Viruses 2015, 7(12), 6570-6589; https://doi.org/10.3390/v7122958
What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?
Henrike Zschach 1, Katrine G. Joensen 2, Barbara Lindhard 1, Ole Lund 1, Marina Goderdzishvili 3, Irina Chkonia 3, Guliko Jgenti 3, Nino Kvatadze 3, Zemphira Alavidze 4, Elizabeth M. Kutter 5
, Henrik Hasman 1 and Mette V. Larsen 1,*
, Henrik Hasman 1 and Mette V. Larsen 1,*
1
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
2
National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
3
Eliava Institute of Bacteriophages, Microbiology and Virology, 3 Gotua Str., Tbilisi 0160, Georgia
4
Eliava Biopreparations LTD,3 Gotua Str., Tbilisi 0160, Georgia
5
Lab 1, The Evergreen State College, Olympia,WA 98505, USA
*
Author to whom correspondence should be addressed.
Academic Editors: Abram Aertsen and Rob Lavigne
Received: 30 September 2015 / Revised: 19 November 2015 / Accepted: 30 November 2015 / Published: 12 December 2015
(This article belongs to the Special Issue 21st Evergreen International Phage Biology Meeting - Emerging Research)
Abstract
Phage therapy, a practice widespread in Eastern Europe, has untapped potential in the combat against antibiotic-resistant bacterial infections. However, technology transfer to Western medicine is proving challenging. Bioinformatics analysis could help to facilitate this endeavor. In the present study, the Intesti phage cocktail, a key commercial product of the Eliava Institute, Georgia, has been tested on a selection of bacterial strains, sequenced as a metagenomic sample, de novo assembled and analyzed by bioinformatics methods. Furthermore, eight bacterial host strains were infected with the cocktail and the resulting lysates sequenced and compared to the unamplified cocktail. The analysis identified 23 major phage clusters in different abundances in the cocktail, among those clusters related to the ICTV genera T4likevirus, T5likevirus, T7likevirus, Chilikevirus and Twortlikevirus, as well as a cluster that was quite distant to the database sequences and a novel Proteus phage cluster. Examination of the depth of coverage showed the clusters to have different abundances within the cocktail. The cocktail was found to be composed primarily of Myoviridae (35%) and Siphoviridae (32%), with Podoviridae being a minority (15%). No undesirable genes were found. View Full-Text
Figure 1
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Zschach, H.; Joensen, K.G.; Lindhard, B.; Lund, O.; Goderdzishvili, M.; Chkonia, I.; Jgenti, G.; Kvatadze, N.; Alavidze, Z.; Kutter, E.M.; Hasman, H.; Larsen, M.V. What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail? Viruses 2015, 7, 6570-6589.