Summary of Study ST002834

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench,, 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.


This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST002834
Study TitleResource competition predicts assembly of in vitro gut bacterial communities- 2021-C18
Study SummaryMicrobiota 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.
Stanford University
Last NameDeFelice
First NameBrian
Address1291 Welch Rd.
Submit Date2023-08-28
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-09-14
Release Version1
Brian DeFelice Brian DeFelice application/zip

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Collection ID:CO002936
Collection Summary:Isolates were obtained via plating of in vitro communities –, derived from culturing fecal samples from humanized mice –, on agar plates made with various complex media and frozen as glycerol stocks, as previously described (, Frozen stocks were streaked onto BHI-blood agar plates (5% defibrinated horse blood in 1.5% w/v agar). Resulting colonies were inoculated into 3 mL of Brain Heart Infusion (BHI) (BD #2237500) or modified Gifu Anaerobic Medium (mGAM) (HyServe #05433) in test tubes. All culturing werewas performed at 37 °C without shaking in an anaerobic chamber (Coy). To minimize potential physiological changes from freeze-thaw cycles and changes in growth medium, cultures were diluted 1:200 every 48 h for 3 passages before growth or metabolomics measurements. After the first passage, subsequent passages were performed in 96-well polystyrene plates (Greiner Bio-One #655161) filled with 200 μL of growth medium.
Sample Type:Bacterial cells