比较基因组学分析不同来源罗伊氏乳杆菌基因多样性及生境适应性
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国家自然科学基金(31430066);内蒙古自然基金(2018MS03041);校优秀青年科学基金(2017XYQ-4)


Comparative genomics analysis of genetic diversity and habitat adaptability of Lactobacillus reuteri from different sources
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    摘要:

    [目的]研究34株不同来源罗伊氏乳杆菌(Lactobacillus reuteri)基因多样性及生境适应性机制,了解该菌株在肠外生境及肠内生境中适应性的异同,为L.reuteri优良菌株的开发提供理论基础。[方法]基于二代测序平台对11株源于发酵食品(酸马奶、酸粥)的L.reuteri进行测序,并应用比较基因组学将其与发酵食品、酸面团、食草动物L.reuteri分离株基因组进行比较分析。[结果]分离自酸马奶、酸粥L.reuteri基因组大小平均为2.14 Mb,GC含量平均为38.77%,且同种来源分离株系统发育关系距离较近。泛-核心基因集分别包含7242个、969个基因家族,其中酸马奶分离株特异性基因最多为459个。功能注释结果显示不同来源菌株碳水化合物、氨基酸相关基因数量及种类差异较大,仅在发酵食品和食草动物株中发现抗生素耐药性基因。注释到的碳水化合物活性酶中仅出现在发酵食品与食草动物分离株的为GH3(β-葡萄糖苷酶等)和GH43(β-木糖苷酶等),特有的分别为AA3(纤维二糖脱氢酶等)和GH66(葡萄糖转移酶等)。[结论]不同来源L.reuteri具有广泛的基因多样性,与生存环境密切相关。发酵食品分离株具有部分食草动物肠道菌株特性且具有其独特的环境适应性特征,体现了与宿主有关的环境适应能力,可加深对食品发酵和肠内环境中细菌生境适应性的理解。

    Abstract:

    [Objective] We studied the genetic diversity and habitat adaptability mechanism of 34 strains of Lactobacillus reuteri from different sources. We aimed to compared the differences of their adaptability in extraintestinal and intraintestinal habitats to provide theoretical basis for the development of Lactobacillus reuteri strains. [Methods] Based on the second generation sequencing platform, We sequenced 11 Lactobacillus reuteri strains from fermented food (yogurt and sour porridge) and compared with the genomes of fermented food, sour dough and herbivore sources of Lactobacillus reuteri strains by comparative genomics. [Results] The average genome size and GC content of L. reuteri isolated from yoghurt and sour porridge were 2.14 Mb and 38.77% respectively, and the phylogenetic relationship between the isolates from the same source was close. Pan-core gene sets consisted of 7242 and 969 gene families, yoghurt isolates had the most specific genes (459). Functional annotation showed that the number and types of carbohydrate and amino acid related genes varied greatly among strains from different sources, and the antibiotic resistance genes were found only in fermented food and herbivores strains. The carbohydrate-active enzymes of GH3 (β-glucosidase etc.) and GH43 (β-xylosidase etc.)only appeared in fermented food herbivore isolates, and the specific ones were AA3 (cellobiose dehydrogenase etc.) and GH66 (dextranase etc.), respectively. [Conclusion] Lactobacillus reuteri from different sources has a wide range of genetic diversity and is closely related to the living environment. Fermented food isolates had the characteristics of some herbivorous intestinal strains and their unique environmental adaptability, and reflected the host environmental adaptability. It can deepen the understanding of food fermentation and bacterial habitat adaptability in intestinal environment.

    参考文献
    [1] Talarico TL, Dobrogosz WJ. Chemical characterization of an antimicrobial substance produced by Lactobacillus reuteri. Antimicrobial Agents and Chemotherapy, 1989, 33(5):674-679.
    [2] Weizman Z, Asli G, Alsheikh A. Effect of a probiotic infant formula on infections in child care centers:comparison of two probiotic agents. Pediatrics, 2005, 115(1):5-9.
    [3] Indrio F, Riezzo G, Raimondi F, Bisceglia M, Cavallo L, Francavilla R. The effects of probiotics on feeding tolerance, bowel habits, and gastrointestinal motility in preterm newborns. The Journal of Pediatrics, 2008, 152(6):801-806.
    [4] Duar RM, Frese SA, Lin XB, Fernando SC, Burkey TE, Tasseva G, Peterson DA, Blom J, Wenzel CQ, Szymanski CM, Walter J. Experimental evaluation of host adaptation of Lactobacillus reuteri to different vertebrate species. Applied and Environmental Microbiology, 2017, 83(12):e00132.
    [5] Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN, Roos S, Walter J. Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. The ISME Journal, 2010, 4(3):377-387.
    [6] Wegmann U, MacKenzie DA, Zheng JS, Goesmann A, Roos S, Swarbreck D, Walter J, Crossman LC, Juge N. The pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract. BMC Genomics, 2015, 16:1023.
    [7] Zheng JS, Zhao X, Lin XB, Gänzle M. Comparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations. Scientific Reports, 2015, 5(1):18234.
    [8] Francis F, Kim J, Ramaraj T, Farmer A, Rush MC, Ham JH. Comparative genomic analysis of two Burkholderia glumae strains from different geographic origins reveals a high degree of plasticity in genome structure associated with genomic islands. Molecular Genetics and Genomics, 2013, 288(3/4):195-203.
    [9] Yu J, Zhao J, Song YQ, Zhang JC, Yu ZJ, Zhang HP, Sun ZH. Comparative genomics of the herbivore gut symbiont Lactobacillus reuteri reveals genetic diversity and lifestyle adaptation. Frontiers in Microbiology, 2018, 9:1151.
    [10] Luo RB, Liu BH, Xie YL, Li ZY, Huang WH, Yuan JY, He GZ, Chen YX, Pan Q, Liu YJ, Tang JB, Wu GX, Zhang H, Shi YJ, Liu Y, Yu C, Wang B, Lu Y, Han CL, Cheung DW, Yiu SM, Peng SL, Xiaoqian Z, Liu GM, Liao XK, Li YR, Yang HM, Wang J, Lam TW, Wang J. SOAPdenovo2:an empirically improved memory-efficient short-read de novo assembler. Gigascience, 2012, 1:18.
    [11] Tatusov RL, Fedorova ND, Jackson JD, Jacobs RA, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. The COG database:an updated version includes eukaryotes. BMC Bioinformatics, 2003, 4(1):41.
    [12] Seemann T. Prokka:rapid prokaryotic genome annotation. Bioinformatics, 2014, 30(14):2068-2069.
    [13] Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, Fookes M, Falush D, Keane JA, Parkhill J. Roary:rapid large-scale prokaryote pan genome analysis. Bioinformatics, 2015, 31(22):3691-3693.
    [14] Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Research, 2016, 44(D1):D457-D462.
    [15] Marchin M, Kelly PT, Fang JW. Tracker:continuous HMMER and BLAST searching. Bioinformatics, 2005, 21(3):388-389.
    [16] Wu H, Zhang Z, Hu SN, Yu J. On the molecular mechanism of GC content variation among eubacterial genomes. Biology Direct, 2012, 7:2.
    [17] Yamagata H, Matoba R, Fujii T, Yukawa H. Application of photosynthetic bacteria for porphyrin production. Studies in Surface Science and Catalysis, 1998, 114:475-478.
    [18] Allison MJ. Biosynthesis of amino acids by ruminal microorganisms. Journal of Animal Science, 1969, 29(5):797-807.
    [19] Qian Y, Yue DM, Peng YK, Liu Y, Xiao L. Occurrence and distribution of antibiotic-resistant bacteria and transfer of resistance genes in Lake Taihu. Microbes and Environments, 2013, 28(4):479-486.
    [20] Sun ZH, Harris HMB, McCann A, Guo CY, Argimon S, Zhang WY, Yang XW, Jeffery IB, Cooney JC, Kagawa TF, Liu WJ, Song YQ, Salvetti E, Wrobel A, Rasinkangas P, Parkhill J, Rea MC, O'Sullivan O, Ritari J, Douillard FP, Paul Ross R, Yang RF, Briner AE, Felis GE, de Vos WM, Barrangou R, Klaenhammer TR, Caufield PW, Cui YJ, Zhang HP, O'Toole PW. Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. Nature Communications, 2015, 6(1):8322.
    [21] Macdonald SS, Blaukopf M, Withers SG. N-acetylglucosaminidases from CAZy family GH3 are really glycoside phosphorylases, thereby explaining their use of histidine as an acid/base catalyst in place of glutamic acid. Journal of Biological Chemistry, 2015, 290(8):4887-4895.
    [22] Di Lauro B, Strazzulli A, Perugino G, La Cara F, Bedini E, Corsaro MM, Rossi M, Moracci M. Isolation and characterization of a new family 42β-galactosidase from the thermoacidophilic bacterium Alicyclobacillus acidocaldarius:identification of the active site residues. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2008, 1784(2):292-301.
    [23] Ozimek LK, van Hijum SAFT, van Koningsveld GA, van der Maarel MJEC, van Geel-Schutten GH, Dijkhuizen L. Site-directed mutagenesis study of the three catalytic residues of the fructosyltransferases of Lactobacillus reuteri 121. FEBS Letters, 2004, 560(1/3):131-133.
    [24] Kim YM, Kiso Y, Muraki T, Kang MS, Nakai H, Saburi W, Lang W, Kang HK, Okuyama M, Mori H, Suzuki R, Funane K, Suzuki N, Momma M, Fujimoto Z, Oguma T, Kobayashi M, Kim D, Kimura A. Novel dextranase catalyzing ycloisomaltooligosaccharide formation and identification of catalytic amino acids and their functions using chemical rescue approach. Journal of Biological Chemistry, 2012, 287(24):19927-19935.
    [25] Sützl L, Laurent CVFP, Abrera AT, Schütz G, Ludwig R, Haltrich D. Multiplicity of enzymatic functions in the CAZy AA3 family. Applied Microbiology and Biotechnology, 2018, 102(6):2477-2492.
    [26] Su MSW, Oh PL, Walter J, Gänzle MG. Intestinal origin of sourdough Lactobacillus reuteri isolates as revealed by phylogenetic, genetic, and physiological analysis. Applied and Environmental Microbiology, 2012, 78(18):6777-6780.
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安晓娜,李伟程,于洁,潘琳,莫蓝馨,姚彩青,张和平. 比较基因组学分析不同来源罗伊氏乳杆菌基因多样性及生境适应性[J]. 微生物学报, 2020, 60(5): 875-886

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  • 收稿日期:2019-07-31
  • 最后修改日期:2019-09-20
  • 在线发布日期: 2020-05-11
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