PHISDetector:A Tool to Detect Diverse In Silico Phage–host Interaction Signals for Virome Studies  

作　　者：Fengxia Zhou Rui Gan Fan Zhang Chunyan Ren Ling Yu Yu Si Zhiwei Huang 

机构地区：[1]HIT Center for Life Sciences,School of Life Science and Technology,Harbin Institute of Technology,Harbin 150080,China [2]Department of Hematology/oncology,Boston Children’s Hospital,Harvard Medical School,Boston,MA 02115,USA

出　　处：《Genomics, Proteomics & Bioinformatics》2022年第3期508-523,共16页基因组蛋白质组与生物信息学报（英文版）

基　　金：supported by the National Natural Science Foundation of China(Grant Nos.31825008,31422014,and 61872117).

摘　　要：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 genomic sequences,defined as phage-host interaction signals(PHISs),which include clustered regularly interspaced short palindromic repeats(CRISPR)targeting,prophage,and protein-protein interaction 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,outperforming 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).The PHISDetector can be run either as a web server(http://www.microbiome-bigdata.com/PHISDetector/)for general users to study individual inputs or as a stand-alone version(https://github.com/HITImmunologyLab/PHISDetector)to process massive phage contigs from virome studies.

关 键 词：Phage-host interaction Virome CRISPR PROPHAGE Machine learning 

分 类 号：Q939.4[生物学—微生物学]