Isolation and characterization of diverse Veillonella phages reveal novel lineages and distinct host interactions

Abstract

The human oral microbiome is diverse and home to many species of bacteria, archaea, microeukaryotes, fungi and viruses. Homeostasis in the oral microbiome is important for health and dysbiosis in these communities leads to periodontal and systemic diseases. Veillonella are gram-negative, anaerobic, lactate-fermenting early colonizers of the mouth and are abundant in healthy oral microbiomes. Although considered commensals, Veillonella serve as bridging species in dental biofilms, promoting later colonization by pathogens, with mounting evidence supporting their roles as accessory pathogens in dental caries and periodontal disease. Bacteriophages are key regulators of bacterial community composition and are important drivers of microbial diversity, evolution, and ecology of the oral environment. Despite the ecological importance of Veillonella in the oral microbiome, phages infecting Veillonella remain largely uncharacterized. Here, we report the isolation of ten phages infecting natural isolates of three Veillonella species, representing seven distinct phage genomes. These phages exhibit diverse morphologies, genome organizations, and host ranges, with infection restricted to strains within the species of isolation. Several phages establish stable lysogeny, confer resistance to superinfection, and differ substantially in spontaneous production of infectious phage progeny. Genetic analysis of resistant mutants implicates lipopolysaccharide O-antigen as the receptor for one phage. Although none of the isolated phages had close matches in existing oral virome catalogs, related sequences were detected in oral metagenomes from geographically diverse populations. Together, these findings establish an experimentally characterized collection of Veillonella phages and connect previously uncharacterized oral viral diversity to bacterial hosts and infection phenotypes.