组学技术在乳酸菌分离鉴定及功能研究中的应用

doi:10.16431/j.cnki.1671-7236.2020.12.010

摘要/Abstract

摘要： 乳酸菌具有黏附宿主细胞或黏膜、抑制病原菌生长、维持机体微生态平衡、增强宿主免疫力等促进宿主健康的作用，同时在食品工业、抗菌剂生产和体内发酵中也发挥重要作用，但目前对乳酸菌发挥益生作用的具体分子机制的描述不多。为探明乳酸菌自身及其在宿主中的新功能和调控机制，可采用组学技术进行研究。根据中心法则衍生出的组学方法包括基因组学、转录组学、蛋白质组学和代谢组学。单组学技术在乳酸菌研究中的应用可深入探索乳酸菌发挥的功能及其作用机制。多组学技术的应用可突破单一组学技术的局限性，从不同维度综合分析乳酸菌的潜在功能，进一步预测乳酸菌自身及其在宿主中发挥的作用。作者综述了几种常用于乳酸菌分离鉴定及功能研究领域的组学技术，阐述了多组学技术在乳酸菌功能及其机制研究中的应用概况，为进一步探明乳酸菌的潜在功能提供可行的技术方法和方向。

关键词: 乳酸菌; 基因组学; 转录组学; 蛋白质组学; 代谢组学; 多组学联合分析

Abstract: Lactic acid bacteria can promote host health by adhering to host cells or mucosa and inhibiting pathogen growth,maintaining microecological balance and enhancing host immunities.It also plays an important role in food industry,antimicrobial production and in vivo fermentation.However,the specific molecular mechanism of probiotics in lactic acid bacteria is rarely described.In order to explore the new function and regulation mechanism of lactic acid bacteria itself and lactic acid bacteria in its host,omics technology can be used for research.The omics methods derived from the central dogma include genomics,transcriptomics,proteomics,and metabolomics.The application of monoomics technology in the study can further explore the function and mechanism of lactic acid bacteria.The application of multi-group technology can break through the limitation of single group technology,the potential function of lactic acid bacteria can be analyzed synthetically from different dimensions,and the lactic acid bacteria itself and its role in the host were further predicted.Several omics techniques which are commonly used in the field of lactic acid bacteria isolation and identification and functional research were reviewed in this paper.The application of multi-omics in the study of function and mechanism of lactic acid bacteria were reviewed.It provided a feasible technical method and direction to further explore the potential function of lactic acid bacteria.

Key words: lactic acid bacteria; genomic; transcriptomics; proteomics; metabolomics; multi-omics

中图分类号:

S852.1

牛春宇, 石琳琳, 孙苗, 刘彦民, 黄少磊, 程超, 李培锋. 组学技术在乳酸菌分离鉴定及功能研究中的应用[J]. 中国畜牧兽医, 2020, 47(12): 3882-3889.

NIU Chunyu, SHI Linlin, SUN Miao, LIU Yanmin, HUANG Shaolei, CHENG Chao, LI Peifeng. Applications of Omics Approaches in Isolation and Identification of Lactic Acid Bacteria and It’s Functional Research[J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(12): 3882-3889.

参考文献

[1] BROOKS G F,BUTEL J S,ORNSTON L N.Jawetz,Melnick and Adelberg's medical microbiology[J].Sultan Qaboos University Medical Journal,2007,7(3):273-275.
[2] AROUTCHEVA A,GARITI D,SIMON M,et al.Defense factors of vaginal Lactobacilli[J].American Journal of Obstetrics & Gynecology,2001,185(2):375-379.
[3] MENDLING W.Vaginal microbiota[J].Advances in Experimental Medicine & Biology,2016,902:83-93.
[4] KRAVTSOV E G,YERMOLAYEV A V,ANOKHINA I V,et al.Adhesion characteristics of Lactobacillus is a criterion of the probiotic choice[J].Bulletin of Experimental Biology & Medicine,2008,145(2):232-234.
[5] SHERMAN P M,OSSA J C,JOHNSON-HENRY K.Unraveling mechanisms of action of probiotics[J].Nutrition in Clinical Practice,2009,24(1):10-14.
[6] STECHER B,HARDT W D.Mechanisms controlling pathogen colonization of the gut[J].Current Opinion in Microbiology,2011,14(1):82-91.
[7] BHAT M I,SOWMYA K,KAPILA S,et al.Potential probiotic Lactobacillus rhamnosus (MTCC-5897) inhibits Escherichia coli impaired intestinal barrier function by modulating the host tight junction gene response[J].Probiotics and Antimicrobial Proteins,2020,12(3):1149-1160.
[8] BAECKHED F,LEY R E,SONNENBURG J L,et al.Host-bacterial mutualism in the human intestine[J].Science,2005,307(5717):1915-1920.
[9] 李桂澜,匡华.高通量测序技术在食品微生物检测中的应用[J].食品安全质量检测学报,2019,10(15):5091-5097. LI G L,KUANG H.Applications of high-throughput sequencing technologies for food microbiome detection[J].Journal of Food Safety and Quality,2019,10(15):5091-5097.(in Chinese)
[10] HUANG S,CHAUDHARY K,GARMIRE LX.More is better:Recent progress in multi-omics data integration methods[J].Frontiers in Genetics,2017,8:84.
[11] LIN E,LANE H Y.Machine learning and systems genomics approaches for multi-omics data[J].Biomarker Research,2017,5:2.
[12] QIN J,YAN B,HU Y,et al.Applications of integrative OMICs approaches to gene regulation studies[J].Quantitative Biology,2016,4(4):283-301.
[13] O' DONNELL S T,ROSS R P,STANTON C.The Progress of multi-omics technologies:Determining function in lactic acid bacteria using a systems level approach[J].Frontiers in Microbiology,2020,10:3084.
[14] WANG Q,WANG K,WU W,et al.Host and microbiome multi-omics integration:Applications and methodologies[J].Biophysical Reviews,2019,11(1):55-65.
[15] SANCHEZ B,RUIZ L,GUEIMONDE M,et al.Omics for the study of probiotic microorganisms[J].Food Research International,2013,54(1):1061-1071.
[16] ZHANG W,LI F,NIE L.Integrating multiple ‘omics’ analysis for microbial biology:Application and methodologies[J].Microbiology,2010,156(Pt 2):287-301.
[17] ALLENDORF F W,HOHENLOHE P A,LUIKART G.Genomics and the future of conservation genetics[J].Nature Reviews Genetics,2010,11(10):697-709.
[18] CHENOLL E,RIVERO M,CODOER F M,et al.Complete genome sequence of Bifidobacterium longum subsp. infantis strain cect 7210,a probiotic strain active against rotavirus infections[J].Genome Announcements,2015,3(2):e00105-15.
[19] SABAT A J,BUDIMIR A,NASHEV D,et al.Overview of molecular typing methods for outbreak detection and epidemiological surveillance[J].Eurosurveillance,2013,18(4):20380.
[20] LOMAN N J,PALLEN M J.Twenty years of bacterial genome sequencing[J].Nature Reviews Microbiology,2015,13(12):787-794.
[21] NEVILLE B A,FORDE B M,CLAESSON M J,et al.Characterization of pro-inflammatory flagellin proteins produced by Lactobacillus ruminis and related motile Lactobacilli[J].PLoS One,2012,7(7):e40592
[22] WALTER J,CHAGNAUD P,TANNOCK G W,et al.A high-molecular-mass surface protein (Lsp) and methionine sulfoxide reductase B (MsrB) contribute to the ecological performance of Lactobacillus reuteri in the murine gut[J].Applied and Environmental Microbiology,2005,71(2):979-986.
[23] O'CONNELL MOTHERWAY M,ZOMER A,LEAHY S C,et al.Functional genome analysis of Bifidobacterium breve UCC2003 reveals type IVb tight adherence (Tad) pili as an essential and conserved host-colonization factor[J].Proceedings of the National Academy of Sciences of the United States of America,2011,108(27):11217-11222.
[24] BUCK B L,ALTERMANN E,SVINGERUD T,et al.Functional analysis of putative adhesion factors in Lactobacillus acidophilus NCFM[J].Applied and Environmental Microbiology,2006,71(12):8344-8351.
[25] MASAHIRO I,YUN-GI K,HIROKAZU T,et al.Transposon mutagenesis of probiotic Lactobacillus casei identifies asnH,an asparagine synthetase gene involved in its immune-activating capacity[J].PLoS One,2014,9(1):e83876.
[26] PAPADIMITRIOU K,POT B,TSAKALIDOU E.How microbes adapt to a diversity of food niches[J].Current Opinion in Food Science.2015,2:29-35.
[27] WEI Y X,ZHANG Z Y,LIU C,et al.Safety assessment of bifidobacterium longum JDM301 based on complete genome sequences[J]. World Journal of Gastroenterology,2012,18(5):479-488.
[28] HANDELSMAN J,RONDON M R,BRADY S F,et al.Molecular biological access to the chemistry of unknown soil microbes:A new frontier for natural products[J]. Chemistry and Biology,1998,5(10):245-249.
[29] HUTTENHOWER C,GEVERS D,KNIGHT R,et al.Structure,function and diversity of the healthy human microbiome[J].Nature,2012,486(7402):207-214.
[30] YANG H,HUANG X,FANG S,et al.Uncovering the composition of microbial community structure and metagenomics among three gut locations in pigs with distinct fatness[J].Scientific Reports,2016,6:27427.
[31] ZHERNAKOVA A,KURILSHIKOV A,BONDER M J,et al.Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity[J].Science,2016,352(6285):565-569.
[32] QIN J,LI R,RAES J,et al.A human gut microbial gene catalogue established by metagenomic sequencing[J].Nature,2010,464(7285):59-65.
[33] SOREK R,COSSART P.Prokaryotic transcriptomics:A new view on regulation,physiology and pathogenicity[J].Nature Reviews Genetics,2009,11(1):9-16.
[34] NIU C,CHENG C,LIU Y,et al.Transcriptome profiling analysis of bovine vaginal epithelial cell response to an isolated Lactobacillus strain[J].mSystems,2019,4(5):e00268-19.
[35] TROOST F J,BAARLEN P V,LINDSEY P,et al.Identification of the transcriptional response of human intestinal mucosa to Lactobacillus plantarum WCFS1in vivo[J].BMC Genomics,2008,9:374.
[36] IONELIA T,DANIELA M,CORNELIA B,et al.In vitro transcriptome response to a mixture of Lactobacilli strains in intestinal porcine epithelial cell line[J].International Journal of Molecular Sciences,2018,19(7):1923.
[37] BASHIARDES S,ZILBERMAN-SCHAPIRA G,ELINAV E.Use of metatranscriptomics in microbiome research[J].Bioinformatics and Biology Insights,2016,10:19-25.
[38] CAGNO R D,ANGELIS M D,CALASSO M,et al.Proteomics of the bacterial cross-talk by quorum sensing[J].Journal of Proteomics,2011,74(1):19-34.
[39] ARUMUGAM M,RAES J,PELLETIER E,et al.Enterotypes of the human gut microbiome[J].Nature,2011,473(7346):174-180.
[40] CASH P.Proteomics in medical microbiology[J]. Electrophoresis,2000,21(6):1187-1201.
[41] SÁNCHEZ B,CHAMPOMIER-VERGÈS M C,ANGLADE P,et al.A preliminary analysis of bifidobacterium longum exported proteins by two-dimensional electrophoresis[J].Journal of Molecular Microbiology and Biotechnology,2008,14(1-3):74-79.
[42] LIPPOLIS R,GNONI A,ABBRESCIA A,et al.Comparative proteomic analysis of four Bacillus clausii strains:Proteomic expression signature distinguishes protein profile of the strains[J]. Journal of Proteomics,2011,74(12):2846-2855.
[43] RUIZ-MOYANO S,TAO N,UNDERWOOD M A,et al.Rapid discrimination of Bifidobacterium animalis subspecies by matrix-assisted laser desorption ionization-time of flight mass spectrometry[J].Food Microbiology,2012,30(2):432-437.
[44] VITALI B,TURRONI S,PIAZ F D,et al.Genetic and proteomic characterization of rifaximin resistance in Bifidobacterium infantis BI07[J].Research in Microbiology,2007,158(4):355-362.
[45] SCHOTT A S,BEHR J,GEISSLER A J,et al.Quantitative proteomics for the comprehensive analysis of stress responses of Lactobacillus paracasei subsp.paracasei F19[J].Journal of Proteome Research,2017,16(10):3816-3829.
[46] RODRÍGUEZ-VALERA F.Environmental genomics,the big picture?[J].FEMS Microbiology Letters,2004,231(2):153-158.
[47] FIEHN O.Metabolomics-The link between genotypes and phenotypes[J].Plant Molecular Biology,2002,48(1-2):155-171.
[48] YUAN Z W,ZHONG L J,JI P,et al.Plasma metabolomics of angelica intervene in blood stasis syndrome rats[J].Natural Product Research and Development, 2018,30:559-567.
[49] 龚霄,齐宁利,林丽静,等.基于气质联用技术的唾液乳杆菌渗胁迫响应代谢组学研究[J].食品研究与开发,2014,35(19):10-12. GONG X,QI N L,LIN L J,et al.GC/MS based metabonomics study on osmotic response of Lactobacillus salivarius[J].Food Research and Development,2014,35(19):10-12.(in Chinese)
[50] SARRUT M,CRÉTIER G,HEINISCH S.Theoretical and practical interest in UHPLC technology for 2D-LC[J].Trends in Analytical Chemistry,2014,63:104-112.
[51] 王晶,杨杏芬,Ong Choon Nam,等.两种气相色谱质谱联用技术在人体尿液代谢组学研究中的应用对比[J].环境与健康杂志,2015,32(4):324-327. WANG J,YANG X F,CHOON NAM O,et al.Comparative study of GC/QTOF-MS and GC/Q-MS in human metabonomics of urine[J].Journal of Environment and Health,2015,32(4):324-327.(in Chinese)
[52] GALLEGOS J,ARCE C,JORDANO R,et al.Target identification of volatile metabolites to allow the differentiation of lactic acid bacteria by gas chromatography-ion mobility spectrometry[J]. Food Chemistry,2017,220:362-370.
[53] TOMITA S,SAITO K,NAKAMURA T,et al.Rapid discrimination of strain-dependent fermentation characteristics among Lactobacillus strains by NMR-based metabolomics of fermented vegetable juice[J].PLoS One,2017,12(7):e0182229.
[54] GAO K,LIU L,DOU X,et al.Doses Lactobacillus reuteri depend on adhesive ability to modulate the intestinal immune response and metabolism in mice challenged with lipopolysaccharide[J].Scientific Reports,2016,6:28332.
[55] GYGI S P,ROCHON Y,FRANZA B R,et al.Correlation between protein and mRNA abundance in yeast[J].Molecular & Cellular Biology,1999,19(3):1720-1730.
[56] NIERMAN W,EISEN J A,FRASER C M.Microbial genome sequencing 2000:New insights into physiology,evolution and expression analysis[J].Research in Microbiology, 2000,151(2):79-84.
[57] ZHAO Y,JOHNSON W E.Exploring host-microbe interactions in lung cancer[J].American Journal of Respiratory and Critical Care Medicine,2018,198(9):1116-1118.
[58] MORGAN X C,KABAKCHIEV B,WALDRON L,et al.Associations between host gene expression,the mucosal microbiome,and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease[J].Genome Biology,2015,16(1):67.
[59] TURRONI F,MILANI C,DURANTI S,et al.Deciphering bifidobacterial-mediated metabolic interactions and their impact on gut microbiota by a multi-omics approach[J].The ISME Journal,2016,10(7):1656-1668.
[60] CHEN G,GHARIB T G,HUANG C C,et al.Discordant protein and mRNA expression in lung adenocarcinomas[J].Molecular and Cellular Proteomics,2002,1(4):304-313.
[61] HERVE-JIMENEZ L,GUILLOUARD I,GUEDON E,et al.Postgenomic analysis of Streptococcus thermophilus cocultivated in milk with Lactobacillus delbrueckii subsp.bulgaricus:Involvement of nitrogen,purine,and iron metabolism[J].Applied and Environ-mental Microbiology,2009,75(7):2062-2073.
[62] KOSKENNIEMI K,LAAKSO K,KOPONEN J,et al.Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG[J].Molecular & Cellular Proteomics,2011,10(2):M110.002741.
[63] ASKENAZI M,DRIGGERS E M,HOLTZMAN D A,et al.Integrating transcriptional and metabolite profiles to direct the engineering of lovastatin-producing fungal strains[J].Nature Biotechnology,2003,21(2):150-156.
[64] WILSON C M,AGGIO R B M,O'TOOLE P W,et al.Transcriptional and metabolomic consequences of luxS inactivation reveal a metabolic rather than quorum-sensing role for LuxS in Lactobacillus reuteri 100-23[J].Journal of Bacteriology,2012,194(7):1743-1746.
[65] KROMER J O,SORGENFREI O,KLOPPROGGE K,et al.In-depth profiling of lysine-producing Corynebac-terium glutamicum by combined analysis of the transcriptome,metabolome,and fluxome[J].Journal of Bacteriology,2004,186(6):1769-1784.