Phage-microbe interactions are appealing systems to study coevolution,and have also been increasingly emphasized due to their roles in human health,disease,and the development of novel therapeutics.Phage-microbe interactions leave diverse signals in bacterial and phage geno-mic sequences,defined as phage-host interaction signals(PHISs),which include clustered regularly interspaced short palindromic repeats(CRISPR)targeting,prophage,and protein-protein interac-tion signals.In the present study,we developed a novel tool phage-host interaction signal detector(PHISDetector)to predict phage-host interactions by detecting and integrating diverse in silico PHISs,and scoring the probability of phage-host interactions using machine learning models based on PHIS features.We evaluated the performance of PHISDetector on multiple benchmark datasets and application cases.When tested on a dataset of 758 annotated phage-host pairs,PHISDetector yields the prediction accuracies of 0.51 and 0.73 at the species and genus levels,respectively,outper-forming other phage-host prediction tools.When applied to 125,842 metagenomic viral contigs(mVCs)derived from 3042 geographically diverse samples,a detection rate of 54.54％could be achieved.Furthermore,PHISDetector could predict infecting phages for 85.6％of 368 multidrug-resistant(MDR)bacteria and 30％of 454 human gut bacteria obtained from the National Institutes of Health(NIH)Human Microbiome Project(HMP).

Fengxia Zhou;Rui Gan;Fan Zhang;Chunyan Ren;Ling Yu;Yu Si;Zhiwei Huang

HIT Center for Life Sciences,School of Life Science and Technology,Harbin Institute of Technology,Harbin 150080,China;Department of Hematology/oncology,Boston Children s Hospital,Harvard Medical School,Boston,MA 02115,USA

基因组蛋白质组与生物信息学报（英文版）

[1]Fengxia Zhou;Rui Gan;Fan Zhang;Chunyan Ren;Ling Yu;Yu Si;Zhiwei Huang-.PHISDetector:A Tool to Detect Diverse In Silico Phage-host Interaction Signals for Virome Studies)[J].基因组蛋白质组与生物信息学报（英文版）,2022(03):508-523

PHISDetector,Virome,PHISs,prophage,PHIS,mVCs

Tool,Diverse,Silico,Phage,host,Interaction,Signals,Studies,microbe,interactions,are,appealing,systems,study,coevolution,have,also,been,increasingly,emphasized,due,their,roles,human,health,disease,development,novel,therapeutics,leave,diverse,signals,bacterial,sequences,defined,which,include,clustered,regularly,interspaced,short,palindromic,repeats,CRISPR,targeting,protein,present,we,developed,detector,by,detecting,integrating,silico,scoring,probability,using,machine,learning,models,features,We,evaluated,performance,multiple,benchmark,datasets,application,cases,When,tested,annotated,pairs,yields,prediction,accuracies,species,genus,levels,respectively,outper,forming,other,tools,applied,metagenomic,viral,contigs,derived,from,geographically,samples,detection,rate,could,achieved,Furthermore,infecting,phages,multidrug,resistant,MDR,gut,obtained,National,Institutes,Health,NIH,Human,Microbiome,Project,HMP

0.554512