mi-atlas: a Microbial Interactions Atlas

Description

A framework was recently suggested to describe interactions occurring between microorganisms using the encoding of several attributes (see below for details) in order to build a catalog amenable to quantitative analyses (Pacheco and Segrè, 2019). Their initial effort described 74 interactions which were unfortunately available only in the Supplementary Material section of the article. Therefore, mi-atlas (pronounced /'mi atlas/ like in Spanish) aims to:

1. propose an interactive exploration of the catalog and
2. enable versioned community contributions to the microbial interactions catalog

Attributes of microbial interactions

Attributes formatting and encoding

The attributes definitions are adapted from the Table 1 of (Pacheco and Segrè, 2019) and can be read as follows:

Attribute type Definition of the attribute. Quantification of the attribute.

The encoding of each of the attributes is described in the following table:

Attributes list

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. Establishment of the reported interaction (e.g. secretion of a metabolite) imposes a fitness burden on an organism involved (i.e. the individual fitness/growth rate of the organism would initially have been greater had it not established 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.). Ternary.

Contact dependence. Interaction is reported to occur only if direct physical contact between the different species is present. Binary.

Time dependence. Interaction is reported to occur only in a specific temporal frame (e.g. occurring only at one point in a circadian cycle). Binary.

Spatial dependence. Interaction is reported to occur only if organisms are in a specific spatial configuration. 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.

Beforehand, each interaction is also described with the scientific names of each participant, the taxonomic resolution (e.g. Genus - species) as well as the domain of each participant (Bacteria, Archaea, Eukarya, Viruses). The exact names of the columns of the .tsv file are listed in the following table where they are grouped in the aforementioned categories.

Contributing

Contributions to the catalog in the form of corrections and/or new entries are welcome and possible. If you are interested, please have a look at the CONTRIBUTING guidelines.

Expected developments

Several milestones are already set for incremental improvements of the two aims of the project.

Spoiler alert: a Shiny application is now used to render the multi-column catalog into human-readable entries upon selection of the interaction of interest. In the future, a builder will be designed to ease the addition of a new entry to the catalog that follows the framework guidelines. And ideally new entries could be discussed and reviewed before acceptance using the pull request review system.

Reference

If you are using the atlas and/or the framework please cite the original article:

Alan R Pacheco, Daniel Segrè, A multidimensional perspective on microbial interactions, FEMS Microbiology Letters, Volume 366, Issue 11, June 2019, fnz125, https://doi.org/10.1093/femsle/fnz125

License

This work is licensed under the terms of the GNU General Public License v3.0. The logo follows the specifications of StickersStandard. It is made up of the following Font Awesome icons (bacteria, atlas and chevron-up) which are licensed under the Creative Commons Attribution 4.0 International and were slightly modified.