A genomic catalog of Earth’s bacterial and archaeal symbionts
TL;DR
Using a novel machine learning framework called symclatron, researchers found that 15 to 23 percent of uncultivated bacteria and archaea across half of all known phyla likely engage in symbiotic lifestyles.
Problem / question
Microbial symbiosis drives the diversification of life on Earth, but it remains heavily underexplored because most symbiotic microbes are extremely difficult to culture in a laboratory setting.
Methods
The authors developed a machine learning framework named symclatron to identify genomic signatures of symbiosis. They applied this tool to hundreds of thousands of microbial genomes derived from diverse environmental metagenome samples and reference genomes.
Key findings
The analysis resulted in the Symbiont Genomes catalog (SymGs), which indicates that 15 to 23 percent of uncultivated microbes are likely symbionts. These symbionts span half of all known bacterial and archaeal phyla. The machine learning models identified key genomic signatures of this lifestyle, specifically the loss of certain metabolic functions and the differential presence of others required for host-dependent living.
Why it matters
The release of the symclatron software and the SymGs catalog provides a massive, accessible resource that will help scientists conduct future mechanistic studies on how microbes and their hosts interact.
Limitations
The provided text does not explicitly mention specific limitations, caveats, or biases of the symclatron model or the resulting catalog.
Takeaway
A new machine learning tool has revealed that up to 23 percent of uncultivated microbes are symbionts, yielding a comprehensive new catalog (SymGs) to study host-microbe evolution.