WebofMicrobes analyzing the chemistry between microbes

WoM Data Sources

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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. In Review. 2018. Data available at https://genome.jgi.doe.gov/portal/ENIBEMetabolites_FD/ENIBEMetabolites_FD.info.html
  6. Detailed Data Sources

    References for WoM data by environment and organism.

    EnvironmentOrganismReference
    A+ minimalThe Environment3
    A+ minimalSynechococcus sp. PCC70023
    A+ with Synechococcus extractThe Environment3
    A+ with Synechococcus extractSynechococcus sp. PCC70023
    A+ with yeast extractThe Environment3
    A+ with yeast extractSynechococcus sp. PCC70023
    A+:MEBM (1:1)The Environment3
    A+:MEBM (1:1)Synechococcus sp. PCC70023
    BG11+6crustisoExtractArthrobacter sp. (D1B45)2
    BG11+6crustisoExtractBacillus sp. 2 (L2B47)2
    BG11+6crustisoExtractBacillus sp. 2 (D1B51)2
    BG11+6crustisoExtractBosea sp. (L1B56)2
    BG11+6crustisoExtractThe Environment2
    BG11+6crustisoExtractMethylobacterium sp. (D1B20)2
    BG11+6crustisoExtractModestobacter sp. (L1B44)2
    BG11+6crustisoExtractMicrocoleus vaginatus (PCC9802)2
    BG11+MvExtractArthrobacter sp. (D1B45)2
    BG11+MvExtractBacillus sp. 2 (L2B47)2
    BG11+MvExtractBacillus sp. 2 (D1B51)2
    BG11+MvExtractBosea sp. (L1B56)2
    BG11+MvExtractThe Environment2
    BG11+MvExtractMethylobacterium sp. (D1B20)2
    BG11+MvExtractModestobacter sp. (L1B44)2
    BG11+MvExtractMicrocoleus vaginatus (PCC9802)2
    Biological Soil Crust Porewater (Green Butte Site, Collection: Rajeev 2013 ISME J. 7(11):2178)Native microbiome: 018min Incubation2
    Biological Soil Crust Porewater (Green Butte Site, Collection: Rajeev 2013 ISME J. 7(11):2178)Native microbiome: 540min Incubation2
    Biological Soil Crust Porewater (Green Butte Site, Collection: Rajeev 2013 ISME J. 7(11):2178)The Environment2
    OE-MinimalGlucoseAAThe Environment4
    OE-MinimalGlucoseAAt0 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica4
    OE-MinimalGlucoseAAt1 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica4
    OE-MinimalGlucoseAAt2 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica4
    OE-MinimalGlucoseAAt3 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica4
    OE-MinimalGlucoseAAt4 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica4
    OE-MinimalGlucoseAAt5 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica4
    OE-MinimalGlucoseAAt6 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica4
    OE-MinimalGlucoseAAt7 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica4
    OE-MinimalGlucoseAAt8 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica4
    OE-MinimalGlucoseAAt9 Triculture: Bacillus cereus, Pseudomonas lini and Pseudomonas baetica4
    R2APhenylobacterium sp. (GW123-8A04)5
    R2AAcidovorax sp. (GW101-3E06)5
    R2ARhizobium sp. (GW101-3B10)5
    R2APseudomonas sp. (FW300-N2E3)5
    R2APseudomonas sp. (GW456-L13)5
    R2AThe Environment5
    R2APseudomonas sp. (FW300-N2A2)5
    R2APseudomonas sp. (GW456-L15)5
    R2APseudomonas sp. (FW507-14TSA)5
    R2APseudomonas sp. (FW300-N2F2)5
    R2ABacillus sp. (FW507-8R2A)5
    ZMMGThe Environment1
    ZMMGZymomonas mobilis strain ZM4 (ATCC 31821)1
    ZMMGEscherichia coli strain BW251131
    ZMMGTheoretical: Escherichia coli JW0233 proA, proline auxotroph1
    ZMMGTheoretical: Escherichia coli JW2580 pheA, phenylalanine auxotroph1
    ZMMGTheoretical: Escherichia coli JW3745 ilvA, isoleucine auxotroph1
    ZMMGTheoretical: Zymomonas mobilis ZMO0748 cysK, cysteine auxotroph1