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. |
| 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:
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 |
