Characterizing prophages in the genus Fusobacterium

Fusobacteria are common residents of the human oral cavity and are regularly detected in subgingival plaque [1]. Fusobacteria may behave as benign commensals, but can also be associated with abscesses of the sinus and liver, skin ulcers, gastrointestinal tract carcinoma, and inflammatory bowel disease [1]. In vitro, fusobacteria display a range of virulence determinants, including host cell invasion [2], cytokine pathway interference [3,4] and biofilm promotion [5]. There is evidence for substantial within-species variation leading to heterogeneity in virulence phenotypes [2,6], therefore looking for genetic islands that are regularly gained or lost over short phylogenetic timescales may shed light on cryptic virulence determinants.

As temperate symbionts, bacteriophages can integrate into host bacterial genomes as prophages and encode fitness factors that positively augment the host microbe's phenotype [7,8]. Prophages are known to encode exotoxins [9], adhesins [10], and other proteins that facilitate opportunistic colonization, invasion, or spread of the bacterial host through mammalian tissue [11,12]. Although most information is available for species outside of the genus Fusobacterium, prophage infection may partially explain the phenotypic and genotypic variation observed in strains of Fusobacterium species.

Little is known about Fusobacterium prophages, with only two induced phages sequenced from lysate to date [13]. The primary goal of this work is to provide the first broad view of Fusobacterium prophage distribution, and the first focused view of prophage induction patterns within a single Fusobacterium strain. To achieve this, we set out to identify and characterize prophages within the genomes of published Fusobacterium strains, and to develop qPCR-based methods to characterize intra- and extra-cellular induction of prophage replication in a variety of environmental contexts. For both these goals, we selected a focal strain for which two prophages have already been induced and sequenced from host lysate [13]: the model invasive pathogen Fusobacterium nucleatum subsp. animalis 7-1 (henceforth referred to as ‘7-1’).

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