高通量测序技术在乳品微生物研究中的应用
|
摘要
近10年来,随着高通量测序技术的快速发展及其在食品、医药和环境等领域的广泛应用,人们对于食品中不可培养微生物的种类、分布及其在食品中功能的定位和认识逐渐改变和加深,对进一步改善食品加工贮藏传统技术和工艺、提高食品风味品质以及保障食品安全具有重要的促进作用。本文对近5年来国内外有关应用高通量测序技术研究乳中微生物及其对乳品质安全影响的相关研究的最新进展进行综述,以期为国内外研究人员开展相关研究提供参考。
In the past decade, due to the rapid development of high-throughput sequencing and its wide application in food, medicinal and environmental fields, knowledge has been continuously updated about the species, distribution and functions of non-culturable microorganisms in foods, which highlights the importance of high-throughput sequencing in improving traditional food processing and preservation technologies, increasing food flavor quality and guaranteeing food safety. This article aims to review the progress that has been made during the last 5 years in the application of high-throughput sequencing in milk microbiology research and in studies on the microbial safety of dairy products. It is hoped that this review will provide useful information for diary researchers.
In the past decade, due to the rapid development of high-throughput sequencing and its wide application in food, medicinal and environmental fields, knowledge has been continuously updated about the species, distribution and functions of non-culturable microorganisms in foods, which highlights the importance of high-throughput sequencing in improving traditional food processing and preservation technologies, increasing food flavor quality and guaranteeing food safety. This article aims to review the progress that has been made during the last 5 years in the application of high-throughput sequencing in milk microbiology research and in studies on the microbial safety of dairy products. It is hoped that this review will provide useful information for diary researchers.
引文
[1]FLAHERTY S,KLAENHAMMER T R.The impact of omic technologies on the study of food microbes[J].Annual Review of Food Science and Technology,2011,2(1):353-371.DOI:10.1146/annurevfood-030810-110338.
[2]ERCOLINI D,COCOLIN L.Molecular techniques in the microbial ecology of fermented foods[M].Berlin:Springer Science and Business Media,2007.
[3]ERCOLINI D.PCR-DGGE fingerprinting:novel strategies for detection of microbes in food[J].Journal of Microbiological Methods,2004,56(3):297-314.DOI:10.1016/j.mimet.2003.11.006.
[4]QUIGLEY L,O’SULLIVAN O,BERESFORD T P,et al.Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese[J].International Journal of Food Microbiology,2011,150(2/3):81-94.DOI:10.1016/j.ijfoodmicro.2011.08.001.
[5]COCOLIN L,DOLCI P,RANTSIOU K.Biodiversity and dynamics of meat fermentations:the contribution of molecular methods for a better comprehension of a complex ecosystem[J].Meat Science,2011,89(3):296-302.DOI:10.1016/j.meatsci.2011.04.011.
[6]GIRAFFA G,NEVIANI E.DNA-based,culture-independent strategies for evaluating microbial communities in food-associated ecosystems[J].International Journal of Food Microbiology,2001,67(1/2):19-34.DOI:10.1016/S0168-1605(01)00445-7.
[7]SHENDURE J,JI H.Next-generation DNA sequencing[J].Nature Biotechnology,2008,26(10):1135-1145.DOI:10.1038/nbt1486.
[8]LIU Lin,LI Yinhu,LI Siliang,et al.Comparison of next-generation sequencing systems[J].Bio Med Research International,2012(7):251364.DOI:10.1155/2012/251364.
[9]LOMAN N J,MISRA R V,DALLMAN T J,et al.Performance comparison of benchtop high-throughput sequencing platforms[J].Nature Biotechnology,2012,30(5):434-439.DOI:10.1038/nbt.2198.
[10]BOKULICH N A,MILLS D A.Next-generation approaches to the microbial ecology of food fermentations[J].BMB Reports,2012,45(7):377-389.DOI:10.5483/BMBRep.2012.45.7.148.
[11]李贺,马莺.羊乳营养及其功能性特性[J].中国乳品工业,2017,45(1):29-33.DOI:10.5297/ser.1201.002.
[12]张敏,张艳,兰国伟,等.高通量测序技术在乳制品微生物多样性中的研究进展[J].中国农学通报,2016,32(32):48-52.
[13]张和平,郑艺.高通量测序技术在乳制品研究中的应用[J].中国食品学报,2015,15(3):1-7.DOI:10.16429/j.1009-7848.2015.03.001.
[14]SHENDURE J,BALASUBRAMANIAN S,CHURCH G M,et al.DNA sequencing at 40:past,present and future[J].Nature,2017,550:345-353.DOI:10.1038/nature24286.
[15]ERCOLINI D.PCR-DGGE fingerprinting:novel strategies for detection of microbes in food[J].Microbiol Method,2004,56:297-314.DOI:10.1038/sj.embor.embor931.
[16]QUAIL M A,KOZAREWA I,SMITH F,et al.A large genome center’s improvements to the Illumina sequencing system[J].Nature Methods,2008,5(12):1005-1010.DOI:10.1038/nmeth.1270.
[17]MEYER M,STENZEL U,HOFREITER M.Parallel tagged sequencing on the 454 platform[J].Nature Protocols,2008,3(2):267-278.DOI:10.1038/nprot.2007.520.
[18]MASON C E,ELEMENTO O.Faster sequencers,larger datasets,new challenges[J].Genome Biology,2012,13(3):314.DOI:10.1186/gb-2012-13-3-314.
[19]秦楠,栗东芳,杨瑞馥.高通量测序技术及其在微生物学研究中的应用[J].微生物学报,2011,51(4):445-457.
[20]EID J,FEHR A,GRAY J,et al.Real-time DNA sequencing from single polymerase molecules[J].Science,2009,323:133-138.DOI:10.1126/science.11 62986.
[21]RUSK N.Cheap third-generation sequencing[J].Nature Methods,2009,6(4):244.DOI:10.1038/nmeth0409-244a.
[22]QUIGLEY L,O’SULLIVAN O,BERESFORD T P,et al.Highthroughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses[J].Applied and Environmental Microbiology,2012,78:5717-5723.DOI:10.1128/AEM.00918-12.
[23]韩瑞芳.利用分子学方法研究生鲜乳中细菌的多样性[D].济南:齐鲁工业大学,2015.
[24]COENYE T,VANDAMME P.Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes[J].FEMS Microbiology Letters,2003,228(1):45-49.DOI:10.1016/S0378-1097(03)00717-1.
[25]QUIGLEY L,MCCARTHY R,O’SULLIVAN O,et al.The microbial content of raw and pasteurized cow milk as determined by molecular approaches[J].Journal of Dairy Science,2013,96(8):4928-4937.DOI:10.3168/jds.2013-6688.
[26]VON NEUBECK M,BAUR C,KREWINKEL M,et al.Biodiversity of refrigerated raw milk microbiota and their enzymatic spoilage potential[J].International Journal of Food Microbiology,2015,211:57-65.DOI:10.1016/j.ijfoodmicro.2015.07.001.
[27]YUAN L,SADIQ F A,LIU T,et al.Psychrotrophic bacterial populations in Chinese raw dairy milk[J].LWT-Food Science and Technology,2017,84:409-418.DOI:10.1016/j.lwt.2017.05.023.
[28]XIN Liang,MENG Zhaoxu,ZHANG Lanwei,et al.The diversity and proteolytic properties of psychrotrophic bacteria in raw cows’milk from North China[J].International Dairy Journal,2017,66:34-41.DOI:10.1016/j.idairyj.2016.10.014.
[29]ERCOLINI D,RUSSO F,FERROCINO I,et al.Molecular identification of mesophilic and psychrotrophic bacteria from raw cow’s milk[J].Food Microbiology,2009,26(2):228-231.DOI:10.1016/j.fm.2008.09.005.
[30]JμNIOR J C R,DE OLIVEIRA A M,SILVA F G,et al.The main spoilage-related psychrotrophic bacteria in refrigerated raw milk[J].Journal of Dairy Science,2018,101(1):75-83.DOI:10.3168/jds.2017-13069.
[31]高佳媛,邵玉宇,雷飞艳,等.陕西关中地区羊乳中细菌多样性的分析[J].食品与发酵工业,2018,44(1):52-59.DOI:10.13995/j.cnki.11-1802/ts.015452.
[32]ZHANG F,WANG Z,LEI F,et al.Bacterial diversity in goat milk from the Guanzhong area of China[J].Journal of Dairy Science,2017,100(10):7812-7824.DOI:10.3168/jds.2017-13244.
[33]张敏,张艳,黄丽丽,等.基于16S r DNA高通量测序方法比较新疆西北部地区乳品中微生物的多样性[J].食品科学,2017,38(20):27-33.DOI:10.7506/spkx1002-6630-201720005.
[34]MCINNIS E A,KALANETRA K M,MILLS D A,et al.Analysis of raw goat milk microbiota:impact of stage of lactation and lysozyme on microbial diversity[J].Food Microbiology,2015,46:121-131.DOI:10.1016/j.fm.2014.07.021.
[35]SOTO DEL RIO M L D,DALMASSO A,CIVERA T,et al.Characterization of bacterial communities of donkey milk by high-throughput sequencing[J].International Journal of Food Microbiology,2017,251:67-72.DOI:10.1016/j.ijfoodmicro.2017.03.023.
[36]ABUSHELAIBI A,AL-MAHADIN S,El-TARABILY K,et al.Characterization of potential probiotic lactic acid bacteria isolated from camel milk[J].LWT-Food Science and Technology,2017,79:316-325.DOI:10.1016/j.lwt.2017.01.041.
[37]张熙桐,关博元,孔繁华,等.人乳、牛乳、羊乳中乳清部分氨基酸组成及乳清蛋白中蛋白质二级结构的对比[J].食品科学,2017,38(24):107-112.DOI:10.7506/spkx1002-6630-201724017.
[38]黄卫强,张家超,张和平.应用宏基因组测序技术检测UHT牛乳中的微生物[J].中国乳品工业,2015,43(7):55-58.
[39]LI L,RENYE J A,FENG L,et al.Characterization of the indigenous microflora in raw and pasteurized buffalo milk during storage at refrigeration temperature by high-throughput sequencing[J].Journal of Dairy Science,2016,99(9):7016-7024.DOI:10.3168/jds.2016-11041.
[40]DOYLE C J,GLEESON D,O’TOOLE P W,et al.High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions[J].International Journal of Food Microbiology,2017,255:1-6.DOI:10.1016/j.ijfoodmicro.2017.05.019.
[41]PORCELLATO D,ASPHOLM M,SKEIE S B,et al.Microbial diversity of consumption milk during processing and storage[J].International Journal of Food Microbiology,2018,266:21-30.DOI:10.1016/j.ijfoodmicro.2017.11.004.
[42]MARCHAND S,DE BLOCK J,DE JONGHE V,et al.Biofilm formation in milk production and processing environments;influence on milk quality and safety[J].Comprehensive Reviews in Food Science and Food Safety,2012,11(2):133-147.DOI:10.1111/j.1541-4337.2011.00183.x.
[43]VITHANAGE N R,DISSANAYAKE M,BOLGE G,et al.Biodiversity of culturable psychrotrophic microbiota in raw milk attributable to refrigeration conditions,seasonality and their spoilage potential[J].International Dairy Journal,2016,57:80-90.DOI:10.1016/j.idairyj.2016.02.042.
[44]VACHEYROU M,NORMAND A C,GUYOT P,et al.Cultivable microbial communities in raw cow milk and potential transfers from stables of sixteen French farms[J].International Journal of Food Microbiology,2011,146(3):253-262.DOI:10.1016/j.ijfoodmicro.2011.02.033.
[45]METZGER S A,HERNANDEZ L L,SKARLUPKA J H,et al.Influence of sampling technique and bedding type on the milk microbiota:results of a pilot study[J].Journal of Dairy Science,2018.DOI:10.3168/jds.2017-14212.
[2]ERCOLINI D,COCOLIN L.Molecular techniques in the microbial ecology of fermented foods[M].Berlin:Springer Science and Business Media,2007.
[3]ERCOLINI D.PCR-DGGE fingerprinting:novel strategies for detection of microbes in food[J].Journal of Microbiological Methods,2004,56(3):297-314.DOI:10.1016/j.mimet.2003.11.006.
[4]QUIGLEY L,O’SULLIVAN O,BERESFORD T P,et al.Molecular approaches to analysing the microbial composition of raw milk and raw milk cheese[J].International Journal of Food Microbiology,2011,150(2/3):81-94.DOI:10.1016/j.ijfoodmicro.2011.08.001.
[5]COCOLIN L,DOLCI P,RANTSIOU K.Biodiversity and dynamics of meat fermentations:the contribution of molecular methods for a better comprehension of a complex ecosystem[J].Meat Science,2011,89(3):296-302.DOI:10.1016/j.meatsci.2011.04.011.
[6]GIRAFFA G,NEVIANI E.DNA-based,culture-independent strategies for evaluating microbial communities in food-associated ecosystems[J].International Journal of Food Microbiology,2001,67(1/2):19-34.DOI:10.1016/S0168-1605(01)00445-7.
[7]SHENDURE J,JI H.Next-generation DNA sequencing[J].Nature Biotechnology,2008,26(10):1135-1145.DOI:10.1038/nbt1486.
[8]LIU Lin,LI Yinhu,LI Siliang,et al.Comparison of next-generation sequencing systems[J].Bio Med Research International,2012(7):251364.DOI:10.1155/2012/251364.
[9]LOMAN N J,MISRA R V,DALLMAN T J,et al.Performance comparison of benchtop high-throughput sequencing platforms[J].Nature Biotechnology,2012,30(5):434-439.DOI:10.1038/nbt.2198.
[10]BOKULICH N A,MILLS D A.Next-generation approaches to the microbial ecology of food fermentations[J].BMB Reports,2012,45(7):377-389.DOI:10.5483/BMBRep.2012.45.7.148.
[11]李贺,马莺.羊乳营养及其功能性特性[J].中国乳品工业,2017,45(1):29-33.DOI:10.5297/ser.1201.002.
[12]张敏,张艳,兰国伟,等.高通量测序技术在乳制品微生物多样性中的研究进展[J].中国农学通报,2016,32(32):48-52.
[13]张和平,郑艺.高通量测序技术在乳制品研究中的应用[J].中国食品学报,2015,15(3):1-7.DOI:10.16429/j.1009-7848.2015.03.001.
[14]SHENDURE J,BALASUBRAMANIAN S,CHURCH G M,et al.DNA sequencing at 40:past,present and future[J].Nature,2017,550:345-353.DOI:10.1038/nature24286.
[15]ERCOLINI D.PCR-DGGE fingerprinting:novel strategies for detection of microbes in food[J].Microbiol Method,2004,56:297-314.DOI:10.1038/sj.embor.embor931.
[16]QUAIL M A,KOZAREWA I,SMITH F,et al.A large genome center’s improvements to the Illumina sequencing system[J].Nature Methods,2008,5(12):1005-1010.DOI:10.1038/nmeth.1270.
[17]MEYER M,STENZEL U,HOFREITER M.Parallel tagged sequencing on the 454 platform[J].Nature Protocols,2008,3(2):267-278.DOI:10.1038/nprot.2007.520.
[18]MASON C E,ELEMENTO O.Faster sequencers,larger datasets,new challenges[J].Genome Biology,2012,13(3):314.DOI:10.1186/gb-2012-13-3-314.
[19]秦楠,栗东芳,杨瑞馥.高通量测序技术及其在微生物学研究中的应用[J].微生物学报,2011,51(4):445-457.
[20]EID J,FEHR A,GRAY J,et al.Real-time DNA sequencing from single polymerase molecules[J].Science,2009,323:133-138.DOI:10.1126/science.11 62986.
[21]RUSK N.Cheap third-generation sequencing[J].Nature Methods,2009,6(4):244.DOI:10.1038/nmeth0409-244a.
[22]QUIGLEY L,O’SULLIVAN O,BERESFORD T P,et al.Highthroughput sequencing for detection of subpopulations of bacteria not previously associated with artisanal cheeses[J].Applied and Environmental Microbiology,2012,78:5717-5723.DOI:10.1128/AEM.00918-12.
[23]韩瑞芳.利用分子学方法研究生鲜乳中细菌的多样性[D].济南:齐鲁工业大学,2015.
[24]COENYE T,VANDAMME P.Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes[J].FEMS Microbiology Letters,2003,228(1):45-49.DOI:10.1016/S0378-1097(03)00717-1.
[25]QUIGLEY L,MCCARTHY R,O’SULLIVAN O,et al.The microbial content of raw and pasteurized cow milk as determined by molecular approaches[J].Journal of Dairy Science,2013,96(8):4928-4937.DOI:10.3168/jds.2013-6688.
[26]VON NEUBECK M,BAUR C,KREWINKEL M,et al.Biodiversity of refrigerated raw milk microbiota and their enzymatic spoilage potential[J].International Journal of Food Microbiology,2015,211:57-65.DOI:10.1016/j.ijfoodmicro.2015.07.001.
[27]YUAN L,SADIQ F A,LIU T,et al.Psychrotrophic bacterial populations in Chinese raw dairy milk[J].LWT-Food Science and Technology,2017,84:409-418.DOI:10.1016/j.lwt.2017.05.023.
[28]XIN Liang,MENG Zhaoxu,ZHANG Lanwei,et al.The diversity and proteolytic properties of psychrotrophic bacteria in raw cows’milk from North China[J].International Dairy Journal,2017,66:34-41.DOI:10.1016/j.idairyj.2016.10.014.
[29]ERCOLINI D,RUSSO F,FERROCINO I,et al.Molecular identification of mesophilic and psychrotrophic bacteria from raw cow’s milk[J].Food Microbiology,2009,26(2):228-231.DOI:10.1016/j.fm.2008.09.005.
[30]JμNIOR J C R,DE OLIVEIRA A M,SILVA F G,et al.The main spoilage-related psychrotrophic bacteria in refrigerated raw milk[J].Journal of Dairy Science,2018,101(1):75-83.DOI:10.3168/jds.2017-13069.
[31]高佳媛,邵玉宇,雷飞艳,等.陕西关中地区羊乳中细菌多样性的分析[J].食品与发酵工业,2018,44(1):52-59.DOI:10.13995/j.cnki.11-1802/ts.015452.
[32]ZHANG F,WANG Z,LEI F,et al.Bacterial diversity in goat milk from the Guanzhong area of China[J].Journal of Dairy Science,2017,100(10):7812-7824.DOI:10.3168/jds.2017-13244.
[33]张敏,张艳,黄丽丽,等.基于16S r DNA高通量测序方法比较新疆西北部地区乳品中微生物的多样性[J].食品科学,2017,38(20):27-33.DOI:10.7506/spkx1002-6630-201720005.
[34]MCINNIS E A,KALANETRA K M,MILLS D A,et al.Analysis of raw goat milk microbiota:impact of stage of lactation and lysozyme on microbial diversity[J].Food Microbiology,2015,46:121-131.DOI:10.1016/j.fm.2014.07.021.
[35]SOTO DEL RIO M L D,DALMASSO A,CIVERA T,et al.Characterization of bacterial communities of donkey milk by high-throughput sequencing[J].International Journal of Food Microbiology,2017,251:67-72.DOI:10.1016/j.ijfoodmicro.2017.03.023.
[36]ABUSHELAIBI A,AL-MAHADIN S,El-TARABILY K,et al.Characterization of potential probiotic lactic acid bacteria isolated from camel milk[J].LWT-Food Science and Technology,2017,79:316-325.DOI:10.1016/j.lwt.2017.01.041.
[37]张熙桐,关博元,孔繁华,等.人乳、牛乳、羊乳中乳清部分氨基酸组成及乳清蛋白中蛋白质二级结构的对比[J].食品科学,2017,38(24):107-112.DOI:10.7506/spkx1002-6630-201724017.
[38]黄卫强,张家超,张和平.应用宏基因组测序技术检测UHT牛乳中的微生物[J].中国乳品工业,2015,43(7):55-58.
[39]LI L,RENYE J A,FENG L,et al.Characterization of the indigenous microflora in raw and pasteurized buffalo milk during storage at refrigeration temperature by high-throughput sequencing[J].Journal of Dairy Science,2016,99(9):7016-7024.DOI:10.3168/jds.2016-11041.
[40]DOYLE C J,GLEESON D,O’TOOLE P W,et al.High-throughput metataxonomic characterization of the raw milk microbiota identifies changes reflecting lactation stage and storage conditions[J].International Journal of Food Microbiology,2017,255:1-6.DOI:10.1016/j.ijfoodmicro.2017.05.019.
[41]PORCELLATO D,ASPHOLM M,SKEIE S B,et al.Microbial diversity of consumption milk during processing and storage[J].International Journal of Food Microbiology,2018,266:21-30.DOI:10.1016/j.ijfoodmicro.2017.11.004.
[42]MARCHAND S,DE BLOCK J,DE JONGHE V,et al.Biofilm formation in milk production and processing environments;influence on milk quality and safety[J].Comprehensive Reviews in Food Science and Food Safety,2012,11(2):133-147.DOI:10.1111/j.1541-4337.2011.00183.x.
[43]VITHANAGE N R,DISSANAYAKE M,BOLGE G,et al.Biodiversity of culturable psychrotrophic microbiota in raw milk attributable to refrigeration conditions,seasonality and their spoilage potential[J].International Dairy Journal,2016,57:80-90.DOI:10.1016/j.idairyj.2016.02.042.
[44]VACHEYROU M,NORMAND A C,GUYOT P,et al.Cultivable microbial communities in raw cow milk and potential transfers from stables of sixteen French farms[J].International Journal of Food Microbiology,2011,146(3):253-262.DOI:10.1016/j.ijfoodmicro.2011.02.033.
[45]METZGER S A,HERNANDEZ L L,SKARLUPKA J H,et al.Influence of sampling technique and bedding type on the milk microbiota:results of a pilot study[J].Journal of Dairy Science,2018.DOI:10.3168/jds.2017-14212.