Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts

Patrick A de Jonge; F A Bastiaan von Meijenfeldt; Ana Rita Costa; Franklin L Nobrega; Stan J J Brouns; Bas E Dutilh

doi:10.1016/j.isci.2020.101439

Adsorption Sequencing as a Rapid Method to Link Environmental Bacteriophages to Hosts

iScience. 2020 Aug 6;23(9):101439. doi: 10.1016/j.isci.2020.101439. eCollection 2020 Sep 25.

Authors

Patrick A de Jonge^{1

2}, F A Bastiaan von Meijenfeldt¹, Ana Rita Costa², Franklin L Nobrega², Stan J J Brouns², Bas E Dutilh¹

Affiliations

¹ Theoretical Biology and Bioinformatics, Science4Life, Utrecht University, 3584 CH Utrecht, the Netherlands.
² Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ Delft, the Netherlands.

Abstract

An important viromics challenge is associating bacteriophages to hosts. To address this, we developed adsorption sequencing (AdsorpSeq), a readily implementable method to measure phages that are preferentially adsorbed to specific host cell envelopes. AdsorpSeq thus captures the key initial infection cycle step. Phages are added to cell envelopes, adsorbed phages are isolated through gel electrophoresis, after which adsorbed phage DNA is sequenced and compared with the full virome. Here, we show that AdsorpSeq allows for separation of phages based on receptor-adsorbing capabilities. Next, we applied AdsorpSeq to identify phages in a wastewater virome that adsorb to cell envelopes of nine bacteria, including important pathogens. We detected 26 adsorbed phages including common and rare members of the virome, a minority being related to previously characterized phages. We conclude that AdsorpSeq is an effective new tool for rapid characterization of environmental phage adsorption, with a proof-of-principle application to Gram-negative host cell envelopes.

Keywords: Ecology; Environmental Science; Microbiology; Techniques in Genetics.