Phylogenomic analyses and host range prediction of cluster P mycobacteriophages

Abstract

Bacteriophages, infecting bacterial hosts in every environment on our planet, are a driver of adaptive evolution in bacterial communities. At the same time, the host range of many bacteriophages—and thus one of the selective pressures acting on complex microbial systems in nature—remains poorly characterized. Here, we computationally inferred the putative host ranges of 40 cluster P mycobacteriophages, including members from six sub-clusters (P1-P6). A series of comparative genomic analyses revealed that mycobacteriophages of sub-cluster P1 are restricted to the Mycobacterium genus, whereas mycobacteriophages of sub-clusters P2 to P6 are likely also able to infect other genera, several of which are commonly associated with human disease. Further genomic analysis highlighted that the majority of cluster P mycobacteriophages harbor a conserved integration-dependent immunity system, hypothesized to be the ancestral state of a genetic switch that controls the shift between lytic and lysogenic life cycles—a temperate characteristic that impedes their usage in anti-bacterial applications.

Microbacterium Cluster EA Bacteriophages: Phylogenomic Relationships and Host Range Predictions

“…To obtain insights into which Microbacterium species each bacteriophage might be able to infect, COUSIN v.0.4 [ 25 ] was used to determine the COdon Usage Similarity INdex (COUSIN 59 ) for each of the 125 cluster EA bacteriophages ( Supplementary Table S1 ) across 14 putative microbacterial host species ( Supplementary Table S2 ), including M. foliorum B-24224 (i.e., the experimentally validated host for the majority of the isolated cluster EA bacteriophages). Following Howell, Versoza et al [ 26 ], host ranges were predicted using both exploratory and confirmatory methods—PHERI v.0.2 [ 27 ] and WIsH v.1.1 [ 19 ], respectively. PHERI is a machine-learning-based tool that capitalizes on protein sequence similarity, while WIsH utilizes the oligonucleotide frequency profiles of bacteriophages to predict prospective hosts.…”