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 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.
Institute
Stanford University
Last NameDeFelice
First NameBrian
Address1291 Welch Rd.
Emailbcdefelice@ucdavis.edu
Phone5303564485
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
https://dx.doi.org/10.21228/M8DB1F
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

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Factors:

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

mb_sample_id local_sample_id Genotype Treatment
SA306907metaboproj_165C_20220203Pos_BK6Analytical Blank Method Blank
SA306908metaboproj_165C_20220203Neg_BK8Analytical Blank Method Blank
SA306909metaboproj_165C_20220203Pos_BK5Analytical Blank Method Blank
SA306910metaboproj_165C_20220203Pos_BK3Analytical Blank Method Blank
SA306911metaboproj_165C_20220203Pos_BK2Analytical Blank Method Blank
SA306912metaboproj_165C_20220203Pos_BK7Analytical Blank Method Blank
SA306913metaboproj_165C_20220203Pos_BK4Analytical Blank Method Blank
SA306914metaboproj_165C_20220203Pos_BK8Analytical Blank Method Blank
SA306915metaboproj_165C_20220203Neg_BK3Analytical Blank Method Blank
SA306916metaboproj_165C_20220203Neg_BK2Analytical Blank Method Blank
SA306917metaboproj_165C_20220203Neg_BK5Analytical Blank Method Blank
SA306918metaboproj_165C_20220203Neg_BK4Analytical Blank Method Blank
SA306919metaboproj_165C_20220203Neg_BK6Analytical Blank Method Blank
SA306920metaboproj_165C_20220203Neg_BK7Analytical Blank Method Blank
SA306933metaboproj_165C_20220203_Neg_1_MSA0051bacterial community mGAM fresh
SA306934metaboproj_165C_20220203_Pos_1_MSA0045bacterial community mGAM fresh
SA306935metaboproj_165C_20220203_Pos_1_MSA0051bacterial community mGAM fresh
SA306936metaboproj_165C_20220203_Pos_1_MSA0018bacterial community mGAM fresh
SA306937metaboproj_165C_20220203_Neg_1_MSA0045bacterial community mGAM fresh
SA306938metaboproj_165C_20220203_Neg_1_MSA0018bacterial community mGAM fresh
SA306939metaboproj_165C_20220203_Pos_1_MSA0034bacterial community mGAM spent by Bacteroides fragilis
SA306940metaboproj_165C_20220203_Pos_1_MSA0022bacterial community mGAM spent by Bacteroides fragilis
SA306941metaboproj_165C_20220203_Pos_1_MSA0020bacterial community mGAM spent by Bacteroides fragilis
SA306942metaboproj_165C_20220203_Neg_1_MSA0020bacterial community mGAM spent by Bacteroides fragilis
SA306943metaboproj_165C_20220203_Neg_1_MSA0022bacterial community mGAM spent by Bacteroides fragilis
SA306944metaboproj_165C_20220203_Neg_1_MSA0034bacterial community mGAM spent by Bacteroides fragilis
SA306945metaboproj_165C_20220203_Neg_1_MSA0038bacterial community mGAM spent by Bacteroides thetaiotaomicron
SA306946metaboproj_165C_20220203_Neg_1_MSA0052bacterial community mGAM spent by Bacteroides thetaiotaomicron
SA306947metaboproj_165C_20220203_Neg_1_MSA0048bacterial community mGAM spent by Bacteroides thetaiotaomicron
SA306948metaboproj_165C_20220203_Pos_1_MSA0048bacterial community mGAM spent by Bacteroides thetaiotaomicron
SA306949metaboproj_165C_20220203_Pos_1_MSA0052bacterial community mGAM spent by Bacteroides thetaiotaomicron
SA306950metaboproj_165C_20220203_Pos_1_MSA0038bacterial community mGAM spent by Bacteroides thetaiotaomicron
SA306951metaboproj_165C_20220203_Neg_1_MSA0003bacterial community mGAM spent by Bacteroides uniformis
SA306952metaboproj_165C_20220203_Pos_1_MSA0009bacterial community mGAM spent by Bacteroides uniformis
SA306953metaboproj_165C_20220203_Pos_1_MSA0063bacterial community mGAM spent by Bacteroides uniformis
SA306954metaboproj_165C_20220203_Pos_1_MSA0003bacterial community mGAM spent by Bacteroides uniformis
SA306955metaboproj_165C_20220203_Neg_1_MSA0009bacterial community mGAM spent by Bacteroides uniformis
SA306956metaboproj_165C_20220203_Neg_1_MSA0063bacterial community mGAM spent by Bacteroides uniformis
SA306957metaboproj_165C_20220203_Pos_1_MSA0028bacterial community mGAM spent by Blautia producta
SA306958metaboproj_165C_20220203_Neg_1_MSA0028bacterial community mGAM spent by Blautia producta
SA306959metaboproj_165C_20220203_Pos_1_MSA0004bacterial community mGAM spent by Blautia producta
SA306960metaboproj_165C_20220203_Neg_1_MSA0004bacterial community mGAM spent by Blautia producta
SA306961metaboproj_165C_20220203_Neg_1_MSA0005bacterial community mGAM spent by Blautia producta
SA306962metaboproj_165C_20220203_Pos_1_MSA0005bacterial community mGAM spent by Blautia producta
SA306963metaboproj_165C_20220203_Pos_1_MSA0013bacterial community mGAM spent by Clostridium clostridioforme
SA306964metaboproj_165C_20220203_Neg_1_MSA0013bacterial community mGAM spent by Clostridium clostridioforme
SA306965metaboproj_165C_20220203_Pos_1_MSA0024bacterial community mGAM spent by Clostridium clostridioforme
SA306966metaboproj_165C_20220203_Neg_1_MSA0017bacterial community mGAM spent by Clostridium clostridioforme
SA306967metaboproj_165C_20220203_Pos_1_MSA0017bacterial community mGAM spent by Clostridium clostridioforme
SA306968metaboproj_165C_20220203_Neg_1_MSA0049bacterial community mGAM spent by Clostridium hathewayi
SA306969metaboproj_165C_20220203_Neg_1_MSA0056bacterial community mGAM spent by Clostridium hathewayi
SA306970metaboproj_165C_20220203_Pos_1_MSA0049bacterial community mGAM spent by Clostridium hathewayi
SA306971metaboproj_165C_20220203_Pos_1_MSA0056bacterial community mGAM spent by Clostridium hathewayi
SA306972metaboproj_165C_20220203_Pos_1_MSA0014bacterial community mGAM spent by Clostridium hathewayi
SA306973metaboproj_165C_20220203_Pos_1_MSA0055bacterial community mGAM spent by Clostridium hylemonae
SA306974metaboproj_165C_20220203_Pos_1_MSA0023bacterial community mGAM spent by Clostridium hylemonae
SA306975metaboproj_165C_20220203_Neg_1_MSA0023bacterial community mGAM spent by Clostridium hylemonae
SA306976metaboproj_165C_20220203_Neg_1_MSA0055bacterial community mGAM spent by Clostridium hylemonae
SA306977metaboproj_165C_20220203_Neg_1_MSA0042bacterial community mGAM spent by Clostridium hylemonae
SA306978metaboproj_165C_20220203_Pos_1_MSA0042bacterial community mGAM spent by Clostridium hylemonae
SA306979metaboproj_165C_20220203_Neg_1_MSA0044bacterial community mGAM spent by Clostridium scindens
SA306980metaboproj_165C_20220203_Neg_1_MSA0035bacterial community mGAM spent by Clostridium scindens
SA306981metaboproj_165C_20220203_Neg_1_MSA0046bacterial community mGAM spent by Clostridium scindens
SA306982metaboproj_165C_20220203_Pos_1_MSA0046bacterial community mGAM spent by Clostridium scindens
SA306983metaboproj_165C_20220203_Pos_1_MSA0035bacterial community mGAM spent by Clostridium scindens
SA306984metaboproj_165C_20220203_Pos_1_MSA0044bacterial community mGAM spent by Clostridium scindens
SA306985metaboproj_165C_20220203_Neg_1_MSA0053bacterial community mGAM spent by Clostridium symbiosum
SA306986metaboproj_165C_20220203_Pos_1_MSA0010bacterial community mGAM spent by Clostridium symbiosum
SA306987metaboproj_165C_20220203_Pos_1_MSA0001bacterial community mGAM spent by Clostridium symbiosum
SA306988metaboproj_165C_20220203_Pos_1_MSA0053bacterial community mGAM spent by Clostridium symbiosum
SA306989metaboproj_165C_20220203_Neg_1_MSA0010bacterial community mGAM spent by Clostridium symbiosum
SA306990metaboproj_165C_20220203_Pos_1_MSA0058bacterial community mGAM spent by Enterococcus faecalis
SA306991metaboproj_165C_20220203_Neg_1_MSA0058bacterial community mGAM spent by Enterococcus faecalis
SA306992metaboproj_165C_20220203_Pos_1_MSA0019bacterial community mGAM spent by Enterococcus faecalis
SA306993metaboproj_165C_20220203_Neg_1_MSA0021bacterial community mGAM spent by Enterococcus faecalis
SA306994metaboproj_165C_20220203_Pos_1_MSA0021bacterial community mGAM spent by Enterococcus faecalis
SA306995metaboproj_165C_20220203_Neg_1_MSA0019bacterial community mGAM spent by Enterococcus faecalis
SA306996metaboproj_165C_20220203_Neg_1_MSA0059bacterial community mGAM spent by Enterococcus faecium
SA306997metaboproj_165C_20220203_Neg_1_MSA0060bacterial community mGAM spent by Enterococcus faecium
SA306998metaboproj_165C_20220203_Neg_1_MSA0036bacterial community mGAM spent by Enterococcus faecium
SA306999metaboproj_165C_20220203_Pos_1_MSA0060bacterial community mGAM spent by Enterococcus faecium
SA307000metaboproj_165C_20220203_Pos_1_MSA0036bacterial community mGAM spent by Enterococcus faecium
SA307001metaboproj_165C_20220203_Pos_1_MSA0059bacterial community mGAM spent by Enterococcus faecium
SA307002metaboproj_165C_20220203_Neg_1_MSA0029bacterial community mGAM spent by Enterococcus hirae
SA307003metaboproj_165C_20220203_Neg_1_MSA0025bacterial community mGAM spent by Enterococcus hirae
SA307004metaboproj_165C_20220203_Pos_1_MSA0029bacterial community mGAM spent by Enterococcus hirae
SA307005metaboproj_165C_20220203_Neg_1_MSA0011bacterial community mGAM spent by Enterococcus hirae
SA307006metaboproj_165C_20220203_Pos_1_MSA0011bacterial community mGAM spent by Enterococcus hirae
SA307007metaboproj_165C_20220203_Pos_1_MSA0025bacterial community mGAM spent by Enterococcus hirae
SA307008metaboproj_165C_20220203_Neg_1_MSA0062bacterial community mGAM spent by Escherichia fergusonii
SA307009metaboproj_165C_20220203_Neg_1_MSA0054bacterial community mGAM spent by Escherichia fergusonii
SA307010metaboproj_165C_20220203_Pos_1_MSA0002bacterial community mGAM spent by Escherichia fergusonii
SA307011metaboproj_165C_20220203_Pos_1_MSA0054bacterial community mGAM spent by Escherichia fergusonii
SA307012metaboproj_165C_20220203_Pos_1_MSA0062bacterial community mGAM spent by Escherichia fergusonii
SA307013metaboproj_165C_20220203_Neg_1_MSA0002bacterial community mGAM spent by Escherichia fergusonii
SA307014metaboproj_165C_20220203_Pos_1_MSA0031bacterial community mGAM spent by Flavonifractor plautii
SA307015metaboproj_165C_20220203_Pos_1_MSA0039bacterial community mGAM spent by Flavonifractor plautii
SA307016metaboproj_165C_20220203_Neg_1_MSA0031bacterial community mGAM spent by Flavonifractor plautii
SA307017metaboproj_165C_20220203_Neg_1_MSA0033bacterial community mGAM spent by Flavonifractor plautii
SA307018metaboproj_165C_20220203_Neg_1_MSA0039bacterial community mGAM spent by Flavonifractor plautii
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