WoM Data Sources
- Kosina SM, Danielewicz MA, Mohammed M, Ray J, Suh Y, Yilmaz S, et al. Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism. ACS Synth Biol. 2016;5:569–76. DOI: 10.1021/acssynbio.5b00236.
- Baran R, Brodie EL, Mayberry-Lewis J, Hummel E, Da Rocha UN, Chakraborty R, et al. Exometabolite niche partitioning among sympatric soil bacteria. Nat Commun. 2015;6:8289. DOI: 10.1038/ncomms9289.
- Baran R, Bowen BP, Northen TR. Untargeted metabolic footprinting reveals a surprising breadth of metabolite uptake and release by Synechococcus sp. PCC 7002. Mol Biosyst. 2011;7:3200. DOI: 10.1039/c1mb05196b.
- Erbilgin O, Bowen BP, Kosina SM, Jenkins S, Lau RK, Northen TR. Dynamic substrate preferences and predicted metabolic properties of a simple microbial consortium. 2016. DOI: 10.1186/s12859-017-1478-2.
- Kosina SM, Greiner A, Lau RK, Jenkins S, Baran R, Bowen BP, Northen TR. Web of Microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes. BMC Microbiology, September 12, 2018 DOI: 10.1186/s12866-018-1256-y. Data available at https://genome.jgi.doe.gov/portal/ENIBEMetabolites_FD/ENIBEMetabolites_FD.info.html
- Zhalnina, K., Louie, K.B., Hao, Z., Mansoori, N., da Rocha, U.N., Shi, S., Cho, H., Karaoz, U., Loqué, D., Bowen, B.P., Firestone, M.K., Northen, T.R., Brodie, E.L., 2018. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nature Microbiology 3, 470–480. doi:10.1038/s41564-018-0129-3 DOI: https://doi.org/10.1038/s41564-018-0129-3. Data available at https://www.nature.com/articles/s41564-018-0129-3#Sec23
Detailed Data Sources
References for WoM data by environment and organism.
| Environment | Organism | Reference |
|---|---|---|
| A+ minimal | The Environment | 3 |
| A+ minimal | Synechococcus sp. PCC7002 | 3 |
| A+ with Synechococcus extract | The Environment | 3 |
| A+ with Synechococcus extract | Synechococcus sp. PCC7002 | 3 |
| A+ with yeast extract | The Environment | 3 |
| A+ with yeast extract | Synechococcus sp. PCC7002 | 3 |
| A+:MEBM (1:1) | The Environment | 3 |
| A+:MEBM (1:1) | Synechococcus sp. PCC7002 | 3 |
| Avena barbata root exudate (2018KZ) | The Environment | 6 |
| BG11+6crustisoExtract | Arthrobacter sp. (D1B45) | 2 |
| BG11+6crustisoExtract | Bacillus sp. 2 (L2B47) | 2 |
| BG11+6crustisoExtract | Bacillus sp. 2 (D1B51) | 2 |
| BG11+6crustisoExtract | Bosea sp. (L1B56) | 2 |
| BG11+6crustisoExtract | The Environment | 2 |
| BG11+6crustisoExtract | Methylobacterium sp. (D1B20) | 2 |
| BG11+6crustisoExtract | Modestobacter sp. (L1B44) | 2 |
| BG11+6crustisoExtract | Microcoleus vaginatus (PCC9802) | 2 |
| BG11+MvExtract | Arthrobacter sp. (D1B45) | 2 |
| BG11+MvExtract | Bacillus sp. 2 (L2B47) | 2 |
| BG11+MvExtract | Bacillus sp. 2 (D1B51) | 2 |
| BG11+MvExtract | Bosea sp. (L1B56) | 2 |
| BG11+MvExtract | The Environment | 2 |
| BG11+MvExtract | Methylobacterium sp. (D1B20) | 2 |
| BG11+MvExtract | Modestobacter sp. (L1B44) | 2 |
| BG11+MvExtract | Microcoleus vaginatus (PCC9802) | 2 |
| Biological Soil Crust Porewater (Green Butte Site, Collection: Rajeev 2013 ISME J. 7(11):2178) | Native microbiome: 018min Incubation | 2 |
| Biological Soil Crust Porewater (Green Butte Site, Collection: Rajeev 2013 ISME J. 7(11):2178) | Native microbiome: 540min Incubation | 2 |
| Biological Soil Crust Porewater (Green Butte Site, Collection: Rajeev 2013 ISME J. 7(11):2178) | The Environment | 2 |
| OE-MinimalGlucoseAA | The Environment | 4 |
| OE-MinimalGlucoseAA | t0 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica | 4 |
| OE-MinimalGlucoseAA | t1 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica | 4 |
| OE-MinimalGlucoseAA | t2 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica | 4 |
| OE-MinimalGlucoseAA | t3 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica | 4 |
| OE-MinimalGlucoseAA | t4 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica | 4 |
| OE-MinimalGlucoseAA | t5 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica | 4 |
| OE-MinimalGlucoseAA | t6 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica | 4 |
| OE-MinimalGlucoseAA | t7 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica | 4 |
| OE-MinimalGlucoseAA | t8 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica | 4 |
| OE-MinimalGlucoseAA | t9 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica | 4 |
| R2A | Phenylobacterium sp. (GW123-8A04) | 5 |
| R2A | Acidovorax sp. (GW101-3E06) | 5 |
| R2A | Rhizobium sp. (GW101-3B10) | 5 |
| R2A | Pseudomonas sp. (FW300-N2E3) | 5 |
| R2A | Pseudomonas sp. (GW456-L13) | 5 |
| R2A | The Environment | 5 |
| R2A | Pseudomonas sp. (FW300-N2A2) | 5 |
| R2A | Pseudomonas sp. (GW456-L15) | 5 |
| R2A | Pseudomonas sp. (FW507-14TSA) | 5 |
| R2A | Pseudomonas sp. (FW300-N2F2) | 5 |
| R2A | Bacillus sp. (FW507-8R2A) | 5 |
| ZMMG | The Environment | 1 |
| ZMMG | Zymomonas mobilis strain ZM4 (ATCC 31821) | 1 |
| ZMMG | Escherichia coli strain BW25113 | 1 |
| ZMMG | Theoretical: Escherichia coli JW0233 proA, proline auxotroph | 1 |
| ZMMG | Theoretical: Escherichia coli JW2580 pheA, phenylalanine auxotroph | 1 |
| ZMMG | Theoretical: Escherichia coli JW3745 ilvA, isoleucine auxotroph | 1 |
| ZMMG | Theoretical: Zymomonas mobilis ZMO0748 cysK, cysteine auxotroph | 1 |
