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These assertions are based on direct experimental evidence obtained through exometabolomic analyses. Currently, the database containes results from carefully curated mass spectrometry datasets from the Northen Metabolomics Lab located at the Joint Genome Institute, a DOE National User Facility of Lawrence Berkeley National Laboratory. WoM captures assertions: metabolite compositions of environments and the changes to metabolite abundances metabolites by organisms in the environment. It is important to note that these transformations are only interpretable in the context of the specific environment since the manner in which an organism may interact with a metabolite in one environment may differ in another.
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
‘Environment’ is the starting metabolite pool that is transformed by the organism(s) and may include anything from synthetic mixtures of metabolites, rich medias, plant exudates, microbial extracts, soil extracts, plant materials, etc. |
‘Metabolite’ includes organic compounds that can be accurately identified and measured in comparison of control and transformed environments.
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‘Organism’ is the transforming agent that results in the increase or decrease of metabolites within an environment and may be a monoculture or consortia of organisms (plants, bacterial isolates, native microbial communities from soil, etc.) |
The WoM features four data viewing tabs: The first, "The Web", links the actions of microorganisms on metabolites from within a single environment. The other three, "One Environment", "One Metabolite" and "One Organism", allow the user to constrain the data to the dimension as indicated on the tab. For example "One Metabolite" will display a table linking the actions of organisms on the user specified metabolite from within multiple environments. These metabolic actions include the increase or decrease of a metabolite after exposure of an environment to a transforming agent (one or more organsims). There are two types of assertions that are made on the WoM:
Compatibility predictions: On the "One Environment" tab, compatibility scores are calculated to provide either a measure of compatibility between an organism and an environment or between two organisms. Scores are displayed in the column headers after the user selects a reference column by clicking on the column header. The current reference column is marked in yellow, and scores are calculated for all other columns (the scored organsims) in relation to the reference column (reference organism). When "The Environment" is selected as the reference, the Environmental Use Scores are displayed for all scored organisms. When an organsism is displayed as the reference, competition and exchange scores are displayed for all of the scored organsims.
Caveats: Our goal is to make assertions of presence and relative abundances. The shading does not indicate absolute/quantified abundances, thus it is not possible to use the shading to compare abundances of different metabolites (given dramatic differences in certain instrument response functions for metabolites). For example, with mass spectrometry, some abundant metabolites may not be detectable due to poor ionization (e.g. hydrocarbons). Further, the increase/decrease of a metabolite may be due to a number of factors including, for example, active or passive transmembrane transport, extracellular enzymes, and adsorption onto cellular, mineral or culture vessel surfaces.
Metabolite names and IDs: Metabolite names are given to the level of structural information available. Typically, we are making identifications from samples based on two orthogonal and independent parameters as compared with pure reference standards. In other cases, where we only have limited evidence for an assignment (for example comparison of sample metabolite with an online spectral database) we are making a putative annotation. Right now, these are indicated with parentheses around the metabolite name. In other cases, where only limited structural information is available, a chemical formula, detection value (retention time + m/z) or chemical class is used as the metabolite name.
The WoM features data viewing tabs: "One Environment", "One Compound" and "One Organism" allow the user to constrain the data to the dimension as indicated on the tab. For example "One Compound" will display a table linking the actions of organisms on the user specified metabolite from within multiple environments. These metabolic actions include the increase or decrease of a metabolite after exposure of an environment to a transforming agent (one or more organisms). There are two types of assertions that are made on the WoM:
Caveats: Our goal is to make assertions of presence and relative abundances. The shading does not indicate absolute/quantified abundances, thus it is not possible to use the shading to compare abundances of different metabolites (given dramatic differences in certain instrument response functions for metabolites). For example, with mass spectrometry, some abundant metabolites may not be detectable due to poor ionization (e.g. hydrocarbons). Further, the increase/decrease of a metabolite may be due to a number of factors including, for example, active or passive transmembrane transport, extracellular enzymes, and adsorption onto cellular, mineral or culture vessel surfaces.
To contact us with questions, comments, or requests for submitting data, please email webofmicrobes@lbl.gov.
The WoM features data viewing tabs: "One Environment", "One Compound" and "One Organism" allow the user to constrain the data to the dimension as indicated on the tab. For example "One Compound" will display a table linking the actions of organisms on the user specified metabolite from within multiple environments. These metabolic actions include the increase or decrease of a metabolite after exposure of an environment to a transforming agent (one or more organisms). There are two types of assertions that are made on the WoM:
Compatibility predictions: On the "One Environment" tab, compatibility scores are calculated to provide either a measure of compatibility between an organism and an environment or between two organisms. Scores are displayed in the column headers after the user selects a reference column by clicking on the column header. The current reference column is marked in yellow, and scores are calculated for all other columns (the scored organisms) in relation to the reference column (reference organism). When "The Environment" is selected as the reference, the Environmental Use Scores are displayed for all scored organisms. When an organism is displayed as the reference, competition and exchange scores are displayed for all of the scored organisms.
Caveats: Our goal is to make assertions of presence and relative abundances. The shading does not indicate absolute/quantified abundances, thus it is not possible to use the shading to compare abundances of different metabolites (given dramatic differences in certain instrument response functions for metabolites). For example, with mass spectrometry, some abundant metabolites may not be detectable due to poor ionization (e.g. hydrocarbons). Further, the increase/decrease of a metabolite may be due to a number of factors including, for example, active or passive transmembrane transport, extracellular enzymes, and adsorption onto cellular, mineral or culture vessel surfaces.