BaseClear
BaseClear is a Dutch contract research laboratory specializing in microbial genomics and DNA-based analysis, serving enterprise clients in pharmaceutical, food and beverage, personal care, animal health, and academic research sectors since 1993.
- Company typePrivate
- Founded1993
- HeadquartersLeiden, Netherlands
- Headcount51–100
- GTM typeB2B
- OfferingServices
What BaseClear does
BaseClear B.V. is a Dutch contract research laboratory specializing in microbial genomics and DNA-based analysis, founded in 1993 and headquartered in Leiden, Netherlands, with additional sites on Galileiweg and a PO Box address in the same city. The company serves enterprise clients in pharmaceutical, food and beverage, personal care, animal health, and academic research with a portfolio built around three service pillars: sequencing (Illumina, Oxford Nanopore, Sanger, whole genome), microbiome analysis and bioinformatics (metagenomics, amplicon profiling, metatranscriptomics, pathogen detection, biomarker discovery), and regulatory affairs and microbiology (strain discovery, safety assessment, EFSA compliance dossiers). GMP-certified testing is delivered through its wholly-owned ProBase Pharma subsidiary, and the company also distributes Zymo Research, Base-Gene, and Kisker Biotech products in Europe.
Technically, BaseClear integrates multiple sequencing platforms with proprietary bioinformatics pipelines, including a shallow-shotgun Infant Microbiome Pipeline with a customized database (Kraken 2/Bracken), low-biomass sample handling using proprietary qPCR-based QC, an AMR gene screening pipeline (CARD/VFDB), and a 2025-launched ML-powered Key Microbiome Pipeline for biomarker discovery using ensemble learning. The team comprises 65+ PhD-level molecular biologists, microbiome specialists, and bioinformatics experts, and the company maintains a 30-year proprietary knowledge base in microbial genomics.
Commercially, BaseClear operates a project-based professional services model priced in euros (orders up to €5,000 invoiced in full on acceptance; orders of €5,000+ require 50% upfront with the balance invoiced after draft report, net 14 days). Go-to-market is sales-led and event-driven: direct enterprise engagement through an online ordering portal and request-quotation workflow, supported by recurring Experts Meetings, webinars, scientific content, and conferences. Named customers include Abbott Biologicals, DSM, Reckitt Benckiser, Danone, IFF, Lesaffre, Jennewein Biotechnologie, CHDR, and Wageningen University. The company is privately held (B.V.), with no disclosed external funding or M&A activity.
BaseClear firmographics
Firmographics- Name
- BaseClear
- Legal name
- BaseClear B.V.
- Website
- https://baseclear.com
- Company type
- Private
- Founded year
- 1993
- Operating status
- Operating
- Headcount range
- 51–100 employees
- Short description
- BaseClear is a Dutch contract research laboratory specializing in microbial genomics and DNA-based analysis, serving enterprise clients in pharmaceutical, food and beverage, personal care, animal health, and academic research sectors since 1993.
- Ownership category
- akta.pro rank
BaseClear industry classification
Industry- Product category
- Contract Research Laboratory Services
- NAICS
- Research and Development in Biotechnology (except Nanobiotechnology) (541714)
- SIC
- Services-Commercial Physical & Biological Research (8731)
- akta.pro primary industry
- Microbiome Analytics, Sequencing & Bioinformatics Platforms (HLAAAFAI)
- akta.pro secondary industries
- Molecular Biology & Genomics Instruments (PCR/qPCR, Sequencing, Microarrays) (HLAGAIAF), Microbiology & Infectious Disease Diagnostics (culture, rapid antigen, syndromic panels) (HLAAALAC)
Keywords
Where BaseClear is headquartered
LocationHeadquarters
- HQ city
- Leiden
- HQ country
- Netherlands
- HQ region
- Europe
Offices3 records
Markets served
BaseClear business model
Business model- GTM type
- B2B
- Offering type
- Services
- Cost components
- Personnel, Technology or R&D, Operations, Marketing or Sales, Infrastructure, Supply Chain
Revenue model
- Laboratory Services - Sequencing: BaseClear provides comprehensive sequencing services including Next-Generation Sequencing (Illumina, Nanopore), Whole Genome Sequencing, and Sanger sequencing. These services are delivered as project-based engagements with GMP and non-GMP options.
- Microbiome Analysis & Bioinformatics: Turnkey microbiome analysis services including study design consultancy, sampling solutions, DNA/RNA extraction, sequencing, and downstream bioinformatics and biostatistical analysis. Delivered as project-based professional services.
- Regulatory Affairs & Microbiology: Regulatory affairs services including GMM dossier preparation, novel food applications, EFSA compliance, and safety assessment dossiers. Microbiology services include strain discovery, safety assessment, and product IP & regulatory scoping.
- Microbial Identification & Quality Testing: Rapid microbial identification services using MicroSEQ and MALDI-TOF, microbial strain typing, cell line characterization, mycoplasma detection, and adventitious agents testing. GMP-certified options available for pharmaceutical quality control.
- Lab Products Distribution: Distribution of third-party lab products including Zymo Research (sample collection, DNA/RNA purification, epigenetics, microbiomics), Base-Gene, and Kisker Biotech products.
Pricing tiers
| Model | Billing | Price |
|---|---|---|
| Other | Pay-as-you-go | Project-based laboratory services |
Go-to-market motion3 records
Distribution channels4 records
Marketing channels6 records
BaseClear product offering
Product offeringCore offering
BaseClear is a contract research laboratory specializing in microbial genomics and DNA-based analysis. The company delivers sequencing services (Illumina, Nanopore, Sanger, whole genome), comprehensive microbiome analysis with bioinformatics, microbial identification and quality control testing, and regulatory affairs support covering safety assessment and EFSA/FDA/EMA compliance for food, pharmaceutical, personal care, and animal health clients.
Product overview
BaseClear is a microbial genomics contract research organization established in 1993, offering a comprehensive portfolio of laboratory services organized around three core pillars: (1) Sequencing Services covering Illumina and Nanopore next-generation sequencing, whole genome sequencing, and Sanger sequencing; (2) Microbiome Analysis & Bioinformatics including shotgun metagenomics, amplicon profiling, metatranscriptomics, and the newly launched ML-powered Key Microbiome Pipeline for biomarker discovery; and (3) Regulatory Affairs & Microbiology providing safety assessments, strain discovery, and EFSA compliance support. The company also operates ProBase Pharma as its GMP-certified brand for rapid molecular testing and quality control. Additional offerings include distributed lab products from Zymo Research, Base-Gene, and Kisker Biotech. Results are delivered through BaseClear's proprietary Genome Explorer online portal.
Differentiator
Problem solved
Functional benefit
Products and services
- Next-Generation Sequencing Services Illumina and Nanopore next-generation sequencing services for microbial genomics applications, including real-time qPCR services, targeted at pharma, food, personal care, and academic clients requiring high-resolution microbial DNA analysis.
- Whole Genome Sequencing Complete microbial genome sequencing service providing finished genome assemblies for bacteria, yeast, and other microorganisms for research and industrial clients.
- Sanger Sequencing Traditional capillary DNA sequencing for validation, verification, and confirmation of genetic material, including plasmid/viral vector verification and cell line identity confirmation.
- ProBase Pharma (GMP Sequencing & Quality Control) GMP-certified DNA-based quality control testing for raw materials, process intermediates, and finished products in food and pharmaceutical industries, offered under the ProBase Pharma brand.
- Microbiome Analysis & Bioinformatics Comprehensive microbiome analysis including shotgun metagenomics, 16S/ITS amplicon profiling, (meta)transcriptomics, pathogen detection, comparative genomics, RNA-seq analysis, and key microbial biomarker detection with interactive data visualization through the Genome Explorer portal.
- Infant Microbiome Pipeline Specialized shallow shotgun sequencing pipeline with a customized infant microbiome database providing strain-level abundance profiles across multiple microbial kingdoms (bacteria, fungi, archaea, viruses) for infant nutrition and health research clients.
- Key Microbiome Pipeline (ML-powered Biomarker Discovery) Machine learning-powered bioinformatics service for identifying microbial biomarkers linked to disease states or treatment responses in clinical trials, using ensemble ML frameworks combining support vector machines, random forest classifiers, and clustering algorithms.
- Microbial Identification Services Rapid molecular identification of bacteria and fungi using qPCR, DNA sequencing, and MALDI-TOF technology, including the FDA- and EMA-endorsed MicroSEQ system, with results delivered in 1-3 working days.
- Regulatory Affairs & Microbiology Services Comprehensive regulatory support including novel strain discovery, safety assessment, product IP scoping, EFSA compliance dossier preparation, GMM dossier preparation, novel food applications, and antimicrobial susceptibility (MIC) testing.
- Antimicrobial Resistance (AMR) Analysis Whole-genome shotgun metagenomics pipeline for characterizing antibiotic resistance genes using CARD and VFDB databases, with EFSA AMR compliance testing including WGS-based AMR gene screening, MIC testing, and antimicrobial production analysis.
- Human Gut Microbiome Analysis Complete gut microbiome analysis including sampling logistics, DNA/RNA extraction, shotgun metagenomics, and biostatistical analysis for clinical trials, probiotic development, and human health research.
- Skin Microbiome Analysis Species-level taxonomic profiling for skin and low-biomass samples using shotgun metagenomics with proprietary qPCR-based QC assessment, supporting personal care product development and microbiome-friendly claims.
- Animal Microbiome Analysis Complete microbiome analysis services for various animal species including swine, poultry, aquaculture, and ruminants, covering feed efficiency, gut health, antimicrobial resistance monitoring, and probiotic development.
- Methane Metabolism & Antimicrobial Screening In-house methane metabolism pipeline for analyzing gut microbiome function and screening for antimicrobial compounds, particularly relevant to ruminant agriculture and climate research.
- Lab Products Distribution (Zymo Research, Base-Gene, Kisker Biotech) Authorized European distribution of Zymo Research products (sample collection, DNA/RNA purification, epigenetics, microbiomics), Base-Gene, and Kisker Biotech laboratory products.
Quantifiable outcome
- Delivery time of 1-3 working days for microbial identification using MALDI-TOF
- +4 more outcomes
Companies that use BaseClear
Customer profileNamed customers11 records
Segments8 records
Ideal customer profiles4 records
BaseClear technology and API
TechnologyTechnology focussed Yes
API detail
- Has API
- No
- API docs
- API detail
Core technology
AI maturity
App detail
AI capability3 records
Feature8 records
BaseClear partnerships and signals
Strategic signalPartnerships
16 partnerships are on record, tiered core, strategic and minor.
- DanonecoreDr. Kaouther Ben Amor, Senior Team Leader Probiotics at Danone, spoke at BaseClear's Infant & Pregnancy Microbiome Experts Meeting. Danone conducted clinical trials on C-section infant microbiome restoration using pre- and probiotic mixtures.
- Oxford Nanopore TechnologiescoreCollaborative partnership to scale Oxford Nanopore sequencing capacity for microbial insights. BaseClear worked with Oxford Nanopore to develop future-ready long-read sequencing services supporting advanced microbial discovery for complex projects like soil metagenomics.
- Center for Human Drug Research (CHDR)coreCHDR collaborates with BaseClear for skin and gut microbiome analysis in clinical trials. BaseClear is involved from project application through study design, providing technical, scientific, and logistical support. Partnership includes sampling logistics with barcode-labeled tubes and bioinformatics collaboration.
- DSM Nutritional ProductscoreCollaboration between BaseClear and DSM scientists to advance sequencing technologies and microbiome research. Dr. Riccardo Sfriso from DSM participated in interviews on skin microbiome trends, and BaseClear provides state-of-the-art microbiome analyses for DSM's personal care product development.
- ARTIS MicropiastrategicBaseClear partnered with Micropia ARTIS on the 'Primate Rewilding Project' to understand and identify primate gut microbiome, carbohydrate pathway analysis, and link to high-fibre natural diet. BaseClear led the genomics perspective including study design, sampling collection, and analysis.
- Vrije UniversitystrategicPartnership with Prof. Remco Kort from Vrije University on the Primate Rewilding Project. Vrije University provided the foundational database for primate gut microbial genomics that BaseClear built upon.
- Zymo ResearchcoreBaseClear is an authorized distributor of Zymo Research products in Europe, offering sample collection & preservation, DNA/RNA purification, epigenetics, microbiomics, E.coli, and yeast products.
- Base-GeneminorBaseClear offers Base-Gene products as part of their lab product offerings.
- Kisker BiotechminorBaseClear distributes Kisker Biotech products as part of their lab product portfolio.
- Reckitt BenckisercoreDr. Maciej Chichlowski from Reckitt Benckiser participated in expert meeting on infant microbiome hosted by BaseClear. Discussion focused on role of nutrition in infant microbiome development and collaboration on preclinical studies involving microbiome in pediatric nutrition.
- Jennewein BiotechnologiestrategicDr. Katja Parschat from Jennewein spoke at BaseClear's expert meeting on Human Milk Oligosaccharides (HMOs) as functional food ingredients. Active in infant nutrition and microbiome research collaboration.
- Wageningen UniversitystrategicDr. Clara Belzer from Wageningen University presented at BaseClear's expert meeting. Academic collaboration on microbiome research including gut-brain axis and early infant microbiome development.
- University of HelsinkistrategicDr. Katri Korpela from University of Helsinki presented research on effects of birth mode and antibiotics on mother-infant microbiome at BaseClear's expert meeting.
- UMCG (University Medical Center Groningen)strategicDr. Marijke Faas from UMCG presented research on gut microbiome and immune changes during pregnancy at BaseClear's expert meeting.
- Quadram Institute BiosciencesstrategicDr. Steve James from Quadram Institute Biosciences presented on infant gut mycobiome at BaseClear's expert meeting on infant and pregnancy microbiome.
- RB/Mead Johnson NutritioncoreDr. Maciej Chichlowski from RB/Mead Johnson Nutrition presented on 'healthy' gut microbiome at BaseClear's expert meeting. Active collaboration on infant nutrition and microbiome research.
Scale indicators3 records
Recent moves6 records
Expansion highlights6 records
BaseClear competitors and assessment
Company assessmentDirect peers
- CosmosID: CosmosID provides commercial microbiome analytics services using proprietary sequencing-based microbial identification and bioinformatics pipelines. It directly competes with BaseClear in shotgun metagenomics, AMR gene screening, and microbiome bioinformatics for pharmaceutical, food, and consumer health customers.
- Diversigen (OraSure Technologies): Diversigen is a US-based microbiome services provider offering 16S, shotgun metagenomics, and bioinformatics for pharma, nutrition, and academic clients. It is a direct competitor to BaseClear's microbiome analysis pipeline, with overlapping technology stack and target customers.
- Microsynth: Microsynth is a European (Switzerland/Germany/Austria) contract genomics provider offering Sanger, NGS, and custom sequencing services. It competes with BaseClear for European biotech and academic sequencing projects with similar turnaround expectations and service-level positioning.
- MR DNA (Molecular Research LP): MR DNA is a US-based molecular research lab specializing in 16S, shotgun metagenomics, and environmental microbiome sequencing. It is a direct competitor to BaseClear's microbiome services, particularly for agricultural, environmental, and animal health microbiome projects.
Broad incumbents
- QIAGEN (Genomics Services): QIAGEN offers genomic services and bioinformatics tools for microbial typing, microbiome analysis, and pharmaceutical QC. It competes with BaseClear's microbial identification and metagenomics work while also supplying the underlying sample-prep and analysis tools used by many microbiome researchers.
- Eurofins Genomics: Eurofins Genomics is the sequencing services arm of Eurofins Scientific, one of the world's largest testing services groups. It offers Sanger, NGS, and synthesis services globally, overlapping with BaseClear's sequencing portfolio while operating at substantially larger scale across multiple service lines beyond microbial genomics.
- LGC Group (Genomics Division): LGC Group operates a genomics division offering Sanger, NGS, and genotyping services alongside its standards and measurement science business. It competes with BaseClear for European sequencing and microbial identification work, particularly in regulated industries.
- Charles River Laboratories: Charles River Laboratories is a large preclinical CRO offering microbial identification, cell line characterization, and GMP testing services. Its microbial solutions overlap with BaseClear's ProBase Pharma GMP offerings while serving broader biopharmaceutical development needs.
Emerging players
- Zymo Research: Zymo Research manufactures sample collection, DNA/RNA purification, and microbiome kits, and is a key supplier whose products BaseClear distributes in Europe. Zymo is also expanding into service offerings, making it both a partner and an emerging competitor in microbiome analysis services.
- Second Genome (now part of Pfizer): Second Genome is a microbiome drug discovery and services company using metagenomics and bioinformatics to identify therapeutic targets. It overlaps with BaseClear's ML biomarker discovery and clinical trial microbiome services, particularly for pharma-sponsored studies.
Market position
Strengths5 records
Weaknesses5 records
Competitive moat6 records
Key risks6 records
Key highlights7 records
Customer concentration
BaseClear social profiles
Digital presenceBaseClear compliance and trust
Trust signalCompliance3 records
BaseClear financial estimates
Financial estimateRevenue estimate
Valuation estimate
BaseClear leadership team
Management profileNumber of profiles
Profiles10 records
BaseClear subsidiaries and ownership
Company hierarchySubsidiaries1 record
BaseClear funding detail
Funding detailFunding overview
Funding rounds
Investors
Funding detail is available on the Subscription and Enterprise plan.Contact sales →
BaseClear M&A and investment
M&A and investmentM&A
Investments
M&A and investment is available on the Subscription and Enterprise plan.Contact sales →
Frequently asked questions about BaseClear
What does BaseClear do?
BaseClear is a contract research laboratory specializing in microbial genomics and DNA-based analysis. The company delivers sequencing services (Illumina, Nanopore, Sanger, whole genome), comprehensive microbiome analysis with bioinformatics, microbial identification and quality control testing, and regulatory affairs support covering safety assessment and EFSA/FDA/EMA compliance for food, pharmaceutical, personal care, and animal health clients.
Is BaseClear a public or private company?
BaseClear is a private company. It is classified as founder individual operated bootstrapped and is currently operating.
When was BaseClear founded?
BaseClear was founded in 1993. It employs 51 to 100 people.
Where is BaseClear based?
BaseClear is headquartered in Leiden, Netherlands, in the Europe region.
How does BaseClear make money?
Five revenue lines are on record. Laboratory Services - Sequencing is the primary driver. The others are microbiome Analysis & Bioinformatics, regulatory Affairs & Microbiology, microbial Identification & Quality Testing and lab Products Distribution.
Who are BaseClear's main competitors?
Direct peers on record are CosmosID, Diversigen (OraSure Technologies), Microsynth and MR DNA (Molecular Research LP). Broad incumbents are QIAGEN (Genomics Services), Eurofins Genomics, LGC Group (Genomics Division) and Charles River Laboratories. Emerging players are Zymo Research and Second Genome (now part of Pfizer).
Does BaseClear have an API?
No public API is recorded for BaseClear.
What industry is BaseClear in?
BaseClear's product category is Contract Research Laboratory Services. Its primary akta.pro industry code is HLAAAFAI, Microbiome Analytics, Sequencing & Bioinformatics Platforms, with a secondary code of HLAGAIAF, Molecular Biology & Genomics Instruments (PCR/qPCR, Sequencing, Microarrays). Its NAICS code is 541714 and its SIC code is 8731.