宏基因组学及其在鱼类肠道微生物中的研究进展
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摘要
<正>传统的微生物研究方法主要利用微生物培养技术,但自然界中只有不到1%的微生物可以通过传统培养方法获得[1],极大的限制了微生物相关研究。宏基因组学最早由Handelsman等提出,自环境样品中提取出含有的总微生物DNA构建微生物宏基因组文库[2]。宏基因组学方法共包括全宏基因组技术及16SrRNA片段扩增技术,通过高通量测序,打破了传统以培养为主的微生物研究方式,又比变性梯度凝胶电泳和末端片段长度多态性等
引文
[1]Torsvik V,Ovreas L.Microbial diversity and function in soil:from genes to ecosystems[J].Current Opinion in Microbiology,2002,5(3):240-245.
[2]Logares R,Sunagawa S,Salazar G,et al.Metagenomic16SrDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities[J].Environmental Microbiology,2014,16(9):2659-2671.
[3]斯日古楞,特木仑,明亮,等.宏基因组学及其应用前景[J].中国畜牧兽医,2014,41(3):115-118.
[4]Franzosa E A,Morgan X C,Segata N,et al.Relating the metatranscriptome and metagenome of the human gut[J].Proceedings of the National Academy of Sciences of the United States of America,2014,111(22):2329-2338.
[5]Handelsman J,Rondon M R,Brady S F,et al.Molecular biological accesses to the chemistry of unknown soil microbes:a new frontier for natural products[J].Chemistry Biology,1998,5(10):245-249.
[6]刘艳超,郝文利,宿庄,等.自来水中细菌宏基因组DNA的浓度与细菌菌落总数的相关性分析[J].科学技术与工程,2015(32):143-146.
[7]Xia X Q,Bollinger J,Ogram A,et al.Molecular genetic analysis of the response of three soil microbial communities to the application of 2,4-D[J].Molecular Ecology,1995,4(1):17-28.
[8]Li A,Cui D,Wang J H,et al.Extraction method of metagenomic DNA used for the new generation sequencing technology[J].Journal of Harbin Institute of Technology,2012,44(6):20-23.
[9]Zhou J Z,Bruns M A,Tiedje J M.DNA recovery from soils of diverse composition[J].Applied and Environment Microbiology,1996,62(2):316-322.
[10]Barry K A,Middelbos I S,Vester Boler B M,et al.Effects of dietary fiber on the feline gastrointestinal metagenome[J].Journal of Proteome Research,2012,11(12):5924-5933.
[11]Courtois S,Cappelano C M,Ball M.Recombinant environmental libraries provide access to microbial diversity of drug discovery from natural products[J].Appl Environ Microbiol,2003,69(7):49-55.
[12]Henne A,Daniel R,Schmitz R A,et al.Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate[J].Applied&Environmental Microbiology,1999,65(9):3901-3907.
[13]Entcheva P,Liebl W,Johann A,et al.Direct cloning from enrichment cultures,a reliable strategy for isolation of complete operons and genes from microbial consortia[J].Appl Environ Microbiol,2001,67(9):89-99.
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[17]Martinez A,Kolvek S J,Hopke J,et al.Environmental DNA fragment conferring early and increased sporulation and antibiotic production in Streptomyces species[J].Appl Environ Microbiol,2005,71(3):1638-1641.
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[29]Singh B,Gautam S K,Verma V,et al.Metagenomics in animal gastrointestinal ecosystem:potential biotechnological prospects[J].Anaerobe,2008,14(3):138-144.
[30]吴森,张莺莺,昝林森.基于高通量测序的宏基因组学技术在动物胃肠道微生物方面的研究进展[J].生物技术进展,2015(2):77-84.
[31]Gajardo K,Rodiles A,Kortner T M,et al.A highresolution map of the gut microbiota in Atlantic salmon(Salmo salar):a basis for comparative gut microbial research[J].Scientific Reports,2016,6(3):1-10.
[32]Gatesoupe F J.Live yeasts in the gut:natural occurrence,dietary introduction,and their effects on fish health and development[J].Aquaculture,2007,267(1/4):20-30.
[33]Saha S,Roy R N,Sen S K,et al.Characterization of cellulase-producing bacteria from the digestive tract of tilapia,Oreochromis mossambica,(Peters)and grass carp,Ctenopharyngodon idella,(Valenciennes)[J].Aquaculture Research,2006,37(4):380-388.
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[37]Vesta S,Aniolas S,Dalius B,et al.Phylogenetic analysis of intestinal bacteria of freshwater salmon Salmo salar and sea trout Salmo trutta truttaand diet[J].Fisheries Science,2008,74(6):1307-1314.
[38]Verner-Jeffreys D W,Shields R J,Bricknell I R,et al.Changes in the gut-associated microflora during the development of Atlantic halibut(Hippoglossus hippoglossus,L.)larvae in three British hatcheries[J].Aquaculture,2003,219(1):21-42.
[39]Pond M J,Stone D M,Alderman D J.Comparison of conventional and molecular techniques to investigate the intestinal microflora of rainbow trout(Oncorhynchus mykiss)[J].Aquaculture,2006,261(1):194-203.
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[41]Sullam K E,Rubin B E,Dalton C M,et al.Divergence across diet,time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies[J].ISME Journal,2015,9(7):1508-1522.
[42]Hennersdorf P,Mrotzek G,Abdul-Aziz M A,et al.Metagenomic analysis between free-living and cultured Epinephelus fuscoguttatus,under different environmental conditions in Indonesian waters[J].Marine Pollution Bulletin,2016,110(2):726-734.
[43]Christos G,Detmer S,Hauke S,et al.The impact of rearing environment on the development of gut microbiota in tilapia larvae[J].Scientific Reports,2015,5(1):1-15.
[44]Rawls J F,Samuel B S,Gordon J I.Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota[J].Proceedings of the National Academy of Sciences of the United States of America,2004,101(13):4596-4601.
[45]Stagaman K,Burns A R,Guillemin K,et al.The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish[J].Isme Journal,2017,11(7):1630-1639.
[46]Li T,Long M,Ji C,et al.Alterations of the gut microbiome of largemouth bronze gudgeon(Coreius guichenoti)suffering from furunculosis[J].Scientific Reports,2016(6):1-12.
[47]Jankauskien3R.Defence mechanisms in fish:frequency of the genus Lactobacillus bacteriain the intestinal tract microflora of carps[J].Biologia,2002,7(2):13-17.
[48]Navarrete P,Mardones P,Opazo R,et al.Oxytetracycline treatment reduces bacterial diversity of intestinal microbiota of Atlantic salmon[J].Journal of A-quatic Animal Health,2008,20(3):177-183.
[49]沈佳斌,张雪敬,吴蔚,等.雉科鸟类肠道微生物的多样性与功能及其对食性的适应[J].南京师大学报:自然科学版,2016,39(2):90-95.
[50]Llewellyn M S,Leadbeater S,Garcia C,et al.Parasitism perturbs the mucosal microbiome of Atlantic salmon[J].Scientific Reports,2017,7(3):1-10.
[51]Fjellheim A J,Playfoot K J,Skjermo J,et al.Vibrionaceae,dominates the microflora antagonistic towards Listonella anguillarum,in the intestine of cultured Atlantic cod(Gadus morhua,L.)larvae[J].Aquaculture,2007,269(4):98-106.
[52]RingE,Olsen R E.The effect of diet on aerobic bacterial flora associated with intestine of Arctic charr(Salvelinus alpinus,L.)[J].Journal of Applied Microbiology,1999,37(1):891-897.
[53]Li J,Ni J,Li J,et al.Comparative study on gastrointestinal microbiota of eight fish species with different feeding habits[J].Journal of Applied Microbiology,2014,117(6):1750-1760.
[54]Mikaelyan A,Dietrich C,K9hler T,et al.Diet is the primary determinant of bacterial community structure in the guts of higher termites[J].Molecular Ecology,2015,24(20):5284-5295.
[55]Ingerslev H C,Jrgensen L V G,Strube M L,et al.The development of the gut microbiota in rainbow trout(Oncorhynchus mykiss)is affected by first feeding and diet type[J].Aquaculture,2014,425(2):24-34.
[56]Bairagi A,Ghosh K S,Sen S K,et al.Enzyme producing bacterial flora isolated from fish digestive tracts[J].Aquaculture International,2002,10(2):109-121.
[57]Ni J J,Yu Y H,Zhang T L,et al.Comparison of intestinal bacterial communities in grass carp,Ctenopharyngodon idellus,from two different habitats[J].Chinese Journal of Oceanology and Limnology,2012,30(5):757-765.
[58]Wu S,Wang G,Angert E R,et al.Composition,diversity,and origin of the bacterial community in grass carp intestine[J].Plos One,2012,7(2):1-11.
[59]Sen S K.Characterization of bacilli isolated from the gut of rohu,fingerlings and its significance in digestion[J].Journal of Applied Aquaculture,2002,12(3):33-42.
[60]Ghosh K,Sen S K,Ray A K.Characterization of bacilli isolated from the gut of rohu,Labeo rohita,fingerlings and its significance in digestion[J].Journal of Applied Aquaculture,2002,12(3):33-42.
[61]Peixoto S B,Cladera-Olivera F,Daroit D J,et al.Cellulase-producing Bacillus,strains isolated from the intestine of Amazon basin fish[J].Aquaculture Research,2011,42(6):887-891.
[62]Liu H,Guo X,Gooneratne R,et al.The gut microbiome and degradation enzyme activity of wild freshwater fishes influenced by their trophic levels[J].Scientific Reports,2016(6):1-12.
[63]Ghanbari M,Kneifel W,Domig K J.A new view of the fish gut microbiome:advances from next-generation sequencing[J].Aquaculture,2015,448(391):464-475.
[64]翟万营,郭安宁.鱼类肠道微生物研究进展[J].河南水产,2016,7(4):11-17.
[65]Ramírez C,Romero J.Fine flounder(Paralichthys adspersus)microbiome showed important differences between wild and reared specimens[J].Frontiers in Microbiology,2017,8(3):271-283.
[66]Gosalbes M J,Durbán A,Pignatelli M,et al.Metatranscriptomic approach to analyze the functional human gut microbiota[J].Plos One,2011,6(3):1-17.
[2]Logares R,Sunagawa S,Salazar G,et al.Metagenomic16SrDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities[J].Environmental Microbiology,2014,16(9):2659-2671.
[3]斯日古楞,特木仑,明亮,等.宏基因组学及其应用前景[J].中国畜牧兽医,2014,41(3):115-118.
[4]Franzosa E A,Morgan X C,Segata N,et al.Relating the metatranscriptome and metagenome of the human gut[J].Proceedings of the National Academy of Sciences of the United States of America,2014,111(22):2329-2338.
[5]Handelsman J,Rondon M R,Brady S F,et al.Molecular biological accesses to the chemistry of unknown soil microbes:a new frontier for natural products[J].Chemistry Biology,1998,5(10):245-249.
[6]刘艳超,郝文利,宿庄,等.自来水中细菌宏基因组DNA的浓度与细菌菌落总数的相关性分析[J].科学技术与工程,2015(32):143-146.
[7]Xia X Q,Bollinger J,Ogram A,et al.Molecular genetic analysis of the response of three soil microbial communities to the application of 2,4-D[J].Molecular Ecology,1995,4(1):17-28.
[8]Li A,Cui D,Wang J H,et al.Extraction method of metagenomic DNA used for the new generation sequencing technology[J].Journal of Harbin Institute of Technology,2012,44(6):20-23.
[9]Zhou J Z,Bruns M A,Tiedje J M.DNA recovery from soils of diverse composition[J].Applied and Environment Microbiology,1996,62(2):316-322.
[10]Barry K A,Middelbos I S,Vester Boler B M,et al.Effects of dietary fiber on the feline gastrointestinal metagenome[J].Journal of Proteome Research,2012,11(12):5924-5933.
[11]Courtois S,Cappelano C M,Ball M.Recombinant environmental libraries provide access to microbial diversity of drug discovery from natural products[J].Appl Environ Microbiol,2003,69(7):49-55.
[12]Henne A,Daniel R,Schmitz R A,et al.Construction of environmental DNA libraries in Escherichia coli and screening for the presence of genes conferring utilization of 4-hydroxybutyrate[J].Applied&Environmental Microbiology,1999,65(9):3901-3907.
[13]Entcheva P,Liebl W,Johann A,et al.Direct cloning from enrichment cultures,a reliable strategy for isolation of complete operons and genes from microbial consortia[J].Appl Environ Microbiol,2001,67(9):89-99.
[14]Rondon M R,August P R,Bettermann A D,et al.Cloning the metagenome:a strategy for accessing the genetic and funcitional diversity of uncultured microorganisms[J].Appl Environ Microbiol,2000,66(31):2541-2547.
[15]Henne A,Schmitz R A,Bomeke M,et al.Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli[J].Appl Environ Microbiol,2000,66(1):3113-3116.
[16]Brady S F,Chao C J,Handelsman J,et al.Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA[J].Organic Letters,2001,3(13):1981-1984.
[17]Martinez A,Kolvek S J,Hopke J,et al.Environmental DNA fragment conferring early and increased sporulation and antibiotic production in Streptomyces species[J].Appl Environ Microbiol,2005,71(3):1638-1641.
[18]Knietsch A,Waschkowitz T,Bowien S,et al.Construction and screening of metagenomic libraries derived from enrichment cultures:generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli[J].Appl Environ Microbiol,2003,699(3):1408-1416.
[19]Wang G,Graziani E,Waters B,et al.Novel natural products from soil DNA libraries in a streptomycete host[J].Organic Letters,2000,2(16):2401-2404.
[20]Daniel R.The soil metagenome a rich resource for the discovery of novel natural products[J].Current Opinion in Biotechnology,2004,15(3):199-204.
[21]Knietsch A,Bowien S,Whited G,et al.Identification and characterization of coenzyme B12-dependent glycerol dehydratase and diol dehydratase-encoding genes from metagenomic DNA libraries derived from enrichment cultures[J].Appl Environ Microbiol,2003,69(6):3048-3060.
[22]Uchiyama T,Watanabe K.Substrate-induced gene expression(SIGEX)screening of metagenome libraries[J].Nature Protocols,2008,3(7):1202-1212.
[23]Callaway E.‘Young poo'makes aged fish live longer[J].Nature,2017,544(7649):147-178.
[24]Li J,Sung C Y,Lee N,et al.Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice[J].Proceedings of the National Academy of Sciences of the United States of America,2016,113(9):2-10.
[25]Hu X,Wang T,Jin F.Alzheimer′s disease and gut microbiota[J].Science China Life Sciences,2016,59(10):1006-1023.
[26]Sukantak N.Role of gastrointestinal microbiota in fish[J].Aquaculture Research,2010,41(11):1553-1573.
[27]ArbacˇiauskienéV S.Proteolytic activity of the roach(Rutilus Rutilus L.)intestinal microflora[J].Acta Zoologica Lituanica,2000,10(3):69-77.
[28]Skrodenyte A V,Sruoga A,Butkauskas D.Assessment of microbial diversity in the river trout Salmo trutta fario L.intestinal tract identified by partial 16SrRNA gene sequence analysis[J].Fisheries Science,2006,72(3):597-602.
[29]Singh B,Gautam S K,Verma V,et al.Metagenomics in animal gastrointestinal ecosystem:potential biotechnological prospects[J].Anaerobe,2008,14(3):138-144.
[30]吴森,张莺莺,昝林森.基于高通量测序的宏基因组学技术在动物胃肠道微生物方面的研究进展[J].生物技术进展,2015(2):77-84.
[31]Gajardo K,Rodiles A,Kortner T M,et al.A highresolution map of the gut microbiota in Atlantic salmon(Salmo salar):a basis for comparative gut microbial research[J].Scientific Reports,2016,6(3):1-10.
[32]Gatesoupe F J.Live yeasts in the gut:natural occurrence,dietary introduction,and their effects on fish health and development[J].Aquaculture,2007,267(1/4):20-30.
[33]Saha S,Roy R N,Sen S K,et al.Characterization of cellulase-producing bacteria from the digestive tract of tilapia,Oreochromis mossambica,(Peters)and grass carp,Ctenopharyngodon idella,(Valenciennes)[J].Aquaculture Research,2006,37(4):380-388.
[34]Gómez G D.A review on the interactions between gut microbiota and innate immunity of fish[J].Pathogens and Disease,2008,52(2):145-154.
[35]RingE,Olsen R E,Mayhew T M,et al.Electron microscopy of the intestinal microflora of fish[J].Aquaculture,2003,227(4):395-415.
[36]Xia J H,Lin G,Fu G H,et al.The intestinal microbiome of fish under starvation[J].BMC Genomics,2014,15(1):1-11.
[37]Vesta S,Aniolas S,Dalius B,et al.Phylogenetic analysis of intestinal bacteria of freshwater salmon Salmo salar and sea trout Salmo trutta truttaand diet[J].Fisheries Science,2008,74(6):1307-1314.
[38]Verner-Jeffreys D W,Shields R J,Bricknell I R,et al.Changes in the gut-associated microflora during the development of Atlantic halibut(Hippoglossus hippoglossus,L.)larvae in three British hatcheries[J].Aquaculture,2003,219(1):21-42.
[39]Pond M J,Stone D M,Alderman D J.Comparison of conventional and molecular techniques to investigate the intestinal microflora of rainbow trout(Oncorhynchus mykiss)[J].Aquaculture,2006,261(1):194-203.
[40]Einar R,Sigmund S,Fjeld K O,et al.Use of 16SrRNA gene sequencing analysis to characterize culturable intestinal bacteria in Atlantic salmon(Salmo salar)fed diets with cellulose or non-starch polysaccharides from soy[J].Aquaculture Research,2008,39(10):1087-1100.
[41]Sullam K E,Rubin B E,Dalton C M,et al.Divergence across diet,time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies[J].ISME Journal,2015,9(7):1508-1522.
[42]Hennersdorf P,Mrotzek G,Abdul-Aziz M A,et al.Metagenomic analysis between free-living and cultured Epinephelus fuscoguttatus,under different environmental conditions in Indonesian waters[J].Marine Pollution Bulletin,2016,110(2):726-734.
[43]Christos G,Detmer S,Hauke S,et al.The impact of rearing environment on the development of gut microbiota in tilapia larvae[J].Scientific Reports,2015,5(1):1-15.
[44]Rawls J F,Samuel B S,Gordon J I.Gnotobiotic zebrafish reveal evolutionarily conserved responses to the gut microbiota[J].Proceedings of the National Academy of Sciences of the United States of America,2004,101(13):4596-4601.
[45]Stagaman K,Burns A R,Guillemin K,et al.The role of adaptive immunity as an ecological filter on the gut microbiota in zebrafish[J].Isme Journal,2017,11(7):1630-1639.
[46]Li T,Long M,Ji C,et al.Alterations of the gut microbiome of largemouth bronze gudgeon(Coreius guichenoti)suffering from furunculosis[J].Scientific Reports,2016(6):1-12.
[47]Jankauskien3R.Defence mechanisms in fish:frequency of the genus Lactobacillus bacteriain the intestinal tract microflora of carps[J].Biologia,2002,7(2):13-17.
[48]Navarrete P,Mardones P,Opazo R,et al.Oxytetracycline treatment reduces bacterial diversity of intestinal microbiota of Atlantic salmon[J].Journal of A-quatic Animal Health,2008,20(3):177-183.
[49]沈佳斌,张雪敬,吴蔚,等.雉科鸟类肠道微生物的多样性与功能及其对食性的适应[J].南京师大学报:自然科学版,2016,39(2):90-95.
[50]Llewellyn M S,Leadbeater S,Garcia C,et al.Parasitism perturbs the mucosal microbiome of Atlantic salmon[J].Scientific Reports,2017,7(3):1-10.
[51]Fjellheim A J,Playfoot K J,Skjermo J,et al.Vibrionaceae,dominates the microflora antagonistic towards Listonella anguillarum,in the intestine of cultured Atlantic cod(Gadus morhua,L.)larvae[J].Aquaculture,2007,269(4):98-106.
[52]RingE,Olsen R E.The effect of diet on aerobic bacterial flora associated with intestine of Arctic charr(Salvelinus alpinus,L.)[J].Journal of Applied Microbiology,1999,37(1):891-897.
[53]Li J,Ni J,Li J,et al.Comparative study on gastrointestinal microbiota of eight fish species with different feeding habits[J].Journal of Applied Microbiology,2014,117(6):1750-1760.
[54]Mikaelyan A,Dietrich C,K9hler T,et al.Diet is the primary determinant of bacterial community structure in the guts of higher termites[J].Molecular Ecology,2015,24(20):5284-5295.
[55]Ingerslev H C,Jrgensen L V G,Strube M L,et al.The development of the gut microbiota in rainbow trout(Oncorhynchus mykiss)is affected by first feeding and diet type[J].Aquaculture,2014,425(2):24-34.
[56]Bairagi A,Ghosh K S,Sen S K,et al.Enzyme producing bacterial flora isolated from fish digestive tracts[J].Aquaculture International,2002,10(2):109-121.
[57]Ni J J,Yu Y H,Zhang T L,et al.Comparison of intestinal bacterial communities in grass carp,Ctenopharyngodon idellus,from two different habitats[J].Chinese Journal of Oceanology and Limnology,2012,30(5):757-765.
[58]Wu S,Wang G,Angert E R,et al.Composition,diversity,and origin of the bacterial community in grass carp intestine[J].Plos One,2012,7(2):1-11.
[59]Sen S K.Characterization of bacilli isolated from the gut of rohu,fingerlings and its significance in digestion[J].Journal of Applied Aquaculture,2002,12(3):33-42.
[60]Ghosh K,Sen S K,Ray A K.Characterization of bacilli isolated from the gut of rohu,Labeo rohita,fingerlings and its significance in digestion[J].Journal of Applied Aquaculture,2002,12(3):33-42.
[61]Peixoto S B,Cladera-Olivera F,Daroit D J,et al.Cellulase-producing Bacillus,strains isolated from the intestine of Amazon basin fish[J].Aquaculture Research,2011,42(6):887-891.
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