基于组学技术研究反刍动物瘤胃微生物及其代谢功能的进展

doi:10.11843/j.issn.0366-6964.2019.06.001

Abstract

Abstract: Rumen microbes play a vital role in the production efficiency, health status of ruminants and greenhouse gas emissions. It is hot spots and highlights that the different research methods are used to reveal the structural composition and metabolic function of microbial communities in rumen ecosystems. This article reviews recent advances in rumen microbial composition, genomic function and metabolism in ruminants using omics technologies (metagenome, metatranscriptome, metaproteome and metabolomics) combined with evolving instrumental analysis and bioinformatics technologies. It aims to provide new technical methods and theoretical basis for further regulating rumen microbiome to improve ruminant production and reduce environmental pollution.

CLC Number:

S813.2

NIU Huaxin, CHANG Jie, HU Zongfu, WANG Yuxi. Research Progress on Rumen Microbiomes and Their Metabolic Functions in Ruminants Based on Omics Technology[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2019, 50(6): 1113-1122.

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References

[1] RIPPLE W J,SMITH P,HABERL H,et al.Ruminants,climate change and climate policy[J].Nat Clim Change,2014,4(1):2-5.
[2] 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].Front Microbiol,2018,9:2161.
[3] 郭威,郭晓军,周贤,等.复合菌剂发酵玉米秸秆对绵羊瘤胃液细菌多样性的影响[J].畜牧兽医学报,2018,49(4):736-745.
GUO W,GUO X J,ZHOU X,et al.Effect ofcorn stalk fermented by complex bacterial on rumen bacterial diversity in sheep[J].Acta Veterinaria et Zootechnica Sinica,2018,49(4):736-745.(in Chinese)
[4] MACKIE R I,AMINOV R I,WHITE B A,et al.Molecular ecology and diversity in gut microbial ecosystems[M]//CRONJE P B.Ruminant Physiology:Digestion,Metabolism,Growth and Reproduction.Wallingford:CABI Publishing,2000.
[5] ZHANG J,SHI H T,WANG Y J,et al.Effect of dietary forage to concentrate ratios on dynamic profile changes and interactions of ruminal microbiota and metabolites in Holstein heifers[J].Front Microbiol,2017,8:2206.
[6] WALLACE R J,ROOKE J A,MCKAIN N,et al.The rumen microbial metagenome associated with high methane production in cattle[J].BMC Genomics,2015,16:839.
[7] HUNGATE R E.The rumen and its microbes[M].New York:Academic Press,1966.
[8] YOUSSEF N,SHEIK C S,KRUMHOLZ L R,et al.Comparison of species richness estimates obtained using nearly complete fragments and simulated pyrosequencing-generated fragments in 16S rRNA gene-based environmental surveys[J].Appl Environ Microbiol, 2009,75(16):5227-5236.
[9] SESHADRI R,LEAHY S C,ATTWOOD G T,et al.Cultivation and sequencing of rumen microbiome members from the hungate1000 collection[J].Nat Biotechnol,2018,36(4):359-367.
[10] TRINGE S G,VON MERING C,KOBAYASHI A,et al.Comparative metagenomics of microbial communities[J]. Science, 2005, 308(5721):554-557.
[11] HE S M,WURTZEL O,SINGH K,et al.Validation of two ribosomal RNA removal methods for microbial metatranscriptomics[J].Nat Methods,2010,7(10):807-812.
[12] SCHNEIDER T,KEIBLINGER K M,SCHMID E,et al.Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions[J].ISME J,2012,6(9):1749-1762.
[13] SCALBERT A,BRENNAN L,FIEHN O,et al.Mass-spectrometry-based metabolomics:limitations and recommendations for future progress with particular focus on nutrition research[J].Metabolomics,2009,5(4):435-458.
[14] JANSSON J K,BAKER E S.A multi-omic future for microbiome studies[J].Nat Microbiol,2016,1(5):16049.
[15] 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].Sci Rep,2015,5:14567.
[16] 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].Appl Environ Microbiol,2012,78(14):4949-4958.
[17] 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.
[18] ANGLY F E,WILLNER D,ROHWER F,et al.Grinder:a versatile amplicon and shotgun sequence simulator[J].Nucleic Acids Res,2012,40(12):e94.
[19] KITTELMANN S,SEEDORF H,WALTERS W A,et al.Simultaneous amplicon sequencing to explore co-occurrence patterns of bacterial,archaeal and eukaryotic microorganisms in rumen microbial communities[J].PLoS One,2013,8(2):e47879.
[20] WILKINSON T J,HUWS S A,EDWARDS J E,et al.CowPI:a rumen microbiome focussed version of the PICRUSt functional inference software[J].Front Microbiol,2018,9:1095.
[21] BRULC J M,ANTONOPOULOS D A,MILLER M E B,et al.Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases[J].Proc Natl Acad Sci U S A,2009,106(6):1948-1953.
[22] JAMI E,ISRAEL A,KOTSER A,et al.Exploring the bovine rumen bacterial community from birth to adulthood[J].ISME J,2013,7(6):1069-1079.
[23] DENMAN S E,MARTINEZ FERNANDEZ G,SHINKAI T,et al.Metagenomic analysis of the rumen microbial community following inhibition of methane formation by a halogenated methane analog[J].Front Microbiol,2015,6:1087.
[24] ZHOU Z M,FANG L,MENG Q X,et al.Assessment of ruminal bacterial and archaeal community structure in Yak (Bos grunniens)[J].Front Microbiol,2017,8:179.
[25] ISHAQ S L,ALZAHAL O,WALKER N,et al.An investigation into rumen Fungal and Protozoal diversity in three rumen fractions,during high-fiber or grain-induced sub-acute ruminal acidosis conditions,with or without active dry yeast supplementation[J]. Front Microbiol,2017,8:1943.
[26] XIE X,YANG C L,GUAN L L,et al.Persistence of cellulolytic bacteria Fibrobacter and Treponema after short-term corn stover-based dietary intervention reveals the potential to improve rumen fibrolytic function[J].Front Microbiol,2018,9:1363.
[27] MCGOVERN E,KENNY D A,MCCABE M S,et al.16s rRNA sequencing reveals relationship between potent cellulolytic genera and feed efficiency in the rumen of bulls[J].Front Microbiol,2018,9:1842.
[28] ZEHAVI T,PROBST M,MIZRAHI I.Insights into culturomics of the rumen microbiome[J].Front Microbiol,2018,9:1999.
[29] POPE P B,MACKENZIE A K,GREGOR I,et al.Metagenomics of the Svalbard reindeer rumen microbiome reveals abundance of polysaccharide utilization loci[J].PLoS One,2012,7(6):e38571.
[30] CHENG Y F,WANG Y,LI Y F,et al.Progressive colonization of bacteria and degradation of rice straw in the rumen by Illumina sequencing[J]. Front Microbiol, 2017,8:2165.
[31] UFARTÉ L,POTOCKI-VERONESE G,CECCHINI D,et al.Highly promiscuous oxidases discovered in the bovine rumen microbiome[J]. Front Microbiol,2018,9:861.
[32] QI M,WANG P,O'TOOLE N,et al.Snapshot of the eukaryotic gene expression in muskoxen rumen-a metatranscriptomic approach[J]. PLoS One,2011,6(5):e20521.
[33] DAI X,TIAN Y,LI J T,et al.Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen[J].Appl Environ Microbiol,2015,81(4):1375-1386.
[34] NEVES A L A,LI F Y,GHOSHAL B,et al.Enhancing the resolution of rumen microbial classification from Metatranscriptomic data using Kraken and Mothur[J].Front Microbiol,2017,8:2445.
[35] COMTET-MARRE S,PARISOT N,LEPERCQ P,et al.Metatranscriptomics reveals the active bacterial and Eukaryotic Fibrolytic communities in the rumen of dairy cow fed a mixed diet[J].Front Microbiol,2017,8:67.
[36] GRUNINGER R J,NGUYEN T T M,REID I D,et al.Application of transcriptomics to compare the carbohydrate active enzymes that are expressed by diverse genera of anaerobic Fungi to degrade plant cell wall carbohydrates[J].Front Microbiol,2018,9:1581.
[37] INGOLIA N T,GHAEMMAGHAMI S,NEWMAN J R S,et al.Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling[J].Science,2009,324(5924):218-223.
[38] WILMES P,BOND P L.The application of two-dimensional polyacrylamide gel electrophoresis and downstream analyses to a mixed community of prokaryotic microorganisms[J].Environ Microbiol,2004,6(9):911-920.
[39] TOYODA A,ⅡO W,MITSUMORI M,et al.Isolation and identification of cellulose-binding proteins from sheep rumen contents[J].Appl Environ Microbiol,2009,75(6):1667-1673.
[40] SNELLING T J,WALLACE R J.The rumen microbial metaproteome as revealed by SDS-PAGE[J].BMC Microbiol,2017,17:9.
[41] DEUSCH S,SEIFERT J.Catching the tip of the iceberg-evaluation of sample preparation protocols for metaproteomic studies of the rumen microbiota[J].Proteomics,2015,15(20):3590-3595.
[42] HART E H,CREEVEY C J,HITCH T,et al.Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria[J].Sci Rep,2018,8(1):10504.
[43] MUTH T,BEHNE A,HEYER R,et al.The MetaProteomeAnalyzer:a powerful open-source software suite for metaproteomics data analysis and interpretation[J].J Proteome Res,2015,14(3):1557-1565.
[44] YI L Z,SHI S T,WANG Y,et al.Serum metabolic profiling reveals altered metabolic pathways in patients with post-traumatic cognitive impairments[J].Sci Rep,2016,6:21320.
[45] BUNDY J G,DAVEY M P,VIANT M R.Environmental metabolomics:a critical review and future perspectives[J]. Metabolism, 2015,5:3.
[46] PATEJKO M,JACYNA J,MARKUSZEWSKI M J.Sample preparation procedures utilized in microbial metabolomics:an overview[J]. J Chromatogr B,2017,1043:150-157.
[47] GOLDANSAZ S A,GUO A C,SAJED T,et al.Livestock metabolomics and the livestock metabolome:a systematic review[J].PLoS One,2017,12:e0177675.
[48] WANG M X,CARVER J J,PHELAN V V,et al.Sharing and community curation of mass spectrometry data with global natural products social molecular networking[J].Nat Biotechnol,2016,34(8):828-837.
[49] PATTI G J,YANESO,SIUZDAK G.Metabolomics:the apogee of the omics trilogy[J].Nat Rev Mol Cell Biol,2012,13(4):263-269.
[50] AMETAJ B N,ZEBELI Q,SALEEM F,et al.Metabolomics reveals unhealthy alterations in rumen metabolism with increased proportion of cereal grain in the diet of dairy cows[J].Metabolism,2010,6(4):583-594.
[51] SALEEM F,BOUATRA S,GUO A C,et al.The bovine ruminal fluid metabolome[J].Metabolomics,2013,9(2):360-378.
[52] ZHANG J,ZHAO S G,ZHANG Y D,et al.New primers targeting full-length ciliate 18S rRNA genes and evaluation of dietary effect on rumen ciliate diversity in dairy cows[J].Curr Microbiol,2015,71(6):650-657.
[53] ZHANG R Y,ZHU W Y,JIANG L S,et al.Comparative metabolome analysis of ruminal changes in Holstein dairy cows fed low- or high-concentrate diets[J].Metabolomics,2017,13:74.
[54] ARTEGOITIA V M,FOOTE A P,LEWIS R M,et al.Rumen fluid metabolomics analysis associated with feed efficiency on crossbred steers[J].Sci Rep,2017,7(1):2864.
[55] KINGSTON-SMITH A H,DAVIES T E,REES STEVENS P,et al.Comparative metabolite fingerprinting of the rumen system during colonisation of three forage grass (Lolium perenne L.) varieties[J].PLoS One,2013,8(11):e82801.
[56] ZHAO S,ZHAO J,BU D,et al.Metabolomics analysis reveals large effect of roughage types on rumen microbial metabolic profile in dairy cows[J].Lett Appl Microbiol,2014,59(1):79-85.
[57] MAO S Y,HUO W J,ZHU W Y.Microbiome-metabolome analysis reveals unhealthy alterations in the composition and metabolism of ruminal microbiota with increasing dietary grain in a goat model[J].Environ Microbiol,2016,18(2):525-541.
[58] XUE F G,PAN X H,JIANG L S,et al.GC-MS analysis of the ruminal metabolome response to thiamine supplementation during high grain feeding in dairy cows[J].Metabolomics,2018,14(5):67.
[59] O'CALLAGHAN T,VÁZQUEZ-FRESNO R,SERRA-CAYUELA A.Pasture feeding changes the bovine rumen and milk metabolome[J].Metabolites,2018,8(2):27.
[60] SHI W B,MOON C D,LEAHY S C,et al.Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome[J].Genome Res,2014,24(3):1517-1525.
[61] RUBINO F,CARBERRY C,WATERS S M,et al.Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome[J].ISME J,2017,11(4):932-944.
[62] CASPI R,ALTMAN T,DREHER K,et al.The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases[J].Nucleic Acids Res,2012,44(D1):D742-D752.
[63] 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.
[64] PALOMBA A,TANCA A,FRAUMENE C,et al.Multi-omic biogeography of the gastrointestinal microbiota of a pre-weaned lamb[J].Proteomes,2017,5(4):36.
[65] ELLIOTT C L,EDWARDS J E,WILKINSON T J,et al.Using' omic approaches to compare temporal bacterial colonization of Lolium perenne,Lotus corniculatus,and Trifolium pratense in the rumen[J].Front Microbiol,2018,9:2184.
[66] MORGAVI D P, RATHAHAO-PARIS E, POPOVA M, et al. Rumen microbial communities influence metabolic phenotypes in lambs[J]. Front Microbiol, 2015, 6:1060.
[67] DEUSCH S, CAMARINHA-SILVA A, CONRAD J, et al. A structural and functional elucidation of the rumen microbiome influenced by various diets and microenvironments[J]. Front Microbiol, 2017, 8:1605.
[68] ABECIA L, FERNANDEZ MARTINEZ G, WADDAMS K, et al. Analysis of the rumen microbiome and metabolome to study the effect of an antimethanogenic treatment applied in early life of kid goats[J]. Front Microbiol, 2018, 9:2227.

Research Progress on Rumen Microbiomes and Their Metabolic Functions in Ruminants Based on Omics Technology

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