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Food, Feed & Ingredients

From strain discovery and microbiome research to regulatory safety assessment, BaseClear provides food, feed, and ingredient companies with the genomic insights and scientific evidence needed to develop, validate, and commercialize innovative products with confidence.

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Driving Innovation in Food, Feed & Ingredients

Food, feed, and ingredient innovation increasingly relies on a deep understanding of microorganisms, microbial functions, and product safety. BaseClear helps organizations translate complex microbial data into actionable insights through integrated genomics, microbiome analysis, strain characterization, and regulatory support.

From strain discovery and microbiome research to microbial safety assessment and regulatory dossier generation, BaseClear provides end-to-end scientific solutions that accelerate product development, support market approval, and reduce technical risk. Our combination of laboratory expertise, advanced sequencing technologies, bioinformatics, and regulatory knowledge makes us a trusted partner for companies developing the next generation of food, feed, and ingredient products.

How we support you

Microbial Safety Assessment & Regulatory Services

Microbial Safety Assessment & Regulatory Services help food, feed, and ingredient companies generate the scientific evidence required to demonstrate the safety of microbial strains, products, and ingredients. This service cluster is designed for organizations seeking regulatory approval, supporting applications such as EFSA, FDA, Novel Foods, feed additives, probiotics, postbiotics, and microbial-based ingredients through integrated testing, genomics, and regulatory expertise.

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Microbiome Research

Microbiome Research services help organizations understand the composition, function, and biological impact of microbial communities across clinical, consumer health, food, feed, and environmental applications. This service cluster is designed for biotechnology companies, food and ingredient developers, pharmaceutical organizations, and academic researchers seeking actionable insights through microbiome sequencing, bioinformatics, and advanced data analysis.

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Strain Discovery

Strain Discovery services help organizations identify, isolate, and characterize novel microorganisms with valuable functional properties for food, feed, biotechnology, agricultural, and pharmaceutical applications. This service cluster is designed for companies and researchers seeking proprietary microbial strains, supported by advanced culturomics, genome sequencing, genome mining, and functional characterization.

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Sterility Testing

We perform comprehensive sterility testing according to applicable regulatory standards to verify the absence of contaminating microorganisms in clean rooms, pharmaceutical products, biologics, medical devices, and other sterile materials.

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MIC Testing for Antimicrobial Resistance Assessment

Minimum Inhibitory Concentration (MIC) testing determines whether a microbial production strain exhibits resistance to clinically relevant antimicrobials. BaseClear performs standardized broth microdilution testing according to CLSI guidelines and interprets results against EFSA cut-off values to support microbial safety assessments and regulatory submissions for food enzymes, feed additives, probiotics, and novel foods.

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Assessment of the Presence of Viable Cells in Microbial Products

Assessment of the presence of viable cells demonstrates whether living production organisms remain present in a final product. BaseClear develops and validates strain-specific detection methods using optimized culture conditions and molecular confirmation techniques to generate the evidence required for EFSA and other regulatory submissions involving food enzymes, feed additives, fermentation products, and other microbial-derived ingredients.

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Taxonomic Profiling Using Amplicon & WGS Sequencing

Taxonomic Profiling identifies and quantifies the microorganisms present in a sample, providing detailed insights into the composition and diversity of microbial communities. BaseClear offers both targeted amplicon sequencing (16S rRNA and ITS) and shotgun metagenomic sequencing to characterize bacteria, archaea, fungi, and other microorganisms across clinical, food, feed, environmental, and industrial microbiome studies.

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Assessment of the Presence of DNA in Final Products

Assessment of the Presence of DNA determines whether residual genetic material from a production organism remains detectable in a final product. BaseClear develops sensitive PCR-based assays targeting strain-specific or gene-specific sequences to demonstrate the absence of detectable DNA within validated limits, supporting regulatory submissions for food enzymes, feed additives, fermentation products, and other microbial-derived ingredients.

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Antimicrobial production Testing for Microbial Safety

Antimicrobial activity testing evaluates whether a microbial strain produces compounds that inhibit the growth of other microorganisms. This is a key component of microbial safety assessment, as antimicrobial metabolites may impact microbiota or contribute to the spread of antimicrobial resistance. BaseClear provides standardized antimicrobial activity testing using culture supernatants or final products to detect biologically active compounds.

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In Vitro Cytotoxicity Testing for Microbial Toxigenicity Assessment

In vitro cytotoxicity testing is used to evaluate whether microbial strains produce biologically active compounds that may have harmful effects on mammalian cells. In line with EFSA guidance on the characterisation of microorganisms used in the food chain, cytotoxicity testing is applied to assess toxigenic potential, particularly for strains where genomic analysis indicates the presence of biosynthetic gene clusters, virulence factors, or other risk indicators.

 

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Regulatory Strategy & Dossier Development

Regulatory Strategy & Dossier Development helps companies navigate complex regulatory requirements and generate the scientific evidence needed for successful product approval. BaseClear supports clients from the earliest stages of regulatory planning through dossier preparation and post-submission support, translating regulatory expectations into a clear, actionable development roadmap. The service is designed to reduce regulatory uncertainty, identify data requirements early, and ensure that studies are aligned with the expectations of authorities such as EFSA, FDA, NHC, and other global regulatory agencies.

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Whole Genome Sequencing for Microbial Safety Assessment

WGS is a key requirement for the safety assessment of microbial production strains used in food, feed, and biotechnology applications. BaseClear delivers high-quality WGS integrated with advanced bioinformatics analysis to enable comprehensive genome characterization, including taxonomic identification, genetic modification (GM) confirmation, and the detection of genes of concern such as antimicrobial resistance (AMR), virulence factors, toxins, and mobile genetic elements.

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Clinical Microbiomics

BaseClear provides clinical microbiome sequencing services for studies that need reliable stool DNA extraction, high-throughput sequencing, documented quality control, and secure data delivery. The service can cover the full workflow from sample collection advice and sample receipt through DNA extraction, library preparation, sequencing, run QC, technical reporting, and data package release.

 

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Functional Metagenomics Analysis

Functional metagenomics analysis goes beyond identifying which microorganisms are present in a sample by revealing what those microorganisms are capable of doing. Using shotgun metagenomic sequencing data, BaseClear reconstructs metagenomes, predicts genes, and annotates biological functions to characterize the metabolic potential of microbial communities. This enables researchers to investigate functional pathways, carbohydrate metabolism, antimicrobial resistance genes, virulence factors, and other biological mechanisms that may influence health, disease, product performance, or environmental processes.

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Key Microbial Biomarker Detection

Key Microbial Biomarker Detection is a specialized microbiome analysis service that identifies microbial species, genes, pathways, or microbial signatures associated with specific phenotypes, health conditions, treatment responses, or product performance. By analyzing complex microbiome datasets, BaseClear helps clients uncover biologically relevant biomarkers that can support scientific discovery, product development, diagnostics, patient stratification, and personalized interventions.

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Microbiome-Friendly Assessment

Microbiome-Friendly Assessment is a scientific testing service that evaluates whether a product, ingredient, or formulation significantly alters the composition and diversity of the microbiome. Using microbiome sequencing and advanced bioinformatics, BaseClear determines whether microbial communities remain stable and balanced following product exposure. This enables companies to substantiate microbiome-friendly claims with objective, data-driven evidence and gain a deeper understanding of how their products interact with the microbiome.

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RNA-Seq Analysis

RNA-Seq analysis is a powerful transcriptomics approach used to measure and compare gene expression levels across biological samples. By sequencing RNA molecules, researchers can determine which genes are actively expressed, quantify transcript abundance, and identify changes in gene expression under different conditions. BaseClear offers RNA-Seq analysis for both bacterial and eukaryotic samples, supporting applications such as functional genomics, strain characterization, pathway analysis, host response studies, product development, and biomarker discovery. De novo transcriptome assembly is not part of this service; analyses are performed against a reference genome provided by the customer.

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Competitive Product Genomics

Competitive Product Genomics is a sequencing-based service that enables the identification of microbial production strains, enzyme-encoding genes, and other genetic signatures present in commercial products. By recovering and analyzing trace amounts of DNA from complex industrial matrices, BaseClear helps clients gain insights into the microorganisms and biotechnology platforms used in competitor products. The service is specifically designed for samples where microbial DNA is present at very low concentrations and may be masked by challenging formulation components such as detergents, surfactants, enzymes, salts, and stabilizers.

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Why Food, Feed & Ingredient Innovators Choose BaseClear

Established Since 1993

For more than 30 years, BaseClear has supported food, feed, and ingredient innovators with microbial genomics, sequencing, and safety assessment services. This long-standing expertise enables clients to make confident development and regulatory decisions based on scientifically robust data.

Regulatory-Ready Quality

BaseClear operates under ISO 17025 accreditation and offers GMP-compliant services for selected workflows, ensuring high standards of quality, traceability, and data integrity. Clients receive structured, regulatory-ready reports designed to support EFSA and other global regulatory submissions.

End-to-End Microbial Expertise

From strain discovery and whole genome sequencing to microbiome research, AMR assessment, viable cell testing, and DNA detection, BaseClear provides a complete portfolio of microbial safety and characterization services under one roof. This integrated approach reduces project complexity, accelerates timelines, and ensures consistency from discovery through regulatory approval.

Proven Expertise

ISO17025

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Number of Regulatory Projects

Ready to support your food safety submission

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