[1] LEY R E,HAMADY M,LOZUPONE C,et al.Evolution of mammals and their gut microbes[J].Science,2008,320(5883):1647-1651.
[2] BENSON A K,KELLY S A,LEGGE R,et al.Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors[J].Proceedings of the National Academy of Sciences of the United States of America,2010,107(44):18933-18938.
[3] TURNBAUGH P J,RIDAURA V K,FAITH J J,et al.The effect of diet on the human gut microbiome:a metagenomic analysis in humanized gnotobiotic mice[J].Science Translational Medicine,2009,1(6):6ra14.
[4] TURNBAUGH P J,HAMADY M,YATSUNENKO T,et al.A core gut microbiome in obese and lean twins[J].Nature,2009,457(7228):480-484.
[5] 朱伟云,余凯凡,慕春龙,等.猪的肠道微生物与宿主营养代谢[J].动物营养学报,2014,26(10):3046-3051.
[6] XIA L C,CRAM J A,CHEN T,et al.Accurate genome relative abundance estimation based on shotgun metagenomic reads[J].PLoS One,2011,6(12):e27992.
[7] GARMENDIA L,HERNANDEZ A,SANCHEZ M B,et al.Metagenomics and antibiotics[J].Clinical Microbiology and Infection,2012,18(Suppl 4):27-31.
[8] FAUST K,RAES J.Microbial interactions:from networks to models[J].Nature Reviews Microbiology,2012,10(8):538-550.
[9] CHISTOSERDOVA L.Functional metagenomics:recent advances and future challenges[J].Biotechnology and Genetic Engineering Reviews,2009,26(1):335-352.
[10] SIEZEN R J,KLEEREBEZEM M.The human gut microbiome:are we our enterotypes?[J].Microbial Biotechnology,2011,4(5):550-553.
[11] EISEN J A.Environmental shotgun sequencing:its potential and challenges for studying the hidden world of microbes[J].PLoS Biology,2007,5(3):e82.
[12] TURNBAUGH P J,QUINCE C,FAITH J J,et al.Organismal,genetic,and transcriptional variation in the deeply sequenced gut microbiomes of identical twins[J].Proceedings of the National Academy of Sciences of the United States of America,2010,107(16):7503-7508.
[13] ECKBURG P B,BIK E M,BERNSTEIN C N,et al.Diversity of the human intestinal microbial flora[J].Science,2005,308(5728):1635-1638.
[14] SUCHODOLSKI J S.Companion animals symposium:microbes and gastrointestinal health of dogs and cats[J].Journal of Animal Science,2011,89(5):1520-1530.
[15] DAI X,ZHU Y X,LUO Y F,et al.Metagenomic insights into the fibrolytic microbiome in yak rumen[J].PLoS One,2012,7(7):e40430.
[16] TILG H,KASER A.Gut microbiome,obesity,and metabolic dysfunction[J].The Journal of Clinical Investigation,2011,121(6):2126-2132.
[17] SHANAHAN F.The gut microbiota-a clinical perspective on lessons learned[J].Nature Reviews Gastroenterology & Hepatology,2012,9(10):609-614.
[18] WALLACE B D,WANG H W,LANE K T,et al.Alleviating cancer drug toxicity by inhibiting a bacterial enzyme[J].Science,2010,330(6005):831-835.
[19] VITALI B,NDAGIJIMANA M,CRUCIANI F,et al.Impact of a synbiotic food on the gut microbial ecology and metabolic profiles[J].BMC Microbiology,2010,10:4.
[20] USHAKOVA N A,ABRAMOV V M,KHLEBNIKOV V S,et al.Properties of the probiotic strain Lactobacillus plantarum 8-RA-3 grown in a biofilm by solid substrate cultivation method[J].Probiotics and Antimicrobial Proteins,2012,4(3):180-186.
[21] PAGNINI C,SAEED R,BAMIAS G,et al.Probiotics promote gut health through stimulation of epithelial innate immunity[J].Proceedings of the National Academy of Sciences of the United States of America,2010,107(1):454-459.
[22] KALLIOMÄKI M,ANTOINE J M,HERZ U,et al.Guidance for substantiating the evidence for beneficial effects of probiotics:prevention and management of allergic diseases by probiotics[J].The Journal of Nutrition,2010,140(3):713S-721S.
[23] KINROSS J M,DARZI A W,NICHOLSON J K.Gut microbiome-host interactions in health and disease[J].Genome Medicine,2011,3(3):14.
[24] HEMARAJATA P,VERSALOVIC J.Effects of probiotics on gut microbiota:mechanisms of intestinal immunomodulation and neuromodulation[J].Therapeutic Advances in Gastroenterology,2013,6(1):39-51.
[25] Jumpstart Consortium Human Microbiome Project Data Generation Working Group.Evaluation of 16S rDNA-based community profiling for human microbiome research[J].PLoS One,2012,7(6):e39315.
[26] MARKOWITZ V M,CHEN I M A,CHU K,et al.IMG/M:the integrated metagenome data management and comparative analysis system[J].Nucleic Acids Research,2012,40(D1):D123-D129.
[27] KARLSSON F,TREMAROLI V,NIELSEN J,et al.Assessing the human gut microbiota in metabolic diseases[J].Diabetes,2013,62(10):3341-3349.
[28] CAPORASO J G,KUCZYNSKI J,STOMBAUGH J,et al.QⅡME allows analysis of high-throughput community sequencing data[J].Nature Methods,2010,7(5):335-336.
[29] SCHLOSS P D,WESTCOTT S L,RYABIN T,et al.Introducing mothur:open-source,platform-independent,community-supported software for describing and comparing microbial communities[J].Applied and Environmental Microbiology,2009,75(23):7537-7541.
[30] LI W Z.Analysis and comparison of very large metagenomes with fast clustering and functional annotation[J].BMC Bioinformatics,2009,10:359.
[31] LUO R B,LIU B H,XIE Y L,et al.SOAPdenovo2:an empirically improved memory-efficient short-read de novo assembler[J].Gigascience,2012,1(1):18-18.
[32] KULTIMA J R,SUNAGAWA S,LI J H,et al.MOCAT:a metagenomics assembly and gene prediction toolkit[J].PLoS One,2012,7(10):e47656.
[33] ARUMUGAM M,HARRINGTON E D,FOERSTNER K U,et al.Smash Community:a metagenomic annotation and analysis tool[J].Bioinformatics,2010,26(23):2977-2978.
[34] ABUBUCKER S,SEGATA N,GOLL J,et al.Metabolic reconstruction for metagenomic data and its application to the human microbiome[J].PLoS Computational Biology,2012,8(6):e1002358.
[35] GUILLOTEAU P,ZABIELSKI R,HAMMON H M,et al.Nutritional programming of gastrointestinal tract development.Is the pig a good model for man?[J].Nutrition Research Reviews,2010,23(1):4-22.
[36] SANGILD P T,THYMANN T,SCHMIDT M,et al.Invited review:the preterm pig as a model in pediatric gastroenterology[J].Journal of Animal Science,2013,91(10):4713-4729.
[37] POROYKO V,MOROWITZ M,BELL T,et al.Diet creates metabolic niches in the "immature gut" that shape microbial communities[J].Nutricion Hospitalaria,2011,26(6):1283-1295.
[38] PUIMAN P,STOLL B,MØLBAK L,et al.Modulation of the gut microbiota with antibiotic treatment suppresses whole body urea production in neonatal pigs[J].American Journal of Physiology:Gastrointestinal and Liver Physiology,2013,304(3):G300-G310.
[39] VERASTEGUI Y,CHENG J,ENGEL K,et al.Multisubstrate isotope labeling and metagenomic analysis of active soil bacterial communities[J].mBio,2014,5(4):e01157-14.
[40] QU A N,BRULC J M,WILSON M K,et al.Comparative metagenomics reveals host specific metavirulomes and horizontal gene transfer elements in the chicken cecum microbiome[J].PLoS One,2008,3(8):e2945.
[41] 李倩,洪梦佳,章雨牧,等.海洋鱼类胃肠道微生物的研究进展[J].药物生物技术,2016,23(6):561-564.
[42] 王津.宏基因组技术研究羊、鸡和猪胃肠道微生物菌群多样性[D].博士学位论文.天津:天津大学,2017.
[43] 李旦,王加启,卜登攀,等.荷斯坦奶牛瘤胃微生物元基因组Fosmid文库的构建与分析[J]微生物学杂志,2009,29(6):1-4.
[44] LIU K L,WANG J Q,BU D P,et al.Isolation and biochemical characterization of two lipases from a metagenomic library of China Holstein cow rumen[J].Biochemical and Biophysical Research Communications,2009,385(4):605-611.
[45] 袁静.黑山羊胃肠微生物宏基因组文库构建及多样性研究[D].硕士学位论文.长沙:湖南农业大学,2012.
[46] 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.
[47] SAMUEL B S,HANSEN E E,MANCHESTER J K,et al.Genomic and metabolic adaptations of Methanobrevibacter smithii to the human gut[J].Proceedings of the National Academy of Sciences of the United States of America,2007,104(25):10643-10648.
[48] NEILL A R,GRIME D W,DAWSON R M C.Conversion of choline methyl groups through trimethylamine into methane in the rumen[J].Biochemical Journal,1978,170(3):529-535.
[49] WANG Z N,KLIPFELL E,BENNETT B J,et al.Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease[J].Nature,2011,472(7341):57-63.
[50] RENFREE M B.Review:marsupials:placental mammals with a difference[J].Placenta,2010,31(Suppl 1):S21-S26.
[51] FOLEY W J.Marsupial nutrition[J].Pacific Conservation Biology,1999,5(3):240.
[52] KEMPTON T J,MURRAY R M,LENG R A.Methane production and digestibility measurements in the grey kangaroo and sheep[J].Australian Journal of Biological Sciences,1976,29(3):209-214.
[53] MADSEN J,BERTELSEN M F.Methane production by red-necked wallabies (Macropus rufogriseus)[J].Journal of Animal Science,2012,90(4):1364-1370.
[54] MORRISON M,MCSWEENEY C S,WRIGHT A D G.The vertebrate animal gut in context-microbiomes,metagenomes and methane[J].Microbiology Australia,2007,28(3):107-110.
[55] MORRISON M,POPE P B,DENMAN S E,et al.Plant biomass degradation by gut microbiomes:more of the same or something new?[J].Current Opinion in Biotechnology,2009,20(3):358-363.
[56] EVANS P N,HINDS L A,SLY L I,et al.Community composition and density of methanogens in the foregut of the tammar wallaby (Macropus eugenii)[J].Applied and Environmental Microbiology,2009,75(8):2598-2602.
[57] GAGEN E J,DENMAN S E,PADMANABHA J,et al.Functional gene analysis suggests different acetogen populations in the bovine rumen and tammar wallaby forestomach[J].Applied and Environmental Microbiology,2010,76(23):7785-7795.
[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] BRULC J M,ANTONOPOULOS D A,BERG MILLER M E,et al.Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases[J].Proceedings of the National Academy of Sciences of the United States of America,2009,106(6):1948-1953.
[60] 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(Suppl 1):184-201.
[61] 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.
京公网安备 11010802041926号