Summary of Study ST002833

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 ID	ST002833
Study Title	Resource competition predicts assembly of in vitro gut bacterial communities- 2022-C18
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	2023-08-25
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:	SU002942
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
SA306907	metaboproj_165C_20220203Pos_BK6	Analytical Blank	Method Blank
SA306908	metaboproj_165C_20220203Neg_BK8	Analytical Blank	Method Blank
SA306909	metaboproj_165C_20220203Pos_BK5	Analytical Blank	Method Blank
SA306910	metaboproj_165C_20220203Pos_BK3	Analytical Blank	Method Blank
SA306911	metaboproj_165C_20220203Pos_BK2	Analytical Blank	Method Blank
SA306912	metaboproj_165C_20220203Pos_BK7	Analytical Blank	Method Blank
SA306913	metaboproj_165C_20220203Pos_BK4	Analytical Blank	Method Blank
SA306914	metaboproj_165C_20220203Pos_BK8	Analytical Blank	Method Blank
SA306915	metaboproj_165C_20220203Neg_BK3	Analytical Blank	Method Blank
SA306916	metaboproj_165C_20220203Neg_BK2	Analytical Blank	Method Blank
SA306917	metaboproj_165C_20220203Neg_BK5	Analytical Blank	Method Blank
SA306918	metaboproj_165C_20220203Neg_BK4	Analytical Blank	Method Blank
SA306919	metaboproj_165C_20220203Neg_BK6	Analytical Blank	Method Blank
SA306920	metaboproj_165C_20220203Neg_BK7	Analytical Blank	Method Blank
SA306933	metaboproj_165C_20220203_Neg_1_MSA0051	bacterial community	mGAM fresh
SA306934	metaboproj_165C_20220203_Pos_1_MSA0045	bacterial community	mGAM fresh
SA306935	metaboproj_165C_20220203_Pos_1_MSA0051	bacterial community	mGAM fresh
SA306936	metaboproj_165C_20220203_Pos_1_MSA0018	bacterial community	mGAM fresh
SA306937	metaboproj_165C_20220203_Neg_1_MSA0045	bacterial community	mGAM fresh
SA306938	metaboproj_165C_20220203_Neg_1_MSA0018	bacterial community	mGAM fresh
SA306939	metaboproj_165C_20220203_Pos_1_MSA0034	bacterial community	mGAM spent by Bacteroides fragilis
SA306940	metaboproj_165C_20220203_Pos_1_MSA0022	bacterial community	mGAM spent by Bacteroides fragilis
SA306941	metaboproj_165C_20220203_Pos_1_MSA0020	bacterial community	mGAM spent by Bacteroides fragilis
SA306942	metaboproj_165C_20220203_Neg_1_MSA0020	bacterial community	mGAM spent by Bacteroides fragilis
SA306943	metaboproj_165C_20220203_Neg_1_MSA0022	bacterial community	mGAM spent by Bacteroides fragilis
SA306944	metaboproj_165C_20220203_Neg_1_MSA0034	bacterial community	mGAM spent by Bacteroides fragilis
SA306945	metaboproj_165C_20220203_Neg_1_MSA0038	bacterial community	mGAM spent by Bacteroides thetaiotaomicron
SA306946	metaboproj_165C_20220203_Neg_1_MSA0052	bacterial community	mGAM spent by Bacteroides thetaiotaomicron
SA306947	metaboproj_165C_20220203_Neg_1_MSA0048	bacterial community	mGAM spent by Bacteroides thetaiotaomicron
SA306948	metaboproj_165C_20220203_Pos_1_MSA0048	bacterial community	mGAM spent by Bacteroides thetaiotaomicron
SA306949	metaboproj_165C_20220203_Pos_1_MSA0052	bacterial community	mGAM spent by Bacteroides thetaiotaomicron
SA306950	metaboproj_165C_20220203_Pos_1_MSA0038	bacterial community	mGAM spent by Bacteroides thetaiotaomicron
SA306951	metaboproj_165C_20220203_Neg_1_MSA0003	bacterial community	mGAM spent by Bacteroides uniformis
SA306952	metaboproj_165C_20220203_Pos_1_MSA0009	bacterial community	mGAM spent by Bacteroides uniformis
SA306953	metaboproj_165C_20220203_Pos_1_MSA0063	bacterial community	mGAM spent by Bacteroides uniformis
SA306954	metaboproj_165C_20220203_Pos_1_MSA0003	bacterial community	mGAM spent by Bacteroides uniformis
SA306955	metaboproj_165C_20220203_Neg_1_MSA0009	bacterial community	mGAM spent by Bacteroides uniformis
SA306956	metaboproj_165C_20220203_Neg_1_MSA0063	bacterial community	mGAM spent by Bacteroides uniformis
SA306957	metaboproj_165C_20220203_Pos_1_MSA0028	bacterial community	mGAM spent by Blautia producta
SA306958	metaboproj_165C_20220203_Neg_1_MSA0028	bacterial community	mGAM spent by Blautia producta
SA306959	metaboproj_165C_20220203_Pos_1_MSA0004	bacterial community	mGAM spent by Blautia producta
SA306960	metaboproj_165C_20220203_Neg_1_MSA0004	bacterial community	mGAM spent by Blautia producta
SA306961	metaboproj_165C_20220203_Neg_1_MSA0005	bacterial community	mGAM spent by Blautia producta
SA306962	metaboproj_165C_20220203_Pos_1_MSA0005	bacterial community	mGAM spent by Blautia producta
SA306963	metaboproj_165C_20220203_Pos_1_MSA0013	bacterial community	mGAM spent by Clostridium clostridioforme
SA306964	metaboproj_165C_20220203_Neg_1_MSA0013	bacterial community	mGAM spent by Clostridium clostridioforme
SA306965	metaboproj_165C_20220203_Pos_1_MSA0024	bacterial community	mGAM spent by Clostridium clostridioforme
SA306966	metaboproj_165C_20220203_Neg_1_MSA0017	bacterial community	mGAM spent by Clostridium clostridioforme
SA306967	metaboproj_165C_20220203_Pos_1_MSA0017	bacterial community	mGAM spent by Clostridium clostridioforme
SA306968	metaboproj_165C_20220203_Neg_1_MSA0049	bacterial community	mGAM spent by Clostridium hathewayi
SA306969	metaboproj_165C_20220203_Neg_1_MSA0056	bacterial community	mGAM spent by Clostridium hathewayi
SA306970	metaboproj_165C_20220203_Pos_1_MSA0049	bacterial community	mGAM spent by Clostridium hathewayi
SA306971	metaboproj_165C_20220203_Pos_1_MSA0056	bacterial community	mGAM spent by Clostridium hathewayi
SA306972	metaboproj_165C_20220203_Pos_1_MSA0014	bacterial community	mGAM spent by Clostridium hathewayi
SA306973	metaboproj_165C_20220203_Pos_1_MSA0055	bacterial community	mGAM spent by Clostridium hylemonae
SA306974	metaboproj_165C_20220203_Pos_1_MSA0023	bacterial community	mGAM spent by Clostridium hylemonae
SA306975	metaboproj_165C_20220203_Neg_1_MSA0023	bacterial community	mGAM spent by Clostridium hylemonae
SA306976	metaboproj_165C_20220203_Neg_1_MSA0055	bacterial community	mGAM spent by Clostridium hylemonae
SA306977	metaboproj_165C_20220203_Neg_1_MSA0042	bacterial community	mGAM spent by Clostridium hylemonae
SA306978	metaboproj_165C_20220203_Pos_1_MSA0042	bacterial community	mGAM spent by Clostridium hylemonae
SA306979	metaboproj_165C_20220203_Neg_1_MSA0044	bacterial community	mGAM spent by Clostridium scindens
SA306980	metaboproj_165C_20220203_Neg_1_MSA0035	bacterial community	mGAM spent by Clostridium scindens
SA306981	metaboproj_165C_20220203_Neg_1_MSA0046	bacterial community	mGAM spent by Clostridium scindens
SA306982	metaboproj_165C_20220203_Pos_1_MSA0046	bacterial community	mGAM spent by Clostridium scindens
SA306983	metaboproj_165C_20220203_Pos_1_MSA0035	bacterial community	mGAM spent by Clostridium scindens
SA306984	metaboproj_165C_20220203_Pos_1_MSA0044	bacterial community	mGAM spent by Clostridium scindens
SA306985	metaboproj_165C_20220203_Neg_1_MSA0053	bacterial community	mGAM spent by Clostridium symbiosum
SA306986	metaboproj_165C_20220203_Pos_1_MSA0010	bacterial community	mGAM spent by Clostridium symbiosum
SA306987	metaboproj_165C_20220203_Pos_1_MSA0001	bacterial community	mGAM spent by Clostridium symbiosum
SA306988	metaboproj_165C_20220203_Pos_1_MSA0053	bacterial community	mGAM spent by Clostridium symbiosum
SA306989	metaboproj_165C_20220203_Neg_1_MSA0010	bacterial community	mGAM spent by Clostridium symbiosum
SA306990	metaboproj_165C_20220203_Pos_1_MSA0058	bacterial community	mGAM spent by Enterococcus faecalis
SA306991	metaboproj_165C_20220203_Neg_1_MSA0058	bacterial community	mGAM spent by Enterococcus faecalis
SA306992	metaboproj_165C_20220203_Pos_1_MSA0019	bacterial community	mGAM spent by Enterococcus faecalis
SA306993	metaboproj_165C_20220203_Neg_1_MSA0021	bacterial community	mGAM spent by Enterococcus faecalis
SA306994	metaboproj_165C_20220203_Pos_1_MSA0021	bacterial community	mGAM spent by Enterococcus faecalis
SA306995	metaboproj_165C_20220203_Neg_1_MSA0019	bacterial community	mGAM spent by Enterococcus faecalis
SA306996	metaboproj_165C_20220203_Neg_1_MSA0059	bacterial community	mGAM spent by Enterococcus faecium
SA306997	metaboproj_165C_20220203_Neg_1_MSA0060	bacterial community	mGAM spent by Enterococcus faecium
SA306998	metaboproj_165C_20220203_Neg_1_MSA0036	bacterial community	mGAM spent by Enterococcus faecium
SA306999	metaboproj_165C_20220203_Pos_1_MSA0060	bacterial community	mGAM spent by Enterococcus faecium
SA307000	metaboproj_165C_20220203_Pos_1_MSA0036	bacterial community	mGAM spent by Enterococcus faecium
SA307001	metaboproj_165C_20220203_Pos_1_MSA0059	bacterial community	mGAM spent by Enterococcus faecium
SA307002	metaboproj_165C_20220203_Neg_1_MSA0029	bacterial community	mGAM spent by Enterococcus hirae
SA307003	metaboproj_165C_20220203_Neg_1_MSA0025	bacterial community	mGAM spent by Enterococcus hirae
SA307004	metaboproj_165C_20220203_Pos_1_MSA0029	bacterial community	mGAM spent by Enterococcus hirae
SA307005	metaboproj_165C_20220203_Neg_1_MSA0011	bacterial community	mGAM spent by Enterococcus hirae
SA307006	metaboproj_165C_20220203_Pos_1_MSA0011	bacterial community	mGAM spent by Enterococcus hirae
SA307007	metaboproj_165C_20220203_Pos_1_MSA0025	bacterial community	mGAM spent by Enterococcus hirae
SA307008	metaboproj_165C_20220203_Neg_1_MSA0062	bacterial community	mGAM spent by Escherichia fergusonii
SA307009	metaboproj_165C_20220203_Neg_1_MSA0054	bacterial community	mGAM spent by Escherichia fergusonii
SA307010	metaboproj_165C_20220203_Pos_1_MSA0002	bacterial community	mGAM spent by Escherichia fergusonii
SA307011	metaboproj_165C_20220203_Pos_1_MSA0054	bacterial community	mGAM spent by Escherichia fergusonii
SA307012	metaboproj_165C_20220203_Pos_1_MSA0062	bacterial community	mGAM spent by Escherichia fergusonii
SA307013	metaboproj_165C_20220203_Neg_1_MSA0002	bacterial community	mGAM spent by Escherichia fergusonii
SA307014	metaboproj_165C_20220203_Pos_1_MSA0031	bacterial community	mGAM spent by Flavonifractor plautii
SA307015	metaboproj_165C_20220203_Pos_1_MSA0039	bacterial community	mGAM spent by Flavonifractor plautii
SA307016	metaboproj_165C_20220203_Neg_1_MSA0031	bacterial community	mGAM spent by Flavonifractor plautii
SA307017	metaboproj_165C_20220203_Neg_1_MSA0033	bacterial community	mGAM spent by Flavonifractor plautii
SA307018	metaboproj_165C_20220203_Neg_1_MSA0039	bacterial community	mGAM spent by Flavonifractor plautii

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Collection:

Collection ID:	CO002935
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 (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 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

Treatment:

Treatment ID:	TR002951
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:	SP002948
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). 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:

SP002948

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). 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	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 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:	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 (https://www.nature.com/articles/s41587-020-0531-2) and queried against a combination of our in-house MS2 library and MassBank of North America, the largest freely available spectral repository (https://doi.org/10.1002/mas.21535). 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

MS:

MS ID:	MS004373
Analysis ID:	AN004627
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:	MS004374
Analysis ID:	AN004628
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