Summary of project PR001620
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001620. The data can be accessed directly via it's Project DOI: 10.21228/M89B04 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Project ID: | PR001620 |
| Project DOI: | doi: 10.21228/M89B04 |
| Project Title: | Systems biology illuminates the alternative metabolic niche of the human gut bacterium Eggerthella lenta |
| Project Type: | Untargeted LC-MS |
| Project Summary: | Human gut bacteria perform diverse metabolic functions with consequences for host health. The prevalent and disease-linked Actinobacterium Eggerthella lenta performs several unusual chemical transformations, but it does not metabolize sugars and its core growth strategy remains unclear. To obtain a comprehensive view of the metabolic network of E. lenta, we generated several complementary resources: defined culture media, metabolomics profiles of strain isolates, and a curated genome-scale metabolic reconstruction. Stable isotope-resolved metabolomics revealed that E. lenta uses acetate as a key carbon source while catabolizing arginine to generate ATP, traits which could be recapitulated in silico by our updated metabolic model. We compared these in vitro findings with metabolite shifts observed in E. lenta-colonized gnotobiotic mice, identifying shared signatures across environments and highlighting catabolism of the host signaling metabolite agmatine as an alternative energy pathway. Together, our results elucidate a distinctive metabolic niche filled by E. lenta in the gut ecosystem. |
| Institute: | University of California, San Francisco |
| Department: | Microbiology and Immunology |
| Laboratory: | Peter Turnbaugh |
| Last Name: | Noecker |
| First Name: | Cecilia |
| Address: | 513 Parnassus Ave HSW1501, San Francisco, CA 94143 |
| Email: | cecilia.noecker@ucsf.edu |
| Phone: | 415-502-3264 |
| Funding Source: | This work was supported by the National Institutes of Health (2R01HL122593; 1R01AT011117; 1R01DK114034 to P.J.T., F32GM140808 to C.N.). P.J.T. is a Chan Zuckerberg Biohub Investigator and held an Investigators in the Pathogenesis of Infectious Disease Award from the Burroughs Wellcome Fund. |
| Publications: | https://doi.org/10.1101/2022.09.19.508335 |
Summary of all studies in project PR001620
| Study ID | Study Title | Species | Institute | Analysis(* : Contains Untargted data) | Release Date | Version | Samples | Download(* : Contains raw data) |
|---|---|---|---|---|---|---|---|---|
| ST002509 | Time course 1: Growth of Eggerthella lenta in defined media | Eggerthella lenta | University of California, San Francisco | MS | 2023-04-04 | 1 | 302 | Uploaded data (12.6G)* |
| ST002510 | Strain supernatants: Strain diversity of Eggerthella lenta metabolites in defined media | Eggerthella lenta | University of California, San Francisco | MS | 2023-04-04 | 1 | 152 | Uploaded data (7.7G)* |
| ST002512 | Gnotobiotic mice: Metabolites in intestinal contents of germ-free mice colonized with strains of gut bacterium Eggerthella lenta | Mus musculus | University of California, San Francisco | MS | 2023-04-10 | 1 | 110 | Uploaded data (5.9G)* |
| ST002513 | Gnotobiotic mice: Metabolites in serum of germ-free mice colonized with strains of gut bacterium Eggerthella lenta | Mus musculus | University of California, San Francisco | MS | 2023-04-10 | 1 | 21 | Uploaded data (1G)* |
| ST002515 | Time course 2: Acetate quantification from growth of Eggerthella lenta in defined media | Eggerthella lenta | University of California, San Francisco | MS | 2023-04-10 | 1 | 114 | Uploaded data (8.5G)* |
| ST002516 | Time course 2: Growth of Eggerthella lenta in defined media with some samples receiving 13C2 stable isotope labeled acetate | Eggerthella lenta | University of California, San Francisco | MS | 2023-04-10 | 1 | 576 | Uploaded data (29.5G)* |
| ST002517 | Time course 2: Growth of Eggerthella lenta in defined media with some samples receiving 13C2 stable isotope labeled acetate (intracellular samples) | Eggerthella lenta | University of California, San Francisco | MS | 2023-04-10 | 1 | 123 | Uploaded data (6.4G)* |
| ST002518 | Time course 3: Growth of Eggerthella lenta in defined media with some samples receiving 13C6 stable isotope labeled arginine | Eggerthella lenta | University of California, San Francisco | MS | 2023-04-09 | 1 | 78 | Uploaded data (2.7G)* |
| ST002519 | Time course 3: Growth of Eggerthella lenta in defined media with some samples receiving 13C6 stable isotope labeled arginine (intracellular samples) | Eggerthella lenta | University of California, San Francisco | MS | 2023-04-09 | 1 | 32 | Uploaded data (1.1G)* |
