多组学技术在自然发酵乳中的应用
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摘要
自然发酵乳食用历史悠久,风味独特并且具有优良的益生作用。与商业化生产发酵乳相比,自然发酵乳具有微生物资源构成更为多样、发酵过程更加复杂等优点,但家庭化的生产方式导致自然发酵乳质量安全难以保证,阻碍其工业化生产。基于高通量检测技术的快速发展,多组学技术为解析自然发酵乳中微生物物种和代谢多样性、差异基因的检测、转录、表达及微生物资源开发利用提供了有效的手段。本文简述了培养组学、基因组学、转录组学、蛋白质组学、代谢组学和宏基因组学在国内外自然发酵乳研究中的应用,并指出多组学联用技术在自然发酵乳中应用的前景,以期为自然发酵乳开发利用、品质调控及工业化生产提供可借鉴的思路。
The usage of naturally fermented milk for food has a long history. It has probiotic properties and desirable sensorial characteristics. Compared with commercially fermented milk, the compositions of microorganisms are more diverse, and the fermentation process is more complicated in naturally fermented milk. However, the family-based production method makes it difficult to guarantee the quality and industrialization of naturally fermented milk. Based on the development of high-throughput technology, multi-omics techniques provide an effective solution for analyzing biological and metabolic diversity, differential gene expression and microbial resource development in naturally fermented milk. This paper reviewed the applications of culturomics, genomics, transcriptomics, proteomics, metabolomics and metagenomics in naturally fermented milk at home and abroad and pointed out the prospect of application of multi-omicstechnology combination in naturally fermented milk. It provided some referential ideas for the development, quality control and industrialization of naturally fermented milk.
The usage of naturally fermented milk for food has a long history. It has probiotic properties and desirable sensorial characteristics. Compared with commercially fermented milk, the compositions of microorganisms are more diverse, and the fermentation process is more complicated in naturally fermented milk. However, the family-based production method makes it difficult to guarantee the quality and industrialization of naturally fermented milk. Based on the development of high-throughput technology, multi-omics techniques provide an effective solution for analyzing biological and metabolic diversity, differential gene expression and microbial resource development in naturally fermented milk. This paper reviewed the applications of culturomics, genomics, transcriptomics, proteomics, metabolomics and metagenomics in naturally fermented milk at home and abroad and pointed out the prospect of application of multi-omicstechnology combination in naturally fermented milk. It provided some referential ideas for the development, quality control and industrialization of naturally fermented milk.
引文
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[17]JARDIN J,MOLLE D,PIOT M,et al.Quantitative proteomic analysis of bacterial enzymes released in cheese during ripening[J].Int J Food Microbiol,2012,155(1/2):19-28.
[18]JOHNSON C H,IVANISEVIC J,SIUZDAK G.Metabolomics:beyond biomarkers and towards mechanisms[J].Nat Rev Mol Cell Biol,2016,17(7):451-459.
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[21]SERVIN A L.Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens[J].FEMS Microbiol Rev,2004,28(4):405-440.
[22]VOLTAN S,MARTINES D,ELLI M,et al.Lactobacillus crispatus M247-derived H2O2 acts as a signal transducing molecule activating peroxisome proliferator activated receptor-γin the intestinal mucosa[J].Gastroenterology,2008,135(4):1216-1227.
[23]MATHUR H,FIELD D,REA M C,et al.Fighting biofilms with lantibiotics and other groups of bacteriocins[J].NPJ Biofilms and Microbiomes,2018,4(1):9.
[24]HOU Q,LI C,LIU Y,et al.Koumiss consumption modulates gut microbiota,increases plasma high density cholesterol,decreases immunoglobulin G and albumin[J].Journal of Functional Foods,2019,52:469-478.
[25]KAMINARIDES S,STAMOU P,MASSOURAS T.Comparison of the characteristics of set type yoghurt made from ovine milk of different fat content[J].International Journal of Food Science&Technology,2007,42(9):1019-1028.
[26]葛武鹏，李元瑞，陈瑛，等.牛羊奶酸奶挥发性风味物质固相微萃取GC/MS分析[J].农业机械学报，2008,39(11):64-69.
[27]PISANO M B,SCANO P,MURGIA A,et al.Metabolomics and microbiological profile of Italian mozzarella cheese produced with buffalo and cow milk[J].Food Chem,2016,192:618-624.
[28]COSTELLO E K,LAUBER C L,HAMADY M,et al.Bacterial community variation in human body habitats across space and time[J].Science,2009,326(5960):1694-1697.
[29]ZHONG Z,HOU Q,KWOK L,et al.Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type[J].J Dairy Sci,2016,99(10):7832-7841.
[30]JIN H,MO L,PAN L,et al.Using PacBio sequencing to investigate the bacterial microbiota of traditional Buryatian cottage cheese and comparison with Italian and Kazakhstan artisanal cheeses[J].Journal of Dairy Science,2018,101(8):1-12.
[31]YU J,MO L,PAN L,et al.Bacterial microbiota and metabolic character of traditional sour cream and butter in Buryatia,Russia[J].Front Microbiol,2018,9:2496.
[32]LI J,ZHENG Y,XU H Y,et al.Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time(SMRT)sequencing and its comparison with Belgian,Kalmykian and Italian artisanal cheeses[J].BMC Microbiology,2017,17:13.
[33]MAO L X,YU J,JIN H,et al.Investigating the bacterial microbiota of traditional fermented dairy products using propidium monoazide with single-molecule real-time sequencing[J].J Dairy Sci,2019,102(5):3912-3923.
[34]WALSH A M,CRISPIE F,DAARI K,et al.Strain-level metagenomic analysis of the fermented dairy beverage nunu highlights potential food safety risks[J].Appl Environ Microbiol,2017,83(16):E1144-E1117.
[35]其木格苏都.自然发酵酸马奶细菌多样性及其基因动态变化研究[D].呼和浩特：内蒙古农业大学，2017.
[36]LAGIER J C,ARMOUGOM F,MILLION M,et al.Microbial culturomics:paradigm shift in the human gut microbiome study[J].Clin Microbiol Infect,2012,18(12):1185-1193.
[37]MARTINO G P,QUINTANA I M,ESPARIZ M,et al.Aroma compounds generation in citrate metabolism of Enterococcus faecium:genetic characterization of type I citrate gene cluster[J].Int J Food Microbiol,2016,218:27-37.
[2]雅梅，哈斯其木格，陈永福，等.内蒙古传统乳制品产业发展现状调研报告[J].中国乳品工业，2016,44(7):28-30.
[3]OBERMAN H,LIBUDZISZ Z.Fermented milks[M].2nd ed.London:Blackie Academic&Professional,1998.
[4]张和平.自然发酵乳制品中乳酸菌生物多样性[M].北京：科学出版社，2012.
[5]LAGIER J C,DUBOURG G,MILLION,M,et al.Culturing the human microbiota and culturomics[J].Nat Rev Microbiol,2018(1):540-550.
[6]DIOP K,DIOP A,LEVASSEUR A,et al.Microbial culturomics broadens human vaginal f lora diversity:genome sequence and description of prevotella lascolaii sp.nov.isolated from a patient with bacterial vaginosis[J].Omics,2018,22(3):210-222.
[7]BILEN M,DUFOUR J C,LAGIER J C,et al.The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species[J].Microbiome,2018,6(1):94.
[8]YU J,ZHAO J,SONG Y,et al.Comparative genomics of the herbivore gut symbiont Lactobacillus reuteri reveals genetic diversity and lifestyle adaptation[J].Front Microbiol,2018,9:1151.
[9]宋宇琴.德氏乳杆菌保加利亚亚种的群体遗传学和功能基因组学研究[D].呼和浩特：内蒙古农业大学，2018.
[10]PAGE J T,HUYNH M D,LIECHTY Z S,et al.Insights into the evolution of cotton diploids and polyploids from whole-genome resequencing[J].Genes-genomes-genetics,2013,3(10):1809-1818.
[11]MAGALHAES K T,DE MELO PEREIRA G V,Campos C R,et al.Brazilian kefir:structure,microbial communities and chemical composition[J].Braz J Microbiol,2011,42(2):693-702.
[12]EIKMEYER F G,HEINL S,MARX H,et al.Identification of oxygen-responsive transcripts in the silage inoculant Lactobacillus buchneri CD034 by RNA sequencing[J].PLoS One,2015,10(7):e0134149.
[13]VAN DER MEULEN S B,DE JONG A,KOK J.Transcriptome landscape of Lactococcus lactis reveals many novel RNAs including a small regulatory RNA involved in carbon uptake and metabolism[J].RNA Biology,2016,13(3):353-366.
[14]ROSS P L,HUANG Y N,MARCHESE J N,et al.Multiplexed protein quantitation in Saccharomyces cerevisiae using aminereactive isobaric tagging reagents[J].Mol Cell Proteomics,2004,3(12):1154-1169.
[15]LAHTVEE P J,ADAMBERG K,ARIKE L,et al.Multi-omics approach to study the growth efficiency and amino acid metabolism in Lactococcus lactis at various specific growth rates[J].Microb Cell Fact,2011,10(1):12.
[16]WU Z,WANG P,HE J,et al.Proteome analysis of Lactobacillus plantarum strain under cheese-like conditions[J].J Proteomics,2016,146:165-171.
[17]JARDIN J,MOLLE D,PIOT M,et al.Quantitative proteomic analysis of bacterial enzymes released in cheese during ripening[J].Int J Food Microbiol,2012,155(1/2):19-28.
[18]JOHNSON C H,IVANISEVIC J,SIUZDAK G.Metabolomics:beyond biomarkers and towards mechanisms[J].Nat Rev Mol Cell Biol,2016,17(7):451-459.
[19]MONTEIRO M S,CARVALHO M,BASTOS M L,et al.Metabolomics analysis for biomarker discovery:advances and challenges[J].Curr Med Chem,2013,20(2):257-271.
[20]SHIBY V K,MISHRA H N.Fermented milks and milk products as functional foods-a review[J].Crit Rev Food Sci Nutr,2013,53(5):482-496.
[21]SERVIN A L.Antagonistic activities of lactobacilli and bifidobacteria against microbial pathogens[J].FEMS Microbiol Rev,2004,28(4):405-440.
[22]VOLTAN S,MARTINES D,ELLI M,et al.Lactobacillus crispatus M247-derived H2O2 acts as a signal transducing molecule activating peroxisome proliferator activated receptor-γin the intestinal mucosa[J].Gastroenterology,2008,135(4):1216-1227.
[23]MATHUR H,FIELD D,REA M C,et al.Fighting biofilms with lantibiotics and other groups of bacteriocins[J].NPJ Biofilms and Microbiomes,2018,4(1):9.
[24]HOU Q,LI C,LIU Y,et al.Koumiss consumption modulates gut microbiota,increases plasma high density cholesterol,decreases immunoglobulin G and albumin[J].Journal of Functional Foods,2019,52:469-478.
[25]KAMINARIDES S,STAMOU P,MASSOURAS T.Comparison of the characteristics of set type yoghurt made from ovine milk of different fat content[J].International Journal of Food Science&Technology,2007,42(9):1019-1028.
[26]葛武鹏，李元瑞，陈瑛，等.牛羊奶酸奶挥发性风味物质固相微萃取GC/MS分析[J].农业机械学报，2008,39(11):64-69.
[27]PISANO M B,SCANO P,MURGIA A,et al.Metabolomics and microbiological profile of Italian mozzarella cheese produced with buffalo and cow milk[J].Food Chem,2016,192:618-624.
[28]COSTELLO E K,LAUBER C L,HAMADY M,et al.Bacterial community variation in human body habitats across space and time[J].Science,2009,326(5960):1694-1697.
[29]ZHONG Z,HOU Q,KWOK L,et al.Bacterial microbiota compositions of naturally fermented milk are shaped by both geographic origin and sample type[J].J Dairy Sci,2016,99(10):7832-7841.
[30]JIN H,MO L,PAN L,et al.Using PacBio sequencing to investigate the bacterial microbiota of traditional Buryatian cottage cheese and comparison with Italian and Kazakhstan artisanal cheeses[J].Journal of Dairy Science,2018,101(8):1-12.
[31]YU J,MO L,PAN L,et al.Bacterial microbiota and metabolic character of traditional sour cream and butter in Buryatia,Russia[J].Front Microbiol,2018,9:2496.
[32]LI J,ZHENG Y,XU H Y,et al.Bacterial microbiota of Kazakhstan cheese revealed by single molecule real time(SMRT)sequencing and its comparison with Belgian,Kalmykian and Italian artisanal cheeses[J].BMC Microbiology,2017,17:13.
[33]MAO L X,YU J,JIN H,et al.Investigating the bacterial microbiota of traditional fermented dairy products using propidium monoazide with single-molecule real-time sequencing[J].J Dairy Sci,2019,102(5):3912-3923.
[34]WALSH A M,CRISPIE F,DAARI K,et al.Strain-level metagenomic analysis of the fermented dairy beverage nunu highlights potential food safety risks[J].Appl Environ Microbiol,2017,83(16):E1144-E1117.
[35]其木格苏都.自然发酵酸马奶细菌多样性及其基因动态变化研究[D].呼和浩特：内蒙古农业大学，2017.
[36]LAGIER J C,ARMOUGOM F,MILLION M,et al.Microbial culturomics:paradigm shift in the human gut microbiome study[J].Clin Microbiol Infect,2012,18(12):1185-1193.
[37]MARTINO G P,QUINTANA I M,ESPARIZ M,et al.Aroma compounds generation in citrate metabolism of Enterococcus faecium:genetic characterization of type I citrate gene cluster[J].Int J Food Microbiol,2016,218:27-37.