Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples.
Viruses shape a diversity of ecosystems by modulating their microbial, eukaryotic, or plant host metabolism. The complexity of virus-host interaction networks is progressively fathomed by novel metagenomic approaches. By using a novel metagenomic method, we explored the virome in mammalian cell cultures and clinical samples to identify an extensive pool of mobile genetic elements in all of these ecosystems. Despite aseptic treatment, cell cultures harbored extensive and diverse phage populations with a high abundance of as yet unknown and uncharacterized viruses (viral dark matter). Unknown phages also predominated in the oropharynx and urine of healthy individuals and patients infected with cytomegalovirus despite demonstration of active cytomegalovirus replication. The novelty of viral sequences correlated primarily with the individual evaluated, whereas relative abundance of encoded protein functions was associated with the ecologic niches probed. Together, these observations demonstrate the extensive presence of viral dark matter in human and artificial ecosystems.-Thannesberger, J., Hellinger, H.-J., Klymiuk, I., Kastner, M.-T., Rieder, F. J. J., Schneider, M., Fister, S., Lion, T., Kosulin, K., Laengle, J., Bergmann, M., Rattei, T., Steininger, C. Viruses comprise an extensive pool of mobile genetic elements in eukaryote cell cultures and human clinical samples.
Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria.
Jakob
J
Thannesberger
CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
Hans-Joerg
HJ
Hellinger
Center for Medical Research, Core Facility Molecular Biology, Medical University of Graz, Graz, Austria.
Ingeborg
I
Klymiuk
Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria.
Marie-Theres
MT
Kastner
Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria.
Franz J J
FJJ
Rieder
Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria.
Martina
M
Schneider
Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Vienna, Austria.
Susanne
S
Fister
Children's Cancer Research Institute, Vienna, Austria.
Thomas
T
Lion
Children's Cancer Research Institute, Vienna, Austria.
Karin
K
Kosulin
Department of General Surgery, Medical University of Vienna, Vienna, Austria.
Johannes
J
Laengle
Department of General Surgery, Medical University of Vienna, Vienna, Austria.
Michael
M
Bergmann
CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
Thomas
T
Rattei
Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Vienna, Austria; christoph.steininger@meduniwien.ac.at.
Christoph
C
Steininger
D002478:Cells, Cultured; D004279:DNA, Viral / Q000235:genetics; D005057:Eukaryotic Cells / Q000166:cytology / Q000821:virology*; D016679:Genome, Viral / Q000235:genetics*; D006801:Humans; D020071:Interspersed Repetitive Sequences / Q000235:genetics; D054892:Metagenome / Q000235:genetics; D056186:Metagenomics / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods
D004279:DNA, Viral
bacteriophages; next-generation sequencing; viral dark matter; viral microbiome