Web of Microbes (WoM): data repository of exometabolomics experiments

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

The data from Web of Microbes are represented by three dimensions:

‘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.

 

‘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.)

When constraining data to two-dimensional tables or web of assertions, the user must select the value for the constraining dimension

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. 

Understanding assertions, compatibility predictions and data viewing features on WoM

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:

  • Assertions of 'present in environment': The metabolite to be annotated as detected in >2/3 replicates. These are indicated by tan table cells or filled in circles. 
  • Assertions of 'increase' or 'decrease' by an organism: Metabolites that were significantly different from the control environment versus the transformed environment are asserted as increased (red cells on tables and red lines) or decreased (blue cells on tables and blue lines) with darker shading indicating a greater fold change. 

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.