A new phage on the ‘Mozzarella’ block: Bacteriophage 5093 shares a low level of homology with other Streptococcus thermophilus phages S. Mills a, c , C. Griffin a, c , O. O’Sullivan a , A. Coffey d , O.E. McAuliffe a , W.C. Meijer c , L.M. Serrano c , R.P. Ross a, b, * a Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland b Alimentary Pharmabiotic Centre, Cork, Ireland c CSK Food Enrichment, Ede, The Netherlands d Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland article info Article history: Received 8 February 2011 Received in revised form 24 May 2011 Accepted 20 June 2011 abstract Streptococcus thermophilus bacteriophage 5093 is a virulent phage that infects the industrial Mozzarella starter CSK939. The genome of phage 5093 is 37,184 base pairs (bps) containing 50 open reading frames (orfs). Genetic analysis revealed that the genome of phage 5093 is highly mosaic when compared with other sequenced S. thermophilus phages. This is particularly apparent in the late gene cluster with regions displaying high homology to prophage sequences of non-dairy streptococci and limited homology to either pac or cos-type S. thermophilus phages. In addition, a definitive antireceptor gene was not observed e suggesting that phage 5093 may have developed a different system for host recognition. Interestingly, the phage does contain a methylase domain that probably evolved as a phage counter- defence mechanism. These findings suggest that phage 5093 may represent a third group of S. thermo- philus phage and provide the link between phages that infect S. thermophilus and its non-dairy ancestors. Ó 2011 Elsevier Ltd. All rights reserved. 1. Introduction Streptococcus thermophilus has followed an evolutionary path divergent to that of pathogenic streptococci, mainly through loss-of- function events due to its adaptation to milk, as revealed by compar- ative genomics (Hols et al., 2005). The global utilization of S. thermophilus in the production of yoghurt, Mozzarella and hard- ‘cooked’ cheeses such as Emmental, Gruyère and Grana (Hols et al., 2005) places it as the second most important industrial starter culture after Lactococcus lactis (Fox, 1993; Hols et al., 2005; Rasic & Kurmann, 1978). However, bacteriophage (phage) infection of S. thermophilus cultures in dairy environments is a continuous problem, resulting in slow fermentations and hence products of inferior quality. This is probably a reflection of more intensive use due to increasing demand for Mozzarella-type cheeses, although it must be emphasized that such phage problems are difficult to quantify due to commercial sensitivities. An understanding of phage evolution should enable researchers to develop strategic methods to combat phage attack in the dairy plant. It has been proposed that all phages infecting S. thermophilus are derived from a common ancestor (Mercenier, 1990) forming a rather homogenous group. Indeed, all S. thermophilus phages isolated to date belong to the Siphoviridae family corresponding to group B as defined by Bradley (1967), in being morphologically very similar and containing long non-contractile tails of varying lengths (230e260 nm in length) and isometric capsids (45e65 nm in diameter). They contain double-stranded linear DNA genomes ranging in size from 31 to 45 kb (Brussow, Bruttin, Desiere, Lucchini, & Foley, 1998). S. thermophilus phages have been further classified into two groups based on their mode of DNA packaging, where cos-type phages have been shown to contain two major structural proteins and several minor proteins and pac-type phages contain three such proteins (Le Marrec et al., 1997). Despite the cos and pac distinction the genomes of S. thermophilus phages display a very similar organization, and the genes coding for DNA replication and host lysis are highly conserved (Guglielmotti et al., 2009). Indeed, Quiberoni, Moineau, Rousseau, Reinheimer, and Ackermann (2010) have recently iden- tified an overall core genome for S. thermophilus phages that consists of either four or five open reading frames (ORFs). Core genomes were also established for cos- and pac-type phages, where each distinct group has been shown to share numerous genes. Various mechanisms have been proposed in the genetic evolution of S. thermophilus phages including point mutations, deletions, * Corresponding author. Tel.: þ353 25 42229; fax: þ353 25 42340. E-mail address: paul.ross@teagasc.ie (R.P. Ross). Contents lists available at ScienceDirect International Dairy Journal journal homepage: www.elsevier.com/locate/idairyj 0958-6946/$ e see front matter Ó 2011 Elsevier Ltd. All rights reserved. doi:10.1016/j.idairyj.2011.06.003 International Dairy Journal 21 (2011) 963e969