Understanding assertions, compatibility predictions and data viewing features on Web of Microbes

2022-11-30

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:

  • 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 on the web.
  • 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 on The Web) or decreased (blue cells on tables and blue lines on The Web) with darker shading indicating a greater fold change.

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.