SOCfinder: a genomic tool for identifying cooperative genes in bacteria

Abstract

Bacteria cooperate by working collaboratively to defend their colonies, share nutrients, and resist antibiotics. Nevertheless, our understanding of these remarkable behaviours primarily comes from studying a few well-characterized species. Consequently, there is a significant gap in our understanding of microbial cooperation, particularly in natural environments. To address this gap, we can use bioinformatic tools to identify cooperative traits and their underlying genes across diverse species. Existing tools address this challenge through two approaches. One approach is to identify genes that encode extracellular proteins, which can provide benefits to neighbouring cells. An alternative approach is to predict gene function using annotation tools. However, these tools have several limitations. Not all extracellular proteins are cooperative, and not all cooperative behaviours are controlled by extracellular proteins. Furthermore, existing functional annotation methods frequently miss known cooperative genes. Here, we introduce SOCfinder as a new tool to find cooperative genes in bacterial genomes. SOCfinder combines information from several methods, considering if a gene is likely to (1) code for an extracellular protein, (2) have a cooperative functional annotation, or (3) be part of the biosynthesis of a cooperative secondary metabolite. We use data on two extensively-studied species (P. aeruginosa & B. subtilis) to show that SOCfinder is better at finding known cooperative genes than existing tools. We also use theory from population genetics to identify a signature of kin selection in SOCfinder cooperative genes, which is lacking in genes identified by existing tools. SOCfinder opens up a number of exciting directions for future research, and is available to download from https://github.com/lauriebelch/SOCfinder. Data SummaryAll code and associated files are available at https://github.com/lauriebelch/SOCfinder. Impact StatementBacteria cooperate by secreting many molecules outside the cell, where they can provide benefits to other cells. While we know much about how bacteria cooperate in the lab, we know much less about bacterial cooperation in nature. Is cooperation equally important in all species? Are all cooperations equally vulnerable to cheating? To answer these questions, we need a way of identifying cooperative genes across a wide range of genomes. Here, we provide such a method - which we name SOCfinder. SOCfinder allows users to find cooperative genes in any bacterial genome. SOCfinder opens up a number of exciting directions for future research. It will allow detailed studies of non-model species, as well as broad comparative studies across species. These studies will allow cooperation in the wild to be studied in new ways.