# Systems-level analysis of the metabolism and ecology of genetically intractable gut bacteria

> **NIH NIH F32** · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · 2021 · $65,994

## Abstract

Project Summary/Abstract
Despite the fundamental importance of the human gut microbiome in health and disease, a cohesive
understanding of the core metabolic pathways of many human gut bacterial species is lacking. The
Actinobacterium Eggerthella lenta is a notable example: it is highly prevalent, associated with bacteremia and
the development of autoimmune disease, and capable of diverse transformations of endogenous and
xenobiotic compounds, yet little is known about its nutrient requirements, metabolic regulation, and ecological
niche. This project will investigate metabolic and ecological properties of E. lenta across multiple scales. It will
use a combination of experimental and computational approaches to evaluate these properties across strains
and species in the family Eggerthellaceae, taking advantage of a new resource of strain isolates and genomes.
Preliminary experiments established defined minimal media formulations that support the growth of
Eggerthellaceae and identified key growth determinants, including an unexpected growth benefit from acetate.
Pilot metabolomics analysis of E. lenta cultured in minimal media revealed context-specific metabolism and
production of host-relevant metabolites. This project will first quantify growth, metabolite fluxes, and gene
expression of Eggerthellaceae strains across minimal nutrient contexts. The resulting data resource will be
used to construct and analyze computational genome-scale metabolic models of these taxa. Next, co-culture
studies of E. lenta strains with other gut microbial taxa will elucidate their ecological interactions and possible
metabolite exchanges. Lastly, newly available collections of Eggerthellaceae genomes assembled from public
metagenomic datasets will be analyzed to evaluate associations of genomic and metabolic features with host
disease, geography, age, and microbiome composition. Overall, this work will provide insights into the
metabolic, ecological, and evolutionary properties of this clade and its role in human health and disease.
Moreover, the integration of in vitro profiling, cross-strain comparative analyses, and computational modeling
demonstrated here is a generalizable framework for expanding scientific understanding of the metabolism of
poorly characterized gut microbes. The fellowship training program will include skill development in
experimental biology, research mentoring, and professional skills; supported by a collaborative and successful
microbiome research community at a top-ranked institution.

## Key facts

- **NIH application ID:** 10150247
- **Project number:** 1F32GM140808-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
- **Principal Investigator:** Cecilia Noecker
- **Activity code:** F32 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $65,994
- **Award type:** 1
- **Project period:** 2021-07-01 → 2023-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10150247

## Citation

> US National Institutes of Health, RePORTER application 10150247, Systems-level analysis of the metabolism and ecology of genetically intractable gut bacteria (1F32GM140808-01). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10150247. Licensed CC0.

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