# The UCSD Microbiome and Metagenomics Center

> **NIH NIH U24** · UNIVERSITY OF CALIFORNIA, SAN DIEGO · 2024 · $3,324,680

## Abstract

Project Summary
The University of California San Diego (UCSD) Microbiome and Metagenomics Center (MMC) as part of the
Nutrition for Precision Health (NPH) consortium will provide rapid, robust stool sample processing, high-quality
metagenomic and metatranscriptomic data generation, and best-in-class bioinformatic analysis. We will optimize
our protocols for DNA and RNA extraction from stool, metagenomic and metatranscriptomic library preparation,
sequencing, and bioinformatics for ultra-high resolution taxonomic and functional profiling of the microbiome,
including bacteria, archaea, eukaryotes, and viruses. We will offer analytical services and expertise on study
design, sample collection, statistics, artificial intelligence, and host-microbe data interpretation to support other
NPH centers and develop standard operation procedures with the Research Coordinating Center (RCC). Our
team has developed uniquely innovative approaches to provide metagenomic and metatranscriptomic data at a
cost that facilitates application to all 17,500 samples provided by the BioBank, with robust quality control to
ensure high-quality raw and processed data products. We are also able to provide absolute quantification of
microbial load through our recent innovation in synthetic DNA ‘spike-ins', which also facilitates rigorous
assessment of contamination and extraction efficiency. Beyond bringing cutting edge technology that we have
developed to the consortium, we also propose 3 Pilot Projects: (i) long-read data assembly; (ii) multiplexed
metaproteomics; and (iii) automated stool sample collection and processing, so as to improve the taxonomic and
functional resolution of profiling and improve biomarker detection sensitivity using dense timeseries. Importantly,
our team is also optimally positioned to develop community consensus for the analysis strategies agreed on
during the planning year, as well as to address the challenges of integrating microbiome data into the NPH
consortium, due to our: existing high-throughput sample processing, sequencing, and data analysis cores; tight
integration among disciplinary groups; access to supercomputing infrastructure; data visualization expertise; and
tight coordination with an international braintrust of scientists who have been selected based on their
complementary expertise in different areas of microbiome and precision nutrition research. This center will also
benefit from cross-campus institutional commitment to provide 4 undergraduate, 5 postgraduate, and 6
postdoctoral fellowships, enabling faculty engagement and the development of innovative technologies and
algorithms to advance NPH consortium goals. Additionally, our existing community outreach experiences can
further support the NPH consortium’s goal to provide respectful, accessible and engaging feedback to the
participants. Essential to the success of the MMC is the 35% time-commitment of the PI who has an outstanding
track record in leading similar scale efforts....

## Key facts

- **NIH application ID:** 10813715
- **Project number:** 5U24DK131617-03
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN DIEGO
- **Principal Investigator:** Jack Anthony Gilbert
- **Activity code:** U24 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $3,324,680
- **Award type:** 5
- **Project period:** 2021-12-23 → 2026-11-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10813715

## Citation

> US National Institutes of Health, RePORTER application 10813715, The UCSD Microbiome and Metagenomics Center (5U24DK131617-03). Retrieved via AI Analytics 2026-05-25 from https://api.ai-analytics.org/grant/nih/10813715. Licensed CC0.

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