Data and code from: Engineering bacteriophages through deep mining of metagenomic motifs

Bacteriophages can adapt to new hosts by altering sequence motifs through
recombination or convergent evolution. Where such motifs exist and what
fitness advantage they confer remains largely unknown. We report a new
method, Metagenomic Sequence Informed Functional Scoring (Meta-SIFT), to
discover sequence motifs in metagenomic datasets to engineer phage
activity. Meta-SIFT uses experimental deep mutational scanning data to
create sequence profiles to mine metagenomes for functional motifs
invisible to other searches. We experimentally tested 17,000 Meta-SIFT
derived sequence motifs in the receptor-binding protein of the T7 phage.
The screen revealed thousands of T7 variants with novel host specificity
with motifs sourced from distant families. Position, substitution and
location preferences dictated specificity across a panel of 20 hosts and
conditions. To demonstrate therapeutic utility, we engineered active T7
variants against foodborne pathogen E. coli O121. Meta-SIFT is a powerful
tool to unlock the potential encoded in phage metagenomes to engineer
bacteriophages.