Summary of Study ST002833

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 IDST002833
Study TitleResource competition predicts assembly of in vitro gut bacterial communities- 2022-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 Date2023-08-25
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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Combined analysis:

Analysis ID AN004627 AN004628
Analysis type MS MS
Chromatography type Reversed phase Reversed phase
Chromatography system Thermo Vanquish Thermo Vanquish
Column Agilent Zorbax SB-C18 column (100 x 3.0 mm, 1.8 um) Agilent Zorbax SB-C18 column (100 x 3.0 mm, 1.8 um)
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Units counts, height counts, height


Chromatography ID:CH003482
Chromatography Summary:Bacterial supernatant were analyzed via reversed phase (C18) coupled to a Thermo Q-Exactive HF high resolution mass spectrometer. Prepared samples were injected onto an Agilent Zorbax SB-C18 column (100 mm length × 3 mm id; 1.8 μm particle size) with an additional Phenomenex KrudKatcher pre-column (2 μm depth x 0.004in ID) maintained at 40°C coupled to an Thermo Vanquish UPLC. The mobile phases were prepared with 0.1% formic acid in either 100% LC-MS grade water for mobile phase (A), 100% water or mobile phase (B), 100% acetonitrile. Gradient elution was performed as follows 3% (B) maintained 0–0.43 min to 97% (B) at 9 min, maintained until 11 min, returning to initial conditions at 11.5 min and equilibrating until the end of the run at 14 min. Flow rate is maintained at 0.4 mL/min. Each sample was analyzed in both positive and negative ionization modes (ESI+, ESI-) via subsequent injections. Full MS-ddMS2 data was collected, an inclusion list was used to prioritize MS2 selection of metabolites from our in-house ‘local’ library, when additional scan bandwidth was available MS2 was collected in a data-dependent manner. Mass range was 60-900 mz, resolution was 60k (MS1) and 15k (MS2), centroid data was collected, loop count was 4, isolation window was 1.5 Da. Metabolomics data was processed using MS-DIAL v4.60 ( and queried against a combination of our in-house MS2 library and MassBank of North America, the largest freely available spectral repository ( Features were excluded from analysis if peak height was not at least 5-fold greater in one or more samples compared to the procedural blank average.
Instrument Name:Thermo Vanquish
Column Name:Agilent Zorbax SB-C18 column (100 x 3.0 mm, 1.8 um)
Column Temperature:40C
Flow Gradient:Gradient elution was performed from 100% (B) at 0–2 min to 70% (B) at 7.7 min, 40% (B) at 9.5 min, 30% (B) at 10.25 min, 100% (B) at 12.75 min, isocratic until 16.75 min with a column flow ofGradient elution was performed as follows 3% (B) maintained 0–0.43 min to 97% (B) at 9 min, maintained until 11 min, returning to initial conditions at 11.5 min and equilibrating until the end of the run at 14 min.
Flow Rate:0.4 mL/min.
Solvent A:Water + 0.1% formic acid
Solvent B:Acetonitrile + 0.1% formic acid
Chromatography Type:Reversed phase