China Animal Husbandry and Veterinary Medicine ›› 2020, Vol. 47 ›› Issue (12): 3882-3889.doi: 10.16431/j.cnki.1671-7236.2020.12.010
• Physiology and Biochemistry • Previous Articles Next Articles
NIU Chunyu1, SHI Linlin1, SUN Miao1, LIU Yanmin2, HUANG Shaolei2, CHENG Chao3, LI Peifeng1
Received:
2020-05-12
Online:
2020-12-20
Published:
2020-12-18
CLC Number:
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.
[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. |
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