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

Genomics, Proteomics & Bioinformatics 2022年第3期20卷 508-523页

作者： Fengxia Zhou Rui Gan Fan Zhang Chunyan Ren Ling Yu Yu Si Zhiwei Huang HIT Center for Life Sciences School of Life Science and TechnologyHarbin Institute of TechnologyHarbin 150080China Department of Hematology/oncology Boston Children’s HospitalHarvard Medical SchoolBostonMA 02115USA

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://***/PHISDetector/)for general users to study individual inputs or as a stand-alone version(https://***/HITImmunologyLab/PHISDetector)to process massive phage contigs from virome studies.

关键词： Phage-host interaction Virome CRISPR prophage Machine learning

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Identification of prophages within the Mycobacterium avium 104 Genome and the Link of Their Function Regarding to Environment Survival

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Advances in Microbiology 2016年第13期6卷 927-941页

作者： Miao Zhao Kerrigan Gilbert Lia Danelishvili Brendan Jeffrey Luiz E. Bermudez Program of Biology Oregon State University Corvallis OR USA Department of Biomedical Sciences College of Veterinary Medicine Oregon State University Corvallis OR USA Department of Microbiology Oregon State University Corvallis OR USA

Mycobacterium avium is an opportunistic bacterium associated with pathogenic behavior in both humans and animals. M. avium has evolved as a pathogen by having an environmental component in its life style. prophages are the integrated viral forms in bacterium genome. They constitute about 10% - 20% of genome of many bacteria and they contribute to pathogenicity of microbes. We investigated whether the M. avium 104 genome contained prophages and evaluated the genes/proteins for putative functions. Three prophage genes were identified in the M. avium 104 database, and sequences were analyzed for specific motifs. The prophage sequences were then cloned in Mycobacterium smegmatis and the bacterial phenotype was evaluated in gain of function assays for environmental stresses, such as tolerance to extreme temperatures, UV light, biofilm formation and resistance to acid as well as macrophage survival. The results indicate that two of the prophage genes, MAV_0696 and MAV_2265, confer M. smegmatis with enhanced ability to produce biofilm. Using a Real-Time PCR, it was determined that MAV_0696 and MAV_2265 transcripts were upregulated upon biofilm formation by M. avium. The expression of MAV_2265 gene was significantly higher at all selected time points. In addition, the expression of MAV_2265 in M. smegmatis also led to significantly greater survival rate at pH 5.0 compared to the wild-type control. None of the other physical abilities were altered by overexpressing the prophage genes in M. smegmatis. In summary, we identified three prophage sequences in M. avium 104, from which two of them were found to be associated with biofilm formation and one with resistance to the acidic environment. Future studies will identify the mechanisms involved in the prophages function.

关键词： Mycobacterum avium prophage Virulence Environment

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Influence of Hot Spring Phages on Community Carbon Metabolism: Win, Lose or Draw?

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Advances in Microbiology 2015年第9期5卷 630-643页

作者： Raymond Kepner Department of Biology Marist College Poughkeepsie New York USA

Abundant virus-like particles were concentrated from large-volume samples from two hot springs. Both addition of viral concentrates and addition of samples induced by addition of mitomycin-C changed patterns of carbon source utilization by hot spring microbial communities. Specific effects of the two treatments depended upon both temperature and incubation period. Increased metabolic capability with greater exposure to free phages, consistent with the view that phages are major lateral transporters of metabolic genes, was observed most clearly in microbes incubated at a temperature lower than that encountered in situ. On the other hand, decreases in the diversity of utilizable C sources upon exposure to phages may have been due to lytic activity in which susceptible bacterial populations were differentially reduced by infective viruses, consistent with the “killing the winner” hypothesis. Treatment of cultures with MC-treated culture extracts, assumed to increase exposure to excised prophages, resulted in higher average metabolic rates after 18 h, but lower rates after 48 h of incubation. With incubation at in situ temperature, this same treatment led to an initial increase in the number of readily utilized C sources, followed by a decrease in community metabolic diversity relative to controls in samples from both hot springs. Thus, treatments designed to increase the interaction between hot spring microbes and either free or newly-excised phages had observable time- and temperature-dependent effects on community metabolism, demonstrating an important, yet complex, ecological role for phages in hot spring waters.

关键词： Hot Springs Virus prophage Thermophiles Carbon Metabolism

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柑橘溃疡病菌全基因组测序与比较基因组分析

柑橘溃疡病菌全基因组测序与比较基因组分析

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作者：陈峰华南农业大学

学位级别：硕士

柑橘溃疡病是柑橘生产上主要的细菌性病害,严重影响树势生长、果实品质和产量,对柑橘产业造成了巨大的损失。该病害是由地毯草黄单胞杆菌柑橘致病变种(Xanthomonas axonopodis pv.citri,Xac)所引起,近年来随着DNA测序技术的快速发展,基... 详细信息

柑橘溃疡病是柑橘生产上主要的细菌性病害,严重影响树势生长、果实品质和产量,对柑橘产业造成了巨大的损失。该病害是由地毯草黄单胞杆菌柑橘致病变种(Xanthomonas axonopodis pv.citri,Xac)所引起,近年来随着DNA测序技术的快速发展,基因组学的研究逐渐成为新的研究热点。本研究选取采自江西的感染溃疡病菌的脐橙进行病原菌的分离培养,利用Illumina Miseq二代测序技术进行病原菌全基因组测序,通过比较基因组学方法分析溃疡病菌A菌株和A菌株的宿主范围和毒性差异的分子机制。主要取得以下几方面的研究进展:1、柑橘溃疡病菌全基因组测序与分析本研究利用Illumina Miseq测序平台对分离的jx-6菌株进行了全基因组序列的测序,并对其基因组缺口进行了人工修补、序列拼装和注释,获得一个环状基因组序列(GenBank登录号:CP011827.1)和两个质粒序列(GenBank登录号分别为:CP013664.1和CP013665.1)。jx-6菌株基因组大小为5,124,792bp,平均GC含量为64.8%,编码4357个CDS,54个tRNA和6个核糖体16S-23S-5S rRNA操纵子,同时还对jx-6菌株基因组中的插入序列、分泌系统、基因岛、噬菌体相关编码基因、CRISPR(clustered regularly interspaced short palindromic repeat)等进行了预测分析并通过实验进行了验证,在jx-6基因组中,预测到了14个可信的IS(Insertion Sequence)元件,42个基因岛区域,3个前噬菌体区域和5个CRISPR位点。2、柑橘溃疡病菌比较基因组学分析将本研究中测序菌株jx-6与GenBank数据库中已经公布全基因组的菌株中选取的2株A菌株(gd3,GenBank收录号:CP009016.1和306,GenBank收录号:AE008923.1)和2株A菌株(A12879,GenBank收录号:CP003778.1和A13,GenBank收录号:CP009031.1)进行比较基因组学分析。直系同源基因聚类分析表明5个菌株核心基因簇共3887个,只有A菌株具有特异基因簇,特异基因簇为216个。对这些特异基因簇进行分析结果显示大部分与生物代谢和细胞代谢过程有关。基因组共线性分析结果显示A菌株基因组存在翻转、易位、倒位等基因组重排事件。另外,对A菌株和A菌株的全基因组进行前噬菌体预测分析,表明A菌株基因组中都含有3个前噬菌体区域,A菌株基因组中都含有5个前噬菌体区域。通过比对发现A菌株中的prophage2与A菌株中的prophage2属于同一种噬菌体,其中A菌株中的prophage4和prophage5两个前噬菌体区域正好插入在两个菌株共线性程度较低的部分。这些前噬菌体的插入及基因组重排有可能是导致A菌株寄主专化性的原因所在。3、柑橘溃疡病菌中CRISPR/cas系统的分析原核生物中,CRISPR/cas系统对外来的质粒和噬菌体序列具有抵抗作用,是一串包含多个间隔的短重复序列的区域。通过对菌株jx-6的分析发现其基因组上共存在5个CRISPR位点,并且CRISPR5在其序列上游区域存在着相关的cas基因,因此推测其在不同菌株中具有潜在的活性。基于上述推测分别对来自广东、广西、江西三地的不同菌株中的CRISPR5进行PCR、克隆测序分析,其结果表明CRISPR5位点的重复单元具有可变性,与推测是相一致的,进一步说明了CRISPR5潜在的活性。4、柑橘溃疡病菌基因组进化分析本研究选取了包括jx-6菌株在内的共22株柑橘溃疡病菌的7个看家基因(atpD,dnaK,efp,fyuA,glnA,gyrB,rpoD),串联后绘制了系统发育进化树,菌株jx-6与BL18的亲缘关系较近,并且所有的A菌株聚为一支,A菌株聚为一支。这一结果与共线性分析和基因同源聚类分析的结果相一致。

关键词：柑橘溃疡病 Xanthomonas axonopodis pv.citri 全基因组测序比较基因组学 CRISPR prophage

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