures consistent and reliable results across projects.
BaseClear can analyze a wide range of microbiome sample types, including human, animal, environmental, food, feed, and industrial samples. Our workflows are optimized for different sample matrices and research objectives, enabling clients to investigate microbial diversity, functional potential, gene expression, and microbiome changes across diverse applications.
Identify genetic elements of concern, including AMR and toxin-related genes
Demonstrate absence of living production organisms using validated culture-based methods
Evaluate functional and toxigenic risks associated with microbial metabolites
Aenean porta velit id sem euismod eleifend. Praesent eget dignissim quam. Nulla lacinia leo nec massa dictum, sed lacinia neque posuere. Aenean porta velit id sem euismod eleifend. Praesent eget dignissim quam.
