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《工程(英文)》 >> 2022年 第17卷 第10期 doi: 10.1016/j.eng.2020.09.016

基于系统发育和比较基因组分析揭示与发酵乳杆菌缓解结肠炎相关的关键基因

a State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
b School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
c National Engineering Research Centre for Functional Food, Jiangnan University, Wuxi, 214122, China
d International Joint Research Laboratory for Probiotics, Jiangnan University, Wuxi, 214122, China
e Beijing Innovation Centre of Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China

收稿日期: 2020-03-16 修回日期: 2020-09-13 录用日期: 2020-09-24 发布日期: 2021-02-05

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摘要

越来越多的研究表明,发酵乳杆菌可以用于溃疡性结肠炎的预防和治疗。本研究中,我们从中国不同地区的人群粪便样本中分离出了105 株发酵乳杆菌,并对其基因组草图进行了测序。我们分析了这些菌株的泛基因组和系统发育特征,并对4 个模型菌株(发酵乳杆菌3872、CECT5716、IFO3956 和VRI003)也进行了分析。系统发育分析表明,发酵乳杆菌基因组的进化方向与宿主的地理位置、性别、族群和年龄没有明显的关系。我们挑选了3 株来自不同的系统发育支系的发酵乳杆菌(FWXBH115、FGDLZR121和FXJCJ61)和发酵乳杆菌模式菌株CECT5716,通过构建右旋糖酐硫酸钠(DSS)诱导的结肠炎小鼠模型,
探究这几株菌的抗炎和免疫调节活性。发酵乳杆菌FXJCJ61 和CECT5716 可以通过缓解所有结肠炎相关的组织学指标,保护黏膜完整性,增加肠道短链脂肪酸(SCFA),显著减轻结肠炎,而其他两株菌未能提供类似的保护作用。发酵乳杆菌FXJCJ61 和CECT5716 的抗炎机制与核转录因子kappa-B(NF-κB)信号通路激活以及促进白细胞介素10(IL-10)的产生有关。比较基因组分析结果表明,这些有益发酵乳杆菌的抗炎作用可能与一些特定基因有关。

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参考文献

[ 1 ] Archer AC, PMJAM Halami. Probiotic attributes of Lactobacillus fermentum isolated from human feces and dairy products. Appl Microbiol Biotechnol 2015;99(19):8113‒23. 链接1

[ 2 ] Lin WH, Yu B, Jang SH, Tsen HY. Different probiotic properties for Lactobacillus fermentum strains isolated from swine and poultry. Anaerobe 2007;13(3‒4):107‒13.

[ 3 ] Morita H, Toh H, Fukuda S, Horikawa H, Oshima K, Suzuki T, et al. Comparative genome analysis of Lactobacillus reuteri and Lactobacillus fermentum reveal a genomic island for reuterin and cobalamin production. DNA Res 2008;15 (3):151‒61. 链接1

[ 4 ] Jayashree S, Pooja S, Pushpanathan M, Rajendhran J, Gunasekaran P. Identification and characterization of bile salt hydrolase genes from the genome of Lactobacillus fermentum MTCC 8711. Appl Biochem Biotechnol 2014;174(2):855‒66. 链接1

[ 5 ] Dan T, Fukuda K, Sugai-Bannai M, Takakuwa N, Motoshima H, Urashima T. Characterization and expression analysis of the exopolysaccharide gene cluster in Lactobacillus fermentum TDS030603. Biosci Biotechnol Biochem 2009;73(12):2656‒64. 链接1

[ 6 ] Oloyede AR, Albert OM, Arowosegbe OA. Detection and molecular characterization of butyrate-producing genes in probiotic lactic acid bacteria for use in livestock. Niger J Biotechnol 2017;33(1):58‒65. 链接1

[ 7 ] Makarova K, Slesarev A, Wolf Y, Sorokin A, Mirkin B, Koonin E, et al. Comparative genomics of the lactic acid bacteria. Proc Natl Acad Sci USA 2006;103(42):15611‒6. 链接1

[ 8 ] Mendes-Soares H, Suzuki H, Hickey RJ, Forney LJ. Comparative functional genomics of Lactobacillus spp. reveals possible mechanisms for specialization of vaginal lactobacilli to their environment. J Bacteriol 2014;196(7):1458‒70. 链接1

[ 9 ] O’Sullivan O, O’Callaghan J, Sangrador-Vegas A, Mcauliffe O, Slattery L, Kaleta P, et al. Comparative genomics of lactic acid bacteria reveals a niche-specific gene set. BMC Microbiol 2009;9(1):50. 链接1

[10] Siezen RJ, Tzeneva VA, Castioni A, Wels M, Phan HTK, Rademaker JLW, et al. Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches. Environ Microbiol Rep 2010;12(3):758‒73. 链接1

[11] Zheng J, Zhao X, Lin XB, Ganzle M. Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations. Sci Rep 2015;5(1):18234. 链接1

[12] Kant R, Rintahaka J, Yu X, Sigvart-Mattila P, Paulin L, Mecklin JP, et al. A comparative pan-genome perspective of niche-adaptable cell-surface protein phenotypes in Lactobacillus rhamnosus. PLoS ONE 2014;9(7). 链接1

[13] Cai H, Thompson R, Budinich MF, Broadbent JR, JLJGB Steele. Genome sequence and comparative genome analysis of Lactobacillus casei: insights into their niche-associated evolution. Genome Biol Evol 2009;1:239‒57. 链接1

[14] Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN, Roos S, et al. Diversification of the gut symbiont Lactobacillus reuteri as a result of hostdriven evolution. ISME J 2010;4(3):377‒87. 链接1

[15] Dan T, Liu W, Song Y, Xu H, Menghe B, Zhang H, et al. The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST). BMC Microbiol 2015;15(1):107. 链接1

[16] Silvi S, Verdenelli MC, Orpianesi C, Cresci A. Cresci AJJoFE. EU project Crownalife: functional foods, gut microflora and healthy ageing:isolation and identification of Lactobacillus and Bifidobacterium strains from faecal samples of elderly subjects for a possible probiotic use in functional foods. J Food Eng 2003;56(2-3):195‒200. 链接1

[17] Morandi S, Brasca M, Lodi R. Technological, phenotypic and genotypic characterisation of wild lactic acid bacteria involved in the production of Bitto PDO Italian cheese. Dairy Sci Technol 2011;91(3):341‒59. 链接1

[18] Blomberg L, Henriksson A, Conway PL. Inhibition of adhesion of Escherichia coli K88 to piglet ileal mucus by Lactobacillus spp.. Appl Environ Microbiol 1993;59(1):34‒9. 链接1

[19] Lehri B, Seddon AM, Karlyshev AV. Lactobacillus fermentum 3872 as a potential tool for combatting Campylobacter jejuni infections. Virulence 2017;8(8):1753‒60. 链接1

[20] Kim BK, Lee IO, Tan PL, Eor JY, Hwang JK, Kim SH. Protective effect of Lactobacillus fermentum LA12 in an alcohol-induced rat model of alcoholic steatohepatitis. Korean J Food Sci Anim Resour 2017;37:931‒9. 链接1

[21] Kullisaar T, Zilmer K, Salum T, Rehema A, Zilmer M. The use of probiotic L. fermentum ME-3 containing reg’activ cholesterol supplement for 4 weeks has a positive influence on blood lipoprotein profiles and inflammatory cytokines: an open-label preliminary study. Nutr J 2016;15(1):93. 链接1

[22] Chen X, Zhao X, Wang H, Yang Z, Li J, Suo H. Prevent effects of Lactobacillus fermentum HY01 on dextran sulfate sodium-induced colitis in mice. Nutrients 2017;9(6):545. 链接1

[23] Zhao Y, Hong K, Zhao J, Zhang H, Zhai Q, Chen W. Lactobacillus fermentum and its potential immunomodulatory properties. J Funct Foods 2019;56:21‒32. 链接1

[24] Rodríguez-Nogales A, Algieri F, Garrido-Mesa J, Vezza T, Utrilla MP, Chueca N, et al. Differential intestinal anti-inflammatory effects of Lactobacillus fermentum and Lactobacillus salivarius in DSS mouse colitis: impact on microRNAs expression and microbiota composition. Mol Nutr Food Res 2017;61(11):1700144. 链接1

[25] Chery J, Dvoskin D, Morato FP, Fahoum B. Lactobacillus fermentum, a pathogen in documented cholecystitis. Int J Surg Case Rep 2013;4(8):662‒4. 链接1

[26] Anderson RC, Ulluwishewa D, Young W, Ryan LJ, Henderson G, Meijerink M, et al. Human oral isolate Lactobacillus fermentum AGR1487 induces a proinflammatory response in germ-free rat colons. Sci Rep 2016;6(1):20318. 链接1

[27] Yao L, Seaton SC, Ndousse-Fetter S, Adhikari AA, DiBenedetto N, Mina AI. A selective gut bacterial bile salt hydrolase alters host metabolism. eLife 2018;7: e37182. 链接1

[28] Guo CJ, Allen BM, Hiam KJ, Dodd D, Van Treuren W, Higginbottom S, et al. Depletion of microbiome-derived molecules in the host using Clostridium genetics. Science 2019;366(6471):eaav1282. 链接1

[29] Kumar R, Rajkumar H, Kumar M, Varikuti SR, Athimamula R, Shujauddin M, et al. Molecular cloning, characterization and heterologous expression of bile salt hydrolase (Bsh) from Lactobacillus fermentum NCDO394. Mol Biol Rep 2013;40(8):5057‒66. 链接1

[30] Hartemink R, Domenech VR, Rombouts FM. LAMVAB—a new selective medium for the isolation of lactobacilli from faeces. J Microbiol Methods 1997;29 (2):77‒84. 链接1

[31] Zheng J, Ruan L, Sun M, Ganzle M. A genomic view of Lactobacilli and Pediococci demonstrates that phylogeny matches ecology and physiology. Appl Environ Microbiol 2015;81(20):7233‒43. 链接1

[32] Verma R, Lee C, Jeun EJ, Yi J, Kim KS, Ghosh A. Cell surface polysaccharides of Bifidobacterium bifidum induce the generation of Foxp3+ regulatory T cells. Sci Immunol 2018;3(28):eaat6975. 链接1

[33] Liu HL, Zhang YL, Yang N, Zhang YX, Liu XQ, Li CG, et al. A functionalized single-walled carbon nanotube-induced autophagic cell death in human lung cells through Akt-TSC2-mTOR signaling. Cell Death Dis 2011;2(5). 链接1

[34] Zhang Z, Wu X, Cao S, Wang L, Wang D, Yang H, et al. Caffeic acid ameliorates colitis in association with increased Akkermansia population in the gut microbiota of mice. Oncotarget 2016;7(22):31790‒9. 链接1

[35] Zhai Q, Wang G, Zhao J, Liu X, Tian F, Zhang H, et al. Protective effects of Lactobacillus plantarum CCFM8610 against acute cadmium toxicity in mice. Appl Environ Microbiol 2013;79(5):1508‒15. 链接1

[36] Tan H, Zhao J, Zhang H, Zhai Q, Chen WJAM. Novel strains of Bacteroides fragilis and Bacteroides ovatus alleviate the LPS-induced inflammation in mice. Appl Microbiol Biotechnol 2019;103(5):2353‒65. 链接1

[37] Xu Q, Li X, Wang E, He Y, Yin B, Fang D, et al. A cellular model for screening of lactobacilli that can enhance tight junctions. RSC Adv 2016;6 (113):111812‒21. 链接1

[38] Mao B, Li D, Ai C, Zhao J, Zhang H, Chen W. Lactulose differently modulates the composition of luminal and mucosal microbiota in C57BL/6J mice. J Agric Food Chem 2016;64(31):6240‒7. 链接1

[39] Sun Y, Jin C, Zhang X, Jia W, Le J, Ye J. Restoration of GLP-1 secretion by Berberine is associated with protection of colon enterocytes from mitochondrial overheating in diet-induced obese mice. Nutr Diabetes 2018;8 (1):53. 链接1

[40] Song YL, Kato N, Liu CX, Matsumiya Y, Kato H, KJFMLWatanabe. Rapid identification of 11 human intestinal Lactobacillus species by multiplex PCR assays using group- and species-specific primers derived from the 16S‍‒‍23S rRNA intergenic spacer region and its flanking 23S rRNA. FEMS Microbiol Lett 2000;187(2):167‒73. 链接1

[41] Bahl MI, Bergstrom A, Licht TR. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis. FEMS Microbiol Lett 2012;‍329(2):193‒7. 链接1

[42] Li P, Gu Q, Yang L, Yu Y, Wang Y. Characterization of extracellular vitamin B12 producing Lactobacillus plantarum strains and assessment of the probiotic potentials. Food Chem 2017;234:494‒501. 链接1

[43] Sulemankhil I, Parent M, Jones ML, Feng Z, Labbe A, Prakash S. In vitro and in vivo characterization and strain safety of Lactobacillus reuteri NCIMB 30253 for probiotic applications. Can J Microbiol 2012;58(6):776‒87. 链接1

[44] Moran NA, Sloan DB. The hologenome concept: helpful or hollow? PLoS Biol 2015;13(12). 链接1

[45] Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, et al. Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun 2017;8(1):14319. 链接1

[46] Duar RM, Lin XB, Zheng J, Martino ME, Grenier T, Perez-Munoz ME, et al. Lifestyles in transition: evolution and natural history of the genus Lactobacillus. FEMS Microbiol Rev 2017;41(Supp 1):S27‒48. 链接1

[47] Guo X, Li S, Zhang J, Wu F, Li X, Wu D, et al. Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diversity, and global distribution in mammalian gut microbiotas. BMC Genomics 2017;18(1):800. 链接1

[48] Ottman N, Reunanen J, Meijerink M, Pietila TE, Kainulainen V, Klievink J, et al. Pili-like proteins of Akkermansia muciniphila modulate host immune responses and gut barrier function. PLoS ONE 2017;12(3). 链接1

[49] Pandurangan AK, Ismail S, Saadatdoust Z, Esa NM. Allicin alleviates dextran sodium sulfate- (DSS-) induced ulcerative colitis in BALB/c mice. Oxid Med Cell Longev 2015;2015. 链接1

[50] Cario E. Toll-like receptors in inflammatory bowel diseases: a decade later. Inflamm Bowel Dis 2010;16(9):1583‒97. 链接1

[51] Takagawa T, Kitani A, Fuss I, Levine B, Brant SR, Peter I, et al. An increase in LRRK2 suppresses autophagy and enhances Dectin-1-induced immunity in a mouse model of colitis. Sci Transl Med 2018;10(444):eaan8162. 链接1

[52] Mittal SK, Roche PA. Suppression of antigen presentation by IL-10. Curr Opin Immunol 2015;34:22‒7. 链接1

[53] Onizawa M, Nagaishi T, Kanai T, Nagano K, Oshima S, Nemoto Y, et al. Signaling pathway via TNF-alpha/NF-kappaB in intestinal epithelial cells may be directly involved in colitis-associated carcinogenesis. Am J Physiol Gastrointest Liver Physiol 2009;296(4):G850‒9. 链接1

[54] Price MN, Wetmore KM, Waters RJ, Callaghan M, Ray J, Liu H, et al. Mutant phenotypes for thousands of bacterial genes of unknown function. Nature 2018;557(7706):503‒9. 链接1

[55] Spaulding CN, Klein RD, Ruer S, Kau AL, Schreiber HL, Cusumano ZT, et al. Selective depletion of uropathogenic E. coli from the gut by a FimH antagonist. Nature 2017;546(7659):528‒32. 链接1

[56] Yang J, Li Q, Henning SM, Zhong J, Hsu M, Lee R, et al. Effects of prebiotic fiber xylooligosaccharide in adenine-induced nephropathy in mice. Mol Nutr Food Res 2018;62(15):1800014. 链接1

[57] Adachi O, Fujii Y, Ano Y, Moonmangmee D, Toyama H, Shinagawa E, et al. Membrane-bound sugar alcohol dehydrogenase in acetic acid bacteria catalyzes L-ribulose formation and NAD-dependent ribitol dehydrogenase is independent of the oxidative fermentation. Biosci Biotechnol Biochem 2001;65(1):115‒25. 链接1

[58] Wen L, Wong FS. Dietary short-chain fatty acids protect against type 1 diabetes. Nat Immunol 2017;18(5):484‒6. 链接1

[59] Zagato E, Pozzi C, Bertocchi A, Schioppa T, Saccheri F, et al. Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth. Nat Microbiol 2020;‍5(3):511‒24. 链接1

[60] Smith PM, Howitt MR, Panikov N, Michaud M, Gallini CA, Bohlooly-Y M, et al. the microbial metabolites, short-chain fatty acids, regulate colonic treg cell homeostasis. Science 2013;341(6145):569‒73. 链接1

[61] Mishiro T, Kusunoki R, Otani A, Ansary MM, Tongu M, Harashima N, et al. Butyric acid attenuates intestinal inflammation in murine DSS-induced colitis model via milk fat globule-EGF factor 8. Lab Invest 2013;93(7):834‒43. 链接1

[62] Laffin M, Fedorak R, Zalasky A, Park H, Gill A, Agrawal A, et al. A high-sugar diet rapidly enhances susceptibility to colitis via depletion of luminal short-chain fatty acids in mice. Sci Rep 2019;9(1):12294. 链接1

[63] Wang M, Wichienchot S, He X, Fu X, Huang Q, Zhang B. In vitro colonic fermentation of dietary fibers: fermentation rate, short-chain fatty acid production and changes in microbiota. Trends Food Sci Technol 2019;88:1‒9. 链接1

[64] Tajik N, Frech M, Schulz O, Schälter F, Lucas S, Azizov V, et al. Targeting zonulin and intestinal epithelial barrier function to prevent onset of arthritis. Nat Commun 2020;11(1):1995. 链接1

[65] Yang C, Gao J, Zhang J, Luo AL. Enterochromaffin cells in the gut: a distant regulator of brain function? Gut 2018;67(8):1557‒8. 链接1

[66] Lee YS, Kim TY, Kim Y, Lee SH, Kim S, Kang SW, et al. Microbiota-derived lactate accelerates intestinal stem-cell-mediated epithelial development. Cell Host Microbe 2018;24(6):833‒46. 链接1

[67] Iraporda C, Errea A, Romanin DE, Cayet D, Pereyra E, Pignataro O, et al. Lactate and short chain fatty acids produced by microbial fermentation downregulate proinflammatory responses in intestinal epithelial cells and myeloid cells. Immunobiology 2015;220(10):1161‒9. 链接1

[68] Witkin SS, Linhares IM. Why do lactobacilli dominate the human vaginal microbiota? BJOG 2017;124(4):606‒11. 链接1

[69] Wulandari AP, Miyazaki J, Kobashi N, Nishiyama M, Hoshino T, Yamane H. Characterization of bacterial homocitrate synthase involved in lysine biosynthesis. FEBS Lett 2002;522(1‒3):35‒40.

[70] Wu R, Sun Z, Wu J, Meng H, Zhang H. Effect of bile salts stress on protein synthesis of Lactobacillus casei Zhang revealed by 2-dimensional gel electrophoresis. J Dairy Sci 2010;93(8):3858‒68. 链接1

[71] Blount KF, Wang JX, Lim J, Sudarsan N, Breaker RR. Antibacterial lysine analogs that target lysine riboswitches. Nat Chem Biol 2007;3(1):44‒9. 链接1

[72] Goh YJ, Barrangou R. Harnessing CRISPR-Cas systems for precision engineering of designer probiotic lactobacilli. Curr Opin Biotechnol 2019;56:163‒71. 链接1

[73] Pontonio E, Mahony J, Di Cagno R, O’Connell Motherway M, Lugli GA, O’Callaghan A, et al. Cloning, expression and characterization of a β-D-xylosidase from Lactobacillus rossiae DSM 15814T. Microb Cell Fact 2016;15(1):72. 链接1

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