RFQ 1232SA26Q0300.pdf

Metagenomic or Shotgun Sequencing

1232SA26Q0300

Description

This is a combined synopsis/solicitation for commercial items prepared in accordance with the format in FAR Part 12. This announcement constitutes the only solicitation; offers are being requested, and a separate written solicitation will not be issued.

Solicitation number 1232SA26Q0300 is issued as a Request for Quotation (RFQ) for Metagenomic or Shotgun Sequencing.

This acquisition is set-aside for small business concerns. This solicitation incorporates provisions and clauses by reference. The full text of provisions and clauses may be accessed electronically at www.acquisition.gov.

The applicable North American Industry Classification Standard Code is 541380 Testing Laboratories and Services The small business size standard is $19M This acquisition is a Total Small Business Set-Aside. All responsible sources may submit a quotation which will be considered by the agency.

See “RFQ 1232SA26Q0300” for applicable clauses, instructions, and evaluation criteria.

Statement of Requirement

1) ERRC scientists will send extracted DNA from bacterial pellets to be shipped overnight on dry ice for shotgun sequencing. Bacterial pellets will be derived from in vitro culturing of the gut microbiota.

• Important: There will be two shipments of two independent experiments. The first experiment will have 177 samples, and the second experiment will have 133 samples.

The total sample number will be 310. The date of the shipments is unknown but will occur within the 12-month period of performance identified in the contract. Once samples are received the vendor will have 45 days to finish the sequencing and transfer the data files.

2) After thawing the samples, the vendor will perform metagenomic sequencing (shallow shotgun) using the Illumina pipeline. The Illumina pipeline is required in order to best match previous sequencing data with current sequencing data. I.E. other data generated for this project has been performed using the Illumina pipeline and the current data must be comparable. General steps required for generating the data are listed below. All steps must be performed by the vendor. All steps must be specifically outlined in the provided quote.

3) Steps required by the vendor are as follows:

a. Generation of the DNA library. Steps include fragmentation of DNA (method of fragmentation must be provided by vendor), the addition of adaptors and molecular barcode indices (specific adaptors and barcodes used must be provided by vendor), http://www.acquisition.gov/ and pooling of samples. Quality control of the DNA library must be monitored with DNA quantifications (for example pico green) and/or gel electrophoresis.

b. Controls must be included by the company during library prep, both negative and positive. Negative controls include water used during library prep and positive includes DNA from known samples.

c. Shallow sequencing will be performed using the Illumina platform. Must produce between 3-5 million read pairs per sample.

d. All raw data files will be transferred to scientists at the ERRC. In addition, quality control of raw sequencing reads must be performed which includes demultiplexing, and removal of adaptor sequencing.

4) All data generated must be transferred to the USDA within 45 days. Deliverables are listed below.

5) All work must be done in the United States to avoid thawing of DNA during shipping.

Award Type

It is anticipated that a firm-fixed price contract will be awarded as a result of this synopsis/solicitation.

The Government intends to make one award from this solicitation. Therefore, to be considered responsive, contractors must submit pricing for all items.

Evaluation and Basis for Award

The provision at FAR 52.212-2, Evaluation—Commercial Products and Commercial Services is not applicable to this solicitation. In lieu of this provision, quotes will be evaluated in accordance with FAR 12.203 based on the criteria listed below. Award will be made to the offeror representing the best value to the Government.

The Government will conduct a comparative evaluation of quotes to select the Contractor that is best suited to fulfill the requirement. The evaluation factors are: Price and Technical Capability. The Government reserves the right to select a quote that represents a superior technical solution, even if it is not the lowest priced.

Submission Requirements:

To be considered, provide a quote on company letterhead including:

• Vendor Details: SAM.gov UEI Number.

• Technical Documentation: Descriptive material and a "meets/does not meet" statement for the minimum specifications.

• Pricing: Unit price and total price (inclusive of all shipping/delivery costs).

• Timeline: Estimated lead time/delivery date.

• Validity: Quote must be valid for at least 60 days.

Offerors shall identify where the offered item meets or does not meet each of the Government's functional and performance minimum specifications listed herein.

Please ensure all email correspondence includes the solicitation number in the subject line. Emails without the RFQ number in the subject line may not be seen, read, and /or reviewed and therefore disqualified from consideration.

QUESTIONS REGARDING THIS RFQ ARE DUE TO RICHARD HAWTHORNE at Richard.hawthorne@usda.gov, NO LATER THAN 1:00 p. m. ET, March 11th, 2026. Questions will only be accepted via email and WILL NOT be answered if received after this date/time.

QUOTES REGARDING THIS RFQ ARE DUE TO RICHARD HAWTHORNE at Richard.hawthorne@usda.gov , NO LATER THAN 5:00 p. m. ET, March 12th, 2026

Delivery Information

Place of Performance:

USDA - ARS - DAIRY AND FUNCTIONAL FOODS RESE

600 EAST MERMAID LANE

WYNDMOOR PA 19038

Service Contract Labor Standards - The Service Contract Labor Standards could apply to any contracts awarded through this solicitation.

In accordance with (IAW) FAR 22.1002-3(a)(2), the place of performance for this contract is currently known and has included Wage Determinations for the location as an attachment to this solicitation.

A wage determination shall be incorporated in the resultant contract, and there shall be no adjustment to the contract price.

mailto:Richard.hawthorne@usda.gov

Statement of Work

Background The United Stated Department of Agriculture (USDA), Northeast Area (NEA), Dairy and Functional Foods Research Unit (DFFRU), at the Eastern Regional Research Center (ERRC) in Wyndmoor, PA requires a vendor to provide metagenomic data generated from shallow shotgun sequencing of complex gut microbial samples.

DFFRU scientists perform in vitro studies to determine how diet impacts the gut microbiota.

During the experiments, samples of the gut microbial communities are taken and DNA is extracted. Shallow shotgun sequencing metagenomic data provides information on how the structure of these microbial communities change over time.

Shallow shotgun sequencing is metagenomic sequencing (DNA sequencing) of microbial communities that generates 3-5M read pairs per sample that can be used to generate species level profiles. Specific steps required are provided in the Tasks or Requirements section below.

Scope

ERRC will use this acquisition to obtain metagenomic data derived from shallow shotgun sequencing further their research goals on species-level changes of the gut microbiota in response to diet, which aligns with the goals of their project plan.

Objectives

Scientists from the Dairy and Functional Foods Research Unit (DFFRU) at the ERRC expect to receive metagenomic data derived from shotgun sequencing. Results will be shared to form hypotheses, disseminated in manuscripts and presentations, or techniques developed to improve sequencing results. The data will be used as determined by the ERRC scientists.

Interests Scientists from the ERRC are interested in evaluation of the structural change in the gut microbial ecosystem in response to food, nutrition, and environmental stimuli, using next generation DNA sequencing technology and bioinformatics analysis.

Tasks or Requirements

1) ERRC scientists will send extracted DNA from bacterial pellets to be shipped overnight on dry ice for shotgun sequencing. Bacterial pellets will be derived from in vitro culturing of the gut microbiota.

Important: There will be two shipments of two independent experiments. The first experiment will have 177 samples, and the second experiment will have 133 samples. The total sample number will be 310. The date of the shipments is unknown but will occur within the 12-month period of performance identified in the contract. Once samples are received the vendor will have 45 days to finish the sequencing and transfer the data files.

2) After thawing the samples, the vendor will perform metagenomic sequencing (shallow shotgun) using the Illumina pipeline. The Illumina pipeline is required in order to best match previous sequencing data with current sequencing data. I.E. other data generated for this project has been performed using the Illumina pipeline and the current data must be comparable. General steps required for generating the data are listed below. All steps must be performed by the vendor. All steps must be specifically outlined in the provided quote.

3) Steps required by the vendor are as follows:

a. Generation of the DNA library. Steps include fragmentation of DNA (method of fragmentation must be provided by vendor), the addition of adaptors and molecular barcode indices (specific adaptors and barcodes used must be provided by vendor), and pooling of samples. Quality control of the DNA library must be monitored with DNA quantifications (for example pico green) and/or gel electrophoresis.

b. Controls must be included by the company during library prep, both negative and positive. Negative controls include water used during library prep and positive includes DNA from known samples.

c. Shallow sequencing will be performed using the Illumina platform. Must produce between 3-5 million read pairs per sample.

d. All raw data files will be transferred to scientists at the ERRC. In addition, quality control of raw sequencing reads must be performed which includes demultiplexing, and removal of adaptor sequencing.

4) All data generated must be transferred to the USDA within 45 days. Deliverables are listed below.

5) All work must be done in the United States to avoid thawing of DNA during shipping.

Deliverables

• Deliverable will include the following:

o Detailed protocol as to how the sequencing was performed for the materials and methods section of a manuscript.

o All QC data must be available upon request o Information on adaptors and indexes must be provided on request o All raw data files must be provided. All data must be provided via secure portal download as dictated by the ERRC scientists in accordance with the USDA safety protocols.

o All data generated from demultiplexing and removal of adaptor sequencing must be provided.

o All left over DNA must be returned to the USDA. The USDA will not pay separately for shipping.

• Completion and return of deliverables are required within 45 days after receipt of Government provided samples.

Estimated Period of Performance:

The contract shall be valid for one year after both parties have signed the contract. Estimated period of performance would be 03/25/2026-03/25/2027.

Government-Furnished Property

DFFRU/ERRC scientists will send extracted DNA from bacteria cultures for analysis. If any material is left over after use, it will be shipped back to the ERRC.

Federal Acquisition Regulation (FAR) and United States Department of Aquiculture Acquisition Regulation (AGAR) Clauses and Provisions The clauses and provisions contained herein are applicable to any order awarded as a result of this solicitation. The terms and conditions set forth herein supersede all other terms and conditions.

Acceptance of the order in accordance with (IAW) FAR 12.201-1(b)(2) constitutes acceptance of all terms and conditions contained herein.

As part of the Revolutionary FAR Overhaul (RFO), system updates may lag policy updates. The System for Award Management (SAM) may continue to require entities to complete representations based on provisions that are not included in this solicitation. Contracting officers will rely on representations from offers based on provisions in the solicitation. Entities are not required to, nor are they able to, update their entity registration to remove these representations in SAM.

52.252-2 Clauses Incorporated by Reference Feb 1998 This solicitation incorporates one or more clauses by reference, with the same force and effect as if they were given in full text. Upon request, the Contracting Officer will make their full text available. Also the full text of the clause may be accessed electronically at Internet address https://www.acquisition.gov/far-overhaul/far-part-deviation-guide/far-overhaul-part-52

52.212-4 Terms and Conditions—Commercial Products and Commercial Services (Nov 2025) ☐ Alternate I (Nov 2025) of 52.212-4 52.203-17 Contractor Employee Whistleblower Rights (Nov 2023) 52.203-19 Prohibition on Requiring Certain Internal Confidentiality Agreements or Statements (Jan 2017) 52.222-50 Combating Trafficking in Persons (Nov 2025)

☐ Alternate I (Nov 2025) of 52.222-50 52.226-8 Encouraging Contractor Policies to Ban Text Messaging While Driving (May 2024) 52.232-40 Providing Accelerated Payments to Small Business Subcontractors (Mar 2023) 52.233-3 Protest After Award (Sep 2025) 52.233-4 Applicable Law for Breach of Contract Claim (Sep 2025) 52.240-91 Security Prohibitions and Exclusions (Nov 2025)

☐ Alternate I (Nov 2025) of 52.240-91 52.244-6 Subcontracts for Commercial Products and Commercial Services (Nov 2025)

The following clauses are applicable if checked:

☐ 52.203-6 Restrictions on Subcontractor Sales to the Government (Jun 2020) with Alternate I (Nov 2021) of 52.203-6 ☐ 52.203-13 Contractor Code of Business Ethics and Conduct (Nov 2021) ☐ 52.204-9 Personal Identity Verification of Contractor Personnel Jan 2011 ☒ 52.204-13 System for Award Management—Maintenance (Nov 2025) ☐ 52.209-6 Protecting the Government’s Interest When Subcontracting with

Contractors Debarred, Suspended, or Proposed for Debarment (Sep 2025) ☐ 52.209-9 Updates of Publicly Available Information Regarding Responsibility Matters (Sep 2025) ☒ 52.209-10 Prohibition on Contracting with Inverted Domestic Corporations (Sep 2025) ☐ 52.219-4 Notice of Price Evaluation Preference for HUBZone Small Business Concerns (Nov 2025) ☒ 52.219-6 Notice of Total Small Business Aside (Nov 2025)

☐ Alternate I (Mar 2020).

☐ 52.219-8 Utilization of Small Business Concerns (Nov 2025) ☐ 52.219-14 Limitations on Subcontracting (Nov 2025) ☐ 52.219-33 Nonmanufacturer Rule (Nov 2025) ☒ 52.222-3 Convict Labor (June 2003) ☐ 52.222-35 Equal Opportunity for Veterans (Nov 2025)

☐ Alternate I (Jul 2014) of 52.222-35 ☒ 52.222-36 Equal Opportunity for Workers with Disabilities (Nov 2025)

☐ Alternate I (Jul 2014) of 52.222-36 ☐ 52.222-37 Employment Reports on Veterans (Nov 2025) ☐ 52.222-40 Notification of Employee Rights Under the National Labor Relations Act (Dec 2010) ☐ 52.222-54 Employment Eligibility Verification (Nov 2025) ☐ 52.222-62 Paid Sick Leave Under Executive Order 13706 (Jan 2022) ☐ 52.223-12 Maintenance, Service, Repair, or Disposal of Refrigeration Equipment and Air Conditioners (Nov 2025) ☒ 52.223-23 Sustainable Products and Services ☒ 52.232-33 Payment by Electronic Funds Transfer— System for Award Management (Oct 2018) ☐ 52.232-36 Payment by Third Party (Nov 2025) ☒ 52.240-93 Basic Safeguarding of Covered Contractor Information Systems (No 2025)

The Contractor shall comply with the following FAR Clauses for Commercial Services.

☒ 52.222-41 Service Contract Labor Standards (Aug 2018) ☒ 52.222-42 Statement of Equivalent Rates for Federal Hires (May 2014) ☐ 52.222-43 Fair Labor Standards Act and Service Contract Labor Standards -- Price Adjustment (Multiple Year and Option Contracts) (Aug 2018) ☐ 52.222-44 Fair Labor Standards Act and Service Contract Labor Standards -- Price Adjustment (May 2014) ☐ 52.222-51 Exemption from Application of the Service Contract Labor Standards to Contracts for Maintenance, Calibration, or Repair of Certain Equipment-Requirements (May 2014) ☐ 52.222-53 Exemption from Application of the Service Contract Labor Standards to Contracts for Certain Services-Requirements (Nov 2025)

AGAR Clauses

452.204–70 Modification for Contract Closeout (Nov 2025)

(a) If unliquidated funds in the amount of $1000 or less remain on the contract, the Contracting Officer (Contracting Officer) shall issue a unilateral modification for deobligation. The contractor will receive a copy of the modification but will not be required to provide a signature. The Contracting Officer shall immediately proceed with contract closeout upon completion of the period of performance, receipt and acceptance of supplies or services, and final payment.

(b) Upon contract closeout for contracts utilizing SAP: if unliquidated funds of more than $1000 remain on the contract, the Contracting Officer shall issue a bilateral modification for deobligation.

The contractor will receive a copy of the modification and will be required to provide a signature.

(The Contracting Officer may also request a “Contractor Release of Claims” be completed by the contractor, although not required for contracts and orders using SAP.) If the bilateral modification and Release of Claims are not returned to the Contracting Officer within 60 days, the Contracting Officer shall release the modification as unilateral and proceed with contract closeout upon completion of the period of performance, receipt and acceptance of supplies or services, and final payment.

(c) Upon contract closeout for contracts utilizing anything other than cost reimbursement, if unliquidated funds of more than $1000 remain on the contract, the Contracting Officer shall issue a bilateral modification for deobligation. The contractor will receive a copy of the modification and a ‘‘Contractor Release of Claims’’ and will be required to provide a signature on both forms. If the bilateral modification and Release of Claims are not returned to the Contracting Officer within 120 days, the Contracting Officer shall release the modification as unilateral and proceed with contract closeout upon completion of the period of performance, receipt and acceptance of supplies or services, and final payment.

(End of Clause)

(END OF CLAUSES)

52.252-1 Solicitation Provisions Incorporated by Reference Feb 1998 This solicitation incorporates one or more solicitation provisions by reference, with the same force and effect as if they were given in full text. Upon request, the Contracting Officer will make their full text available. The offeror is cautioned that the listed provisions may include blocks that must be completed by the offeror and submitted with its quotation or offer. In lieu of submitting the full text of those provisions, the offeror may identify the provision by paragraph identifier and provide the appropriate information with its quotation or offer. Also, the full text of a solicitation provision may be accessed electronically at this/these address(es): https://www.acquisition.gov/far-overhaul/far-part-deviation-guide/far-overhaul-part-52

52.212-1 Instructions to Offerors - Commercial Products and Commercial Services (Nov 2025) 52.203-18 Prohibition on Contracting with Entities that Require Certain Internal Confidentiality Agreements or Statements-Representation (Jan 2017) 52.240-90 Security Prohibitions and Exclusions Representations and Certifications (Nov 2025)

The following provisions are applicable if checked:

☐ 52.203-11 Certification and Disclosure Regarding Payments to Influence Certain Federal Transactions (Sep 2024) ☒ 52.204-7 System for Award Management—Registration (Nov 2025)

☐ Alternate I (Nov 2025) to 52.204-7 ☐ 52.207-6 Solicitation of Offers from Small Business Concerns and Small Business Teaming Arrangements or Joint Ventures (Multiple-Award Contracts) (Aug 2024) ☐ 52.209-12 Certification Regarding Tax Matters (Oct 2025) ☐ 52.222-48 Exemption from Application of the Service Contract Labor Standards for Maintenance, Calibration, or Repair of Certain Equipment–Certification (Nov 2025) ☐ 52.222-52 Exemption from Application of the Service Contract Labor Standards for Certain Services-Certification (Nov 2025) ☐ 52.223-4 Recovered Material Certification (May 2008) ☐ 52.225-2 Buy American Certificate (Oct 2022) ☐ 52.225-4 Buy American-Free Trade Agreements-Israeli Trade Act Certificate (Nov 2025) ☐ 52.225-6 Trade Agreements-Certificate (Feb 2021) ☐ 52.229-11 Tax on Certain Foreign Procurements—Notice and Representation (Jul 2025)

(END OF PROVISIONS)

NOTICE FOR FILING AGENCY PROTESTS

United States Department of Agriculture (USDA) Ombudsman Program

The USDA is committed to issuing solicitations and awarding contracts in a fair and prompt manner.

The Ombudsman Program for Agency Protests (OPAP) was established to address protest issues within the agency, providing an alternative to costly and time-consuming litigation. Operating independently, OPAP offers relief comparable to that granted by the Government Accountability Office (GAO). Interested parties are encouraged to resolve concerns through USDA’s internal Alternative Dispute Resolution (ADR) process before pursuing external forums such as the GAO.

Concerns may be addressed informally or through a formal agency protest filed with either the Contracting Officer or the Ombudsman.

Informal Forum with the Ombudsman

1. Initial Point of Contact: Interested parties who believe a specific USDA procurement is unfair or otherwise defective should first direct their concerns to the applicable Contracting Officer.

2. Escalation: If the Contracting Officer is unable to address their concerns, interested parties are encouraged to contact the USDA Ombudsman for Agency Protests. Under this informal process, the agency is not required to suspend contract award performance. Utilization of the informal forum does not suspend any time requirement for filing a formal protest with the agency or other forums.

3. Required Information: To ensure a timely response, interested parties should provide the following information to the Ombudsman: solicitation/contract number, contracting office, Contracting Officer, and solicitation closing date (if applicable).

Formal Agency Protest with the Ombudsman

1. Effort to Resolve: Prior to submitting a formal agency protest, protesters must first use their best efforts to resolve their concerns with the Contracting Officer through open and frank discussions.

2. Independent Review: If the protester’s concerns remain unresolved, an Independent Review is available by the Ombudsman. The protester may file a formal agency protest with either the Contracting Officer or, alternatively, with the Ombudsman under the OPAP program. Contract awards or performance will be suspended during the protest period unless justified in writing for urgent and compelling reasons or determined in writing to be in the best interest of the Government.

3. Resolution Timeline: The agency’s goal is to resolve protests within 35 calendar days from the date of filing.

4. Required Information: Protests shall include the information set forth in FAR 33.104(a)(3).

Failure to submit the required information may result in a delay or dismissal of the protest.

5. Timeliness: Protests must be filed within the timeframes specified in FAR 33.104.

6. Submission: Formal protests under the OPAP program should be submitted electronically to SPE.inquiry@usda.gov and the Contracting Officer.

Election of Forum. By initiating a protest with the USDA, the protester agrees not to pursue the same matter with the Government Accountability Office (GAO) or any other external forum while the agency protest is pending. If a protest is filed externally, the agency protest will be dismissed.

mailto:SPE.inquiry@usda.gov

IPP.gov

How to enroll in IPP

Vendors that are required to submit an invoice through IPP do not need to contact IPP to enroll.

Enrollment will be initiated by the agency they are doing business with and will be completed by IPP.

Once enrolled, vendors will receive two emails with an IPP login ID and a temporary password.

If you already have an IPP.gov account, but do not know your login info, please have your Tax ID Number (TIN) ready when your reach out to IPP.

What happens next?

• After an account is established, you will receive two emails. The first one will include your IPP User ID, and 12 to 24 hours later a second email will give you a 12-character password. Use the ID and password to log onto IPP. You will be asked to change the temporary password to one of your own choosing, agree to the rules for using IPP, and set up the answers to security questions.

As a vendor who provides goods or services to a government agency, once logged in you will be granted access to IPP's Collector module which will allow you to view purchase orders, submit invoices, access payment information, and more.

• Please note that only one Administrator can be initially enrolled in your IPP vendor profile. The Administrator can then add additional users as necessary.

• Allow 5 to 10 business days for registration.

• All government vendors must register and continue to maintain their account data in the System for Award Management (SAM) registry and activate it annually. Please visit http://www.SAM.gov/ for more information.

E-mail notifications of payments are sent when a payment is distributed to your bank account and will include all pertinent payment information. The IPP Customer Support Desk is available to assist users Monday through Friday (excluding bank holidays) from 8:00AM - 6:00PM ET, including answering any questions related to accessing IPP or completing the registration process. Their tollfree number is (866) 973-3131 or they can be reached at: IPPCustomerSupport@fiscal.treasury.gov

Statement of Requirement