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《工程(英文)》 >> 2022年 第16卷 第9期 doi: 10.1016/j.eng.2021.03.028

结直肠癌黏膜组织来源的大肠杆菌菌株间遗传和功能差异研究

a State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
b Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
c Guangdong Provincial Key Laboratory of Gastroenterology, Institute of Gastroenterology of Guangdong Province, &Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
d Shenzhen Center for Disease Control and Prevention, Shenzhen 518055, China

# These authors contributed equally to this work.

收稿日期: 2020-10-09 修回日期: 2021-02-11 录用日期: 2021-03-16 发布日期: 2021-09-30

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摘要

结直肠癌是全球第三大癌症。宏基因组学已被广泛用于基于细菌属或种水平的比较来分析肠道微生物群与结直肠癌之间的关系,为结直肠癌发展中的生态失调提供了证据。然而,这种分析并不能为我们提供菌株水平的信息,进而理解一种细菌在结直肠癌发生发展中菌株水平的作用。本文利用培养组学方法分离结直肠癌黏膜样本,并选择了158株大肠杆菌,通过系统发育分析和炎症诱导实验,揭示它们在基因组学和功能上的差异。基因组比较可以将这些菌株分为5个系统群。选择代表性菌株进行THP-1细胞(人白血病单核细胞)Transwell实验以及动物实验,结果显示不同菌株经刺激后,细胞因子水平有显著性差异。进一步的生物信息学分析揭示了不同系统群间单核苷酸多态性、基因和代谢途径的不同特征,这些结果有助于了解这些菌株之间的表型差异。细菌菌株在基因组学和功能上的差异表明,菌株水平上的功能差异可以进一步了解宿主与肠道细菌的相互作用机制。

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参考文献

[ 1 ] Louis P, Hold GL, Flint HJ. The gut microbiota, bacterial metabolites and colorectal cancer. Nat Rev Microbiol 2014;12(10):661‒72. 链接1

[ 2 ] Peters BA, Dominianni C, Shapiro JA, Church TR, Wu J, Miller G, et al. The gut microbiota in conventional and serrated precursors of colorectal cancer. Microbiome 2016;4(1):69. 链接1

[ 3 ] Sun J, Kato I. Gut microbiota, inflammation and colorectal cancer. Genes Dis 2016;3(2):130‒43. 链接1

[ 4 ] Yu J, Feng Q, Wong SH, Zhang D, Liang QY, Qin Y, et al. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut 2017;66(1):70‒8. 链接1

[ 5 ] Yang Y, Weng W, Peng J, Hong L, Yang L, Toiyama Y, et al. Fusobacterium nucleatum increases proliferation of colorectal cancer cells and tumor development in mice by activating Toll-like receptor 4 signaling to nuclear factor-‍κB, and up-regulating expression of microRNA-21. Gastroenterology 2017;152(4):851‒66.e24. 链接1

[ 6 ] Long X, Wong CC, Tong L, Chu ESH, Ho Szeto C, Go MYY, et al. Peptostreptococcus anaerobius promotes colorectal carcinogenesis and modulates tumour immunity. Nat Microbiol 2019;4(12):2319‒30. 链接1

[ 7 ] Barboza M, Sela DA, Pirim C, LoCascio RG, Freeman SL, German JB, et al. Glycoprofiling bifidobacterial consumption of galacto-oligosaccharides by mass spectrometry reveals strain-specific, preferential consumption of glycans. Appl Environ Microbiol 2009;75(23):7319‒25. 链接1

[ 8 ] Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJM, Garcia-Gil LJ, Flint HJ. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl Environ Microbiol 2012;78(2):420‒8. 链接1

[ 9 ] Wilson ID, Nicholson JK. Gut microbiome interactions with drug metabolism, efficacy, and toxicity. Transl Res 2017;179:204‒22. 链接1

[10] Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Hall AB, et al. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature 2017;550(7674):61‒6. 链接1

[11] Scholz M, Ward DV, Pasolli E, Tolio T, Zolfo M, Asnicar F, et al. Strain-level microbial epidemiology and population genomics from shotgun metagenomics. Nat Methods 2016;13(5):435‒8. 链接1

[12] Lagier JC, Hugon P, Khelaifia S, Fournier PE, La Scola B, Raoult D. The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota. Clin Microbiol Rev 2015;28(1):237‒64. 链接1

[13] Sorbara MT, Littmann ER, Fontana E, Moody TU, Kohout CE, Gjonbalaj M, et al. Functional and genomic variation between human-derived isolates of Lachnospiraceae reveals inter- and intra-species diversity. Cell Host Microbe 2020;28(1):134‒46.e4. 链接1

[14] Allali I, Delgado S, Marron PI, Astudillo A, Yeh JJ, Ghazal H, et al. Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain. Gut Microbes 2015;6(3):161‒72. 链接1

[15] Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WKK, et al. Gut mucosal microbiome across stages of colorectal carcinogenesis. Nat Commun 2015;6(1):8727. 链接1

[16] Ingala MR, Simmons NB, Wultsch C, Krampis K, Speer KA, Perkins SL. Comparing microbiome sampling methods in a wild mammal: fecal and intestinal samples record different signals of host ecology, evolution. Front Microbiol 2018;9:803. 链接1

[17] Didelot X, Falush D. Inference of bacterial microevolution using multilocus sequence data. Genetics 2007;175(3):1251‒66. 链接1

[18] Jaureguy F, Landraud L, Passet V, Diancourt L, Frapy E, Guigon G, et al. Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics 2008;9(1):560. 链接1

[19] Schuijt TJ, Lankelma JM, Scicluna BP, de Sousa e Melo F, Roelofs JJTH, de Boer JD, et al. The gut microbiota plays a protective role in the host defence against pneumococcal pneumonia. Gut 2016;65(4):575‒83. 链接1

[20] Tenaillon O, Skurnik D, Picard B, Denamur E. The population genetics of commensal Escherichia coli. Nat Rev Microbiol 2010;8(3):207‒17. 链接1

[21] Caugant DA, Levin BR, Selander RK. Genetic diversity and temporal variation in the E. coli population of a human host. Genetics 1981;98 (3):467‒90. 链接1

[22] Bian Y, Du Y, Wang R, Chen N, Du X, Wang Y, et al. A comparative study of HAMSCs/HBMSCs transwell and mixed coculture systems. IUBMB Life 2019;71(7):1048‒55.

[23] Croxen MA, Law RJ, Scholz R, Keeney KM, Wlodarska M, Finlay BB. Recent advances in understanding enteric pathogenic Escherichia coli. Clin Microbiol Rev 2013;26(4):822‒80. 链接1

[24] Micenková L, Bosák J, Vrba M, Ševčíková A, Šmajs D. Human extraintestinal pathogenic Escherichia coli strains differ in prevalence of virulence factors, phylogroups, and bacteriocin determinants. BMC Microbiol 2016;16(1):218. 链接1

[25] Lindstedt BA, Finton MD, Porcellato D, Brandal LT. High frequency of hybrid Escherichia coli strains with combined Intestinal Pathogenic Escherichia coli (IPEC) and Extraintestinal Pathogenic Escherichia coli (ExPEC) virulence factors isolated from human faecal samples. BMC Infect Dis 2018;18(1):544. 链接1

[26] Raisch J, Buc E, Bonnet M, Sauvanet P, Vazeille E, de Vallée A, et al. Colon cancer-associated B2 Escherichia coli colonize gut mucosa and promote cell proliferation. World J Gastroenterol 2014;20(21):6560‒72. 链接1

[27] Martinez-Medina M, Garcia-Gil LJ. Escherichia coli in chronic inflammatory bowel diseases: an update on adherent invasive Escherichia coli pathogenicity. World J Gastrointest Pathophysiol 2014;5(3):213‒27. 链接1

[28] Camprubí-Font C, Ewers C, Lopez-Siles M, Martinez-Medina M. Genetic and phenotypic features to screen for putative adherent-invasive Escherichia coli. Front Microbiol 2019;10:108. 链接1

[29] Prorok-Hamon M, Friswell MK, Alswied A, Roberts CL, Song F, Flanagan PK, et al. Colonic mucosa-associated diffusely adherent afaC+ Escherichia coli expressing lpfA and pks are increased in inflammatory bowel disease and colon cancer. Gut 2014;63(5):761‒70. 链接1

[30] Suresh A, Ranjan A, Jadhav S, Hussain A, Shaik S, Alam M, et al. Molecular genetic and functional analysis of pks-harboring, extra-intestinal pathogenic Escherichia coli from India. Front Microbiol 2018;9:2631. 链接1

[31] Nougayrède JP, Homburg S, Taieb F, Boury M, Brzuszkiewicz E, Gottschalk G, et al. Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 2006;313(5788):848‒51. 链接1

[32] Gur C, Ibrahim Y, Isaacson B, Yamin R, Abed J, Gamliel M, et al. Binding of the Fap2 protein of Fusobacterium nucleatum to human inhibitory receptor TIGIT protects tumors from immune cell attack. Immunity 2015;42(2):344‒55. 链接1

[33] Kantele A, Lääveri T, Mero S, Häkkinen IMK, Kirveskari J, Johnston BD, et al. Despite predominance of uropathogenic/extraintestinal pathotypes among travel-acquired extended-spectrum β-lactamase-producing Escherichia coli, the most commonly associated clinical manifestation is travelers’ diarrhea. Clin Infect Dis 2020;70(2):210‒8. 链接1

[34] Terlizzi ME, Gribaudo G, Maffei ME. UroPathogenic Escherichia coli (UPEC) infections: virulence factors, bladder responses, antibiotic, and non-antibiotic antimicrobial strategies. Front Microbiol 2017;8:1566. 链接1

[35] Wijetunge DSS, Gongati S, DebRoy C, Kim KS, Couraud PO, Romero IA, et al. Characterizing the pathotype of neonatal meningitis causing Escherichia coli (NMEC). BMC Microbiol 2015;15(1):211. 链接1

[36] Tyakht AV, Manolov AI, Kanygina AV, Ischenko DS, Kovarsky BA, Popenko AS, et al. Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses. BMC Genomics 2018;19(1):968. 链接1

[37] Chang PH, Pan YP, Fan CW, Tseng WK, Huang JS, Wu TH, et al. Pretreatment serum interleukin-1β, interleukin-6, and tumor necrosis factor-α levels predict the progression of colorectal cancer. Cancer Med 2016;5(3):426‒33. 链接1

[38] Ray AL, Berggren KL, Restrepo Cruz S, Gan GN, Beswick EJ. Inhibition of MK2 suppresses IL-1β, IL-6, and TNF-α-dependent colorectal cancer growth. Int J Cancer 2018;142(8):1702‒11. 链接1

[39] Spurbeck RR, Dinh PC, Walk ST, Stapleton AE, Hooton TM, Nolan LK, et al. Escherichia coli isolates that carry vat, fyuA, chuA, and yfcV efficiently colonize the urinary tract. Infect Immun 2012;80(12):4115‒22. 链接1

[40] Rolhion N, Barnich N, Claret L, Darfeuille-Michaud A. Strong decrease in invasive ability and outer membrane vesicle release in Crohn’s diseaseassociated adherent-invasive Escherichia coli strain LF82 with the yfgL gene deleted. J Bacteriol 2005;187(7):2286‒96. 链接1

[41] Alp D, Kuleaşan H, Korkut Altıntaş A. The importance of the S-layer on the adhesion and aggregation ability of lactic acid bacteria. Mol Biol Rep 2020;47(5):3449‒57. 链接1

[42] Tapader R, Bose D, Basu P, Mondal M, Mondal A, Chatterjee NS, et al. Role in proinflammatory response of YghJ, a secreted metalloprotease from neonatal septicemic Escherichia coli. Int J Med Microbiol 2016;306 (7):554‒65. 链接1

[43] Tapader R, Bose D, Dutta P, Das S, Pal A, Raffatellu M. SslE (YghJ), a cellassociated and secreted lipoprotein of neonatal septicemic Escherichia coli, induces Toll-like receptor 2-dependent macrophage activation and proinflammation through NF-κB and MAP kinase signaling. Infect Immun 2018;86(9):e00399-18. 链接1

[44] Ahern P, Faith J, Gordon J. Mining the human gut microbiota for effector strains that shape the immune system. Immunity 2014;40(6):815‒23. 链接1

[45] Bron PA, van Baarlen P, Kleerebezem M. Emerging molecular insights into the interaction between probiotics and the host intestinal mucosa. Nat Rev Microbiol 2012;10(1):66‒78. 链接1

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