Relatedness of Gardnerella prophages and their endolysins

The Gardnerella genus includes a complex sub-taxonomy of bacterial species and subgroups which have been implicated in bacterial vaginosis. We analyzed G. leopoldii, G. swidsinski, G. piotii , and G. vaginalis genomes available in public databases and predicted proviral sequences using Cenote-Taker3. We clustered 266 prophage sequences into 140 viral genera level groupings that encode four distinct gene clusters and 19 different lysin proteins. Analysis of the bacterial and prophage sequence phylogenies reveals that while there were no specific prophage sequence lineages that infected each bacterial host, there is clustering of the prophage sequences by bacterial species within the Gardnerella genus.

We found that many bacteriophages infecting different Gardnerella species are closely related, and that despite the diversity at the genome scale a small number of endolysin proteins were shared among a large number of prophages.

The bacterial genomes analyzed during the current study are available in the NCBI GenBank and GTDB repositories under the accession numbers listed in Supporting Data Table 1. Additional code for the analysis is available at https://github.com/bmaust/gardnerella_phage .