Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts
Journal article, 2023
The environmental impact of uncultured phages is shaped by their preferred life cycle (lytic or lysogenic). However, our ability to predict it is very limited. We aimed to discriminate between lytic and lysogenic phages by comparing the similarity of their genomic signatures to those of their hosts, reflecting their co-evolution. We tested two approaches: (1) similarities of tetramer relative frequencies, (2) alignment-free comparisons based on exact k = 14 oligonucleotide matches. First, we explored 5126 reference bacterial host strains and 284 associated phages and found an approximate threshold for distinguishing lysogenic and lytic phages using both oligonucleotide-based methods. The analysis of 6482 plasmids revealed the potential for horizontal gene transfer between different host genera and, in some cases, distant bacterial taxa. Subsequently, we experimentally analyzed combinations of 138 Klebsiella pneumoniae strains and their 41 phages and found that the phages with the largest number of interactions with these strains in the laboratory had the shortest genomic distances to K. pneumoniae. We then applied our methods to 24 single-cells from a hot spring biofilm containing 41 uncultured phage-host pairs, and the results were compatible with the lysogenic life cycle of phages detected in this environment. In conclusion, oligonucleotide-based genome analysis methods can be used for predictions of (1) life cycles of environmental phages, (2) phages with the broadest host range in culture collections, and (3) potential horizontal gene transfer by plasmids.
bacteriophages
lysogenic phages
single-cell genomics
genomic signatures
lytic phages
Author
Vicente Arnau
Consejo Nacional de Investigaciones Cientificas y Tecnicas
FISABIO
CIBER - Centro de Investigación Biomédica en Red
Wladimiro Díaz-Villanueva
Consejo Nacional de Investigaciones Cientificas y Tecnicas
CIBER - Centro de Investigación Biomédica en Red
FISABIO
Jorge Mifsut Benet
Student at Chalmers
Paula Villasante
Open University of Catalonia (UOC)
Beatriz Beamud
FISABIO
Consejo Nacional de Investigaciones Cientificas y Tecnicas
Paula Mompó
FISABIO
Rafael Sanjuan
Consejo Nacional de Investigaciones Cientificas y Tecnicas
Fernando González-Candelas
FISABIO
Consejo Nacional de Investigaciones Cientificas y Tecnicas
CIBER - Centro de Investigación Biomédica en Red
Pilar Domingo-Calap
Consejo Nacional de Investigaciones Cientificas y Tecnicas
Mária Džunková
Consejo Nacional de Investigaciones Cientificas y Tecnicas
Viruses
1999-4915 (ISSN) 19994915 (eISSN)
Vol. 15 5 1196Subject Categories (SSIF 2011)
Microbiology
DOI
10.3390/v15051196
PubMed
37243281