Fig. 1: Functional metagenomics by reprogrammed bacteriophage particles.

a, Schematic overview of DEEPMINE. DEEPMINE employs hybrid T7 bacteriophage transducing particles and directed evolution to alter phage host-specificity and efficiency for functional metagenomics in target clinical strains. Environmental DNA in the form of metagenomic plasmid library is then packaged into these bacteriophage particles and transduced into the hosts of interest. Comparative analysis of screening hits is enabled by a dual-barcoded PCR-free DNA fragment sequencing pipeline. b, Functional metagenomic library transduction by specific hybrid T7 bacteriophage particles is at least as efficient as electroporation (electroporation into E. coli vs transduction into K. pneumoniae P = 0.010545, two-sample one-sided t-test, n = 3 biologically independent experiments; electroporation into E. coli vs transduction into S. enterica P = 0.15, two-sample one-sided t-test, n = 3 biologically independent experiments; Supplementary Table 2). Mean ± s.e.m. c,d, Delivered metagenomic DNA fragment lengths (c) and diversities (d), determined by using PCR-free long-read deep sequencing right after electroporation and transduction (Methods). Dashed lines represent the average size of the DNA fragments. Shannon alpha diversity indices (H) were calculated on the basis of the frequency of fragments with identical sequences in the libraries (see Methods, n= 276,899, n = 188,317 and n = 180,497 for E. coli, K. pneumoniae and S. enterica, respectively; Supplementary Table 3). Please note that only a fraction of the delivered libraries was sequenced.