Summary of project PR001774
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 PR001774. The data can be accessed directly via it's Project DOI: 10.21228/M8DB1F This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Project ID: | PR001774 |
| Project DOI: | doi: 10.21228/M8DB1F |
| Project Title: | Resource competition predicts assembly of in vitro gut bacterial communities |
| Project Summary: | Microbiota dynamics arise from a plethora of interspecies interactions, including resource competition, cross-feeding, and pH modulation. The individual contributions of these mechanisms are challenging to untangle, especially in natural or complex laboratory environments where the landscape of resource competition is unclear. Here, we developed a framework to estimate the extent of multi-species niche overlaps by combining metabolomics data of individual species, growth measurements in pairwise spent media, and mathematical models. When applied to an in vitro model system of human gut commensals in complex media, our framework revealed that a simple model of resource competition described most pairwise interactions. By grouping metabolomic features depleted by the same set of species, we constructed a coarse-grained consumer-resource model that predicted assembly compositions to reasonable accuracy. Moreover, deviations from model predictions enabled us to identify and incorporate into the model additional interactions, including pH-mediated effects and cross-feeding, which improved model performance. In sum, our work provides an experimental and theoretical framework to dissect microbial interactions in complex in vitro environments. |
| Institute: | Stanford University |
| Last Name: | DeFelice |
| First Name: | Brian |
| Address: | 1291 Welch Rd., Rm. G0821 (SIM1), Stanford CA, California, 94305, USA |
| Email: | bcdefelice@ucdavis.edu |
| Phone: | 5303564485 |
Summary of all studies in project PR001774
| Study ID | Study Title | Species | Institute | Analysis(* : Contains Untargted data) | Release Date | Version | Samples | Download(* : Contains raw data) |
|---|---|---|---|---|---|---|---|---|
| ST002832 | Resource competition predicts assembly of in vitro gut bacterial communities- HILIC | Bacteroides thetaiotaomicron | Stanford University | MS* | 2023-09-14 | 1 | 402 | Uploaded data (8.4G)* |
| ST002833 | Resource competition predicts assembly of in vitro gut bacterial communities- 2022-C18 | Bacteroides thetaiotaomicron | Stanford University | MS* | 2023-09-14 | 1 | 119 | Uploaded data (3.4G)* |
| ST002834 | Resource competition predicts assembly of in vitro gut bacterial communities- 2021-C18 | Bacteroides thetaiotaomicron | Stanford University | MS* | 2023-09-14 | 1 | 164 | Uploaded data (5.6G)* |
