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.

Study ID	ST002832
Study Title	Resource competition predicts assembly of in vitro gut bacterial communities- HILIC
Study 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.
Email	bcdefelice@ucdavis.edu
Phone	5303564485
Submit Date	2023-08-24
Raw Data Available	Yes
Raw Data File Type(s)	raw(Thermo)
Analysis Type Detail	LC-MS
Release Date	2023-09-14
Release Version	1

Select appropriate tab below to view additional metadata details:

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
SA306505	M00179_20220322_Neg_1_MSA0053	bacterial community	15-member community timepoint 1
SA306506	M00179_20220322_Neg_1_MSA0045	bacterial community	15-member community timepoint 1
SA306507	M00179_20220322_Pos_1_MSA0045	bacterial community	15-member community timepoint 1
SA306508	M00179_20220322_Pos_1_MSA0053	bacterial community	15-member community timepoint 1
SA306509	M00179_20220322_Pos_1_MSA0046	bacterial community	15-member community timepoint 1
SA306510	M00179_20220322_Neg_1_MSA0046	bacterial community	15-member community timepoint 1
SA306511	M00179_20220322_Neg_1_MSA0022	bacterial community	15-member community timepoint 10
SA306512	M00179_20220322_Neg_1_MSA0025	bacterial community	15-member community timepoint 10
SA306513	M00179_20220322_Pos_1_MSA0025	bacterial community	15-member community timepoint 10
SA306514	M00179_20220322_Pos_1_MSA0035	bacterial community	15-member community timepoint 10
SA306515	M00179_20220322_Neg_1_MSA0035	bacterial community	15-member community timepoint 10
SA306516	M00179_20220322_Pos_1_MSA0022	bacterial community	15-member community timepoint 10
SA306517	M00179_20220322_Pos_1_MSA0001	bacterial community	15-member community timepoint 11
SA306518	M00179_20220322_Neg_1_MSA0055	bacterial community	15-member community timepoint 11
SA306519	M00179_20220322_Pos_1_MSA0055	bacterial community	15-member community timepoint 11
SA306520	M00179_20220322_Neg_1_MSA0005	bacterial community	15-member community timepoint 11
SA306521	M00179_20220322_Pos_1_MSA0005	bacterial community	15-member community timepoint 11
SA306522	M00179_20220322_Neg_1_MSA0001	bacterial community	15-member community timepoint 11
SA306523	M00179_20220322_Neg_1_MSA0063	bacterial community	15-member community timepoint 12
SA306524	M00179_20220322_Pos_1_MSA0063	bacterial community	15-member community timepoint 12
SA306525	M00179_20220322_Neg_1_MSA0042	bacterial community	15-member community timepoint 12
SA306526	M00179_20220322_Neg_1_MSA0074	bacterial community	15-member community timepoint 12
SA306527	M00179_20220322_Pos_1_MSA0042	bacterial community	15-member community timepoint 12
SA306528	M00179_20220322_Pos_1_MSA0074	bacterial community	15-member community timepoint 12
SA306529	M00179_20220322_Pos_1_MSA0024	bacterial community	15-member community timepoint 13
SA306530	M00179_20220322_Neg_1_MSA0032	bacterial community	15-member community timepoint 13
SA306531	M00179_20220322_Neg_1_MSA0044	bacterial community	15-member community timepoint 13
SA306532	M00179_20220322_Pos_1_MSA0044	bacterial community	15-member community timepoint 13
SA306533	M00179_20220322_Neg_1_MSA0024	bacterial community	15-member community timepoint 13
SA306534	M00179_20220322_Pos_1_MSA0032	bacterial community	15-member community timepoint 13
SA306535	M00179_20220322_Neg_1_MSA0056	bacterial community	15-member community timepoint 14
SA306536	M00179_20220322_Pos_1_MSA0006	bacterial community	15-member community timepoint 14
SA306537	M00179_20220322_Neg_1_MSA0006	bacterial community	15-member community timepoint 14
SA306538	M00179_20220322_Neg_1_MSA0033	bacterial community	15-member community timepoint 14
SA306539	M00179_20220322_Pos_1_MSA0056	bacterial community	15-member community timepoint 14
SA306540	M00179_20220322_Pos_1_MSA0033	bacterial community	15-member community timepoint 14
SA306541	M00179_20220322_Neg_1_MSA0054	bacterial community	15-member community timepoint 15
SA306542	M00179_20220322_Neg_1_MSA0064	bacterial community	15-member community timepoint 15
SA306543	M00179_20220322_Pos_1_MSA0054	bacterial community	15-member community timepoint 15
SA306544	M00179_20220322_Neg_1_MSA0062	bacterial community	15-member community timepoint 15
SA306545	M00179_20220322_Pos_1_MSA0064	bacterial community	15-member community timepoint 15
SA306546	M00179_20220322_Pos_1_MSA0062	bacterial community	15-member community timepoint 15
SA306547	M00179_20220322_Pos_1_MSA0023	bacterial community	15-member community timepoint 16
SA306548	M00179_20220322_Pos_1_MSA0050	bacterial community	15-member community timepoint 16
SA306549	M00179_20220322_Pos_1_MSA0039	bacterial community	15-member community timepoint 16
SA306550	M00179_20220322_Neg_1_MSA0050	bacterial community	15-member community timepoint 16
SA306551	M00179_20220322_Neg_1_MSA0039	bacterial community	15-member community timepoint 16
SA306552	M00179_20220322_Neg_1_MSA0023	bacterial community	15-member community timepoint 16
SA306553	M00179_20220322_Pos_1_MSA0029	bacterial community	15-member community timepoint 17
SA306554	M00179_20220322_Neg_1_MSA0029	bacterial community	15-member community timepoint 17
SA306555	M00179_20220322_Neg_1_MSA0047	bacterial community	15-member community timepoint 17
SA306556	M00179_20220322_Neg_1_MSA0078	bacterial community	15-member community timepoint 17
SA306557	M00179_20220322_Pos_1_MSA0047	bacterial community	15-member community timepoint 17
SA306558	M00179_20220322_Pos_1_MSA0078	bacterial community	15-member community timepoint 17
SA306559	M00179_20220322_Pos_1_MSA0019	bacterial community	15-member community timepoint 18
SA306560	M00179_20220322_Neg_1_MSA0019	bacterial community	15-member community timepoint 18
SA306561	M00179_20220322_Neg_1_MSA0052	bacterial community	15-member community timepoint 18
SA306562	M00179_20220322_Pos_1_MSA0052	bacterial community	15-member community timepoint 18
SA306563	M00179_20220322_Pos_1_MSA0015	bacterial community	15-member community timepoint 18
SA306564	M00179_20220322_Neg_1_MSA0015	bacterial community	15-member community timepoint 18
SA306565	M00179_20220322_Pos_1_MSA0004	bacterial community	15-member community timepoint 19
SA306566	M00179_20220322_Neg_1_MSA0021	bacterial community	15-member community timepoint 19
SA306567	M00179_20220322_Pos_1_MSA0034	bacterial community	15-member community timepoint 19
SA306568	M00179_20220322_Neg_1_MSA0034	bacterial community	15-member community timepoint 19
SA306569	M00179_20220322_Pos_1_MSA0021	bacterial community	15-member community timepoint 19
SA306570	M00179_20220322_Neg_1_MSA0004	bacterial community	15-member community timepoint 19
SA306571	M00179_20220322_Pos_1_MSA0040	bacterial community	15-member community timepoint 2
SA306572	M00179_20220322_Pos_1_MSA0038	bacterial community	15-member community timepoint 2
SA306573	M00179_20220322_Pos_1_MSA0018	bacterial community	15-member community timepoint 2
SA306574	M00179_20220322_Neg_1_MSA0018	bacterial community	15-member community timepoint 2
SA306575	M00179_20220322_Neg_1_MSA0040	bacterial community	15-member community timepoint 2
SA306576	M00179_20220322_Neg_1_MSA0038	bacterial community	15-member community timepoint 2
SA306577	M00179_20220322_Pos_1_MSA0036	bacterial community	15-member community timepoint 20
SA306578	M00179_20220322_Pos_1_MSA0069	bacterial community	15-member community timepoint 20
SA306579	M00179_20220322_Neg_1_MSA0036	bacterial community	15-member community timepoint 20
SA306580	M00179_20220322_Neg_1_MSA0069	bacterial community	15-member community timepoint 20
SA306581	M00179_20220322_Pos_1_MSA0049	bacterial community	15-member community timepoint 20
SA306582	M00179_20220322_Neg_1_MSA0049	bacterial community	15-member community timepoint 20
SA306583	M00179_20220322_Pos_1_MSA0058	bacterial community	15-member community timepoint 21
SA306584	M00179_20220322_Neg_1_MSA0041	bacterial community	15-member community timepoint 21
SA306585	M00179_20220322_Neg_1_MSA0002	bacterial community	15-member community timepoint 21
SA306586	M00179_20220322_Pos_1_MSA0041	bacterial community	15-member community timepoint 21
SA306587	M00179_20220322_Pos_1_MSA0002	bacterial community	15-member community timepoint 21
SA306588	M00179_20220322_Neg_1_MSA0058	bacterial community	15-member community timepoint 21
SA306589	M00179_20220322_Pos_1_MSA0030	bacterial community	15-member community timepoint 22
SA306590	M00179_20220322_Neg_1_MSA0059	bacterial community	15-member community timepoint 22
SA306591	M00179_20220322_Pos_1_MSA0051	bacterial community	15-member community timepoint 22
SA306592	M00179_20220322_Neg_1_MSA0051	bacterial community	15-member community timepoint 22
SA306593	M00179_20220322_Pos_1_MSA0059	bacterial community	15-member community timepoint 22
SA306594	M00179_20220322_Neg_1_MSA0030	bacterial community	15-member community timepoint 22
SA306595	M00179_20220322_Pos_1_MSA0014	bacterial community	15-member community timepoint 23
SA306596	M00179_20220322_Pos_1_MSA0007	bacterial community	15-member community timepoint 23
SA306597	M00179_20220322_Neg_1_MSA0007	bacterial community	15-member community timepoint 23
SA306598	M00179_20220322_Pos_1_MSA0072	bacterial community	15-member community timepoint 23
SA306599	M00179_20220322_Neg_1_MSA0072	bacterial community	15-member community timepoint 23
SA306600	M00179_20220322_Neg_1_MSA0014	bacterial community	15-member community timepoint 23
SA306601	M00179_20220322_Neg_1_MSA0020	bacterial community	15-member community timepoint 3
SA306602	M00179_20220322_Neg_1_MSA0026	bacterial community	15-member community timepoint 3
SA306603	M00179_20220322_Pos_1_MSA0065	bacterial community	15-member community timepoint 3
SA306604	M00179_20220322_Pos_1_MSA0020	bacterial 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.

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