Statement of Work.pdf

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 Contractor to provide shallow shotgun sequencing for hundreds of complex microbial samples. The DFFRU scientists perform complex studies to understand how diet impacts the gut microbiota. These studies require shallow shotgun and shotgun sequencing of the bacterial and fungal communities present in the gut microbiota. Each study produces hundreds of samples that require this sequencing to compare how the bacterial and fungal communities change over the course of a change in diet or treatment.

This project, undertaken by DFFRU scientists, requires accurate and timely sequencing data, as well as the ability to get help with data analysis from the sequencing data.

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.

What the DFFRU will do We will grow bacteria axenically or as a community and treat them with various foods or food compounds. We will harvest the treated bacteria samples via centrifugation, discarding the culture liquid, and freeze them at -80 °C. Samples will be shipped overnight on dry ice to the Contractor for next generation DNA sequencing and bioinformatics analysis. We will interpret the data thus generated.

What The Contractor will do After thawing the samples, The Contractor will extract DNA and perform DNA sequencing. The sequencing reads will be evaluated for quality and subject to bioinformatic analysis in order to identify the sample contents at the strain level. This data will then be sent to the DFFRU scientists in 2 ways: a server-based method of looking at the Operational Taxonomic Units (OTUs) as well as a way to download the raw data file sent directly to the DFFRU scientists in question. The Contractor will also contribute to data interpretation. The Contractor should have the ability to create a user-friendly initial interpretation of the sequencing data. User-friendly in this instance means a server-driven system or app that users can log in to and use to perform standard data manipulations such as alpha diversity and beta diversity measures for the microbial community that was sequenced.

If needed, The Contractor should perform inhouse bioinformatic analysis that goes beyond the initial, user friendly metagenomic analysis available. The Contractor’s capabilities include functional analysis and advanced statistical analysis based on the project goal.

What the DFFRU and The Contractor will do together

Working together, scientists at the ERRC and the Contractor will decipher changes to the commensal gut microbes in response to different foods and food components. The USDA scientists will be responsible for performing the initial experiment and the Contractor scientists will be responsible for sequencing quality. Results will be shared to form hypotheses, disseminated in manuscripts and presentations, or techniques developed to improve sequencing results.

Schedule of Line Items Line Item 01 – Next-Generation Sequencing (Shallow shotgun sequencing, with a minimum of 3 million reads and an ability to go up to at least 20 million reads per sample) 1000 samples will be provided on or before 08/01/2023.

Deliverables

• Deliverable will include the genotyping i.e., data for all sample (OTU files), and the raw data files. All data must be provided via secure portal download that includes an app or similar system for data interpretation.

• Completion and return of deliverable is required within 45 days after receipt of all Government provided samples.