Abstract
In the current report, we describe the identification of three genetically distinct groups of prophages integrated into three different chromosomal sites of human gut-associated Bifidobacterium breve and Bifidobacterium longum strains. These bifidobacterial prophages are distantly related to temperate actinobacteriophages of several hosts. Some prophages, integrated within the dnaJ2 gene, are competent for induction, excision, replication, assembly and lysis, suggesting that they are fully functional and can generate infectious particles, even though permissive hosts have not yet been identified. Interestingly, several of these phages harbor a putative phase variation shufflon (the Rin system) that generates variation of the tail-associated receptor binding protein (RBP). Unlike the analogous coliphage-associated shufflon Min, or simpler Cin and Gin inversion systems, Rin is predicted to use a tyrosine recombinase to promote inversion, the first reported phage-encoded tyrosine-family DNA invertase. The identification of bifidobacterial prophages with RBP diversification systems that are competent for assembly and lysis, yet fail to propagate lytically under laboratory conditions, suggests dynamic evolution of bifidobacteria and their phages in the human gut.
Highlights
Bacteriophages are the most abundant biological entities[1] and exhibit incredible genetic diversity[2]
Prophages have been predicted in several Bifidobacterium strains, many are not characterized, and it is not known if they retain the functional capacity to form infectious particles
We examined a total of eleven prophages present in seven B. breve and three B. longum strains (Fig. 1, Tables 1, 2)
Summary
Bacteriophages are the most abundant biological entities[1] and exhibit incredible genetic diversity[2]. Efforts to characterize bifidobacterial diversity in the human gut have resulted in numerous sequenced B. breve and B. longum isolates[15,16,17,18] The majority of these strains are predicted to contain at least one complete or cryptic prophage[19,20], such as prophages Binf-1 from B. longum subsp. We identified three groups of related prophages in several B. breve and B. longum strains These prophages are distantly related to several types of actinobacteriophages of other hosts, and they are either integrated into a tmRNA gene, a tRNAMet gene, or the dnaJ2 gene, the latter representing an atypical phage integration site that appears to be unique to bifidobacteria/Actinobacteria. Many of them contain a putative tyrosine DNA invertase-mediated phase variation shufflon, Rin, that modulates the receptor binding protein (RBP) allele, analogous to the coliphage Min shufflon
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