Summary of Study ST002832

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

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 IDST002832
Study TitleResource competition predicts assembly of in vitro gut bacterial communities- HILIC
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.
Institute
Stanford University
Last NameDeFelice
First NameBrian
Address1291 Welch Rd.
Emailbcdefelice@ucdavis.edu
Phone5303564485
Submit Date2023-08-24
Raw Data AvailableYes
Raw Data File Type(s)raw(Thermo)
Analysis Type DetailLC-MS
Release Date2023-09-14
Release Version1
Brian DeFelice Brian DeFelice
https://dx.doi.org/10.21228/M8DB1F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Project:

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

Subject:

Subject ID:SU002941
Subject Type:Bacteria
Subject Species:Bacteroides thetaiotaomicron
Taxonomy ID:8188
Subject Comments:Fecal derived communities and isolates, supernatant was assayed

Factors:

Subject type: Bacteria; Subject species: Bacteroides thetaiotaomicron (Factor headings shown in green)

mb_sample_id local_sample_id Genotype Treatment
SA306505M00179_20220322_Neg_1_MSA0053bacterial community 15-member community timepoint 1
SA306506M00179_20220322_Neg_1_MSA0045bacterial community 15-member community timepoint 1
SA306507M00179_20220322_Pos_1_MSA0045bacterial community 15-member community timepoint 1
SA306508M00179_20220322_Pos_1_MSA0053bacterial community 15-member community timepoint 1
SA306509M00179_20220322_Pos_1_MSA0046bacterial community 15-member community timepoint 1
SA306510M00179_20220322_Neg_1_MSA0046bacterial community 15-member community timepoint 1
SA306511M00179_20220322_Neg_1_MSA0022bacterial community 15-member community timepoint 10
SA306512M00179_20220322_Neg_1_MSA0025bacterial community 15-member community timepoint 10
SA306513M00179_20220322_Pos_1_MSA0025bacterial community 15-member community timepoint 10
SA306514M00179_20220322_Pos_1_MSA0035bacterial community 15-member community timepoint 10
SA306515M00179_20220322_Neg_1_MSA0035bacterial community 15-member community timepoint 10
SA306516M00179_20220322_Pos_1_MSA0022bacterial community 15-member community timepoint 10
SA306517M00179_20220322_Pos_1_MSA0001bacterial community 15-member community timepoint 11
SA306518M00179_20220322_Neg_1_MSA0055bacterial community 15-member community timepoint 11
SA306519M00179_20220322_Pos_1_MSA0055bacterial community 15-member community timepoint 11
SA306520M00179_20220322_Neg_1_MSA0005bacterial community 15-member community timepoint 11
SA306521M00179_20220322_Pos_1_MSA0005bacterial community 15-member community timepoint 11
SA306522M00179_20220322_Neg_1_MSA0001bacterial community 15-member community timepoint 11
SA306523M00179_20220322_Neg_1_MSA0063bacterial community 15-member community timepoint 12
SA306524M00179_20220322_Pos_1_MSA0063bacterial community 15-member community timepoint 12
SA306525M00179_20220322_Neg_1_MSA0042bacterial community 15-member community timepoint 12
SA306526M00179_20220322_Neg_1_MSA0074bacterial community 15-member community timepoint 12
SA306527M00179_20220322_Pos_1_MSA0042bacterial community 15-member community timepoint 12
SA306528M00179_20220322_Pos_1_MSA0074bacterial community 15-member community timepoint 12
SA306529M00179_20220322_Pos_1_MSA0024bacterial community 15-member community timepoint 13
SA306530M00179_20220322_Neg_1_MSA0032bacterial community 15-member community timepoint 13
SA306531M00179_20220322_Neg_1_MSA0044bacterial community 15-member community timepoint 13
SA306532M00179_20220322_Pos_1_MSA0044bacterial community 15-member community timepoint 13
SA306533M00179_20220322_Neg_1_MSA0024bacterial community 15-member community timepoint 13
SA306534M00179_20220322_Pos_1_MSA0032bacterial community 15-member community timepoint 13
SA306535M00179_20220322_Neg_1_MSA0056bacterial community 15-member community timepoint 14
SA306536M00179_20220322_Pos_1_MSA0006bacterial community 15-member community timepoint 14
SA306537M00179_20220322_Neg_1_MSA0006bacterial community 15-member community timepoint 14
SA306538M00179_20220322_Neg_1_MSA0033bacterial community 15-member community timepoint 14
SA306539M00179_20220322_Pos_1_MSA0056bacterial community 15-member community timepoint 14
SA306540M00179_20220322_Pos_1_MSA0033bacterial community 15-member community timepoint 14
SA306541M00179_20220322_Neg_1_MSA0054bacterial community 15-member community timepoint 15
SA306542M00179_20220322_Neg_1_MSA0064bacterial community 15-member community timepoint 15
SA306543M00179_20220322_Pos_1_MSA0054bacterial community 15-member community timepoint 15
SA306544M00179_20220322_Neg_1_MSA0062bacterial community 15-member community timepoint 15
SA306545M00179_20220322_Pos_1_MSA0064bacterial community 15-member community timepoint 15
SA306546M00179_20220322_Pos_1_MSA0062bacterial community 15-member community timepoint 15
SA306547M00179_20220322_Pos_1_MSA0023bacterial community 15-member community timepoint 16
SA306548M00179_20220322_Pos_1_MSA0050bacterial community 15-member community timepoint 16
SA306549M00179_20220322_Pos_1_MSA0039bacterial community 15-member community timepoint 16
SA306550M00179_20220322_Neg_1_MSA0050bacterial community 15-member community timepoint 16
SA306551M00179_20220322_Neg_1_MSA0039bacterial community 15-member community timepoint 16
SA306552M00179_20220322_Neg_1_MSA0023bacterial community 15-member community timepoint 16
SA306553M00179_20220322_Pos_1_MSA0029bacterial community 15-member community timepoint 17
SA306554M00179_20220322_Neg_1_MSA0029bacterial community 15-member community timepoint 17
SA306555M00179_20220322_Neg_1_MSA0047bacterial community 15-member community timepoint 17
SA306556M00179_20220322_Neg_1_MSA0078bacterial community 15-member community timepoint 17
SA306557M00179_20220322_Pos_1_MSA0047bacterial community 15-member community timepoint 17
SA306558M00179_20220322_Pos_1_MSA0078bacterial community 15-member community timepoint 17
SA306559M00179_20220322_Pos_1_MSA0019bacterial community 15-member community timepoint 18
SA306560M00179_20220322_Neg_1_MSA0019bacterial community 15-member community timepoint 18
SA306561M00179_20220322_Neg_1_MSA0052bacterial community 15-member community timepoint 18
SA306562M00179_20220322_Pos_1_MSA0052bacterial community 15-member community timepoint 18
SA306563M00179_20220322_Pos_1_MSA0015bacterial community 15-member community timepoint 18
SA306564M00179_20220322_Neg_1_MSA0015bacterial community 15-member community timepoint 18
SA306565M00179_20220322_Pos_1_MSA0004bacterial community 15-member community timepoint 19
SA306566M00179_20220322_Neg_1_MSA0021bacterial community 15-member community timepoint 19
SA306567M00179_20220322_Pos_1_MSA0034bacterial community 15-member community timepoint 19
SA306568M00179_20220322_Neg_1_MSA0034bacterial community 15-member community timepoint 19
SA306569M00179_20220322_Pos_1_MSA0021bacterial community 15-member community timepoint 19
SA306570M00179_20220322_Neg_1_MSA0004bacterial community 15-member community timepoint 19
SA306571M00179_20220322_Pos_1_MSA0040bacterial community 15-member community timepoint 2
SA306572M00179_20220322_Pos_1_MSA0038bacterial community 15-member community timepoint 2
SA306573M00179_20220322_Pos_1_MSA0018bacterial community 15-member community timepoint 2
SA306574M00179_20220322_Neg_1_MSA0018bacterial community 15-member community timepoint 2
SA306575M00179_20220322_Neg_1_MSA0040bacterial community 15-member community timepoint 2
SA306576M00179_20220322_Neg_1_MSA0038bacterial community 15-member community timepoint 2
SA306577M00179_20220322_Pos_1_MSA0036bacterial community 15-member community timepoint 20
SA306578M00179_20220322_Pos_1_MSA0069bacterial community 15-member community timepoint 20
SA306579M00179_20220322_Neg_1_MSA0036bacterial community 15-member community timepoint 20
SA306580M00179_20220322_Neg_1_MSA0069bacterial community 15-member community timepoint 20
SA306581M00179_20220322_Pos_1_MSA0049bacterial community 15-member community timepoint 20
SA306582M00179_20220322_Neg_1_MSA0049bacterial community 15-member community timepoint 20
SA306583M00179_20220322_Pos_1_MSA0058bacterial community 15-member community timepoint 21
SA306584M00179_20220322_Neg_1_MSA0041bacterial community 15-member community timepoint 21
SA306585M00179_20220322_Neg_1_MSA0002bacterial community 15-member community timepoint 21
SA306586M00179_20220322_Pos_1_MSA0041bacterial community 15-member community timepoint 21
SA306587M00179_20220322_Pos_1_MSA0002bacterial community 15-member community timepoint 21
SA306588M00179_20220322_Neg_1_MSA0058bacterial community 15-member community timepoint 21
SA306589M00179_20220322_Pos_1_MSA0030bacterial community 15-member community timepoint 22
SA306590M00179_20220322_Neg_1_MSA0059bacterial community 15-member community timepoint 22
SA306591M00179_20220322_Pos_1_MSA0051bacterial community 15-member community timepoint 22
SA306592M00179_20220322_Neg_1_MSA0051bacterial community 15-member community timepoint 22
SA306593M00179_20220322_Pos_1_MSA0059bacterial community 15-member community timepoint 22
SA306594M00179_20220322_Neg_1_MSA0030bacterial community 15-member community timepoint 22
SA306595M00179_20220322_Pos_1_MSA0014bacterial community 15-member community timepoint 23
SA306596M00179_20220322_Pos_1_MSA0007bacterial community 15-member community timepoint 23
SA306597M00179_20220322_Neg_1_MSA0007bacterial community 15-member community timepoint 23
SA306598M00179_20220322_Pos_1_MSA0072bacterial community 15-member community timepoint 23
SA306599M00179_20220322_Neg_1_MSA0072bacterial community 15-member community timepoint 23
SA306600M00179_20220322_Neg_1_MSA0014bacterial community 15-member community timepoint 23
SA306601M00179_20220322_Neg_1_MSA0020bacterial community 15-member community timepoint 3
SA306602M00179_20220322_Neg_1_MSA0026bacterial community 15-member community timepoint 3
SA306603M00179_20220322_Pos_1_MSA0065bacterial community 15-member community timepoint 3
SA306604M00179_20220322_Pos_1_MSA0020bacterial community 15-member community timepoint 3
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Collection:

Collection ID:CO002934
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 (Cell Host & Microbe (2022). https://doi.org/https://doi.org/10.1016/j.chom.2021.12.008, https://www.biorxiv.org/content/10.1101/2023.01.13.523996v1) 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 was 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

Treatment:

Treatment ID:TR002950
Treatment Summary:Many combinations of bacterial isolates were assayed. details can be found in the publicly available preprint here: https://www.biorxiv.org/content/10.1101/2022.05.30.494065v1.abstract

Sample Preparation:

Sampleprep ID:SP002947
Sampleprep Summary:Spent media were collected as described above and immediately stored at -80 °C. Samples were thawed only once, immediately before LC-MS/MS. Thawed samples were kept on ice, each sample was homogenized by pipetting prior to dispensing. Two 20-µL aliquots of supernatant were removed from each sample well and dispensed into two shallow 96-well polypropylene plates, maintained on ice. Additionally, 5 µL were removed from each sample and combined into a homogenous pool; this pool was dispensed in 20-µL aliquots and prepared in parallel with samples. These pooled samples were used for in-run quality control, injected at predefined intervals over the course of analysis to ensure consistent instrument performance over time. Samples were analyzed using two complementary chromatography methods: reversed phase (C18) and hydrophilic interaction chromatography (HILIC). HILIC data include in this study, C18 data can be found uploaded in a separate study. All samples were analyzed by positive and negative mode electrospray ionization (ESI+, ESI-). Sample analysis order was randomized to minimize potential bias in data acquisition. Procedural blanks were prepared by extracting 20 µL of water in place of bacterial supernatant. Procedural blanks were inserted throughout the run as additional quality control.

Combined analysis:

Analysis ID AN004625 AN004626
Analysis type MS MS
Chromatography type HILIC HILIC
Chromatography system Thermo Vanquish Thermo Vanquish
Column Waters Acquity BEH Amide (150 x 2.1mm, 1.7um) Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
MS Type ESI ESI
MS instrument type Orbitrap Orbitrap
MS instrument name Thermo Q Exactive HF hybrid Orbitrap Thermo Q Exactive HF hybrid Orbitrap
Ion Mode POSITIVE NEGATIVE
Units counts, height counts, height

Chromatography:

Chromatography ID:CH003481
Chromatography Summary:Bacterial supernatant were analyzed via hydrophilic interaction liquid chromatography (HILIC) coupled to a Thermo Q-Exactive HF high resolution mass spectrometer. 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 (https://www.nature.com/articles/s41587-020-0531-2) and queried against a combination of our in-house MS2 library (https://www.nature.com/articles/s41586-021-03707-9) and MassBank of North America, the largest freely available spectral repository (https://doi.org/10.1002/mas.21535). Annotations were scored using guidelines from the metabolomics standards initiative (https://www.nature.com/articles/nbt0807-846b). 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:Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)
Column Temperature:45C
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 of
Flow Rate:0.4 mL/min.
Solvent A:Water + 10mM ammonium formate + 0.125% formic acid
Solvent B:95% acetonitrile + 10mM ammonium formate + 0.125% formic acid
Chromatography Type:HILIC

MS:

MS ID:MS004371
Analysis ID:AN004625
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments: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. 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.
Ion Mode:POSITIVE
  
MS ID:MS004372
Analysis ID:AN004626
Instrument Name:Thermo Q Exactive HF hybrid Orbitrap
Instrument Type:Orbitrap
MS Type:ESI
MS Comments: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. 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.
Ion Mode:NEGATIVE
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