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Applied and Environmental Microbiology, December 2005, p. 8692-8705, Vol. 71, No. 12
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.12.8692-8705.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

Prophage-Like Elements in Bifidobacteria: Insights from Genomics, Transcription, Integration, Distribution, and Phylogenetic Analysis

Marco Ventura,1* Ju-Hoon Lee,2 Carlos Canchaya,1 Ralf Zink,3 S. Leahy,1 J. A. Moreno-Munoz,1 M. O'Connell-Motherway,1 D. Higgins,1 Gerald F. Fitzgerald,1 Daniel J. O'Sullivan,2 and Douwe van Sinderen1

Alimentary Pharmabiotic Centre and Department of Microbiology, Biosciences Institute, National University of Ireland, Western Road, Cork, Ireland,1 Department of Food Science and Nutrition, University of Minnesota, Minneapolis, Minnesota,2 Department of Nutrition and Health, Cognis, Düsseldorf, Germany3

Received 27 April 2005/ Accepted 25 July 2005

So far, there is only fragmentary and unconfirmed information on bacteriophages infecting the genus Bifidobacterium. In this report we analyzed three prophage-like elements that are present in the genomes of Bifidobacterium breve UCC 2003, Bifidobacterium longum NCC 2705, and Bifidobacterium longum DJO10A, designated Bbr-1, Bl-1, and Blj-1, respectively. These prophagelike elements exhibit homology with genes of double-stranded DNA bacteriophages spanning a broad phylogenetic range of host bacteria and are surprisingly closely related to bacteriophages infecting low-G+C bacteria. All three prophage-like elements are integrated in a tRNAMet gene, which appears to be reconstructed following phage integration. Analysis of the distribution of this integration site in many bifidobacterial species revealed that the attB sites are well conserved. The Blj-1 prophage is 36.9 kb long and was induced when a B. longum DJO10A culture was exposed to mitomycin C or hydrogen peroxide. The Bbr-1 prophage-like element appears to consist of a noninducible 28.5-kb chimeric DNA fragment composed of a composite mobile element inserted into prophage-like sequences, which do not appear to be widely distributed among B. breve strains. Northern blot analysis of the Bbr-1 prophage-like element showed that large parts of its genome are transcriptionally silent. Interestingly, a gene predicted to encode an extracellular beta-glucosidase carried within the Bbr-1 prophage-like element was shown to be transcribed.

* Corresponding author. Present address: Department of Genetics, Evolution and Anthropology, Laboratory of Microbial Biotechnology, University of Parma, Parco Area della Scienze 11A, Parma, Italy. Phone: 39 (521) 905479. Fax: 39 (521) 905604. E-mail: marco.ventura{at}unipr.it.

Applied and Environmental Microbiology, December 2005, p. 8692-8705, Vol. 71, No. 12
0099-2240/05/$08.00+0     doi:10.1128/AEM.71.12.8692-8705.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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