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Viruses. 2015 Dec 12;7(12):6570-89. doi: 10.3390/v7122958.

What Can We Learn from a Metagenomic Analysis of a Georgian Bacteriophage Cocktail?

Author information

1
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark. henrike@cbs.dtu.dk.
2
National Food Institute, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark. kagjo@food.dtu.dk.
3
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark. b.lindhard@live.dk.
4
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark. lund@cbs.dtu.dk.
5
Eliava Institute of Bacteriophages, Microbiology and Virology, 3 Gotua Str., Tbilisi 0160, Georgia. mgoderdzishvili@gtu.ge.
6
Eliava Institute of Bacteriophages, Microbiology and Virology, 3 Gotua Str., Tbilisi 0160, Georgia. irinachkonia@yahoo.com.
7
Eliava Institute of Bacteriophages, Microbiology and Virology, 3 Gotua Str., Tbilisi 0160, Georgia. gulikojgenti@yahoo.com.
8
Eliava Institute of Bacteriophages, Microbiology and Virology, 3 Gotua Str., Tbilisi 0160, Georgia. ninqvatadze@yahoo.com.
9
Eliava Biopreparations LTD,3 Gotua Str., Tbilisi 0160, Georgia. z.i.alavidze@gmail.com.
10
Lab 1, The Evergreen State College, Olympia,WA 98505, USA. KutterB@evergreen.edu.
11
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark. henh@ssi.dk.
12
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark. metteb@cbs.dtu.dk.

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.

KEYWORDS:

Eliava Intestiphage; metagenomics; phage therapy; whole genome sequence analysis

PMID:
26703713
PMCID:
PMC4690881
DOI:
10.3390/v7122958
[Indexed for MEDLINE]
Free PMC Article
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