宏组学在发酵食品微生物群落研究中的应用进展
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摘要
发酵食品是人类饮食的重要组成部分,深入研究其中的微生物群落结构、代谢及其活性,对于充分探索微生物资源、促进发酵食品的质量具有深远意义。目前,随着后基因组学时代的到来,测序技术的迅猛发展及其成本的降低,主要基于宏基因组学、宏转录组学,宏蛋白质组学和代谢组学在内的宏组学技术已经应用于微生物群落的多样性、结构及潜在基因功能等方面,为发酵食品潜在分子机制的研究奠定了基础。总结了在发酵食品中应用的宏组学(宏基因组学、宏转录组学,宏蛋白质组学和代谢组学)技术。随后,对奶酪、发酵酒精饮料、发酵蔬菜、发酵茶、发酵豆制品和食醋环境中微生物群落结构和功能方面的宏组学研究进行了综述,揭示了发酵食品中有益基因和生物活性物质的来源,并简单概述了这些技术的优势及其现阶段所存在的不足,旨为未来发酵食品的科学研究和工业生产提供一定参考。
Fermented food is an important part of human diet,thus it is far-reaching significance to fully explore the microbial resources and promote the quality of fermented foods via thoroughly studying the microbial community structures,metabolisms and activity.With the advent of the post-genomics era,the rapid development of sequencing technology and the reduction of its cost,meta-omics mainly based on metagenomics,metatranscriptomics,metaproteomics and metabolomics has been applied to the diversity,structure and potential gene functions of microbial communities,laying a foundation for studying potential molecular mechanisms of fermented foods. This paper summarizes the techniques of meta-omics(metagenomics,metatranscriptomics,metaproteomics and metabolomics)used in fermented foods.Subsequently,the paper reviews the meta-omics study on the structure and function of microbial communities in cheese,fermented alcoholic beverages,fermented vegetables,fermented tea,fermented soy products and vinegar environment,and reveals rich sources of valuable genes and bioactive substances in fermented foods. It also briefly outlines the advantages of these technologies and the shortcomings of them at current stage,aiming at providing a reference for future research and industrial production of fermented foods.
Fermented food is an important part of human diet,thus it is far-reaching significance to fully explore the microbial resources and promote the quality of fermented foods via thoroughly studying the microbial community structures,metabolisms and activity.With the advent of the post-genomics era,the rapid development of sequencing technology and the reduction of its cost,meta-omics mainly based on metagenomics,metatranscriptomics,metaproteomics and metabolomics has been applied to the diversity,structure and potential gene functions of microbial communities,laying a foundation for studying potential molecular mechanisms of fermented foods. This paper summarizes the techniques of meta-omics(metagenomics,metatranscriptomics,metaproteomics and metabolomics)used in fermented foods.Subsequently,the paper reviews the meta-omics study on the structure and function of microbial communities in cheese,fermented alcoholic beverages,fermented vegetables,fermented tea,fermented soy products and vinegar environment,and reveals rich sources of valuable genes and bioactive substances in fermented foods. It also briefly outlines the advantages of these technologies and the shortcomings of them at current stage,aiming at providing a reference for future research and industrial production of fermented foods.
引文
[1]Bokulich NA,Lewis ZT,Boundy-Mills K,et al.A new perspective on microbial landscapes within food production[J].Curr Opin Biotechnol,2016,37:182-189.
[2]Handelsman J,Rondon MR,Brady SF,et al.Molecular biological access to the chemistry of unknown soil microbes:a new frontier for natural products[J].Chem Biol,1998,5(10):245-249.
[3]Albantoglu U,Cakar A,et al.Metagenomic analysis of the microbial community in kefir grains[J].Food Microbiol,2014,41:42-51.
[4]Poretsky RS,Bano N,Buchan A,et al.Analysis of microbial gene transcripts in environmental samples[J].Applied and Environmental Microbiology,2005,71(7):4121-4126.
[5]Reyes A,Haynes M,Hanson N,et al.Viruses in the faecal microbiota of monozygotic twins and their mothers[J].Nat,2010,466(7304):334-338.
[6]Lacerda C,Choe LH,Reardon KF.Metaproteomic analysis of a bacterial community response to cadmium exposure[J].JProteome Res,2007,6:1145-1152.
[7]Park C,Helm RF.Application of metaproteomic analysis for studying extracellular polymeric substances(EPS)in activated sludge flocs and their fate in sludge digestion[J].Water Sci Technol,2008,57:2009-2015.
[8]于仁涛,高培基,韩黎,等.宏蛋白质组学研究策略及应用[J].生物工程学报,2009,25(7):961-967.
[9]Wilmes P,Heintz-Buschart A,Bond PL.A decade of metaproteomics:where we stand and what the future holds[J].Proteomics,2015,15(20):3409-3417.
[10]Mangiapane E,Mazzoli R,et al.Ten years of subproteome investigations in lactic acid bacteria:a key for food starter and probiotic typing[J].J Proteomics,2015,127:332-339.
[11]Mozzi F,Ortiz ME,et al.Metabolomics as a tool for the comprehensive understanding of fermented and functional foods with lactic acid bacteria[J].Food Res Inter,2013,54(1):1152-1161.
[12]Reaves ML,Rabinowitz JD.Metabolomics in systems microbiology[J].Curr Opin Biotechnol,2011,22(1):17-25.
[13]Nicholson JK,Lindon JC.Systems biology:metabonomics[J].Nat,2008,455(7216):1054-1056.
[14]黄强,尹沛源,路鑫,等.色谱-质谱联用技术在代谢组学中的应用[J].色谱,2009,27(5):566-572.
[15]German JB,Hammock BD,Watkins SM.Metabolomics:building on a century of biochemistry to guide human health[J].Metabolomics,2005,1(1):3-9.
[16]Wolfe BE,Button JE,Santarelli M,et al.Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity[J].Cell,2014,158(2):422-433.
[17]Almeida M,Hébert A,Abraham AL,et al.Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products[J].BMCGenomics,2014,15(1):1101.
[18]Escobar-Zepeda A,Sanchez-Flores A,Baruch MQ.Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota[J].Food Microbiology,2016,57:116-127.
[19]Monnet C,Dugat-Bony E,Swennen D,et al.Investigation of the activity of the microorganisms in a reblochon-style cheese by metatranscriptomic analysis[J].Front Microbiol,2016,7:536.
[20]De Filippis F,Genovese A,Ferranti P,et al.Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate[J].Sci Rep,2016,6:21871.
[21]Dugat-Bony E,Straub C,Teissandier A,et al.Overview of a surface-ripened cheese community functioning by meta-omics analyses[J].PLoS One,2015,10,e0124360.
[22]Bokulich NA,Ohta M,Lee M,Mills DA.Indigenous bacteria and fungi drive traditional kimoto sake fermentations[J].Applied and Environmental Microbiology,2014,80(17):5522-5529.
[23]Zhang L,Zhou R,Niu M,Zheng J,Wu C.Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology[J].J Appl Microbiol,2015,119(5):1345-1356.
[24]Bokulich NA,Thorngate JH,et al.Microbial biogeography of wine grapes is conditioned by cultivar,vintage,and climate[J].Proc Natl Acad Sci USA,2014,111(1):E139-148.
[25]Bora SS,Keot J,Das S,et al.Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture(Xaj-pitha)of Assam,India[J].Biotech,2016,6(2):153.
[26]Chen B,et al.Filamentous fungal diversity and community structure associated with the solid state fermentation of Chinese Maotaiflavor liquor[J].Int J Food Microbiol,2014,179:80-84.
[27]Hu XL,Du H,Xu Y.Identification and quantification of the caproic acid-producing bacterium Clostridium kluyveri in the fermentation of pit mud used for Chinese strong-aroma type liquor production[J].Int J Food Microbiol,2015,214:116-122.
[28]Lu X,Wu Q,et al.Genomic and transcriptomic analyses of the Chinese Maotai-flavored liquor yeast MT1 revealed its unique multicarbon co-utilization[J].BMC Genomics,2015,16(1):1064.
[29]Song G,Dickins BJA,Demeter J,et al.AGAPE(automated genome analysis PipelinE)for Pan-genome analysis of Saccharomyces cerevisiae[J].PLoS One,2015,10(3):e0120671.
[30]Zheng Q,Lin B,Wang Y,et al.Proteomic and high-throughput analysis of protein expression and microbial diversity of microbes from 30-and 300-year pit muds of Chinese Luzhou-flavor liquor[J].Food Res Inter,2015,75:305-314.
[31]Wu Q,Chen B,Xu Y.Regulating yeast flavor metabolism by controlling saccharification reaction rate in simultaneous saccharification and fermentation of Chinese Maotai-flavor liquor[J].Int J Food Microbiol,2015,200:39-46.
[32]Zhi Y,Wu Q,Du H,et al.Biocontrol of geosmin-producing Streptomyces spp.by two Bacillus strains from Chinese liquor[J].Int J Food Microbiol,2016,231:1-9.
[33]Jeong SH,Jung JY,et al.Microbial succession and metabolite changes during fermentation of dongchimi,traditional Korean watery kimchi[J].Int J Food Microbiol,2013,164(1):46-53.
[34]Park SE,Yoo SA,Seo SH,et al.GC-MS based metabolomics approach of Kimchi for the understanding of Lactobacillus plantarum fermentation characteristics[J].LWT-Food Science and Technology,2016,68:313-321.
[35]Jung JY,Lee SH,Kim JM,et al.Metagenomic analysis of kimchi,the Korean traditional fermented food[J].Applied and Environmental Microbiology,2011,77(7):2264-2274.
[36]Xu A,Wang Y,Wen J,et al.Fungal community associated with fermentation and storage of Fuzhuan brick-tea[J].Int J Food Microbiol,2011,146(1):14-22.
[37]Lv H,Zhang Y,Lin Z,et al.Processing and chemical constituents of Pu-erh tea:a review[J].Food Res Inter,2013,53(2):608-618.
[38]Tian J,Zhu Z,Wu B,et al.Bacterial and fungal communities in Pu’er tea samples of different ages[J].J food Sci,2013,78(8):M1249-M1256.
[39]Lyu C,Chen C,Ge F,et al.A preliminary metagenomic study of puer tea during pile fermentation[J].Journal of the Science of Food and Agriculture,2013,93(13):3165-3174.
[40]Zhao M,Zhang D,Su X,et al.An integrated metagenomics/metaproteomics investigation of the microbial communities and enzymes in solid-state fermentation of Pu-erh tea[J].Scientific Reports,2015,5:10117.
[41]Tan J,Dai W,Lu M,et al.Study of the dynamic changes in the non-volatile chemical constituents of black tea during fermentation processing by a non-targeted metabolomics approach[J].Food Res Inter,2016,79:106-113.
[42]Wang Q,Gong J,Chisti Y,et al.Fungal isolates from a Pu-Erh type tea fermentation and their ability to convert tea polyphenols to theabrownins[J].J food Sci,2015,80(4):M809-M817.
[43]Chettri R,Tamang JP.Bacillus species isolated from tungrymbai and bekang,naturally fermented soybean foods of India[J].Int JFood Microbiol,2015,197:72-76.
[44]Chettri R,Bhutia MO,Tamang JP.Poly-γ-glutamic acid(PGA)-producing Bacillus species isolated from Kinema,Indian fermented soybean food[J].Front Microbiol,2016,7:971.
[45]Jung WY,et al.Functional characterization of bacterial communities responsible for fermentation of Doenjang:a traditional Korean fermented soybean paste[J].Front Microbiol,2016,7:827.
[46]Lee MH,Lee J,Nam YD,et al.Characterization of antimicrobial lipopeptides produced by Bacillus sp.LM7 isolated from chungkookjang,a Korean traditional fermented soybean food[J].Int J Food Microbiol,2016,221:12-18.
[47]Zhao G,Yao Y,et al.Comparative genomic analysis of Aspergillus oryzae strains 3.042 and RIB40 for soy sauce fermentation[J].Int J Food Microbiol,2013,164(2-3):148-154.
[48]Zhao G,Yao Y,Hao G,et al.Gene regulation in Aspergillus oryzae promotes hyphal growth and flavor formation in soy sauce koji[J].Rsc Advances,2015,5(31):24224-24230.
[49]Sulaiman J,Gan HM,Yin WF,et al.Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine[J].Front Microbiol,2014,5:556.
[50]Li S,Li P,Feng F,et al.Microbial diversity and their roles in the vinegar fermentation process[J].Applied Microbiology and Biotechnology,2015,99(12):4997-5024.
[51]Wu JJ,Gullo M,Chen FS,et al.Diversity of Acetobacter pasteurianus strains isolated from solid-state fermentation of cereal vinegars[J].Current Microbiology,2010,60(4):280-286.
[52]Wang ZM,Lu ZM,Yu YJ,et al.Batch-to-batch uniformity of bacterial community succession and flavor formation in the fermentation of Zhenjiang aromatic vinegar[J].Food Microbiology,2015,50:64-69.
[53]Wang ZM,Lu ZM,Shi JS,et al.Exploring flavour-producing core microbiota in multispecies solid-state fermentation of traditional Chinese vinegar[J].Scientific Reports,2016,6:26818.
[54]Zhang GQ,Xu Q,Bian C,et al.The Dendrobium catenatum Lindl.genome sequence provides insights into polysaccharide synthase,floral development and adaptive evolution[J].Scientific Reports,2016,6:19029.
[2]Handelsman J,Rondon MR,Brady SF,et al.Molecular biological access to the chemistry of unknown soil microbes:a new frontier for natural products[J].Chem Biol,1998,5(10):245-249.
[3]Albantoglu U,Cakar A,et al.Metagenomic analysis of the microbial community in kefir grains[J].Food Microbiol,2014,41:42-51.
[4]Poretsky RS,Bano N,Buchan A,et al.Analysis of microbial gene transcripts in environmental samples[J].Applied and Environmental Microbiology,2005,71(7):4121-4126.
[5]Reyes A,Haynes M,Hanson N,et al.Viruses in the faecal microbiota of monozygotic twins and their mothers[J].Nat,2010,466(7304):334-338.
[6]Lacerda C,Choe LH,Reardon KF.Metaproteomic analysis of a bacterial community response to cadmium exposure[J].JProteome Res,2007,6:1145-1152.
[7]Park C,Helm RF.Application of metaproteomic analysis for studying extracellular polymeric substances(EPS)in activated sludge flocs and their fate in sludge digestion[J].Water Sci Technol,2008,57:2009-2015.
[8]于仁涛,高培基,韩黎,等.宏蛋白质组学研究策略及应用[J].生物工程学报,2009,25(7):961-967.
[9]Wilmes P,Heintz-Buschart A,Bond PL.A decade of metaproteomics:where we stand and what the future holds[J].Proteomics,2015,15(20):3409-3417.
[10]Mangiapane E,Mazzoli R,et al.Ten years of subproteome investigations in lactic acid bacteria:a key for food starter and probiotic typing[J].J Proteomics,2015,127:332-339.
[11]Mozzi F,Ortiz ME,et al.Metabolomics as a tool for the comprehensive understanding of fermented and functional foods with lactic acid bacteria[J].Food Res Inter,2013,54(1):1152-1161.
[12]Reaves ML,Rabinowitz JD.Metabolomics in systems microbiology[J].Curr Opin Biotechnol,2011,22(1):17-25.
[13]Nicholson JK,Lindon JC.Systems biology:metabonomics[J].Nat,2008,455(7216):1054-1056.
[14]黄强,尹沛源,路鑫,等.色谱-质谱联用技术在代谢组学中的应用[J].色谱,2009,27(5):566-572.
[15]German JB,Hammock BD,Watkins SM.Metabolomics:building on a century of biochemistry to guide human health[J].Metabolomics,2005,1(1):3-9.
[16]Wolfe BE,Button JE,Santarelli M,et al.Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity[J].Cell,2014,158(2):422-433.
[17]Almeida M,Hébert A,Abraham AL,et al.Construction of a dairy microbial genome catalog opens new perspectives for the metagenomic analysis of dairy fermented products[J].BMCGenomics,2014,15(1):1101.
[18]Escobar-Zepeda A,Sanchez-Flores A,Baruch MQ.Metagenomic analysis of a Mexican ripened cheese reveals a unique complex microbiota[J].Food Microbiology,2016,57:116-127.
[19]Monnet C,Dugat-Bony E,Swennen D,et al.Investigation of the activity of the microorganisms in a reblochon-style cheese by metatranscriptomic analysis[J].Front Microbiol,2016,7:536.
[20]De Filippis F,Genovese A,Ferranti P,et al.Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate[J].Sci Rep,2016,6:21871.
[21]Dugat-Bony E,Straub C,Teissandier A,et al.Overview of a surface-ripened cheese community functioning by meta-omics analyses[J].PLoS One,2015,10,e0124360.
[22]Bokulich NA,Ohta M,Lee M,Mills DA.Indigenous bacteria and fungi drive traditional kimoto sake fermentations[J].Applied and Environmental Microbiology,2014,80(17):5522-5529.
[23]Zhang L,Zhou R,Niu M,Zheng J,Wu C.Difference of microbial community stressed in artificial pit muds for Luzhou-flavour liquor brewing revealed by multiphase culture-independent technology[J].J Appl Microbiol,2015,119(5):1345-1356.
[24]Bokulich NA,Thorngate JH,et al.Microbial biogeography of wine grapes is conditioned by cultivar,vintage,and climate[J].Proc Natl Acad Sci USA,2014,111(1):E139-148.
[25]Bora SS,Keot J,Das S,et al.Metagenomics analysis of microbial communities associated with a traditional rice wine starter culture(Xaj-pitha)of Assam,India[J].Biotech,2016,6(2):153.
[26]Chen B,et al.Filamentous fungal diversity and community structure associated with the solid state fermentation of Chinese Maotaiflavor liquor[J].Int J Food Microbiol,2014,179:80-84.
[27]Hu XL,Du H,Xu Y.Identification and quantification of the caproic acid-producing bacterium Clostridium kluyveri in the fermentation of pit mud used for Chinese strong-aroma type liquor production[J].Int J Food Microbiol,2015,214:116-122.
[28]Lu X,Wu Q,et al.Genomic and transcriptomic analyses of the Chinese Maotai-flavored liquor yeast MT1 revealed its unique multicarbon co-utilization[J].BMC Genomics,2015,16(1):1064.
[29]Song G,Dickins BJA,Demeter J,et al.AGAPE(automated genome analysis PipelinE)for Pan-genome analysis of Saccharomyces cerevisiae[J].PLoS One,2015,10(3):e0120671.
[30]Zheng Q,Lin B,Wang Y,et al.Proteomic and high-throughput analysis of protein expression and microbial diversity of microbes from 30-and 300-year pit muds of Chinese Luzhou-flavor liquor[J].Food Res Inter,2015,75:305-314.
[31]Wu Q,Chen B,Xu Y.Regulating yeast flavor metabolism by controlling saccharification reaction rate in simultaneous saccharification and fermentation of Chinese Maotai-flavor liquor[J].Int J Food Microbiol,2015,200:39-46.
[32]Zhi Y,Wu Q,Du H,et al.Biocontrol of geosmin-producing Streptomyces spp.by two Bacillus strains from Chinese liquor[J].Int J Food Microbiol,2016,231:1-9.
[33]Jeong SH,Jung JY,et al.Microbial succession and metabolite changes during fermentation of dongchimi,traditional Korean watery kimchi[J].Int J Food Microbiol,2013,164(1):46-53.
[34]Park SE,Yoo SA,Seo SH,et al.GC-MS based metabolomics approach of Kimchi for the understanding of Lactobacillus plantarum fermentation characteristics[J].LWT-Food Science and Technology,2016,68:313-321.
[35]Jung JY,Lee SH,Kim JM,et al.Metagenomic analysis of kimchi,the Korean traditional fermented food[J].Applied and Environmental Microbiology,2011,77(7):2264-2274.
[36]Xu A,Wang Y,Wen J,et al.Fungal community associated with fermentation and storage of Fuzhuan brick-tea[J].Int J Food Microbiol,2011,146(1):14-22.
[37]Lv H,Zhang Y,Lin Z,et al.Processing and chemical constituents of Pu-erh tea:a review[J].Food Res Inter,2013,53(2):608-618.
[38]Tian J,Zhu Z,Wu B,et al.Bacterial and fungal communities in Pu’er tea samples of different ages[J].J food Sci,2013,78(8):M1249-M1256.
[39]Lyu C,Chen C,Ge F,et al.A preliminary metagenomic study of puer tea during pile fermentation[J].Journal of the Science of Food and Agriculture,2013,93(13):3165-3174.
[40]Zhao M,Zhang D,Su X,et al.An integrated metagenomics/metaproteomics investigation of the microbial communities and enzymes in solid-state fermentation of Pu-erh tea[J].Scientific Reports,2015,5:10117.
[41]Tan J,Dai W,Lu M,et al.Study of the dynamic changes in the non-volatile chemical constituents of black tea during fermentation processing by a non-targeted metabolomics approach[J].Food Res Inter,2016,79:106-113.
[42]Wang Q,Gong J,Chisti Y,et al.Fungal isolates from a Pu-Erh type tea fermentation and their ability to convert tea polyphenols to theabrownins[J].J food Sci,2015,80(4):M809-M817.
[43]Chettri R,Tamang JP.Bacillus species isolated from tungrymbai and bekang,naturally fermented soybean foods of India[J].Int JFood Microbiol,2015,197:72-76.
[44]Chettri R,Bhutia MO,Tamang JP.Poly-γ-glutamic acid(PGA)-producing Bacillus species isolated from Kinema,Indian fermented soybean food[J].Front Microbiol,2016,7:971.
[45]Jung WY,et al.Functional characterization of bacterial communities responsible for fermentation of Doenjang:a traditional Korean fermented soybean paste[J].Front Microbiol,2016,7:827.
[46]Lee MH,Lee J,Nam YD,et al.Characterization of antimicrobial lipopeptides produced by Bacillus sp.LM7 isolated from chungkookjang,a Korean traditional fermented soybean food[J].Int J Food Microbiol,2016,221:12-18.
[47]Zhao G,Yao Y,et al.Comparative genomic analysis of Aspergillus oryzae strains 3.042 and RIB40 for soy sauce fermentation[J].Int J Food Microbiol,2013,164(2-3):148-154.
[48]Zhao G,Yao Y,Hao G,et al.Gene regulation in Aspergillus oryzae promotes hyphal growth and flavor formation in soy sauce koji[J].Rsc Advances,2015,5(31):24224-24230.
[49]Sulaiman J,Gan HM,Yin WF,et al.Microbial succession and the functional potential during the fermentation of Chinese soy sauce brine[J].Front Microbiol,2014,5:556.
[50]Li S,Li P,Feng F,et al.Microbial diversity and their roles in the vinegar fermentation process[J].Applied Microbiology and Biotechnology,2015,99(12):4997-5024.
[51]Wu JJ,Gullo M,Chen FS,et al.Diversity of Acetobacter pasteurianus strains isolated from solid-state fermentation of cereal vinegars[J].Current Microbiology,2010,60(4):280-286.
[52]Wang ZM,Lu ZM,Yu YJ,et al.Batch-to-batch uniformity of bacterial community succession and flavor formation in the fermentation of Zhenjiang aromatic vinegar[J].Food Microbiology,2015,50:64-69.
[53]Wang ZM,Lu ZM,Shi JS,et al.Exploring flavour-producing core microbiota in multispecies solid-state fermentation of traditional Chinese vinegar[J].Scientific Reports,2016,6:26818.
[54]Zhang GQ,Xu Q,Bian C,et al.The Dendrobium catenatum Lindl.genome sequence provides insights into polysaccharide synthase,floral development and adaptive evolution[J].Scientific Reports,2016,6:19029.