Table 1.
Definitions of key interaction attributes. We describe microbial interactions using a number of attributes, each of which is assigned a numerical value based on experimental observations. Each attribute defined here corresponds to a column in our interaction catalog (Supplementary Table 1). We quantify most features in a binary way: using a ‘0’ if the interaction does not exhibit a certain attribute and a ‘1’ if it does. For example, if an interaction involved the exchange of a peptide, it would contain a ‘1’ in the ‘peptides’ column. Costs and ecological outcomes are specific to the organisms in the interactions, that is, there are columns for costs and outcomes for each of the participants. In a pairwise commensal interaction, for instance, there would be a ‘0’ in the column corresponding to the outcome gained by participant 1 and a ‘1’ in the column corresponding to the outcome gained by participant 2.
| Attribute | Definition | Quantification |
|---|---|---|
| Specificity | The reported mechanism of interaction is deployed in a manner specific to the recipient (e.g. signaling molecules specific to one species vs. nonspecific secretion of waste products). | Binary |
| Cost | Engagement in the reported interaction (e.g. secreting a metabolite) imposes a fitness burden on a participant (i.e. the individual fitness/growth rate of an organism would initially have been greater had it not been involved in the interaction). | Binary |
| Ecological outcome | The ultimate ecological effect the interaction confers on each participant. Combining these values for both participants in a pairwise interaction yields its overall ecological outcome (e.g. 1,-1 corresponds to selfishness; 1,1 corresponds to mutualism, etc.). |
|
| Contact dependence | Reported interaction features organisms engaging in direct physical contact. | Binary |
| Time dependence | Reported relationship features organisms interacting according specific temporal frames (e.g. occurring only at one point in a circadian cycle). | Binary |
| Spatial dependence | Reported interaction features organisms displaying particular spatial configurations (e.g. colonies separated by some distance on an agar plate as opposed to interacting in mixed cultures). | Binary |
| Site | The site, relative to the microbes involved, in which the interaction is reported to take place: extracellular (e.g. signaling molecule release or metabolic exchange), membrane (e.g. protein docking or conjugation), or cytoplasm (e.g. direct predation). | Binary value for each site |
| Habitat | The biome(s) in which the interaction or participating organisms have been observed: aquatic, biofilm, food product, multicellular host, soil, synthetic, or ubiquitous. | Binary value for each habitat |
| Compounds involved | The type of molecule that mediates the interaction: small molecules (e.g. carbohydrates or metabolic intermediates, but not secondary metabolites), nucleic acids (e.g. DNA), peptides (e.g. amino acids), or secondary metabolites (e.g. quorum sensing molecules). | Binary value for each compound type |