Diversity-generating retroelements enable phages to expand their host range in the human gut.

Abstract

Diversity-generating retroelements (DGRs) are genetic elements that use error-prone reverse transcription to hypermutate specific target genes, most often the receptor-binding proteins of phages. They are enriched in human gut viruses, where they are hypothesised to enable phages expand their host range. Yet DGR-mediated host-range expansion across bacterial species has so far only been predicted in silico and has not been examined directly within complex microbial communities. To test this hypothesis in situ, we tracked phage-host interactions in the human gut, combining bulk metagenomic, virus-like particle (VLP), and Hi-C sequencing of longitudinal faecal samples collected over a five-week period. This culture-independent approach identified 380 interactions between 97 phages and 76 bacterial hosts. Nearly a third of these phages (31 of 97) encoded a DGR, and DGR-encoding phages were more likely to interact with multiple bacterial species. Moreover, nucleotide diversity in DGR-targeted genes increased with the number of hosts a phage interacted with and was concentrated in the surface-exposed, DGR-targeted variable region of its receptor-binding proteins. Together, these results provide in situ evidence that DGRs enable phages to expand their host range in the human gut.