[1] SHABAT S K,SASSON G,DORON-FAIGENBOIM A,et al.Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants[J].The ISME Journal,2016,10(12):2958-2972.

[2] FIRKINS J L,YU Z.Ruminant nutrition symposium:how to use data on the rumen microbiome to improve our understanding of ruminant nutrition[J].Journal of Animal Science,2015,93(4):1450-1470.

[3] JAMI E,WHITE B A,MIZRAHI I.Potential role of the bovine rumen microbiome in modulating milk composition and feed efficiency[J].PLoS One,2014,9(1):e85423.
[4] CARBERRY C A,KENNY D A,HAN S,et al.Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle[J].Applied and Environmental Microbiology,2012,78(14):4949-4958.

[5] HUWS S A,CREEVEY C J,OYAMA L B,et al.Addressing global ruminant agricultural challenges through understanding the rumen microbiome:past,present,and future[J].Frontiers in Microbiology,2018(9):2161-2161.
[6] XUE M Y,SUN H Z,WU X H,et al.Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance[J].Microbiome,2020,8(1):64.
[7] BICKHART D M,WEIMER P J.Symposium review:host-rumen microbe interactions may be leveraged to improve the productivity of dairy cows[J].Journal of Dairy Science,2018,101(8):7680-7689.

[8] SEED K D,YEN M,SHAPIRO B J,et al.Evolutionary consequences of intra-patient phage predation on microbial populations[J].eLife,2014(3):e3497.
[9] HURWITZ B L,WESTVELD A H,BRUM J R,et al.Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses[J].Proceedings of the National Academy of Sciences,2014,111(29):10714-10719.

[10] HURWITZ B L,BRUM J R,SULLIVAN M B.Depth-stratified functional and taxonomic niche specialization in the ‘core’ and ‘flexible’ Pacific Ocean Virome[J].The ISME Journal,2015,9(2):472-484.

[11] BRUM J R,IGNACIO-ESPINOZA J C,ROUX S,et al.Ocean plankton.Patterns and ecological drivers of ocean viral communities[J].Science,2015,348(6237):1261498.
[12] TWORT F W.Further investigations on the nature of ultra-microscopic viruses and their cultivation[J].Journal of Hygiene,1936,36(2):204-235.

[13] CHANISHVILI N.Phage therapy-history from Twort and d'Herelle through Soviet experience to current approaches[J].Advances in Virus Research,2012,83:3-40.
[14] SMITH H W,HUGGINS M B.Effectiveness of phages in treating experimental Escherichia coli diarrhoea in calves,piglets and lambs[J].Journal of General Microbiology,1983,129(8):2659-2675.
[15] ADAMS J C,GAZAWAY J A,BRAILSFORD M D,et al.Isolation of bacteriophages from the bovine rumen[J].Experientia,1966(22):717-718.
[16] BRADLEY D E.Ultrastructure of bacteriophage and bacteriocins[J].Bacteriological Reviews,1967,31(4):230-314.

[17] KLIEVE A V,BAUCHOP T.Morphological diversity of ruminal bacteriophages from sheep and cattle[J].Applied and Environmental Microbiology,1988,54(6):1637-1641.

[18] HOOGENRAAD N J,HIRK F J,HOLMES I,et al.Bacteriophages in rumen contents of sheep[J].Journal of General Virology,1967,1(4):575-576.

[19] PAYNTER M J,EWERT D L,CHALUPA W.Some morphological types of bacteriophages in bovine rumen contents[J].Applied Microbiology,1969,18(5):942-943.

[20] TARAKANOV B V.Biological properties of
Streptococcus bovis bacteriophages isolated from lysogenic cultures and sheep rumen[J].Mikrobiologiia,1976,45(4):695-700.
[21] TARAKANOV B V.Bacteriophages in the contents of cattle rumen[J].Mikrobiologiia,1971,40(3):544-550.
[22] JIANG W H,PATTERSON J A,STEENSON L R.Isolation and characterization of a temperate bacteriophage from a ruminal acetogen[J].Current Microbiology,1995,31(6):336-339.

[23] AMBROZIC J,FERME D,GRABNAR M,et al.The bacteriophages of ruminal prevotellas[J].Folia Microbiol,2001,46(1):37-39.

[24] IVERSON W G,MILLIS N F.Characterization of
Streptococcus bovis bacteriophages[J].Canadian Journal of Microbiology,1976,22(6):847-852.

[25] SWAIN R A,NOLAN J V,KLIEVE A V.Natural variability and diurnal fluctuations within the bacteriophage population of the rumen[J].Applied and Environmental Microbiology,1996,62(3):994-997.

[26] NEMCOVA R,STYRIAK I,STACHOVA M,et al.Isolation and partial characterization of three rumen
Lactobacillus plantarum bacteriophages[J].New Microbiologica,1993,16(2):177-180.
[27] STYRIAK I,KMET V,SPANOVA A.Isolation and characterization of two rumen
Streptococcus bovis bacteriophages[J].Microbiologica,1989,12(4):317-322.
[28] LOCKINGTON R A,ATTWOOD G T,BROOKER J D.Isolation and characterization of a temperate bacteriophage from the ruminal anaerobe
Selenomonas ruminantium[J].Applied and Environmental Microbiology,1988,54(6):1575-1580.

[29] KLIEVE A V,BAIN P A,YOKOYAMA M T,et al.Bacteriophages that infect the cellulolytic ruminal bacterium
Ruminococcus albus AR67[J].Letters in Applied Microbiology,2004,38(4):333-338.

[30] 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].Frontiers in Microbiology,2017(8):2340.
[31] PARMAR N R,JAKHESARA S J,MOHAPATRA A J C G.Rumen virome:an assessment of viral communities and their functions in the rumen of an Indian buffalo[J].Current Science,2016,111:919-925.
[32] FRIEDERSDORFF J,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].Frontiers in Microbiology,2020.DOI:10.3389/fmicb.2020.01588.
[33] NAMONYO S,WAGACHA M,MAINA S,et al.A metagenomic study of the rumen virome in domestic caprids[J].Archives of Virology,2018,163(12):3415-3419.

[34] 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.
[35] SOLDEN L M,NAAS A E,ROUX S,et al.Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem[J].Nature Microbiology,2018,3(11):1274-1284.

[36] HENDERSON G,COX F,GANESH S,et al.Rumen microbial community composition varies with diet and host,but a core microbiome is found across a wide geographical range[J].Scientific Reports,2016(6):14567.
[37] FLINT H J,BAYER E A,RINCON M T,et al.Polysaccharide utilization by gut bacteria:potential for new insights from genomic analysis[J].Nature Reviews Microbiology,2008,6(2):121-131.

[38] ZEINELDIN M,BARAKAT R,ELOLIMY A,et al.Synergetic action between the rumen microbiota and bovine health[J].Microbial Pathogenesis,2018,124:106-115.
[39] VEIRA D M.The role of ciliate protozoa in nutrition of the ruminant[J].Journal of Animal Science,1986,63(5):1547-1560.

[40] KRAUSE D O,NAGARAJA T G,WRIGHT A D,et al.Board-invited review:rumen microbiology:leading the way in microbial ecology[J].Journal of Animal Science,2013,91(1):331-341.

[41] KLIEVE A V,SWAIN R A.Estimation of ruminal bacteriophage numbers by pulsed-field gel electrophoresis and laser densitometry[J].Applied and Environmental Microbiology,1993,59(7):2299-2303.

[42] THOMPSON L R,ZENG Q,KELLY L,et al.Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism[J].Proceedings of the National Academy of Sciences,2011,108(39):E757-E764.
[43] ROSS E M,PETROVSKI S,MOATE P J,et al.Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle[J].BMC Microbiology,2013(13):242.
[44] GILBERT R A,TOWNSEND E M,CREW K S,et al.Rumen virus populations:technological advances enhancing current understanding[J].Frontiers in Microbiology,2020(11):450.
[45] ORPIN C G,MUNN E A.The occurrence of bacteriophages in the rumen and their influence on rumen bacterial populations[J].Experientia,1974,30(9):1018-1020.

[46] ACKERMANN H W.Bacteriophage electron microscopy[J].Advances in Virus Research,2012,821-32.
[47] ACKERMANN H W.Sad state of phage electron microscopy.Please shoot the messenger[J].Microorganisms,2013,2(1):1-10.

[48] WILLIAMSON K E,HELTON R R,WOMMACK K E.Bias in bacteriophage morphological classification by transmission electron microscopy due to breakage or loss of tail structures[J].Microscopy Research and Technique,2012,75(4):452-457.

[49] ACKERMANN H W,PRANGISHVILI D.Prokaryote viruses studied by electron microscopy[J].Archives of Virology,2012,157(10):1843-1849.

[50] SHKOPOROV A N,KHOKHLOVA E V,FITZGERALD C B,et al.PhiCrAss001 represents the most abundant bacteriophage family in the human gut and infects
Bacteroides intestinalis[J].Nature Communications,2018,9(1):4781.
[51] KAELBER J T,HRYC C F,CHIU W.Electron cryomicroscopy of viruses at near-atomic resolutions[J].Annual Review of Virology,2017,4(1):287-308.

[52] LETAROV A V,KULIKOV E E.Adsorption of bacteriophages on bacterial cells[J].Biochemistry (Moscow),2017,82(13):1632-1658.

[53] TAMADA H,HARASAWA R,SHINJO T.Isolation of a bacteriophage in
Fusobacterium necrophorum[J].Nihon Juigaku Zasshi,1985,47(3):483-486.

[54] STYRIAK I,SPANOVA A,MONTAGOVA H,et al.Isolation and characterization of a new ruminal bacteriophage lytic to
Streptococcus bovis[J].Current Microbiology,1994,28:355-358.
[55] KLIEVE A V,GREGG K,BAUCHOP T.Isolation and characteristics of lytic phages from
Bacteroides ruminicola ss brevis[J].Current Microbiology,1991,23:183-187.
[56] 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.
[57] PARMAR N R,SOLANKI J V,PATEL A B,et al.Metagenome of Mehsani buffalo rumen microbiota:an assessment of variation in feed-dependent phylogenetic and functional classification[J].Journal of Molecular Microbiology and Biotechnology,2014,24(4):249-261.

[58] HESS M,SCZYRBA A,EGAN R,et al.Metagenomic discovery of biomass-degrading genes and genomes from cow rumen[J].Science,2011,331(6016):463-467.

[59] KWOK K,NIEUWENHUIJSE D F,PHAN M,et al.Virus metagenomics in farm animals:a systematic review[J].Viruses,2020,12(1):107.
[60] YUTIN N,KAPITONOV V V,KOONIN E V.A new family of hybrid virophages from an animal gut metagenome[J].Biology Direct,2015,10(1):19.
[61] DINSDALE E A,EDWARDS R A,HALL D,et al.Functional metagenomic profiling of nine biomes[J].Nature,2008,452(7187):629-632.

[62] WILLNER D,THURBER R V,ROHWER F.Metagenomic signatures of 86 microbial and viral metagenomes[J].Environmental Microbiology,2009,11(7):1752-1766.

[63] BERG M M,YEOMAN C J,CHIA N,et al.Phage-bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome[J].Environmental Microbiology,2012,14(1):207-227.

[64] CALISHER C H,BRIESE T,BRISTER J R,et al.Strengthening the interaction of the virology community with the International Committee on Taxonomy of Viruses (ICTV) by linking virus names and their abbreviations to virus species[J].Systematic Biology,2019,68(5):828-839.

[65] LEFKOWITZ E J,DEMPSEY D M,HENDRICKSON R C,et al.Virus taxonomy:the database of the International Committee on Taxonomy of Viruses (ICTV)[J].Nucleic Acids Research,2018,46(D1):D708-D717.
[66] PETERS D L,WANG W,ZHANG X,et al.Metaproteomic and metabolomic approaches for characterizing the gut microbiome[J].Proteomics,2019,19(16):e1800363.
[67] HITCH T,EDWARDS J E,GILBERT R A.Metatranscriptomics reveals mycoviral populations in the ovine rumen[J].FEMS Microbiology Letters,2019,366(13):161.
[68] YUAN L,HENSLEY C,MAHSOUB H M,et al.Microbiota in viral infection and disease in humans and farm animals[J].Progress in Molecular Biology and Translational Science,2020,171:15-60.
[69] HURWITZ B L,HALLAM S J,SULLIVAN M B.Metabolic reprogramming by viruses in the sunlit and dark ocean[J].Genome Biology,2013,14(11):R123.
[70] FEINER R,ARGOV T,RABINOVICH L,et al.A new perspective on lysogeny:prophages as active regulatory switches of bacteria[J].Nature Reviews Microbiology,2015,13(10):641-650.

[71] SIEIRO C,AREAL-HERMIDA L,PICHARDO-GALLARDO A,et al.A hundred years of bacteriophages:can phages replace antibiotics in agriculture and aquaculture?[J].Antibiotics (Basel),2020,9(8):493.
[72] JARVIS B D.Lysis of viable rumen bacteria in bovine rumen fluid[J].Applied Microbiology,1968,16(5):714-723.

[73] FIRKINS J L,WEISS W P,PIWONKA E J.Quantification of intraruminal recycling of microbial nitrogen using nitrogen-15[J].Journal of Animal Science,1992,70(10):3223-3233.

[74] HARTINGER T,GRESNER N,SUDEKUM K H.Does intra-ruminal nitrogen recycling waste valuable resources? A review of major players and their manipulation[J].Journal of Animal Science and Biotechnology,2018(9):497-517
[75] BACH A,CALSAMIGLIA S,STERN M D.Nitrogen metabolism in the rumen[J].Journal of Dairy Science,2005,88(Suppl.1):E9-E21.
[76] LENG R A,NOLAN J V.Nitrogen metabolism in the rumen[J].Journal of Dairy Science,1984,67(5):1072-1089.

[77] WELLS J E,RUSSELL J B.Why do many ruminal bacteria die and lyse so quickly?[J].Journal of Dairy Science,1996,79(8):1487-1495.

[78] ARBER W.A beginner's guide to lambda biology[J].Cold Spring Harbor Monograph Archive,1983(13):381-394.
[79] COHEN O,PUPKO T.Inference and characterization of horizontally transferred gene families using stochastic mapping[J].Molecular Biology and Evolution,2010,27(3):703-713.

[80] ROHWER F,PRANGISHVILI D,LINDELL D.Roles of viruses in the environment[J].Environmental Microbiology,2009,11(11):2771-2774.

[81] TOUCHON M,MOURA D S J,ROCHA E P.Embracing the enemy:the diversification of microbial gene repertoires by phage-mediated horizontal gene transfer[J].Current Opinion in Microbiology,2017,38:66-73.
[82] WEINBAUER M G.Ecology of prokaryotic viruses[J].FEMS Microbiology Reviews,2004,28(2):127-181.

[83] MCCUDDIN Z P,CARLSON S A,RASMUSSEN M A,et al.Klebsiella to
Salmonella gene transfer within rumen protozoa:implications for antibiotic resistance and rumen defaunation[J].Veterinary Microbiology,2006,114(3/4):275-284.
[84] TOOMEY N,MONAGHAN A,FANNING S,et al.Transfer of antibiotic resistance marker genes between lactic acid bacteria in model rumen and plant environments[J].Applied and Environmental Microbiology,2009,75(10):3146-3152.

[85] KLIEVE A V,BAUCHOP T.Phage resistance and altered growth habit in a strain of
Streptococcus bovis[J].FEMS Microbiology Letters,1991,64(2/3):155-159.