{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002833","ANALYSIS_ID":"AN004627","VERSION":"1","CREATED_ON":"August 28, 2023, 2:26 pm"},

"PROJECT":{"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"},

"STUDY":{"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"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Bacteroides thetaiotaomicron","TAXONOMY_ID":"8188","SUBJECT_COMMENTS":"Fecal derived communities and isolates, supernatant was assayed"},
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{
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{
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{
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"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0038",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0038.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0039",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Flavonifractor plautii"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0039.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0042",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hylemonae"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0042.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0044",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium scindens"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0044.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0045",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM fresh"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0045.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0046",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium scindens"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0046.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0047",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0047.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0048",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0048.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0049",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hathewayi"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0049.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0050",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Parabacteroides distasonis"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0050.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0051",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM fresh"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0051.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0052",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides thetaiotaomicron"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0052.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0053",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium symbiosum"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0053.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0054",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Escherichia fergusonii"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0054.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0055",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hylemonae"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0055.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0056",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Clostridium hathewayi"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0056.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0058",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Enterococcus faecalis"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0058.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0059",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0059.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0060",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Enterococcus faecium"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0060.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0062",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Escherichia fergusonii"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0062.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203_Pos_1_MSA0063",
"Factors":{"Genotype":"bacterial community","Treatment":"mGAM spent by Bacteroides uniformis"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203_Pos_1_MSA0063.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_BK2",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_BK2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_BK3",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_BK3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_BK4",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_BK4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_BK5",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_BK5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_BK6",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_BK6.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_BK7",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_BK7.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_BK8",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_BK8.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_QC2",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_QC2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_QC3",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_QC3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_QC4",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_QC4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_QC5",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_QC5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_QC6",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_QC6.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Neg_QC7",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Neg_QC7.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_BK2",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_BK2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_BK3",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_BK3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_BK4",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_BK4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_BK5",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_BK5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_BK6",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_BK6.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_BK7",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_BK7.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_BK8",
"Factors":{"Genotype":"Analytical Blank","Treatment":"Method Blank"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_BK8.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_QC2",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_QC2.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_QC3",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_QC3.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_QC4",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_QC4.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_QC5",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_QC5.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_QC6",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_QC6.raw"}
},
{
"Subject ID":"-",
"Sample ID":"metaboproj_165C_20220203Pos_QC7",
"Factors":{"Genotype":"Quality Control","Treatment":"Sample Pool"},
"Additional sample data":{"RAW_FILE_NAME":"metaboproj_165C_20220203Pos_QC7.raw"}
}
],
"COLLECTION":{"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_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"},

"SAMPLEPREP":{"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."},

"CHROMATOGRAPHY":{"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.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Agilent Zorbax SB-C18 column (100 x 3.0 mm, 1.8 um)","SOLVENT_A":"Water + 0.1% formic acid","SOLVENT_B":"Acetonitrile + 0.1% formic acid","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.","COLUMN_TEMPERATURE":"40C"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF hybrid Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","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.","MS_RESULTS_FILE":"ST002833_AN004627_Results.txt UNITS:counts, height Has m/z:Yes Has RT:Yes RT units:Minutes"}

}