October 2019: Borenstein in Nature: Human gut bacteria 'steal' defense systems from other bacteria

Species in the gut microbiome harbor mechanisms to compete with neighboring bacteria. One of these mechanisms is the type VI secretion system, which can inject a variety of toxins into neighboring cells. Bacterial species that carry this mechanism also encode genes for the corresponding immunity factors, allowing them to protect themselves against these toxins. A new study of Prof. Elhanan Borenstein, Edmond J. Safra faculty fellow (CS and Medicine), in collaboration with Mougous lab (University of Washington), published in Nature, reveals that immunity genes are much more widespread in the gut microbiome than previously believed.

Analyzing a large array of metagenomic samples from the gut microbiome, the researchers found that in many samples, the abundance of immunity genes normally encoded by the gut bacteria B. fragilis is much higher than expected based on the estimated abundance of that species. This suggests that other species in the microbiome, including those that do not carry the corresponding toxins, may have ‘stolen’ copies of these immunity genes from B. fragilis and now encode them in their own genomes, likely as a way to protect themselves against assault from B. fragilis. Moreover, genomic and metagenomic analysis of these species demonstrated that they in fact often encode very large clusters of immunity genes, predicted to protect against diverse toxins from a wide range of different species. Follow up experimental work further confirmed that these ‘orphan’ immunity genes indeed confer resistance to such toxins.

These findings suggest that obtaining and maintaining orphan immunity genes is a common mechanism of gut bacteria to defend themselves against interbacterial attacks and survive in the gut environment.