Abstract
The aim of this study was to explore the gut microbiota profiles of colorectal cancer (CRC) patients and to examine the relationship between gut microbiota and other key molecular factors involved in CRC tumorigenesis. In this study, a 16S rDNA sequencing platform was used to identify possible differences in the microbiota signature between CRC and adjacent normal mucosal tissue. Differences in the microbiota composition in different anatomical colorectal tumor sites and their potential association with KRAS mutation were also explored. In this study, the number of Firmicutes and Actinobacteria decreased, while the number of Fusobacteria increased in the gut of CRC patients. In addition, at the genus level, Fusobacterium was identified as the key contributor to CRC tumorigenesis. In addition, a different distribution of gut microbiota in ascending and descending colon cancer samples was observed. Lipopolysaccharide biosynthesis-associated microbial genes were enriched in tumor tissues. Our study suggests that specific mucosa-associated microbiota signature and function are significantly changed in the gut of CRC patients, which may provide insight into the progression of CRC. These findings could also be of value in the creation of new prevention and treatment strategies for this type of cancer.
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Siegel RL, Miller KD, Jemal A (2015) Cancer statistics, 2015. CA Cancer J Clin 65(1):5–29
Chen W, Zheng R, Baade PD, Zhang S, Zeng H, Bray F, Jemal A, Yu XQ, He J (2016) Cancer statistics in China, 2015. CA Cancer J Clin 66(2):115–132
Cancer Genome Atlas Network (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature 487(7407):330–337
Bonnet M, Buc E, Sauvanet P, Darcha C, Dubois D, Pereira B, Déchelotte P, Bonnet R, Pezet D, Darfeuille-Michaud A (2014) Colonization of the human gut by E. coli and colorectal cancer risk. Clin Cancer Res 20(4):859–867
Culpepper T, Ukhanova M, Wang X, Sun Y, Mai V (2014) Associations between diet, gut microbiota and markers of CRC risk. Cancer Metab 2(Suppl 1):P45
Peters U, Bien S, Zubair N (2015) Genetic architecture of colorectal cancer. Gut 64(10):1623–1636
Hagland HR, Søreide K (2015) Cellular metabolism in colorectal carcinogenesis: influence of lifestyle, gut microbiome and metabolic pathways. Cancer Lett 356(2 Pt A):273–280
Zhu Q, Gao R, Wu W, Qin H (2013) The role of gut microbiota in the pathogenesis of colorectal cancer. Tumour Biol 34(3):1285–1300
Garrett WS (2015) Cancer and the microbiota. Science 348(6230):80–86
Flemer B, Lynch DB, Brown JM, Jeffery IB, Ryan FJ, Claesson MJ, O’Riordain M, Shanahan F, O’Toole PW (2017) Tumour-associated and non-tumour-associated microbiota in colorectal cancer. Gut 66(4):633–643
Nakatsu G, Li X, Zhou H, Sheng J, Wong SH, Wu WK, Ng SC, Tsoi H, Dong Y, Zhang N, He Y, Kang Q, Cao L, Wang K, Zhang J, Liang Q, Yu J, Sung JJ (2015) Gut mucosal microbiome across stages of colorectal carcinogenesis. Nat Commun 6:8727
Keku TO, Dulal S, Deveaux A, Jovov B, Han X (2015) The gastrointestinal microbiota and colorectal cancer. Am J Physiol Gastrointest Liver Physiol 308(5):G351–G363
Zackular JP, Baxter NT, Iverson KD, Sadler WD, Petrosino JF, Chen GY, Schloss PD (2013) The gut microbiome modulates colon tumorigenesis. MBio 4(6):e00692-13
DuPont AW, DuPont HL (2011) The intestinal microbiota and chronic disorders of the gut. Nat Rev Gastroenterol Hepatol 8(9):523–531
Morgun A, Dzutsev A, Dong X, Greer RL, Sexton DJ, Ravel J, Schuster M, Hsiao W, Matzinger P, Shulzhenko N (2015) Uncovering effects of antibiotics on the host and microbiota using transkingdom gene networks. Gut 64(11):1732–1743
Engen PA, Green SJ, Voigt RM, Forsyth CB, Keshavarzian A (2015) The gastrointestinal microbiome: alcohol effects on the composition of intestinal microbiota. Alcohol Res 37(2):223–236
Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R (2012) Diversity, stability and resilience of the human gut microbiota. Nature 489(7415):220–230
Halmos EP, Christophersen CT, Bird AR, Shepherd SJ, Gibson PR, Muir JG (2015) Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut 64(1):93–100
Sonnenburg JL, Bäckhed F (2016) Diet–microbiota interactions as moderators of human metabolism. Nature 535(7610):56–64
Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, Sonnenburg JL (2016) Diet-induced extinctions in the gut microbiota compound over generations. Nature 529(7585):212–215
Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, Almeida M, Quinquis B, Levenez F, Galleron N, Gougis S, Rizkalla S, Batto JM, Renault P; ANR MicroObes consortium, Doré J, Zucker JD, Clément K, Ehrlich SD (2013) Dietary intervention impact on gut microbial gene richness. Nature 500(7464):585–588
Yazici C, Wolf PG, Kim H, Cross TL, Vermillion K, Carroll T, Augustus GJ, Mutlu E, Tussing-Humphreys L, Braunschweig C, Xicola RM, Jung B, Llor X, Ellis NA, Gaskins HR (2017) Race-dependent association of sulfidogenic bacteria with colorectal cancer. Gut
Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AV, Larin AK, Karpova IY, Selezneva OV, Semashko TA, Ospanova EA, Babenko VV, Maev IV, Cheremushkin SV, Kucheryavyy YA, Shcherbakov PL, Grinevich VB, Efimov OI, Sas EI, Abdulkhakov RA, Abdulkhakov SR, Lyalyukova EA, Livzan MA, Vlassov VV, Sagdeev RZ, Tsukanov VV, Osipenko MF, Kozlova IV, Tkachev AV, Sergienko VI, Alexeev DG, Govorun VM (2013) Human gut microbiota community structures in urban and rural populations in Russia. Nat Commun 4:2469
Tai N, Wong FS, Wen L (2015) The role of gut microbiota in the development of type 1, type 2 diabetes mellitus and obesity. Rev Endocr Metab Disord 16(1):55–65
Tilg H, Moschen AR (2014) Microbiota and diabetes: an evolving relationship. Gut 63(9):1513–1521
Delzenne NM, Cani PD (2011) Interaction between obesity and the gut microbiota: relevance in nutrition. Annu Rev Nutr 31:15–31
Senthong V, Li XS, Hudec T, Coughlin J, Wu Y, Levison B, Wang Z, Hazen SL, Tang WH (2016) Plasma trimethylamine N-oxide, a gut microbe-generated phosphatidylcholine metabolite, is associated with atherosclerotic burden. J Am Coll Cardiol 67(22):2620–2628
O’Keefe SJ (2016) Diet, microorganisms and their metabolites, and colon cancer. Nat Rev Gastroenterol Hepatol 13(12):691–706
Tlaskalová-Hogenová H, Stěpánková R, Kozáková H, Hudcovic T, Vannucci L, Tučková L, Rossmann P, Hrnčíř T, Kverka M, Zákostelská Z, Klimešová K, Přibylová J, Bártová J, Sanchez D, Fundová P, Borovská D, Srůtková D, Zídek Z, Schwarzer M, Drastich P, Funda DP (2011) The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases. Cell Mol Immunol 8(2):110–120
Gao Z, Guo B, Gao R, Zhu Q, Qin H (2015) Microbiota disbiosis is associated with colorectal cancer. Front Microbiol 6:20
Collins D, Hogan AM, Winter DC (2011) Microbial and viral pathogens in colorectal cancer. Lancet Oncol 12(5):504–512
Sears CL, Garrett WS (2014) Microbes, microbiota, and colon cancer. Cell Host Microbe 15(3):317–328
Burnett-Hartman AN, Newcomb PA, Potter JD (2008) Infectious agents and colorectal cancer: a review of Helicobacter pylori, Streptococcus bovis, JC virus, and human papillomavirus. Cancer Epidemiol Biomarkers Prev 17(11):2970–2979
Zackular JP, Rogers MA, Ruffin MT 4th, Schloss PD (2014) The human gut microbiome as a screening tool for colorectal cancer. Cancer Prev Res (Phila) 7(11):1112–1121
Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, Goedert JJ, Hayes RB, Yang L (2013) Human gut microbiome and risk for colorectal cancer. J Natl Cancer Inst 105(24):1907–1911
Liu S, da Cunha AP, Rezende RM, Cialic R, Wei Z, Bry L, Comstock LE, Gandhi R, Weiner HL (2016) The host shapes the gut microbiota via fecal microRNA. Cell Host Microbe 19(1):32–43
Tahara T, Yamamoto E, Suzuki H, Maruyama R, Chung W, Garriga J, Jelinek J, Yamano HO, Sugai T, An B, Shureiqi I, Toyota M, Kondo Y, Estécio MR, Issa JP (2014) Fusobacterium in colonic flora and molecular features of colorectal carcinoma. Cancer Res 74(5):1311–1318
Langille MG, Zaneveld J, Caporaso JG, McDonald D, Knights D, Reyes JA, Clemente JC, Burkepile DE, Vega Thurber RL, Knight R, Beiko RG, Huttenhower C (2013) Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nat Biotechnol 31(9):814–821
Hägerstrand D, Lindh MB, Peña C, Garcia-Echeverria C, Nistér M, Hofmann F, Ostman A (2010) PI3K/PTEN/Akt pathway status affects the sensitivity of high-grade glioma cell cultures to the insulin-like growth factor-1 receptor inhibitor NVP-AEW541. Neuro Oncol 12(9):967–975
Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ (2013) The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res 41(Database issue):D64–D69
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25(16):2078–2079
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, Kondrashov AS, Sunyaev SR (2010) A method and server for predicting damaging missense mutations. Nat Methods 7(4):248–249
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20(9):1297–1303
Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38(16):e164
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29(1):308–311
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491(7422):56–65
Parsons DW, Jones S, Zhang X, Lin JC, Leary RJ, Angenendt P, Mankoo P, Carter H, Siu IM, Gallia GL, Olivi A, McLendon R, Rasheed BA, Keir S, Nikolskaya T, Nikolsky Y, Busam DA, Tekleab H, Diaz LA Jr, Hartigan J, Smith DR, Strausberg RL, Marie SK, Shinjo SM, Yan H, Riggins GJ, Bigner DD, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW (2008) An integrated genomic analysis of human glioblastoma multiforme. Science 321(5897):1807–1812
Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 31(3):213–219
Boeva V, Zinovyev A, Bleakley K, Vert JP, Janoueix-Lerosey I, Delattre O, Barillot E (2011) Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics 27(2):268–269
Boeva V, Popova T, Bleakley K, Chiche P, Cappo J, Schleiermacher G, Janoueix-Lerosey I, Delattre O, Barillot E (2012) Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics 28(3):423–425
Chen K, Wallis JW, McLellan MD, Larson DE, Kalicki JM, Pohl CS, McGrath SD, Wendl MC, Zhang Q, Locke DP, Shi X, Fulton RS, Ley TJ, Wilson RK, Ding L, Mardis ER (2009) BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods 6(9):677–681
Charlop-Powers Z, Brady SF (2015) phylogeo: an R package for geographic analysis and visualization of microbiome data. Bioinformatics 31(17):2909–2911
Rodriguez-Castaño GP, Caro-Quintero A, Reyes A, Lizcano F (2017) Advances in gut microbiome research, opening new strategies to cope with a western lifestyle. Front Genet 7:224
Rajagopala SV, Vashee S, Oldfield LM, Suzuki Y, Venter JC, Telenti A, Nelson KE (2017) The human microbiome and cancer. Cancer Prev Res (Phila) 10(4):226–234
García-Castillo V, Sanhueza E, McNerney E, Onate SA, García A (2016) Microbiota dysbiosis: a new piece in the understanding of the carcinogenesis puzzle. J Med Microbiol 65(12):1347–1362
Wang X, Yang Y, Huycke MM (2016) Microbiome-driven carcinogenesis in colorectal cancer: models and mechanisms. Free Radic Biol Med 105:3–15
Chen W, Liu F, Ling Z, Tong X, Xiang C (2012) Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer. PLoS One 7(6):e39743
Kostic AD, Chun E, Robertson L, Glickman JN, Gallini CA, Michaud M, Clancy TE, Chung DC, Lochhead P, Hold GL, El-Omar EM, Brenner D, Fuchs CS, Meyerson M, Garrett WS (2013) Fusobacterium nucleatum potentiates intestinal tumorigenesis and modulates the tumor-immune microenvironment. Cell Host Microbe 14(2):207–215
Marchesi JR, Adams DH, Fava F, Hermes GD, Hirschfield GM, Hold G, Quraishi MN, Kinross J, Smidt H, Tuohy KM, Thomas LV, Zoetendal EG, Hart A (2016) The gut microbiota and host health: a new clinical frontier. Gut 65(2):330–339
Bachrach G, Ianculovici C, Naor R, Weiss EI (2005) Fluorescence based measurements of Fusobacterium nucleatum coaggregation and of fusobacterial attachment to mammalian cells. FEMS Microbiol Lett 248(2):235–240
Han YW, Shi W, Huang GT, Kinder Haake S, Park NH, Kuramitsu H, Genco RJ (2000) Interactions between periodontal bacteria and human oral epithelial cells: Fusobacterium nucleatum adheres to and invades epithelial cells. Infect Immun 68(6):3140–3146
Dharmani P, Strauss J, Ambrose C, Allen-Vercoe E, Chadee K (2011) Fusobacterium nucleatum infection of colonic cells stimulates MUC2 mucin and tumor necrosis factor alpha. Infect Immun 79(7):2597–2607
Abed J, Emgård JE, Zamir G, Faroja M, Almogy G, Grenov A, Sol A, Naor R, Pikarsky E, Atlan KA, Mellul A, Chaushu S, Manson AL, Earl AM, Ou N, Brennan CA, Garrett WS, Bachrach G (2016) Fap2 mediates Fusobacterium nucleatum colorectal adenocarcinoma enrichment by binding to tumor-expressed gal-GalNAc. Cell Host Microbe 20(2):215–225
Rubinstein MR, Wang X, Liu W, Hao Y, Cai G, Han YW (2013) Fusobacterium nucleatum promotes colorectal carcinogenesis by modulating E-cadherin/beta-catenin signaling via its FadA adhesin. Cell Host Microbe 14(2):195–206
Yang Y, Weng W, Peng J, Hong L, Yang L, Toiyama Y, Gao R, Liu M, Yin M, Pan C, Li H, Guo B, Zhu Q, Wei Q, Moyer MP, Wang P, Cai S, Goel A, Qin H, Ma Y (2017) Fusobacterium nucleatum increases proliferation of colorectal cancer cells and tumor development in mice by activating toll-like receptor 4 signaling to nuclear factor-kappaB, and up-regulating expression of microRNA-21. Gastroenterology 152(4):851–866.e24
Yu J, Feng Q, Wong SH, Zhang D, Liang QY, Qin Y, Tang L, Zhao H, Stenvang J, Li Y, Wang X, Xu X, Chen N, Wu WK, Al-Aama J, Nielsen HJ, Kiilerich P, Jensen BA, Yau TO, Lan Z, Jia H, Li J, Xiao L, Lam TY, Ng SC, Cheng AS, Wong VW, Chan FK, Xu X, Yang H, Madsen L, Datz C, Tilg H, Wang J, Brünner N, Kristiansen K, Arumugam M, Sung JJ, Wang J (2017) Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut 66(1):70–78
Wong SH, Kwong TN, Chow TC, Luk AK, Dai RZ, Nakatsu G, Lam TY, Zhang L, Wu JC, Chan FK, Ng SS, Wong MC, Ng SC, Wu WK, Yu J, Sung JJ (2016) Quantitation of faecal Fusobacterium improves faecal immunochemical test in detecting advanced colorectal neoplasia. Gut
Mima K, Nishihara R, Qian ZR, Cao Y, Sukawa Y, Nowak JA, Yang J, Dou R, Masugi Y, Song M, Kostic AD, Giannakis M, Bullman S, Milner DA, Baba H, Giovannucci EL, Garraway LA, Freeman GJ, Dranoff G, Garrett WS, Huttenhower C, Meyerson M, Meyerhardt JA, Chan AT, Fuchs CS, Ogino S (2016) Fusobacterium nucleatum in colorectal carcinoma tissue and patient prognosis. Gut 65(12):1973–1980
Mima K, Sukawa Y, Nishihara R, Qian ZR, Yamauchi M, Inamura K, Kim SA, Masuda A, Nowak JA, Nosho K, Kostic AD, Giannakis M, Watanabe H, Bullman S, Milner DA, Harris CC, Giovannucci E, Garraway LA, Freeman GJ, Dranoff G, Chan AT, Garrett WS, Huttenhower C, Fuchs CS, Ogino S (2015) Fusobacterium nucleatum and T cells in colorectal carcinoma. JAMA Oncol 1(5):653–661
Bourgault AM, Rosenblatt JE, Fitzgerald RH (1980) Peptococcus magnus: a significant human pathogen. Ann Intern Med 93(2):244–248
Brook I (1994) Peptostreptococcal infection in children. Scand J Infect Dis 26(5):503–510
Tsoi H, Chu ESH, Zhang X, Sheng J, Nakatsu G, Ng SC, Chan AWH, Chan FKL, Sung JJY, Yu J (2017) Peptostreptococcus anaerobius induces intracellular cholesterol biosynthesis in colon cells to induce proliferation and causes dysplasia in mice. Gastroenterology 152(6):1419–1433.e5
Lee MS, Menter DG, Kopetz S (2017) Right versus left colon cancer biology: integrating the consensus molecular subtypes. J Natl Compr Canc Netw 15(3):411–419
Ishihara S, Murono K, Sasaki K, Yasuda K, Otani K, Nishikawa T, Tanaka T, Kiyomatsu T, Kawai K, Hata K, Nozawa H, Sugihara K, Watanabe T (2017) Impact of primary tumor location on postoperative recurrence and subsequent prognosis in nonmetastatic colon cancers: a multicenter retrospective study using a propensity score analysis. Ann Surg
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We thank Majorbio Biological Technology Co., Ltd. for the technical assistance in the study.
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RG, CK, and HL wrote the manuscript; RG, CK, and LH collected the clinical data; RG and ZL provided the samples; RG, HL, XQ, and ZL analyzed the data. PL, JW, and HQ designed and supervised the study.
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This work was supported by grants from the National Natural Science Foundation of China (nos. 81230057, 81200264, 81372615 and 81472262) and Emerging Cutting-Edge Technology Joint Research projects of Shanghai (no. SHDC12012106). Tongji University Subject Pilot Program (no.162385).
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This study has been approved by the ethical committees of Shanghai Tenth People’s Hospital. and the Sixth Affiliated Hospital, Sun Yat-sen University.
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Gao, R., Kong, C., Huang, L. et al. Mucosa-associated microbiota signature in colorectal cancer. Eur J Clin Microbiol Infect Dis 36, 2073–2083 (2017). https://doi.org/10.1007/s10096-017-3026-4
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DOI: https://doi.org/10.1007/s10096-017-3026-4