反刍动物瘤胃噬菌体的宏基因组学研究方法及进展

doi:10.11843/j.issn.0366-6964.2022.01.003

Abstract

Abstract: Viruses are ubiquitous to the gastrointestinal tracts of various types of animals, including the rumen of ruminants. The rumen is a dense and taxonomically diverse consortium of bacteria, fungi, protozoa, archaea and virus. Nowadays, most of the researches by multi-omics and bioinformatics have focused on rumen bacteria. Studies have shown that diet, environment and host genotype have great impact on the diversity and community structure of rumen bacteria; meanwhile, rumen bacteria also affect the host’s metabolism, growth performance and health status in turn. Compared with rumen bacteria, rumen phages have received relatively fewer attention. With the development of molecular biology technology, high-throughput sequencing has paved way for the study of virome. Many novel viruses in rumen have been discovered by viral metagenomics, which largely enriches the understanding of the diversity of rumen viruses. Starting from the concept of rumen phage, this review focused on the analytical methods including virus DNA extraction, sequencing and bioinformatics. Then discussed the virome analytical methods both in the rumen and other ecosystems, and finally summarized the application prospects of rumen virome research.

Key words: rumen, virus, bacteriophage, metagenomics, high-throughput sequencing

CLC Number:

S852.65

WU Yicheng, RAN Tao, ZHOU Chuanshe, TAN Zhiliang. Rumen Bacteriophage in Ruminants: Metagenome Analytical Methods and Research Progress[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(1): 20-31.

References 71

[1]	WOMMACK K E,COLWELL R R.Virioplankton:Viruses in aquatic ecosystems[J].Microbiol Mol Biol Rev,2000,64(1):69-114.
[2]	FOCARDI A,OSTROWSKI M,GOOSSEN K,et al.Investigating the diversity of marine bacteriophage in contrasting water masses associated with the East Australian Current (EAC) system[J].Viruses,2020,12(3):317.
[3]	SHKOPOROV A N,RYAN F J,DRAPER L A,et al.Reproducible protocols for metagenomic analysis of human faecal phageomes[J].Microbiome,2018,6(1):68.
[4]	BRAILSFORD M D, HARTMAN P A. Characterization of Streptococcus durans bacteriophages [J]. Can J Microbiol, 1968, 14(4): 397-402.
[5]	HOOGENRAAD N J,HIRD F J R,HOLMES I,et al.Bacteriophages in rumen contents of sheep[J].J Gen Virol,1967,1(4):575-576.
[6]	GILBERT R A,TOWNSEND E M,CREW K S,et al.Rumen virus populations:Technological advances enhancing current understanding[J].Front Microbiol,2020,11:450.
[7]	KLIEVE A V,BAUCHOP T.Morphological diversity of ruminal bacteriophages from sheep and cattle[J].Appl Environ Microbiol,1988,54(6):1637-1641.
[8]	MARTINEZ-MARTINEZ J, SWAN B K, WILSON W H. Marine viruses, a genetic reservoir revealed by targeted viromics [J]. ISME J, 2014, 8(5): 1079-1088.
[9]	PAEZ-ESPINO D,ELOE-FADROSH E A,PAVLOPOULOS G A,et al.Uncovering earth’s virome[J].Nature,2016,536(7617):425-430.
[10]	SUTTON T D S,HILL C.Gut bacteriophage:Current understanding and challenges[J].Front Endocrinol,2019,10:784.
[11]	MANRIQUE P,BOLDUC B,WALK S T,et al.Healthy human gut phageome[J].Proc Natl Acad Sci U S A,2016,113(37):10400-10405.
[12]	DENMAN S E,MORGAVI D P,MCSWEENEY C S.Review:The application of omics to rumen microbiota function[J].Animal,2018,12(S2):S233-S245.
[13]	MORGAVI D P,KELLY W J,JANSSEN P H,et al.Rumen microbial (meta)genomics and its application to ruminant production[J].Animal,2013,7(S1):184-201.
[14]	BERGEN W G.Quantitative determination of rumen ciliate protozoal biomass with real-time PCR[J].J Nutr,2004,134(12):3223-3224.
[15]	JANSSEN P H,KIRS M.Structure of the archaeal community of the rumen[J].Appl Environ Microbiol,2008,74(12):3619-3625.
[16]	DENG W D,XI D M,MAO H M,et al.The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies:a review[J].Mol Biol Rep,2008,35(2):265-274.
[17]	PARMAR N R,JAKHESARA S J,MOHAPATRA A,et al.Rumen virome:an assessment of viral communities and their functions in the rumen of an Indian buffalo[J].Curr Sci,2016,111(5):919-925.
[18]	NAMONYO S,WAGACHA M,MAINA S,et al.A metagenomic study of the rumen virome in domestic caprids[J].Arch Virol,2018,163(12):3415-3419.
[19]	BARYLSKI J,ENAULT F,DUTILH B E,et al.Analysis of spounaviruses as a case study for the overdue reclassification of tailed phages[J].Syst Biol,2020,69(1):110-123.
[20]	ADAMS J C,GAZAWAY J A Jr,BRAILSFORD M D,et al.Isolation of bacteriophages from the bovine rumen[J].Experientia,1966,22(11):717-718.
[21]	MILLER M E B,YEOMAN C J,CHIA N,et al.Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome[J].Environ Microbiol,2012,14(1):207-227.
[22]	SWAIN R A,NOLAN J V,KLIEVE A V.Natural variability and diurnal fluctuations within the bacteriophage population of the rumen[J].Appl Environ Microbiol,1996,62(3):994-997.
[23]	ANDERSON C L,SULLIVAN M B,FERNANDO S C.Dietary energy drives the dynamic response of bovine rumen viral communities[J].Microbiome,2017,5(1):155.
[24]	ROSS E M,PETROVSKI S,MOATE P J,et al.Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle[J].BMC Microbiol,2013,13(1):242.
[25]	POPOV V L,TESH R B,WEAVER S C,et al.Electron microscopy in discovery of novel and emerging viruses from the collection of the world reference center for emerging viruses and arboviruses (WRCEVA)[J].Viruses,2019,11(5):477.
[26]	SU Z Q,TONG P P,ZHANG L,et al.First isolation and molecular characterization of blaCTX-M-121-producing Escherichia coli O157:H7 from cattle in Xinjiang,China[J].Front Vet Sci,2021,8:574801.
[27]	KLIEVE A V, HEGARTY R S.Opportunities for biological control of ruminal methanogenesis[J]. Aust J Agr Res, 1991, 50: 1315-1319.
[28]	TAMADA H,HARASAWA R,SHINJO T.Isolation of a bacteriophage in Fusobacterium necrophorum[J].Nihon Juigaku Zasshi,1985,47(3):483-486.
[29]	GILBERT R A,KELLY W J,ALTERMANN E,et al.Toward understanding phage:host interactions in the rumen; complete genome sequences of lytic phages infecting rumen bacteria[J].Front Microbiol,2017,8:2340.
[30]	FRIEDERSDORFF J C A,KINGSTON-SMITH A H,PACHEBAT J A,et al.The isolation and genome sequencing of five novel bacteriophages from the rumen active against Butyrivibrio fibrisolvens[J].Front Microbiol,2020,11:1588.
[31]	KLIEVE A V,GREGG K,BAUCHOP T.Isolation and characterization of lytic phages from Bacterioides ruminicola ss brevis[J].Curr Microbiol,1991,23(4):183-187.
[32]	CUERVO A,CARRASCOSA J L.Observation of bacteriophage ultrastructure by cryo-electron microscopy[J].Methods Mol Biol,2018,1693:43-55.
[33]	HANDELSMAN J.Metagenomics:application of genomics to uncultured microorganisms[J].Microbiol Mol Biol Rev,2004,68(4):669-685.
[34]	何彪,涂长春.病毒宏基因组学的研究现状及应用[J].畜牧兽医学报,2012,43(12):1865-1870.HE B,TU C C.The advances and applications of viral metagenomics[J].Acta Veterinaria et Zootechnica Sinica,2012,43(12):1865-1870.(in Chinese)
[35]	EISENHOFER R,MINICH J J,MAROTZ C,et al.Contamination in low microbial biomass microbiome studies:issues and recommendations[J].Trends Microbiol,2019,27(2):105-117.
[36]	HUNGATE R E.The rumen and its microbes[M].New York:Academic Press,1966:13-14.
[37]	陈金华.环境微生物的宏基因组学研究进展[J].吉林农业,2010(6):44-45,49.CHEN J H.Progress in the study of macrogenomics of environmental microorganisms[J].Jilin Agricultural,2010(6):44-45,49 (in Chinese).
[38]	CONCEIÇÃO-NETO N,ZELLER M,LEFRōRE H,et al.Modular approach to customise sample preparation procedures for viral metagenomics:a reproducible protocol for virome analysis[J].Sci Rep,2015,5:16532.
[39]	DUAN Y,LLORENTE C,LANG S,et al.Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease[J].Nature,2019,575(7783):505-511.
[40]	CARROLL-PORTILLO A,COFFMAN C N,VARGA M G,et al.Standard bacteriophage purification procedures cause loss in numbers and activity[J].Viruses,2021,13(2):328.
[41]	CORDOVA A,DESERNO M,GELBART W M,et al.Osmotic shock and the strength of viral capsids[J].Biophys J,2003,85(1):70-74.
[42]	D’HUMIèRES C,TOUCHON M,DION S,et al.A simple,reproducible and cost-effective procedure to analyse gut phageome:from phage isolation to bioinformatic approach[J].Sci Rep,2019,9(1):11331.
[43]	QIAO Y,LIU W L,LU N,et al.Rapid droplet multiple displacement amplification based on the droplet regeneration strategy[J].Anal Chim Acta,2021,1141:173-179.
[44]	RUSSELL D A.Sequencing,assembling,and finishing complete bacteriophage genomes[J].Methods Mol Biol,2018,1681:109-125.
[45]	ARDUI S,AMEUR A,VERMEESCH J R,et al.Single molecule real-time (SMRT) sequencing comes of age:applications and utilities for medical diagnostics[J].Nucleic Acids Res,2018,46(5):2159-2168.
[46]	CAO J B,ZHANG Y Q,DAI M,et al.Profiling of human gut virome with Oxford nanopore technology[J].Med Microecol,2020,4:100012.
[47]	ROUX S,ENAULT F,HURWITZ B L,et al.VirSorter:Mining viral signal from microbial genomic data[J].PeerJ,2015,3:e985.
[48]	REN J,AHLGREN N A,LU Y Y,et al.VirFinder:A novel k-mer based tool for identifying viral sequences from assembled metagenomic data[J].Microbiome,2017,5(1):69.
[49]	AMGARTEN D,BRAGA L P P,DA SILVA A M,et al.MARVEL,a tool for prediction of bacteriophage sequences in metagenomic bins[J].Front Genet,2018,9:304.
[50]	ZHENG T T,LI J,NI Y Q,et al.Mining,analyzing,and integrating viral signals from metagenomic data[J].Microbiome,2019,7(1):42.
[51]	KIEFT K,ZHOU Z C,ANANTHARAMAN K.VIBRANT:automated recovery,annotation and curation of microbial viruses,and evaluation of viral community function from genomic sequences[J].Microbiome,2020,8(1):90.
[52]	GUO J R,BOLDUC B,ZAYED A A,et al.VirSorter2:a multi-classifier,expert-guided approach to detect diverse DNA and RNA viruses[J].Microbiome,2021,9(1):37.
[53]	SHARMA V K,KUMAR N,PRAKASH T,et al.MetaBioME:a database to explore commercially useful enzymes in metagenomic datasets[J].Nucleic Acids Res,2010,38:D468-D472.
[54]	KANEHISA M,FURUMICHI M,TANABE M,et al.KEGG:new perspectives on genomes,pathways,diseases and drugs[J].Nucleic Acids Res,2017,45(D1):D353-D361.
[55]	GALPERIN M Y,MAKAROVA K S,WOLF Y I,et al.Expanded microbial genome coverage and improved protein family annotation in the COG database[J].Nucleic Acids Res,2015,43(D1):D261-D269.
[56]	FINN R D,COGGILL P,EBERHARDT R Y,et al.The Pfam protein families database:towards a more sustainable future[J].Nucleic Acids Res,2016,44(D1):D279-D285.
[57]	ALCOCK B P,RAPHENYA A R,LAU T T Y,et al.CARD 2020:Antibiotic resistome surveillance with the comprehensive antibiotic resistance database[J].Nucleic Acids Res,2020,48(D1):D517-D525.
[58]	YUTIN N,KAPITONOV V V,KOONIN E V.A new family of hybrid virophages from an animal gut metagenome[J].Biol Direct,2015,10(1):19.
[59]	SOLDEN L M,NAAS A E,ROUX S,et al.Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem[J].Nat Microbiol,2018,3(11):1274-1284.
[60]	VAN ECK N J,WALTMAN L.Software survey:VOSviewer,a computer program for bibliometric mapping[J].Scientometrics,2010,84(2):523-538.
[61]	MARTINEZ-HERNANDEZ F,FORNAS O,GOMEZ M L,et al.Single-virus genomics reveals hidden cosmopolitan and abundant viruses[J].Nat Commun,2017,8(1):15892.
[62]	BREITBART M, SALAMON P, ANDRESEN B,et al.Genomic analysis of uncultured marine viral communities[J].Proc Natl Acad Sci U S A,2002,99(22):14250-14255.
[63]	GREGORY A C,ZAYED A A,CONCEIÇÃO-NETO N,et al.Marine DNA viral macro- and microdiversity from pole to pole[J].Cell,2019,177(5):1109-1123.e14.
[64]	CLOKIE M R J,MILLARD A D,LETAROV A V,et al.Phages in nature[J].Bacteriophage,2011,1(1):31-45.
[65]	GRUNINGER R J,RIBEIRO G O,CAMERON A,et al.Invited review:Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants[J].Animal,2019,13(9):1843-1854.
[66]	EMERSON J B,ROUX S,BRUM J R,et al.Host-linked soil viral ecology along a permafrost thaw gradient[J].Nat Microbiol,2018,3(8):870-880.
[67]	BRUM J R,IGNACIO-ESPINOZA J C,KIM E H,et al.Illuminating structural proteins in viral “dark matter” with metaproteomics[J].Proc Natl Acad Sci U S A,2016,113(9):2436-2441.
[68]	ALLEN L Z,MCCROW J P,ININBERGS K,et al.The Baltic Sea virome:diversity and transcriptional activity of DNA and RNA viruses[J].mSystems,2017,2(1):e00125-16.
[69]	BRUM J R,HURWITZ B L,SCHOFIELD O,et al.Seasonal time bombs:dominant temperate viruses affect Southern Ocean microbial dynamics[J].ISME J,2016,10(2):437-449.
[70]	KNOWLES B,SILVEIRA C B,BAILEY B A,et al.Lytic to temperate switching of viral communities[J].Nature,2016,531(7595):466-470.
[71]	SHKOPOROV A N,HILL C.Bacteriophages of the human gut:the “known unknown” of the microbiome[J].Cell Host Microbe,2019,25(2):195-209.

Rumen Bacteriophage in Ruminants: Metagenome Analytical Methods and Research Progress

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 71

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	LI Jiannan, YUAN Liming, HUA Jinlian. Progress on the Application of CD46 in Breeding of Livestock for Disease Resistance [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 1866-1874.
[2]	LONG Tanghui, ZHOU Jianghui, ZHAN Yanbo, ZHANG Jian, ZHAO Xianghui, LI Yanjiao, OUYANG Kehui, QIU Qinghua. Research Progress on LuxS/AI-2 Quorum Sensing of Rumen Microbe in Ruminants [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 1893-1903.
[3]	YU Zuhua, GAO Mengru, QI Zhiying, ZHANG Jingyu, HE Lei, CHEN Jian, DING Ke. Research Progress on the Function of RNA Binding Protein ELAVL1 and Its Regulation of Viral Replication [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 1914-1925.
[4]	HUANG Jin, LI Siyuan, MAO Li, CAI Xuhang, XIE Lingling, WANG Fu, ZHOU Hua, LI Jizong, LI Bin. Eukaryotic Expression of Bovine Coronavirus S1 Protein and Establishment and Application of Indirect ELISA [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2050-2060.
[5]	HAN Yang, GUAN Shuaiyin, LI Zhen, ZHOU Saisai, YUAN Honggen, SONG Yunfeng. Prokaryotic Expression and Protein Activity of Porcine Circovirus Type 3 Rep [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2061-2071.
[6]	ZHOU Yang, WU Weizi, CAO Weisheng, WANG Fuguang, XU Xiuqiong, ZHONG Wenxia, WU Liyang, YE Jian, LU Shousheng. A Whole Genome Sequencing Method for African Swine Fever Virus based on Nanopore Sequencing Technology was Established [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2080-2089.
[7]	XU Hong, SHANG Hongqi, ZHANG Xue, QIAN Jiali, WANG Chuanhong, SONG Xu, BAO Meiying, LIU Shiyu, ZHANG Gege, GUO Rongli, ZHAO Yongxiang, FAN Baochao, LI Bin. Inhibition Effect of C8orf4 Gene Encoding Protein on in vitro Replication of Porcine Epidemic Diarrhea Virus [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2100-2108.
[8]	XIONG Ting, HE Xianming, ZHAO Xiya, ZHUANG Tingting, HUANG Meizhen, LIANG Shijin, YU Chuanzhao, LIANG Xuejing, CHEN Ruiai. Whole Genome Analysis of Three Predominant Epidemic Strains of Chicken Infectious Bronchitis Virus and Their Pathogenicity [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2109-2122.
[9]	LÜ Yadi, YANG Jie, XIE Wenting, XU Ting, CHEN Ruiai. Construction and Evaluation of the Immune Effect of Recombinant Genotype Ⅶ NDV Strain Co-expressing Membrane-bound and Water-soluble HA Protein of Avian Influenza Virus H9N2 [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2123-2134.
[10]	WANG Jing, ZHANG Shujuan, HU Xia, LIU Xiangyang, ZHANG Xingcui, SONG Zhenhui. CD44 Regulates Na⁺/H⁺ Exchanger 3 Activity by Influencing Porcine Epidemic Diarrhea Virus Replication [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2176-2185.
[11]	ZHANG Ying, SONG Chunlian, ZHANG Ying, SHEN Hong, SHU Xianghua, YANG Honggui. Study on the Damage of Blood-brain Barrier by Tight Junction Protein Mediated by MMP-9 in Pseudorabies Virus-infected Mice [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2186-2194.
[12]	LI Pengfei, GAO Guiqin, ZHOU Guangqing, WU Jinyan, YAN Xinmin, CAO Xiaoan, HE Jijun, YUAN Ligang, SHANG Youjun. Establishment and Application of TaqMan Fluorescence Quantitative RT-PCR Detection Method for Enzootic Nasal Tumor Virus of Goats [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2259-2266.
[13]	HU Zeqi, LI Runcheng, TAN Zuming, XIE Xiuyan, WANG Jiangping, QIN Lejuan, LI Rong, GE Meng. Establishment and Preliminary Application of PEDV, PoRVA and PDCoV TaqMan Triple RT-qPCR Assay [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 2267-2272.
[14]	GUO Xuelian, LI Yongqin, LI Ruiqian, LI Hao, JIN Shuangyuan, WANG Xueyan, DU Jiawei, XU Lihua. Biological Functions of Bovine Respiratory Syncytial Virus G and F Proteins [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1478-1487.
[15]	LIU Weiye, HUANG Xuewei. Research Progress of Non-coding RNA in Infectious Bursal Disease Virus Infection [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(4): 1488-1498.