Metagenomics Adoption in EFSA Risk Assessment

European Food Safety Authority (EFSA) tender to procure scientific and technical services to develop harmonised laboratory and bioinformatics metagenomics protocols and analytical frameworks for regulatory risk assessment of complex microbial mixtures. Estimated contract value €1,250,000, duration 24 months, awarded as a direct service contract. Evaluation weighting is quality 70% and price 30% and submission is electronic via the EU Funding & Tenders Portal with deadline 12 August 2026 14:30:59 CEST. Eligible applicants are legal entities or consortia with demonstrated metagenomics, bioinformatics and regulatory risk assessment expertise; consult the tender documents for full specifications and selection criteria.

Opportunity Type

EU tender (EFSA)

Procurement for scientific and technical services to develop harmonised laboratory and bioinformatics metagenomics protocols and analytical frameworks for regulatory risk assessment of complex microbial mixtures, and to provide recommendations for integrating metagenomics into EFSA workflows ¹.

Estimated contract value and duration:Total estimated amount €1,250,000; planned implementation period 24 months.

1. 1Who can apply: legal entities or consortia able to provide scientific, laboratory and bioinformatics services (research organisations, specialised laboratories, consultancies with relevant expertise).
2. 2Lead contracting authority: European Food Safety Authority (EFSA).
3. 3Submission method: electronic submission via the Funding & Tenders Portal (eSubmission).

Award criteria weightings emphasise quality (70) and price (30). See tender documents for detailed requirements, deliverables and selection criteria ¹.

Footnotes

1. 1Tender details and documents are available on the Funding & Tenders Portal: Tender page.

Opportunity Identification and Administrative Data

Basic Reference and Links

Call identifier EFSA/2026/OP/0009. Published on 2026-05-19. Tender type:procurement for services (contract nature: services, CPV 73000000). Lead contracting authority: European Food Safety Authority (EFSA) EFSA homepage. Full tender dossier and documents are available from the EU Funding & Tenders Portal tender-details page (primary URL provided in the published record) EU Funding & Tenders Portal opportunity ¹.

Estimated Contract Value:The estimated overall contract amount is €1,250,000 for the full duration of the contract.

Planned Duration:Planned period 24 months (tender validity period specified as 9 months for tenderers).

Deadlines and Key Dates

Two dates appear in the raw metadata:an initial deadline entry 2026-01-01T12:30:59.000Z and the official closing date published in the tender record 2026-08-12T14:30:59+00:00. The published and authoritative submission deadline for eSubmission is 12 August 2026 at 14:30:59 (CEST/CET depending on portal timezone declarations). An open tender event is scheduled for 13 August 2026 at 14:30 (see tender documentation). Additional information request period ends 4 August 2026.

Scope and Objectives

Purpose:to procure scientific and technical support to develop harmonised and standardised metagenomics laboratory protocols and bioinformatics analytical frameworks tailored for regulatory risk assessment of complex microbial mixtures. Deliverables will include establishment and validation of laboratory and bioinformatics methods, preparation of recommendations for integrating metagenomics approaches into EFSA risk assessment workflows, and outputs supporting safety evaluation and future EFSA guidance development.

Work Content and Expected Technical Outputs

The contract will require technical activities across laboratory workflows, sequencing methodologies, quality assurance measures, bioinformatics pipelines, reproducibility assessments, reference material strategies, data interpretation frameworks and reporting templates compatible with regulatory assessment. Outputs are expected to include standard operating procedures (SOPs), validated bioinformatics workflows, benchmarking and sensitivity/specificity analyses, documentation of limitations and uncertainty, recommendations for risk assessment decision points, and integration guidelines for EFSA assessment processes.

Eligible Applicant Types

The tender is a public procurement for services; eligible applicants are legal entities capable of performing the required scientific and technical services. Specifically expected and appropriate applicant types include: research institutes and national reference laboratories, universities and academic centres with metagenomics expertise, contract research organisations (CROs) and specialised analytical laboratories, bioinformatics providers and software houses with regulatory analytics experience, large enterprises and SMEs active in genomics and laboratory services, non-governmental laboratories with accreditation, and consortia combining the above. Public authorities may participate where legally permitted by procurement rules. Individuals cannot be sole contractors unless forming an eligible legal entity or consortium.

Funding Type and Contractual Modality

This is a procurement contract (service contract) awarded following an open tender procedure. The primary financial mechanism is a direct service contract (procurement), not a grant, loan, equity or voucher. The tender dossier includes an Annex Draft Direct Service Contract and tender specifications that will govern payment terms, deliverables, reporting and contract management.

Consortium Requirement and Participation Model

The procurement record indicates a single procurement lot (LOT-0001) and allows submission by tenderers meeting selection criteria. The procurement documentation includes selection and award criteria and accommodates tenderers who may be single legal entities or consortia. The tendering terms include standard qualification requests and specific tenderer requirements indicated in the procurement documents; subcontracting is possible in line with the tender specifications. Tenderers should consult the tender specifications for consortium form (lead partner designation, power of attorney, joint venture statements) and evidence required for members and subcontractors.

Geographic Eligibility and Beneficiary Scope

The contracting authority is EFSA (an EU agency). The call is published on the EU Funding & Tenders Portal and follows EU procurement rules. While the tender record does not list an exclusive country-by-country eligibility list in the scraped fields, standard EU procurement practice for EFSA tenders allows economic operators established in the EU Member States and potentially in countries deemed equivalent under the EU procurement rules; tenderers should check the tender specifications and selection criteria for exact nationality, establishment and exclusion/clawback requirements. In practice likely eligible: EU (Member States) and possibly EEA/third countries as specified in the tender documents.

Target Sector and Thematic Areas

Primary thematic sectors:food safety, microbial risk assessment, metagenomics, laboratory sciences, bioinformatics, regulatory science and biotechnology. Secondary areas: public health surveillance, reference laboratory capacity building, standardisation and methods development, data management and reproducible computational workflows.

Project Stage and Expected Maturity

The contract expects activities across method development, validation and demonstration phases. Expected project maturity: from development and validation through demonstration and preparation for regulatory integration. Work will include experimental method validation and bioinformatics benchmarking rather than basic discovery research.

Funding Amount and Financial Details

Estimated overall contract amount:€1,250,000. The tender specifications and draft contract in the procurement documents define detailed payment schedules, milestone payments, liability, insurance and invoicing rules. The award weighting indicates quality 70% and price 30% as deciding factors in evaluation.

Application and Submission Process

Application method:open eSubmission via the EU Funding & Tenders Portal (submission method code ESUBMISSION is required). The portal eForms and submission tools must be used; the tender record references eforms and Funding and Tenders Portal access. Tenderers must upload required documents (invitation letter, tender specifications, draft contract, requested forms) before the published deadline. An additional information request period ends 4 August 2026, after which clarifications may be consolidated in corrigenda.

Evaluation, Award Criteria and Application Stages

Evaluation uses award criteria split between quality (70%) and price (30%). Quality sub-criteria are detailed in the tender specifications and will cover technical approach, methodology, team competence, relevant experience, workplan, deliverables, data management and quality assurance. Selection criteria and exclusion grounds will follow standard procurement checks (financial and operational capacity, professional and technical ability). The process appears to be a single-stage tender with evaluation of submitted bids against selection and award criteria; there is an open tender event date and the process includes evaluation and contract award. Therefore applicants should plan for one main submission followed by evaluation and then contract award (practical stages: submission, evaluation, possible clarification requests, award).

Number of Application Stages:Effectively 1 main submission stage followed by evaluation and award (described as a single-stage competitive procurement process).

Success Rates and Competition

The tender record does not publish historic success rates. As an open procurement with a single contract lot and an estimated contract value of €1,250,000, the success rate will depend on the number and quality of bids received. No explicit maximum number of awards is indicated; typically one contractor will be awarded the service contract for the lot.

Co-funding and Financial Contribution Requirements

No co-funding from the applicant is required in the manner of grants. The contract is a remunerated service contract: the contracting authority will pay the contractor according to contractual payment terms. Tenderers must account for their costs in the price proposal; no matching funds or co-financing conditions apply other than budgetary and financial capacity requirements specified in the procurement documents.

Submission Templates and Required Documents

The tender record lists three primary documents in the tender dossier:OC Invitation to tender (Invitation letter), Tender specifications (detailed requirements and evaluation criteria), and Annex 2_Draft Direct Service Contract (contract template). Tenderers must consult and complete the forms and templates contained in the tender specifications and eForms package on the Funding and Tenders Portal. Typical required documentation will include: administrative forms (legal entity form, declaration on honour), proof of enrolment/registration, financial capacity statements, professional and technical capacity evidence (CVs, references, similar contracts), technical proposal (methodology, workplan, deliverables), price proposal, consortium agreements or power of attorney for joint bids, and any requested certificates or accreditations. The procurement documents specify precise templates and fillable eForms to be used for submission.

1. 1Download full tender dossier from the Funding & Tenders Portal (Invitation letter, Tender specifications, Draft contract).
2. 2Prepare administrative and selection evidence as required (legal entity, financial statements, declarations).
3. 3Prepare technical proposal addressing SOP development, laboratory validation, bioinformatics pipelines, benchmarking, deliverables, data management and integration recommendations.
4. 4Prepare detailed price schedule consistent with the draft contract payment provisions and explain assumptions.
5. 5If bidding as a consortium, prepare consortium agreement, lead partner designation and powers of attorney, and assign responsibilities for deliverables.
6. 6Submit all documents via eSubmission before 12 August 2026 14:30:59 (portal time).

Technical and Scientific Requirements (summary of expected content)

The technical requirements will be detailed in the Tender specifications and are expected to include: development and harmonisation of laboratory protocols for sample handling, nucleic acid extraction, library preparation and sequencing for complex microbial mixtures; quality control and contamination control measures; design and validation of bioinformatics pipelines for taxonomic and functional profiling; sensitivity and specificity benchmarking using mock communities and reference materials; reproducibility and inter-laboratory comparisons; uncertainty and limits of detection assessments; guidelines for result interpretation in regulatory risk assessment contexts; secure data management, FAIR data principles application and reporting templates; training materials and stakeholder engagement to facilitate EFSA integration and future guidance drafting.

Tenderers should be prepared to demonstrate practical laboratory capacity (including sequencing platforms), bioinformatics competence (pipeline development, containerisation, reproducibility and workflow management), experience with regulatory or standards bodies, previous projects in metagenomics or microbial community analysis, and robust project management and quality assurance systems.

What Applicants Must Verify in Tender Specifications

• Eligibility conditions and permitted nationalities or establishments (check procurement documents for any third-country restrictions).
• Specific exclusion and selection grounds and the documentary evidence required.
• Exact format and content of technical and financial proposals expressed in the tender specifications and eForms.
• Data protection, confidentiality, intellectual property and publication rules in the draft contract.
• Insurance, liability and warranty clauses in the draft direct service contract.
• Subcontracting rules and limits, and rules for consortium submissions.

Mentioned Countries and Geographic References

The tender metadata explicitly names the European Food Safety Authority as contracting authority and references the EU Funding & Tenders Portal. No individual Member States are specified in the scraped content. Geographical eligibility should be verified in the tender specifications, but the scope is EU-centric (EFSA).

Co-funding and Financial Obligations

No co-funding requirement is specified in the tender metadata. The contract is a paid procurement: tenderers propose a price for execution of the work; the awarding authority pays the contracted amount under the contract terms. Tenderers must ensure the price proposal covers all obligations, compliance costs, travel, consumables and deliverables as required.

Summary and Strategic Advice

This open procurement offers a single service contract to deliver harmonised metagenomics methods and bioinformatics frameworks for EFSA risk assessment of complex microbial mixtures. It is aimed at organisations with demonstrable laboratory and bioinformatics expertise and experience in method validation and regulatory contexts. The tender has a clear quality emphasis (70% weighting) meaning technical quality, scientific rigour, workplan credibility and team competence will be decisive alongside competitive pricing. Interested parties should download and study the Invitation to tender, Tender specifications and Draft contract immediately, plan consortium arrangements if multidisciplinary coverage is needed, and prepare a rigorous technical proposal with reproducible computational workflows, inter-laboratory validation strategy and clear integration pathways for EFSA risk assessment workflows. Submit via the Funding & Tenders Portal before 12 August 2026 at 14:30:59 portal time. ¹

Footnotes

1. 1Primary tender page and documents are available via the EU Funding & Tenders Portal opportunity page: ec.europa.eu. Consult the Tender specifications PDF and Draft Direct Service Contract attached to the opportunity for complete legal and technical requirements.

Opportunity Summary and Objectives

This tender seeks scientific and technical support to develop harmonised and standardised metagenomics protocols and analytical frameworks for the regulatory risk assessment of complex microbial mixtures, specifically focusing on competitive exclusion products ¹. The project aims to establish laboratory and bioinformatics methods and produce recommendations for integrating metagenomics approaches into EFSA risk assessment workflows to support safety evaluation and future guidance development ².

Key Tasks:Applicants must develop standardised metagenomics workflows from sample to safety assessment, including sample preparation, sequencing, taxonomic characterization, species identification, and relative abundances ¹. Additionally, the project requires establishing a bioinformatics framework to evaluate analytical pipelines, provide recommendations for risk assessment contexts, and define quality control standards ¹.

Contract Details and Financials

The estimated overall contract amount is €1,250,000, covering a planned period of 24 months ³. The contract is a direct service agreement, and the tender validity period is 9 months ³.

Eligibility and Award Criteria

Tenders will be evaluated based on quality (70% weight) and price (30% weight), with quality criteria focusing on the technical merit and feasibility of the proposed metagenomics protocols and bioinformatics frameworks ³. Applicants must consult the procurement documents for specific selection criteria and tenderer requirements ³.

Required Expertise:Successful applicants must demonstrate expertise in metagenomics, bioinformatics, and regulatory risk assessment, with the ability to implement safety genomic screening for pathogen identification, antimicrobial resistance (AMR) genes, and virulence factors ¹.

Application Process and Resources

1. 1Read the full call for tenders and tender specifications on the EU Funding & Tenders Portal EFSA Tender Portal
2. 2Review the EFSA guidance for tenderers and complete the required forms in the instructions for tendering ⁴
3. 3Submit your proposal electronically via the EU Funding & Tenders Portal before the deadline of 12 August 2026 ⁴
4. 4Contact EFSAProcurement@efsa.europa.eu for specific questions regarding the procurement process ⁴

The submission method is electronic (esubmission), and all procurement documents, including the invitation letter and draft contract, are available on the portal ³. Questions can be submitted through the EU Funding and Tenders Portal until 4 August 2026 ³.

Footnotes

1. 1EFSA Funding Opportunities 2026-27 Master File, detailing the objective and tasks for the Adoption of metagenomics approaches for risk assessment EFSA Master File.
2. 2EU Funding & Tenders Portal tender description for Metagenomics Adoption in EFSA Risk Assessment EU Portal.
3. 3Tender specifications and procurement lot details including contract amount, duration, and award criteria EU Portal Lot Details.
4. 4EFSA Procurement page listing the call for tenders and submission instructions EFSA Procurement.