TY - JOUR AU - Sender, R. AU - Fuchs, S. AU - Milo, R. PY - 2016 DA - 2016// TI - Revised estimates for the number of human and bacteria cells in the body JO - PLoS Biol VL - 14 UR - https://doi.org/10.1371/journal.pbio.1002533 DO - 10.1371/journal.pbio.1002533 ID - Sender2016 ER - TY - JOUR AU - Li, J. AU - Jia, H. AU - Cai, X. AU - Zhong, H. AU - Feng, Q. AU - Sunagawa, S. PY - 2014 DA - 2014// TI - An integrated catalog of reference genes in the human gut microbiome JO - Nat Biotechnol VL - 32 UR - https://doi.org/10.1038/nbt.2942 DO - 10.1038/nbt.2942 ID - Li2014 ER - TY - JOUR AU - Dominguez-Bello, M. G. AU - Godoy-Vitorino, F. AU - Knight, R. AU - Blaser, M. J. PY - 2019 DA - 2019// TI - Role of the microbiome in human development JO - Gut. VL - 68 UR - https://doi.org/10.1136/gutjnl-2018-317503 DO - 10.1136/gutjnl-2018-317503 ID - Dominguez-Bello2019 ER - TY - JOUR AU - Kennedy, E. A. AU - King, K. Y. AU - Baldridge, M. T. PY - 2018 DA - 2018// TI - Mouse microbiota models: comparing germ-free mice and antibiotics treatment as tools for modifying gut bacteria JO - Front Physiol VL - 9 UR - https://doi.org/10.3389/fphys.2018.01534 DO - 10.3389/fphys.2018.01534 ID - Kennedy2018 ER - TY - JOUR AU - Bäckhed, F. PY - 2011 DA - 2011// TI - Programming of host metabolism by the gut microbiota JO - Ann Nutr Metab VL - 58 UR - https://doi.org/10.1159/000328042 DO - 10.1159/000328042 ID - Bäckhed2011 ER - TY - JOUR AU - Dobrijevic, D. AU - Abraham, A. -. L. AU - Jamet, A. AU - Maguin, E. AU - Guchte, M. PY - 2016 DA - 2016// TI - Functional comparison of bacteria from the human gut and closely related non-gut bacteria reveals the importance of conjugation and a paucity of motility and chemotaxis functions in the gut environment JO - PLoS One VL - 11 UR - https://doi.org/10.1371/journal.pone.0159030 DO - 10.1371/journal.pone.0159030 ID - Dobrijevic2016 ER - TY - JOUR AU - Björkholm, B. AU - Bok, C. M. AU - Lundin, A. AU - Rafter, J. AU - Hibberd, M. L. AU - Pettersson, S. PY - 2009 DA - 2009// TI - Intestinal microbiota regulate xenobiotic metabolism in the liver JO - PLoS One VL - 4 UR - https://doi.org/10.1371/journal.pone.0006958 DO - 10.1371/journal.pone.0006958 ID - Björkholm2009 ER - TY - JOUR AU - Coryell, M. AU - McAlpine, M. AU - Pinkham, N. V. AU - McDermott, T. R. AU - Walk, S. T. PY - 2018 DA - 2018// TI - The gut microbiome is required for full protection against acute arsenic toxicity in mouse models JO - Nat Commun VL - 9 UR - https://doi.org/10.1038/s41467-018-07803-9 DO - 10.1038/s41467-018-07803-9 ID - Coryell2018 ER - TY - JOUR AU - Selwyn, F. P. AU - Cheng, S. L. AU - Bammler, T. K. AU - Prasad, B. AU - Vrana, M. AU - Klaassen, C. PY - 2015 DA - 2015// TI - Developmental regulation of drug-processing genes in livers of germ-free mice JO - Toxicol Sci VL - 147 UR - https://doi.org/10.1093/toxsci/kfv110 DO - 10.1093/toxsci/kfv110 ID - Selwyn2015 ER - TY - JOUR PY - 2012 DA - 2012// TI - Structure, function and diversity of the healthy human microbiome JO - Nature. VL - 486 UR - https://doi.org/10.1038/nature11234 DO - 10.1038/nature11234 ID - ref10 ER - TY - JOUR AU - Weiss, G. A. AU - Hennet, T. PY - 2017 DA - 2017// TI - Mechanisms and consequences of intestinal dysbiosis JO - Cell Mol Life Sci VL - 74 UR - https://doi.org/10.1007/s00018-017-2509-x DO - 10.1007/s00018-017-2509-x ID - Weiss2017 ER - TY - JOUR AU - Gensollen, T. AU - Iyer, S. S. AU - Kasper, D. L. AU - Blumberg, R. S. PY - 2016 DA - 2016// TI - How colonization by microbiota in early life shapes the immune system JO - Science. VL - 352 UR - https://doi.org/10.1126/science.aad9378 DO - 10.1126/science.aad9378 ID - Gensollen2016 ER - TY - JOUR AU - Thursby, E. AU - Juge, N. PY - 2017 DA - 2017// TI - Introduction to the human gut microbiota JO - Biochem J VL - 474 UR - https://doi.org/10.1042/BCJ20160510 DO - 10.1042/BCJ20160510 ID - Thursby2017 ER - TY - JOUR AU - Sinha, R. AU - Abu-Ali, G. AU - Vogtmann, E. AU - Fodor, A. A. AU - Ren, B. AU - Amir, A. PY - 2017 DA - 2017// TI - Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium JO - Nat Biotechnol VL - 35 UR - https://doi.org/10.1038/nbt.3981 DO - 10.1038/nbt.3981 ID - Sinha2017 ER - TY - JOUR AU - Costea, P. I. AU - Zeller, G. AU - Sunagawa, S. AU - Pelletier, E. AU - Alberti, A. AU - Levenez, F. PY - 2017 DA - 2017// TI - Towards standards for human fecal sample processing in metagenomic studies JO - Nat Biotechnol VL - 35 UR - https://doi.org/10.1038/nbt.3960 DO - 10.1038/nbt.3960 ID - Costea2017 ER - TY - JOUR AU - Greathouse, K. L. AU - Sinha, R. AU - Vogtmann, E. PY - 2019 DA - 2019// TI - DNA extraction for human microbiome studies: the issue of standardization JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1843-8 DO - 10.1186/s13059-019-1843-8 ID - Greathouse2019 ER - TY - JOUR AU - Debelius, J. AU - Song, S. J. AU - Vazquez-Baeza, Y. AU - Xu, Z. Z. AU - Gonzalez, A. AU - Knight, R. PY - 2016 DA - 2016// TI - Tiny microbes, enormous impacts: what matters in gut microbiome studies? JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-1086-x DO - 10.1186/s13059-016-1086-x ID - Debelius2016 ER - TY - JOUR AU - Mallick, H. AU - Ma, S. AU - Franzosa, E. A. AU - Vatanen, T. AU - Morgan, X. C. AU - Huttenhower, C. PY - 2017 DA - 2017// TI - Experimental design and quantitative analysis of microbial community multiomics JO - Genome Biol VL - 18 UR - https://doi.org/10.1186/s13059-017-1359-z DO - 10.1186/s13059-017-1359-z ID - Mallick2017 ER - TY - JOUR AU - Parkin, D. M. PY - 2006 DA - 2006// TI - The global health burden of infection-associated cancers in the year 2002 JO - Int J Cancer VL - 118 UR - https://doi.org/10.1002/ijc.21731 DO - 10.1002/ijc.21731 ID - Parkin2006 ER - TY - JOUR AU - Warren, J. R. PY - 2000 DA - 2000// TI - Gastric pathology associated with Helicobacter pylori JO - Gastroenterol Clin N Am VL - 29 UR - https://doi.org/10.1016/S0889-8553(05)70139-4 DO - 10.1016/S0889-8553(05)70139-4 ID - Warren2000 ER - TY - JOUR AU - Fox, J. G. AU - Wang, T. C. PY - 2007 DA - 2007// TI - Inflammation, atrophy, and gastric cancer JO - J Clin Invest VL - 117 UR - https://doi.org/10.1172/JCI30111 DO - 10.1172/JCI30111 ID - Fox2007 ER - TY - JOUR AU - Karimi, P. AU - Islami, F. AU - Anandasabapathy, S. AU - Freedman, N. D. AU - Kamangar, F. PY - 2014 DA - 2014// TI - Gastric cancer: descriptive epidemiology, risk factors, screening, and prevention JO - Cancer Epidemiol Biomark Prev VL - 23 UR - https://doi.org/10.1158/1055-9965.EPI-13-1057 DO - 10.1158/1055-9965.EPI-13-1057 ID - Karimi2014 ER - TY - JOUR AU - Chen, J. AU - Domingue, J. C. AU - Sears, C. L. PY - 2017 DA - 2017// TI - Microbiota dysbiosis in select human cancers: evidence of association and causality JO - Semin Immunol VL - 32 UR - https://doi.org/10.1016/j.smim.2017.08.001 DO - 10.1016/j.smim.2017.08.001 ID - Chen2017 ER - TY - JOUR AU - Polyzos, S. A. AU - Zeglinas, C. AU - Artemaki, F. AU - Doulberis, M. AU - Kazakos, E. AU - Katsinelos, P. PY - 2018 DA - 2018// TI - Helicobacter pylori infection and esophageal adenocarcinoma: a review and a personal view JO - Ann Gastroenterol Hepatol VL - 31 ID - Polyzos2018 ER - TY - JOUR AU - Wang, Z. AU - Shaheen, N. J. AU - Whiteman, D. C. AU - Anderson, L. A. AU - Vaughan, T. L. AU - Corley, D. A. PY - 2018 DA - 2018// TI - Helicobacter pylori infection is associated with reduced risk of Barrett’s esophagus: an analysis of the Barrett’s and Esophageal Adenocarcinoma Consortium JO - Am J Gastroenterol VL - 113 UR - https://doi.org/10.1038/s41395-018-0070-3 DO - 10.1038/s41395-018-0070-3 ID - Wang2018 ER - TY - JOUR AU - Prakash, O. AU - Bardot, S. F. AU - Cole, J. T. PY - 2007 DA - 2007// TI - Chicken sarcoma to human cancers: a lesson in molecular therapeutics JO - Ochsner J VL - 7 ID - Prakash2007 ER - TY - JOUR AU - Harden, M. E. AU - Munger, K. PY - 2017 DA - 2017// TI - Human papillomavirus molecular biology JO - Mutat Res - Rev Mut Res VL - 772 UR - https://doi.org/10.1016/j.mrrev.2016.07.002 DO - 10.1016/j.mrrev.2016.07.002 ID - Harden2017 ER - TY - STD TI - Hau PM, Tsao SW. Epstein-Barr virus hijacks DNA damage response transducers to orchestrate its life cycle. Viruses. 2017;9. Available from: https://doi.org/10.3390/v9110341. ID - ref28 ER - TY - JOUR AU - Amarante, M. K. AU - Sousa, P. N. AU - Vitiello, G. A. F. AU - Watanabe, M. A. E. PY - 2019 DA - 2019// TI - Involvement of a mouse mammary tumor virus (MMTV) homologue in human breast cancer: evidence for, against and possible causes of controversies JO - Microb Pathog VL - 130 UR - https://doi.org/10.1016/j.micpath.2019.03.021 DO - 10.1016/j.micpath.2019.03.021 ID - Amarante2019 ER - TY - JOUR AU - Geller, L. T. AU - Barzily-Rokni, M. AU - Danino, T. AU - Jonas, O. H. AU - Shental, N. AU - Nejman, D. PY - 2017 DA - 2017// TI - Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine JO - Science. VL - 357 UR - https://doi.org/10.1126/science.aah5043 DO - 10.1126/science.aah5043 ID - Geller2017 ER - TY - JOUR AU - Lehouritis, P. AU - Cummins, J. AU - Stanton, M. AU - Murphy, C. T. AU - McCarthy, F. O. AU - Reid, G. PY - 2015 DA - 2015// TI - Local bacteria affect the efficacy of chemotherapeutic drugs JO - Sci Rep VL - 5 UR - https://doi.org/10.1038/srep14554 DO - 10.1038/srep14554 ID - Lehouritis2015 ER - TY - JOUR AU - Gopalakrishnan, V. AU - Spencer, C. N. AU - Nezi, L. AU - Reuben, A. AU - Andrews, M. C. AU - Karpinets, T. V. PY - 2018 DA - 2018// TI - Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients JO - Science. VL - 359 UR - https://doi.org/10.1126/science.aan4236 DO - 10.1126/science.aan4236 ID - Gopalakrishnan2018 ER - TY - STD TI - Kwa M, Plottel CS, Blaser MJ, Adams S. The intestinal microbiome and estrogen receptor-positive female breast cancer. J Natl Cancer Inst. 2016;108. Available from: https://doi.org/10.1093/jnci/djw029. ID - ref33 ER - TY - JOUR AU - Yang, J. AU - Tan, Q. AU - Fu, Q. AU - Zhou, Y. AU - Hu, Y. AU - Tang, S. PY - 2017 DA - 2017// TI - Gastrointestinal microbiome and breast cancer: correlations, mechanisms and potential clinical implications JO - Breast Cancer VL - 24 UR - https://doi.org/10.1007/s12282-016-0734-z DO - 10.1007/s12282-016-0734-z ID - Yang2017 ER - TY - JOUR AU - Dubin, K. AU - Callahan, M. K. AU - Ren, B. AU - Khanin, R. AU - Viale, A. AU - Ling, L. PY - 2016 DA - 2016// TI - Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms10391 DO - 10.1038/ncomms10391 ID - Dubin2016 ER - TY - JOUR AU - Frankel, A. E. AU - Coughlin, L. A. AU - Kim, J. AU - Froehlich, T. W. AU - Xie, Y. AU - Frenkel, E. P. PY - 2017 DA - 2017// TI - Metagenomic shotgun sequencing and unbiased metabolomic profiling identify specific human gut microbiota and metabolites associated with immune checkpoint therapy efficacy in melanoma patients JO - Neoplasia. VL - 19 UR - https://doi.org/10.1016/j.neo.2017.08.004 DO - 10.1016/j.neo.2017.08.004 ID - Frankel2017 ER - TY - JOUR AU - Cavarretta, I. AU - Ferrarese, R. AU - Cazzaniga, W. AU - Saita, D. AU - Lucianò, R. AU - Ceresola, E. R. PY - 2017 DA - 2017// TI - The microbiome of the prostate tumor microenvironment JO - Eur Urol VL - 72 UR - https://doi.org/10.1016/j.eururo.2017.03.029 DO - 10.1016/j.eururo.2017.03.029 ID - Cavarretta2017 ER - TY - JOUR AU - Banerjee, S. AU - Alwine, J. C. AU - Wei, Z. AU - Tian, T. AU - Shih, N. AU - Sperling, C. PY - 2019 DA - 2019// TI - Microbiome signatures in prostate cancer JO - Carcinogenesis. VL - 40 UR - https://doi.org/10.1093/carcin/bgz008 DO - 10.1093/carcin/bgz008 ID - Banerjee2019 ER - TY - JOUR AU - Urbaniak, C. AU - Gloor, G. B. AU - Brackstone, M. AU - Scott, L. AU - Tangney, M. AU - Reid, G. PY - 2016 DA - 2016// TI - The microbiota of breast tissue and its association with breast cancer JO - Appl Environ Microbiol VL - 82 UR - https://doi.org/10.1128/AEM.01235-16 DO - 10.1128/AEM.01235-16 ID - Urbaniak2016 ER - TY - JOUR AU - Hieken, T. J. AU - Chen, J. AU - Hoskin, T. L. AU - Walther-Antonio, M. AU - Johnson, S. AU - Ramaker, S. PY - 2016 DA - 2016// TI - The microbiome of aseptically collected human breast tissue in benign and malignant disease JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep30751 DO - 10.1038/srep30751 ID - Hieken2016 ER - TY - JOUR AU - Cicinelli, E. AU - Ziegler, D. AU - Nicoletti, R. AU - Colafiglio, G. AU - Saliani, N. AU - Resta, L. PY - 2008 DA - 2008// TI - Chronic endometritis: correlation among hysteroscopic, histologic, and bacteriologic findings in a prospective trial with 2190 consecutive office hysteroscopies JO - Fertil Steril VL - 89 UR - https://doi.org/10.1016/j.fertnstert.2007.03.074 DO - 10.1016/j.fertnstert.2007.03.074 ID - Cicinelli2008 ER - TY - JOUR AU - Walther-António, M. R. S. AU - Chen, J. AU - Multinu, F. AU - Hokenstad, A. AU - Distad, T. J. AU - Cheek, E. H. PY - 2016 DA - 2016// TI - Potential contribution of the uterine microbiome in the development of endometrial cancer JO - Genome Med. VL - 8 UR - https://doi.org/10.1186/s13073-016-0368-y DO - 10.1186/s13073-016-0368-y ID - Walther-António2016 ER - TY - JOUR AU - Wu, P. AU - Zhang, G. AU - Zhao, J. AU - Chen, J. AU - Chen, Y. AU - Huang, W. PY - 2018 DA - 2018// TI - Profiling the urinary microbiota in male patients with bladder cancer in China JO - Front Cell Infect Microbiol VL - 8 UR - https://doi.org/10.3389/fcimb.2018.00167 DO - 10.3389/fcimb.2018.00167 ID - Wu2018 ER - TY - JOUR AU - Bajic, P. AU - Wolfe, A. J. AU - Gupta, G. N. PY - 2019 DA - 2019// TI - The urinary microbiome: implications in bladder cancer pathogenesis and therapeutics JO - Urology. VL - 126 UR - https://doi.org/10.1016/j.urology.2018.12.034 DO - 10.1016/j.urology.2018.12.034 ID - Bajic2019 ER - TY - JOUR AU - Bučević Popović, V. AU - Šitum, M. AU - Chow, C. -. E. T. AU - Chan, L. S. AU - Roje, B. AU - Terzić, J. PY - 2018 DA - 2018// TI - The urinary microbiome associated with bladder cancer JO - Sci Rep VL - 8 UR - https://doi.org/10.1038/s41598-018-29054-w DO - 10.1038/s41598-018-29054-w ID - Bučević Popović2018 ER - TY - JOUR AU - Pushalkar, S. AU - Hundeyin, M. AU - Daley, D. AU - Zambirinis, C. P. AU - Kurz, E. AU - Mishra, A. PY - 2018 DA - 2018// TI - The pancreatic cancer microbiome promotes oncogenesis by induction of innate and adaptive immune suppression JO - Cancer Discov VL - 8 UR - https://doi.org/10.1158/2159-8290.CD-17-1134 DO - 10.1158/2159-8290.CD-17-1134 ID - Pushalkar2018 ER - TY - JOUR AU - Riquelme, E. AU - Zhang, Y. AU - Zhang, L. AU - Montiel, M. AU - Zoltan, M. AU - Dong, W. PY - 2019 DA - 2019// TI - Tumor microbiome diversity and composition influence pancreatic cancer outcomes JO - Cell VL - 178 UR - https://doi.org/10.1016/j.cell.2019.07.008 DO - 10.1016/j.cell.2019.07.008 ID - Riquelme2019 ER - TY - JOUR AU - Malmgren, R. A. AU - Flanigan, C. C. PY - 1955 DA - 1955// TI - Localization of the vegetative form of Clostridium tetani in mouse tumors following intravenous spore administration JO - Cancer Res VL - 15 ID - Malmgren1955 ER - TY - JOUR AU - Wouters, B. G. AU - Koritzinsky, M. AU - Chiu, R. K. AU - Theys, J. AU - Buijsen, J. AU - Lambin, P. PY - 2003 DA - 2003// TI - Modulation of cell death in the tumor microenvironment JO - Semin Radiat Oncol VL - 13 UR - https://doi.org/10.1053/srao.2003.50004 DO - 10.1053/srao.2003.50004 ID - Wouters2003 ER - TY - JOUR AU - Zu, C. AU - Wang, J. PY - 2014 DA - 2014// TI - Tumor-colonizing bacteria: a potential tumor targeting therapy JO - Crit Rev Microbiol VL - 40 UR - https://doi.org/10.3109/1040841X.2013.776511 DO - 10.3109/1040841X.2013.776511 ID - Zu2014 ER - TY - JOUR AU - Bashiardes, S. AU - Tuganbaev, T. AU - Federici, S. AU - Elinav, E. PY - 2017 DA - 2017// TI - The microbiome in anti-cancer therapy JO - Semin Immunol VL - 32 UR - https://doi.org/10.1016/j.smim.2017.04.001 DO - 10.1016/j.smim.2017.04.001 ID - Bashiardes2017 ER - TY - JOUR AU - Dang, L. H. AU - Bettegowda, C. AU - Huso, D. L. AU - Kinzler, K. W. AU - Vogelstein, B. PY - 2001 DA - 2001// TI - Combination bacteriolytic therapy for the treatment of experimental tumors JO - Proc Natl Acad Sci U S A VL - 98 UR - https://doi.org/10.1073/pnas.251543698 DO - 10.1073/pnas.251543698 ID - Dang2001 ER - TY - JOUR AU - Castellarin, M. AU - Warren, R. L. AU - Freeman, J. D. AU - Dreolini, L. AU - Krzywinski, M. AU - Strauss, J. PY - 2012 DA - 2012// TI - Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.126516.111 DO - 10.1101/gr.126516.111 ID - Castellarin2012 ER - TY - JOUR AU - Kostic, A. D. AU - Gevers, D. AU - Pedamallu, C. S. AU - Michaud, M. AU - Duke, F. AU - Earl, A. M. PY - 2012 DA - 2012// TI - Genomic analysis identifies association of fusobacterium with colorectal carcinoma JO - Genome Res VL - 22 UR - https://doi.org/10.1101/gr.126573.111 DO - 10.1101/gr.126573.111 ID - Kostic2012 ER - TY - JOUR AU - Brennan, C. A. AU - Garrett, W. S. PY - 2016 DA - 2016// TI - Gut microbiota, inflammation, and colorectal cancer JO - Annu Rev Microbiol VL - 70 UR - https://doi.org/10.1146/annurev-micro-102215-095513 DO - 10.1146/annurev-micro-102215-095513 ID - Brennan2016 ER - TY - JOUR AU - Shang, F. -. M. AU - Liu, H. -. L. PY - 2018 DA - 2018// TI - Fusobacterium nucleatum and colorectal cancer: a review JO - World J Gastrointest Oncol VL - 10 UR - https://doi.org/10.4251/wjgo.v10.i3.71 DO - 10.4251/wjgo.v10.i3.71 ID - Shang2018 ER - TY - JOUR AU - Li, S. AU - Konstantinov, S. R. AU - Smits, R. AU - Peppelenbosch, M. P. PY - 2017 DA - 2017// TI - Bacterial biofilms in colorectal cancer initiation and progression JO - Trends Mol Med VL - 23 UR - https://doi.org/10.1016/j.molmed.2016.11.004 DO - 10.1016/j.molmed.2016.11.004 ID - Li2017 ER - TY - JOUR AU - Boleij, A. AU - Hechenbleikner, E. M. AU - Goodwin, A. C. AU - Badani, R. AU - Stein, E. M. AU - Lazarev, M. G. PY - 2015 DA - 2015// TI - The Bacteroides fragilis toxin gene is prevalent in the colon mucosa of colorectal cancer patients JO - Clin Infect Dis VL - 60 UR - https://doi.org/10.1093/cid/ciu787 DO - 10.1093/cid/ciu787 ID - Boleij2015 ER - TY - JOUR AU - Keenan, J. I. AU - Aitchison, A. AU - Purcell, R. V. AU - Greenlees, R. AU - Pearson, J. F. AU - Frizelle, F. A. PY - 2016 DA - 2016// TI - Screening for enterotoxigenic Bacteroides fragilis in stool samples JO - Anaerobe. VL - 40 UR - https://doi.org/10.1016/j.anaerobe.2016.05.004 DO - 10.1016/j.anaerobe.2016.05.004 ID - Keenan2016 ER - TY - JOUR AU - Wei, M. -. Y. AU - Shi, S. AU - Liang, C. AU - Meng, Q. -. C. AU - Hua, J. AU - Zhang, Y. -. Y. PY - 2019 DA - 2019// TI - The microbiota and microbiome in pancreatic cancer: more influential than expected JO - Mol Cancer VL - 18 UR - https://doi.org/10.1186/s12943-019-1008-0 DO - 10.1186/s12943-019-1008-0 ID - Wei2019 ER - TY - JOUR AU - Wong, S. AU - Slavcev, R. A. PY - 2015 DA - 2015// TI - Treating cancer with infection: a review on bacterial cancer therapy JO - Lett Appl Microbiol VL - 61 UR - https://doi.org/10.1111/lam.12436 DO - 10.1111/lam.12436 ID - Wong2015 ER - TY - JOUR AU - Din, M. O. AU - Danino, T. AU - Prindle, A. AU - Skalak, M. AU - Selimkhanov, J. AU - Allen, K. PY - 2016 DA - 2016// TI - Synchronized cycles of bacterial lysis for in vivo delivery JO - Nature. VL - 536 UR - https://doi.org/10.1038/nature18930 DO - 10.1038/nature18930 ID - Din2016 ER - TY - JOUR AU - Martinson, J. A. AU - Tenorio, A. R. AU - Montoya, C. J. AU - Al-Harthi, L. AU - Gichinga, C. N. AU - Krieg, A. M. PY - 2007 DA - 2007// TI - Impact of class A, B and C CpG-oligodeoxynucleotides on in vitro activation of innate immune cells in human immunodeficiency virus-1 infected individuals JO - Immunology. VL - 120 UR - https://doi.org/10.1111/j.1365-2567.2007.02530.x DO - 10.1111/j.1365-2567.2007.02530.x ID - Martinson2007 ER - TY - JOUR AU - Makkouk, A. AU - Joshi, V. B. AU - Wongrakpanich, A. AU - Lemke, C. D. AU - Gross, B. P. AU - Salem, A. K. PY - 2015 DA - 2015// TI - Biodegradable microparticles loaded with doxorubicin and CpG ODN for in situ immunization against cancer JO - AAPS J VL - 17 UR - https://doi.org/10.1208/s12248-014-9676-6 DO - 10.1208/s12248-014-9676-6 ID - Makkouk2015 ER - TY - JOUR AU - Czerwinski, D. K. AU - Frank, M. J. AU - Shree, T. AU - Khodadoust, M. S. AU - Long, S. R. AU - Levy, R. PY - 2018 DA - 2018// TI - Intratumoral injection of CpG-ODN plus systemic ibrutinib induces an anti-tumor immune response affecting T cell subsets in the microenvironment of both injected and non-injected tumor sites in patients with low-grade lymphoma JO - Blood Am Soc Hematol VL - 132 ID - Czerwinski2018 ER - TY - JOUR AU - Appelbe, O. K. AU - Moynihan, K. D. AU - Flor, A. AU - Rymut, N. AU - Irvine, D. J. AU - Kron, S. J. PY - 2017 DA - 2017// TI - Radiation-enhanced delivery of systemically administered amphiphilic-CpG oligodeoxynucleotide JO - J Control Release VL - 266 UR - https://doi.org/10.1016/j.jconrel.2017.09.043 DO - 10.1016/j.jconrel.2017.09.043 ID - Appelbe2017 ER - TY - JOUR AU - Levy, R. AU - Reagan, P. M. AU - Friedberg, J. W. AU - Bartlett, N. L. AU - Gordon, L. I. AU - Leung, A. PY - 2016 DA - 2016// TI - SD-101, a novel class C CpG-oligodeoxynucleotide (ODN) Toll-like receptor 9 (TLR9) agonist, given with low dose radiation for untreated low grade B-cell lymphoma: interim results of a phase 1/2 trial JO - Blood American Society of Hematology VL - 128 ID - Levy2016 ER - TY - STD TI - Search of: CpG ODN | Recruiting, not yet recruiting, active, not recruiting, enrolling by invitation studies | Cancer - List Results - ClinicalTrials.gov. [cited 2019 Jul 11]. Available from: https://clinicaltrials.gov/ct2/results?term=CpG+ODN&cond=Cancer&recrs=b&recrs=a&recrs=f&recrs=d&age_v=&gndr=&type=&rslt=&Search=Apply. UR - https://clinicaltrials.gov/ct2/results?term=CpG+ODN&cond=Cancer&recrs=b&recrs=a&recrs=f&recrs=d&age_v=&gndr=&type=&rslt=&Search=Apply ID - ref68 ER - TY - JOUR AU - Kent, A. PY - 2011 DA - 2011// TI - Cancer screening and survival JO - Rev Obstet Gynecol VL - 4 ID - Kent2011 ER - TY - JOUR AU - Simon, K. PY - 2016 DA - 2016// TI - Colorectal cancer development and advances in screening JO - Clin Interv Aging VL - 11 UR - https://doi.org/10.2147/CIA.S109285 DO - 10.2147/CIA.S109285 ID - Simon2016 ER - TY - JOUR AU - Zackular, J. P. AU - Rogers, M. A. M. AU - Ruffin, M. T. AU - Schloss, P. D. PY - 2014 DA - 2014// TI - The human gut microbiome as a screening tool for colorectal cancer JO - Cancer Prev Res VL - 7 UR - https://doi.org/10.1158/1940-6207.CAPR-14-0129 DO - 10.1158/1940-6207.CAPR-14-0129 ID - Zackular2014 ER - TY - STD TI - Flemer B, Warren RD, Barrett MP, Cisek K, Das A, Jeffery IB, et al. The oral microbiota in colorectal cancer is distinctive and predictive. Gut. 2018;67:1454-63. ID - ref72 ER - TY - JOUR AU - Ilic, M. AU - Ilic, I. PY - 2016 DA - 2016// TI - Epidemiology of pancreatic cancer JO - World J Gastroenterol VL - 22 UR - https://doi.org/10.3748/wjg.v22.i44.9694 DO - 10.3748/wjg.v22.i44.9694 ID - Ilic2016 ER - TY - JOUR AU - Ertz-Archambault, N. AU - Keim, P. AU - Hoff, D. PY - 2017 DA - 2017// TI - Microbiome and pancreatic cancer: a comprehensive topic review of literature JO - World J Gastroenterol VL - 23 UR - https://doi.org/10.3748/wjg.v23.i10.1899 DO - 10.3748/wjg.v23.i10.1899 ID - Ertz-Archambault2017 ER - TY - JOUR AU - Zambirinis, C. P. AU - Pushalkar, S. AU - Saxena, D. AU - Miller, G. PY - 2014 DA - 2014// TI - Pancreatic cancer, inflammation, and microbiome JO - Cancer J VL - 20 UR - https://doi.org/10.1097/PPO.0000000000000045 DO - 10.1097/PPO.0000000000000045 ID - Zambirinis2014 ER - TY - JOUR AU - Vesty, A. AU - Gear, K. AU - Biswas, K. AU - Radcliff, F. J. AU - Taylor, M. W. AU - Douglas, R. G. PY - 2018 DA - 2018// TI - Microbial and inflammatory-based salivary biomarkers of head and neck squamous cell carcinoma JO - Clin Exp Dent Res VL - 4 UR - https://doi.org/10.1002/cre2.139 DO - 10.1002/cre2.139 ID - Vesty2018 ER - TY - JOUR AU - Yang, J. AU - Mu, X. AU - Wang, Y. AU - Zhu, D. AU - Zhang, J. AU - Liang, C. PY - 2018 DA - 2018// TI - Dysbiosis of the salivary microbiome is associated with non-smoking female lung cancer and correlated with immunocytochemistry markers JO - Front Oncol VL - 8 UR - https://doi.org/10.3389/fonc.2018.00520 DO - 10.3389/fonc.2018.00520 ID - Yang2018 ER - TY - JOUR AU - Golombos, D. M. AU - Ayangbesan, A. AU - O’Malley, P. AU - Lewicki, P. AU - Barlow, L. AU - Barbieri, C. E. PY - 2018 DA - 2018// TI - The role of gut microbiome in the pathogenesis of prostate cancer: a prospective JO - Pilot Study Urology VL - 111 ID - Golombos2018 ER - TY - JOUR AU - Zhang, W. -. Q. AU - Zhao, S. -. K. AU - Luo, J. -. W. AU - Dong, X. -. P. AU - Hao, Y. -. T. AU - Li, H. PY - 2018 DA - 2018// TI - Alterations of fecal bacterial communities in patients with lung cancer JO - Am J Transl Res VL - 10 ID - Zhang2018 ER - TY - JOUR AU - Ren, Z. AU - Li, A. AU - Jiang, J. AU - Zhou, L. AU - Yu, Z. AU - Lu, H. PY - 2019 DA - 2019// TI - Gut microbiome analysis as a tool towards targeted non-invasive biomarkers for early hepatocellular carcinoma JO - Gut. VL - 68 UR - https://doi.org/10.1136/gutjnl-2017-315084 DO - 10.1136/gutjnl-2017-315084 ID - Ren2019 ER - TY - JOUR AU - Amirian, E. S. AU - Petrosino, J. F. AU - Ajami, N. J. AU - Liu, Y. AU - Mims, M. P. AU - Scheurer, M. E. PY - 2013 DA - 2013// TI - Potential role of gastrointestinal microbiota composition in prostate cancer risk JO - Infect Agent Cancer VL - 8 UR - https://doi.org/10.1186/1750-9378-8-42 DO - 10.1186/1750-9378-8-42 ID - Amirian2013 ER - TY - JOUR AU - Stanisławska, I. J. AU - Granica, S. AU - Piwowarski, J. P. AU - Szawkało, J. AU - Wiązecki, K. AU - Czarnocki, Z. PY - 2019 DA - 2019// TI - The activity of urolithin A and M4 valerolactone, colonic microbiota metabolites of polyphenols, in a prostate cancer in vitro model JO - Planta Med VL - 85 UR - https://doi.org/10.1055/a-0755-7715 DO - 10.1055/a-0755-7715 ID - Stanisławska2019 ER - TY - JOUR AU - Li, H. AU - He, J. AU - Jia, W. PY - 2016 DA - 2016// TI - The influence of gut microbiota on drug metabolism and toxicity JO - Expert Opin Drug Metab Toxicol VL - 12 UR - https://doi.org/10.1517/17425255.2016.1121234 DO - 10.1517/17425255.2016.1121234 ID - Li2016 ER - TY - JOUR AU - Maurice, C. F. AU - Haiser, H. J. AU - Turnbaugh, P. J. PY - 2013 DA - 2013// TI - Xenobiotics shape the physiology and gene expression of the active human gut microbiome JO - Cell. VL - 152 UR - https://doi.org/10.1016/j.cell.2012.10.052 DO - 10.1016/j.cell.2012.10.052 ID - Maurice2013 ER - TY - JOUR AU - Wilkinson, E. M. AU - Ilhan, Z. E. AU - Herbst-Kralovetz, M. M. PY - 2018 DA - 2018// TI - Microbiota-drug interactions: impact on metabolism and efficacy of therapeutics JO - Maturitas. VL - 112 UR - https://doi.org/10.1016/j.maturitas.2018.03.012 DO - 10.1016/j.maturitas.2018.03.012 ID - Wilkinson2018 ER - TY - JOUR AU - Garrett, W. S. PY - 2015 DA - 2015// TI - Cancer and the microbiota JO - Science. VL - 348 UR - https://doi.org/10.1126/science.aaa4972 DO - 10.1126/science.aaa4972 ID - Garrett2015 ER - TY - JOUR AU - Taur, Y. AU - Jenq, R. R. AU - Perales, M. -. A. AU - Littmann, E. R. AU - Morjaria, S. AU - Ling, L. PY - 2014 DA - 2014// TI - The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation JO - Blood. VL - 124 UR - https://doi.org/10.1182/blood-2014-02-554725 DO - 10.1182/blood-2014-02-554725 ID - Taur2014 ER - TY - JOUR AU - Peled, J. U. AU - Devlin, S. M. AU - Staffas, A. AU - Lumish, M. AU - Khanin, R. AU - Littmann, E. R. PY - 2017 DA - 2017// TI - Intestinal microbiota and relapse after hematopoietic-cell transplantation JO - J Clin Oncol VL - 35 UR - https://doi.org/10.1200/JCO.2016.70.3348 DO - 10.1200/JCO.2016.70.3348 ID - Peled2017 ER - TY - JOUR AU - Iida, N. AU - Dzutsev, A. AU - Stewart, C. A. AU - Smith, L. AU - Bouladoux, N. AU - Weingarten, R. A. PY - 2013 DA - 2013// TI - Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment JO - Science. VL - 342 UR - https://doi.org/10.1126/science.1240527 DO - 10.1126/science.1240527 ID - Iida2013 ER - TY - JOUR AU - Schiavoni, G. AU - Sistigu, A. AU - Valentini, M. AU - Mattei, F. AU - Sestili, P. AU - Spadaro, F. PY - 2011 DA - 2011// TI - Cyclophosphamide synergizes with type I interferons through systemic dendritic cell reactivation and induction of immunogenic tumor apoptosis JO - Cancer Res VL - 71 UR - https://doi.org/10.1158/0008-5472.CAN-10-2788 DO - 10.1158/0008-5472.CAN-10-2788 ID - Schiavoni2011 ER - TY - JOUR AU - Viaud, S. AU - Saccheri, F. AU - Mignot, G. AU - Yamazaki, T. AU - Daillère, R. AU - Hannani, D. PY - 2013 DA - 2013// TI - The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide JO - Science. VL - 342 UR - https://doi.org/10.1126/science.1240537 DO - 10.1126/science.1240537 ID - Viaud2013 ER - TY - JOUR AU - Routy, B. AU - Chatelier, E. AU - Derosa, L. AU - Duong, C. P. M. AU - Alou, M. T. AU - Daillère, R. PY - 2018 DA - 2018// TI - Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors JO - Science. VL - 359 UR - https://doi.org/10.1126/science.aan3706 DO - 10.1126/science.aan3706 ID - Routy2018 ER - TY - JOUR AU - Vétizou, M. AU - Pitt, J. M. AU - Daillère, R. AU - Lepage, P. AU - Waldschmitt, N. AU - Flament, C. PY - 2015 DA - 2015// TI - Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota JO - Science. VL - 350 UR - https://doi.org/10.1126/science.aad1329 DO - 10.1126/science.aad1329 ID - Vétizou2015 ER - TY - JOUR AU - Sivan, A. AU - Corrales, L. AU - Hubert, N. AU - Williams, J. B. AU - Aquino-Michaels, K. AU - Earley, Z. M. PY - 2015 DA - 2015// TI - Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy JO - Science. VL - 350 UR - https://doi.org/10.1126/science.aac4255 DO - 10.1126/science.aac4255 ID - Sivan2015 ER - TY - JOUR AU - Matson, V. AU - Fessler, J. AU - Bao, R. AU - Chongsuwat, T. AU - Zha, Y. AU - Alegre, M. -. L. PY - 2018 DA - 2018// TI - The commensal microbiome is associated with anti-PD-1 efficacy in metastatic melanoma patients JO - Science. VL - 359 UR - https://doi.org/10.1126/science.aao3290 DO - 10.1126/science.aao3290 ID - Matson2018 ER - TY - JOUR AU - Arthur, J. C. AU - Perez-Chanona, E. AU - Mühlbauer, M. AU - Tomkovich, S. AU - Uronis, J. M. AU - Fan, T. -. J. PY - 2012 DA - 2012// TI - Intestinal inflammation targets cancer-inducing activity of the microbiota JO - Science. VL - 338 UR - https://doi.org/10.1126/science.1224820 DO - 10.1126/science.1224820 ID - Arthur2012 ER - TY - JOUR AU - Wang, F. AU - Yin, Q. AU - Chen, L. AU - Davis, M. M. PY - 2018 DA - 2018// TI - Bifidobacterium can mitigate intestinal immunopathology in the context of CTLA-4 blockade JO - Proc Natl Acad Sci U S A VL - 115 UR - https://doi.org/10.1073/pnas.1712901115 DO - 10.1073/pnas.1712901115 ID - Wang2018 ER - TY - JOUR AU - Wang, Y. AU - Wiesnoski, D. H. AU - Helmink, B. A. AU - Gopalakrishnan, V. AU - Choi, K. AU - DuPont, H. L. PY - 2018 DA - 2018// TI - Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis JO - Nat Med VL - 24 UR - https://doi.org/10.1038/s41591-018-0238-9 DO - 10.1038/s41591-018-0238-9 ID - Wang2018 ER - TY - JOUR AU - Zimmermann, M. AU - Zimmermann-Kogadeeva, M. AU - Wegmann, R. AU - Goodman, A. L. PY - 2019 DA - 2019// TI - Mapping human microbiome drug metabolism by gut bacteria and their genes JO - Nature. VL - 570 UR - https://doi.org/10.1038/s41586-019-1291-3 DO - 10.1038/s41586-019-1291-3 ID - Zimmermann2019 ER - TY - JOUR AU - Panebianco, C. AU - Andriulli, A. AU - Pazienza, V. PY - 2018 DA - 2018// TI - Pharmacomicrobiomics: exploiting the drug-microbiota interactions in anticancer therapies JO - Microbiome. VL - 6 UR - https://doi.org/10.1186/s40168-018-0483-7 DO - 10.1186/s40168-018-0483-7 ID - Panebianco2018 ER - TY - STD TI - Koppel N, Maini Rekdal V, Balskus EP. Chemical transformation of xenobiotics by the human gut microbiota. Science. 2017;356. ID - ref101 ER - TY - JOUR AU - Jiang, P. AU - Sellers, W. R. AU - Liu, X. S. PY - 2018 DA - 2018// TI - Big data approaches for modeling response and resistance to cancer drugs JO - Annu Rev Biomed Data Sci VL - 1 UR - https://doi.org/10.1146/annurev-biodatasci-080917-013350 DO - 10.1146/annurev-biodatasci-080917-013350 ID - Jiang2018 ER - TY - JOUR AU - Ma, W. AU - Mao, Q. AU - Xia, W. AU - Dong, G. AU - Yu, C. AU - Jiang, F. PY - 2019 DA - 2019// TI - Gut microbiota shapes the efficiency of cancer therapy JO - Front Microbiol VL - 10 UR - https://doi.org/10.3389/fmicb.2019.01050 DO - 10.3389/fmicb.2019.01050 ID - Ma2019 ER - TY - JOUR AU - Land, M. AU - Hauser, L. AU - Jun, S. -. R. AU - Nookaew, I. AU - Leuze, M. R. AU - Ahn, T. -. H. PY - 2015 DA - 2015// TI - Insights from 20 years of bacterial genome sequencing JO - Funct Integr Genomics VL - 15 UR - https://doi.org/10.1007/s10142-015-0433-4 DO - 10.1007/s10142-015-0433-4 ID - Land2015 ER - TY - JOUR AU - Janda, J. M. AU - Abbott, S. L. PY - 2007 DA - 2007// TI - 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls JO - J Clin Microbiol VL - 45 UR - https://doi.org/10.1128/JCM.01228-07 DO - 10.1128/JCM.01228-07 ID - Janda2007 ER - TY - JOUR AU - Fox, G. E. AU - Wisotzkey, J. D. AU - Jurtshuk, P. PY - 1992 DA - 1992// TI - How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity JO - Int J Syst Bacteriol VL - 42 UR - https://doi.org/10.1099/00207713-42-1-166 DO - 10.1099/00207713-42-1-166 ID - Fox1992 ER - TY - JOUR AU - Lappalainen, T. AU - Scott, A. J. AU - Brandt, M. AU - Hall, I. M. PY - 2019 DA - 2019// TI - Genomic analysis in the age of human genome sequencing JO - Cell. VL - 177 UR - https://doi.org/10.1016/j.cell.2019.02.032 DO - 10.1016/j.cell.2019.02.032 ID - Lappalainen2019 ER - TY - JOUR AU - Luo, C. AU - Knight, R. AU - Siljander, H. AU - Knip, M. AU - Xavier, R. J. AU - Gevers, D. PY - 2015 DA - 2015// TI - ConStrains identifies microbial strains in metagenomic datasets JO - Nat Biotechnol VL - 33 UR - https://doi.org/10.1038/nbt.3319 DO - 10.1038/nbt.3319 ID - Luo2015 ER - TY - JOUR AU - Ranjan, R. AU - Rani, A. AU - Metwally, A. AU - McGee, H. S. AU - Perkins, D. L. PY - 2016 DA - 2016// TI - Analysis of the microbiome: advantages of whole genome shotgun versus 16S amplicon sequencing JO - Biochem Biophys Res Commun VL - 469 UR - https://doi.org/10.1016/j.bbrc.2015.12.083 DO - 10.1016/j.bbrc.2015.12.083 ID - Ranjan2016 ER - TY - STD TI - Hillmann B, Al-Ghalith GA, Shields-Cutler RR, Zhu Q, Gohl DM, Beckman KB, et al. Evaluating the information content of shallow shotgun metagenomics [Internet]. bioRxiv. 2018 [cited 2019 Aug 26]. p. 320986. Available from: https://www.biorxiv.org/content/10.1101/320986v1. UR - https://www.biorxiv.org/content/10.1101/320986v1 ID - ref110 ER - TY - STD TI - NIH HMP Working Group, Peterson J, Garges S, Giovanni M, McInnes P, Wang L, et al. The NIH Human Microbiome Project. Genome Res. 2009;19:2317–2323. ID - ref111 ER - TY - JOUR PY - 2012 DA - 2012// TI - A framework for human microbiome research JO - Nature. VL - 486 UR - https://doi.org/10.1038/nature11209 DO - 10.1038/nature11209 ID - ref112 ER - TY - STD TI - Lloyd-Price J, Mahurkar A, Rahnavard G, Crabtree J, Orvis J, Brantley Hall A, et al. Strains, functions and dynamics in the expanded Human Microbiome Project. Nature. Nature Research; 2017;550:61-66. ID - ref113 ER - TY - JOUR AU - Proctor, L. M. PY - 2011 DA - 2011// TI - The human microbiome project in 2011 and beyond JO - Cell Host Microbe VL - 10 UR - https://doi.org/10.1016/j.chom.2011.10.001 DO - 10.1016/j.chom.2011.10.001 ID - Proctor2011 ER - TY - JOUR AU - Costello, E. K. AU - Lauber, C. L. AU - Hamady, M. AU - Fierer, N. AU - Gordon, J. I. AU - Knight, R. PY - 2009 DA - 2009// TI - Bacterial community variation in human body habitats across space and time JO - Science. VL - 326 UR - https://doi.org/10.1126/science.1177486 DO - 10.1126/science.1177486 ID - Costello2009 ER - TY - JOUR AU - Hallmaier-Wacker, L. K. AU - Lueert, S. AU - Roos, C. AU - Knauf, S. PY - 2018 DA - 2018// TI - The impact of storage buffer, DNA extraction method, and polymerase on microbial analysis JO - Sci Rep VL - 8 UR - https://doi.org/10.1038/s41598-018-24573-y DO - 10.1038/s41598-018-24573-y ID - Hallmaier-Wacker2018 ER - TY - JOUR AU - Kerckhof, F. -. M. AU - Courtens, E. N. P. AU - Geirnaert, A. AU - Hoefman, S. AU - Ho, A. AU - Vilchez-Vargas, R. PY - 2014 DA - 2014// TI - Optimized cryopreservation of mixed microbial communities for conserved functionality and diversity JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0099517 DO - 10.1371/journal.pone.0099517 ID - Kerckhof2014 ER - TY - JOUR AU - Gorzelak, M. A. AU - Gill, S. K. AU - Tasnim, N. AU - Ahmadi-Vand, Z. AU - Jay, M. AU - Gibson, D. L. PY - 2015 DA - 2015// TI - Methods for improving human gut microbiome data by reducing variability through sample processing and storage of stool JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0134802 DO - 10.1371/journal.pone.0134802 ID - Gorzelak2015 ER - TY - JOUR AU - Choo, J. M. AU - Leong, L. E. X. AU - Rogers, G. B. PY - 2015 DA - 2015// TI - Sample storage conditions significantly influence faecal microbiome profiles JO - Sci Rep VL - 5 UR - https://doi.org/10.1038/srep16350 DO - 10.1038/srep16350 ID - Choo2015 ER - TY - JOUR AU - Song, S. J. AU - Amir, A. AU - Metcalf, J. L. AU - Amato, K. R. AU - Xu, Z. Z. AU - Humphrey, G. PY - 2016 DA - 2016// TI - Preservation methods differ in fecal microbiome stability, affecting suitability for field studies JO - mSystems. VL - 1 UR - https://doi.org/10.1128/mSystems.00021-16 DO - 10.1128/mSystems.00021-16 ID - Song2016 ER - TY - JOUR AU - McKain, N. AU - Genc, B. AU - Snelling, T. J. AU - Wallace, R. J. PY - 2013 DA - 2013// TI - Differential recovery of bacterial and archaeal 16S rRNA genes from ruminal digesta in response to glycerol as cryoprotectant JO - J Microbiol Methods VL - 95 UR - https://doi.org/10.1016/j.mimet.2013.10.009 DO - 10.1016/j.mimet.2013.10.009 ID - McKain2013 ER - TY - JOUR AU - Gray, M. A. AU - Pratte, Z. A. AU - Kellogg, C. A. PY - 2013 DA - 2013// TI - Comparison of DNA preservation methods for environmental bacterial community samples JO - FEMS Microbiol Ecol VL - 83 UR - https://doi.org/10.1111/1574-6941.12008 DO - 10.1111/1574-6941.12008 ID - Gray2013 ER - TY - JOUR AU - Al, V. PY - 2015 DA - 2015// TI - Temporal and technical variability of human gut metagenomes JO - Genome Biol VL - 16 UR - https://doi.org/10.1186/s13059-015-0639-8 DO - 10.1186/s13059-015-0639-8 ID - Al2015 ER - TY - JOUR AU - Rintala, A. AU - Pietilä, S. AU - Munukka, E. AU - Eerola, E. AU - Pursiheimo, J. -. P. AU - Laiho, A. PY - 2017 DA - 2017// TI - Gut microbiota analysis results are highly dependent on the 16S rRNA gene target region, whereas the impact of DNA extraction is minor JO - J Biomol Tech VL - 28 UR - https://doi.org/10.7171/jbt.17-2801-003 DO - 10.7171/jbt.17-2801-003 ID - Rintala2017 ER - TY - JOUR AU - Al, H. PY - 2016 DA - 2016// TI - Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability JO - Int J Med Microbiol VL - 306 UR - https://doi.org/10.1016/j.ijmm.2016.03.005 DO - 10.1016/j.ijmm.2016.03.005 ID - Al2016 ER - TY - JOUR AU - Al, H. PY - 2014 DA - 2014// TI - Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects JO - Microbiome. VL - 2 UR - https://doi.org/10.1186/2049-2618-2-5 DO - 10.1186/2049-2618-2-5 ID - Al2014 ER - TY - JOUR AU - Al, H. PY - 2014 DA - 2014// TI - 16S rRNA gene pyrosequencing of reference and clinical samples and investigation of the temperature stability of microbiome profiles JO - Microbiome. VL - 2 UR - https://doi.org/10.1186/2049-2618-2-31 DO - 10.1186/2049-2618-2-31 ID - Al2014 ER - TY - JOUR AU - Al, S. PY - 2015 DA - 2015// TI - Collecting fecal samples for microbiome analyses in epidemiology studies JO - Cancer Epidemiol Biomark Prev VL - 25 ID - Al2015 ER - TY - JOUR AU - Panek, M. AU - Čipčić Paljetak, H. AU - Barešić, A. AU - Perić, M. AU - Matijašić, M. AU - Lojkić, I. PY - 2018 DA - 2018// TI - Methodology challenges in studying human gut microbiota - effects of collection, storage, DNA extraction and next generation sequencing technologies JO - Sci Rep VL - 8 UR - https://doi.org/10.1038/s41598-018-23296-4 DO - 10.1038/s41598-018-23296-4 ID - Panek2018 ER - TY - JOUR AU - Burbach, K. AU - Seifert, J. AU - Pieper, D. H. AU - Camarinha-Silva, A. PY - 2016 DA - 2016// TI - Evaluation of DNA extraction kits and phylogenetic diversity of the porcine gastrointestinal tract based on Illumina sequencing of two hypervariable regions JO - Microbiologyopen. VL - 5 UR - https://doi.org/10.1002/mbo3.312 DO - 10.1002/mbo3.312 ID - Burbach2016 ER - TY - JOUR AU - Al, F. PY - 2010 DA - 2010// TI - Comparison of self-collected and physician-collected vaginal swabs for microbiome analysis JO - J Clin Microbiol VL - 48 UR - https://doi.org/10.1128/JCM.01710-09 DO - 10.1128/JCM.01710-09 ID - Al2010 ER - TY - JOUR AU - Maukonen, J. AU - Simões, C. AU - Saarela, M. PY - 2012 DA - 2012// TI - The currently used commercial DNA-extraction methods give different results of clostridial and actinobacterial populations derived from human fecal samples JO - FEMS Microbiol Ecol VL - 79 UR - https://doi.org/10.1111/j.1574-6941.2011.01257.x DO - 10.1111/j.1574-6941.2011.01257.x ID - Maukonen2012 ER - TY - JOUR AU - Fouhy, F. AU - Deane, J. AU - Rea, M. C. AU - O’Sullivan, Ó. AU - Ross, R. P. AU - O’Callaghan, G. PY - 2015 DA - 2015// TI - The effects of freezing on faecal microbiota as determined using MiSeq sequencing and culture-based investigations JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0119355 DO - 10.1371/journal.pone.0119355 ID - Fouhy2015 ER - TY - STD TI - Tedjo DI, Jonkers DMAE, Savelkoul PH, Masclee AA, van Best N, Pierik MJ, et al. The effect of sampling and storage on the fecal microbiota composition in healthy and diseased subjects. PLoS One 2015;10:e0126685. ID - ref134 ER - TY - JOUR AU - Shaw, A. G. AU - Sim, K. AU - Powell, E. AU - Cornwell, E. AU - Cramer, T. AU - McClure, Z. E. PY - 2016 DA - 2016// TI - Latitude in sample handling and storage for infant faecal microbiota studies: the elephant in the room? JO - Microbiome. VL - 4 UR - https://doi.org/10.1186/s40168-016-0186-x DO - 10.1186/s40168-016-0186-x ID - Shaw2016 ER - TY - JOUR AU - Lewis, Z. T. AU - Davis, J. C. C. AU - Smilowitz, J. T. AU - German, J. B. AU - Lebrilla, C. B. AU - Mills, D. A. PY - 2016 DA - 2016// TI - The impact of freeze-drying infant fecal samples on measures of their bacterial community profiles and milk-derived oligosaccharide content JO - PeerJ. VL - 4 UR - https://doi.org/10.7717/peerj.1612 DO - 10.7717/peerj.1612 ID - Lewis2016 ER - TY - JOUR AU - Al, C. PY - 2012 DA - 2012// TI - Storage conditions of intestinal microbiota matter in metagenomic analysis JO - BMC Microbiol VL - 12 UR - https://doi.org/10.1186/1471-2180-12-158 DO - 10.1186/1471-2180-12-158 ID - Al2012 ER - TY - JOUR AU - Al, N. PY - 2016 DA - 2016// TI - High stability of faecal microbiome composition in guanidine thiocyanate solution at room temperature and robustness during colonoscopy JO - Gut. VL - 65 UR - https://doi.org/10.1136/gutjnl-2016-311937 DO - 10.1136/gutjnl-2016-311937 ID - Al2016 ER - TY - JOUR AU - Al, R. PY - 2009 DA - 2009// TI - Influence of fecal sample storage on bacterial community diversity JO - Open Microbiol J VL - 3 UR - https://doi.org/10.2174/1874285800903010040 DO - 10.2174/1874285800903010040 ID - Al2009 ER - TY - JOUR AU - Bahl, M. I. AU - Bergström, A. AU - Licht, T. R. PY - 2012 DA - 2012// TI - Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis JO - FEMS Microbiol Lett VL - 329 UR - https://doi.org/10.1111/j.1574-6968.2012.02523.x DO - 10.1111/j.1574-6968.2012.02523.x ID - Bahl2012 ER - TY - JOUR AU - Lauber, C. L. AU - Zhou, N. AU - Gordon, J. I. AU - Knight, R. AU - Fierer, N. PY - 2010 DA - 2010// TI - Effect of storage conditions on the assessment of bacterial community structure in soil and human-associated samples JO - FEMS Microbiol Lett VL - 307 UR - https://doi.org/10.1111/j.1574-6968.2010.01965.x DO - 10.1111/j.1574-6968.2010.01965.x ID - Lauber2010 ER - TY - JOUR AU - Hale, V. L. AU - Tan, C. L. AU - Knight, R. AU - Amato, K. R. PY - 2015 DA - 2015// TI - Effect of preservation method on spider monkey (Ateles geoffroyi) fecal microbiota over 8 weeks JO - J Microbiol Methods VL - 113 UR - https://doi.org/10.1016/j.mimet.2015.03.021 DO - 10.1016/j.mimet.2015.03.021 ID - Hale2015 ER - TY - JOUR AU - Ariefdjohan, M. W. AU - Savaiano, D. A. AU - Nakatsu, C. H. PY - 2010 DA - 2010// TI - Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens JO - Nutr J VL - 9 UR - https://doi.org/10.1186/1475-2891-9-23 DO - 10.1186/1475-2891-9-23 ID - Ariefdjohan2010 ER - TY - JOUR AU - Lim, M. Y. AU - Song, E. -. J. AU - Kim, S. H. AU - Lee, J. AU - Nam, Y. -. D. PY - 2018 DA - 2018// TI - Comparison of DNA extraction methods for human gut microbial community profiling JO - Syst Appl Microbiol VL - 41 UR - https://doi.org/10.1016/j.syapm.2017.11.008 DO - 10.1016/j.syapm.2017.11.008 ID - Lim2018 ER - TY - STD TI - Knudsen BE, Bergmark L, Munk P, Lukjancenko O, Priemé A, Aarestrup FM, et al. Impact of sample type and DNA isolation procedure on genomic inference of microbiome composition. mSystems [Internet]. 2016;1. Available from: https://doi.org/10.1128/mSystems.00095-16. ID - ref145 ER - TY - JOUR AU - Eriksson, P. AU - Mourkas, E. AU - González-Acuna, D. AU - Olsen, B. AU - Ellström, P. PY - 2017 DA - 2017// TI - Evaluation and optimization of microbial DNA extraction from fecal samples of wild Antarctic bird species JO - Infect Ecol Epidemiol VL - 7 ID - Eriksson2017 ER - TY - STD TI - Kashinskaya EN, Andree KB, Simonov EP, Solovyev MM. DNA extraction protocols may influence biodiversity detected in the intestinal microbiome: a case study from wild Prussian carp, Carassius gibelio. FEMS Microbiol Ecol 2017;93. Available from: https://doi.org/10.1093/femsec/fiw240. ID - ref147 ER - TY - JOUR AU - Esteves, A. I. S. AU - Amer, N. AU - Nguyen, M. AU - Thomas, T. PY - 2016 DA - 2016// TI - Sample processing impacts the viability and cultivability of the sponge microbiome JO - Front Microbiol VL - 7 UR - https://doi.org/10.3389/fmicb.2016.00499 DO - 10.3389/fmicb.2016.00499 ID - Esteves2016 ER - TY - JOUR AU - Bag, S. AU - Saha, B. AU - Mehta, O. AU - Anbumani, D. AU - Kumar, N. AU - Dayal, M. PY - 2016 DA - 2016// TI - An improved method for high quality metagenomics DNA extraction from human and environmental samples JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep26775 DO - 10.1038/srep26775 ID - Bag2016 ER - TY - JOUR AU - Santiago, A. AU - Panda, S. AU - Mengels, G. AU - Martinez, X. AU - Azpiroz, F. AU - Dore, J. PY - 2014 DA - 2014// TI - Processing faecal samples: a step forward for standards in microbial community analysis JO - BMC Microbiol VL - 14 UR - https://doi.org/10.1186/1471-2180-14-112 DO - 10.1186/1471-2180-14-112 ID - Santiago2014 ER - TY - JOUR AU - Gill, C. AU - Wijgert, J. H. H. M. AU - Blow, F. AU - Darby, A. C. PY - 2016 DA - 2016// TI - Evaluation of lysis methods for the extraction of bacterial DNA for analysis of the vaginal microbiota JO - PLoS One VL - 11 UR - https://doi.org/10.1371/journal.pone.0163148 DO - 10.1371/journal.pone.0163148 ID - Gill2016 ER - TY - JOUR AU - Couch, R. D. AU - Navarro, K. AU - Sikaroodi, M. AU - Gillevet, P. AU - Forsyth, C. B. AU - Mutlu, E. PY - 2013 DA - 2013// TI - The approach to sample acquisition and its impact on the derived human fecal microbiome and VOC metabolome JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0081163 DO - 10.1371/journal.pone.0081163 ID - Couch2013 ER - TY - JOUR AU - Shobar, R. M. AU - Velineni, S. AU - Keshavarzian, A. AU - Swanson, G. AU - DeMeo, M. T. AU - Melson, J. E. PY - 2016 DA - 2016// TI - The effects of bowel preparation on microbiota-related metrics differ in health and in inflammatory bowel disease and for the mucosal and luminal microbiota compartments JO - Clin Transl Gastroenterol VL - 7 UR - https://doi.org/10.1038/ctg.2015.54 DO - 10.1038/ctg.2015.54 ID - Shobar2016 ER - TY - JOUR AU - Al, K. PY - 2009 DA - 2009// TI - Heterogeneity of vaginal microbial communities within individuals JO - J Clin Microbiol VL - 47 UR - https://doi.org/10.1128/JCM.00854-08 DO - 10.1128/JCM.00854-08 ID - Al2009 ER - TY - JOUR AU - Al, G. PY - 2012 DA - 2012// TI - Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota JO - Proc Natl Acad Sci U S A VL - 109 UR - https://doi.org/10.1073/pnas.1107435109 DO - 10.1073/pnas.1107435109 ID - Al2012 ER - TY - JOUR AU - Al, G. -. G. PY - 2013 DA - 2013// TI - A new method for extracting skin microbes allows metagenomic analysis of whole-deep skin JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0074914 DO - 10.1371/journal.pone.0074914 ID - Al2013 ER - TY - JOUR AU - Gohl, D. M. AU - Vangay, P. AU - Garbe, J. AU - MacLean, A. AU - Hauge, A. AU - Becker, A. PY - 2016 DA - 2016// TI - Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies JO - Nat Biotechnol VL - 34 UR - https://doi.org/10.1038/nbt.3601 DO - 10.1038/nbt.3601 ID - Gohl2016 ER - TY - JOUR AU - D’Amore, R. AU - Ijaz, U. Z. AU - Schirmer, M. AU - Kenny, J. G. AU - Gregory, R. AU - Darby, A. C. PY - 2016 DA - 2016// TI - A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling JO - BMC Genomics VL - 17 UR - https://doi.org/10.1186/s12864-015-2194-9 DO - 10.1186/s12864-015-2194-9 ID - D’Amore2016 ER - TY - JOUR AU - Allali, I. AU - Arnold, J. W. AU - Roach, J. AU - Cadenas, M. B. AU - Butz, N. AU - Hassan, H. M. PY - 2017 DA - 2017// TI - A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome JO - BMC Microbiol VL - 17 UR - https://doi.org/10.1186/s12866-017-1101-8 DO - 10.1186/s12866-017-1101-8 ID - Allali2017 ER - TY - JOUR AU - Majaneva, M. AU - Hyytiäinen, K. AU - Varvio, S. L. AU - Nagai, S. AU - Blomster, J. PY - 2015 DA - 2015// TI - Bioinformatic amplicon read processing strategies strongly affect eukaryotic diversity and the taxonomic composition of communities JO - PLoS One VL - 10 UR - https://doi.org/10.1371/journal.pone.0130035 DO - 10.1371/journal.pone.0130035 ID - Majaneva2015 ER - TY - JOUR AU - Callahan, B. J. AU - McMurdie, P. J. AU - Rosen, M. J. AU - Han, A. W. AU - Johnson, A. J. A. AU - Holmes, S. P. PY - 2016 DA - 2016// TI - DADA2: high-resolution sample inference from Illumina amplicon data JO - Nat Methods VL - 13 UR - https://doi.org/10.1038/nmeth.3869 DO - 10.1038/nmeth.3869 ID - Callahan2016 ER - TY - STD TI - Nearing JT, Douglas GM, Comeau AM, Langille MGI. Denoising the denoisers: an independent evaluation of microbiome sequence error-correction methods [Internet]. PeerJ Preprints; 2018 Feb. Report No.: e26566v1. Available from: https://peerj.com/preprints/26566/. UR - https://peerj.com/preprints/26566/ ID - ref162 ER - TY - JOUR AU - Nilakanta, H. AU - Drews, K. L. AU - Firrell, S. AU - Foulkes, M. A. AU - Jablonski, K. A. PY - 2014 DA - 2014// TI - A review of software for analyzing molecular sequences JO - BMC Res Notes VL - 7 UR - https://doi.org/10.1186/1756-0500-7-830 DO - 10.1186/1756-0500-7-830 ID - Nilakanta2014 ER - TY - STD TI - Kopylova E, Navas-Molina JA, Mercier C, Xu ZZ, Mahé F, He Y, et al. Open-source sequence clustering methods improve the state of the art. mSystems [Internet]. 2016;1. Available from: https://doi.org/10.1128/mSystems.00003-15. ID - ref164 ER - TY - STD TI - Xue Z, Kable ME, Marco ML. Impact of DNA sequencing and analysis methods on 16S rRNA gene bacterial community analysis in dairy products [Internet]. bioRxiv. 2018 [cited 2018 Jun 11]. p. 305078. Available from: https://www.biorxiv.org/content/early/2018/04/20/305078. UR - https://www.biorxiv.org/content/early/2018/04/20/305078 ID - ref165 ER - TY - JOUR AU - Edgar, R. C. PY - 2017 DA - 2017// TI - Accuracy of microbial community diversity estimated by closed- and open-reference OTUs JO - PeerJ. VL - 5 UR - https://doi.org/10.7717/peerj.3889 DO - 10.7717/peerj.3889 ID - Edgar2017 ER - TY - JOUR AU - Wang, H. AU - Funchain, P. AU - Bebek, G. AU - Altemus, J. AU - Zhang, H. AU - Niazi, F. PY - 2017 DA - 2017// TI - Microbiomic differences in tumor and paired-normal tissue in head and neck squamous cell carcinomas JO - Genome Med. VL - 9 UR - https://doi.org/10.1186/s13073-017-0405-5 DO - 10.1186/s13073-017-0405-5 ID - Wang2017 ER - TY - JOUR AU - Yang, L. AU - Lu, X. AU - Nossa, C. W. AU - Francois, F. AU - Peek, R. M. AU - Pei, Z. PY - 2009 DA - 2009// TI - Inflammation and intestinal metaplasia of the distal esophagus are associated with alterations in the microbiome JO - Gastroenterology. VL - 137 UR - https://doi.org/10.1053/j.gastro.2009.04.046 DO - 10.1053/j.gastro.2009.04.046 ID - Yang2009 ER - TY - JOUR AU - McCoy, A. N. AU - Araújo-Pérez, F. AU - Azcárate-Peril, A. AU - Yeh, J. J. AU - Sandler, R. S. PY - 2013 DA - 2013// TI - Fusobacterium is associated with colorectal adenomas JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0053653 DO - 10.1371/journal.pone.0053653 ID - McCoy2013 ER - TY - JOUR AU - Geng, J. AU - Fan, H. AU - Tang, X. AU - Zhai, H. AU - Zhang, Z. PY - 2013 DA - 2013// TI - Diversified pattern of the human colorectal cancer microbiome JO - Gut Pathog VL - 5 UR - https://doi.org/10.1186/1757-4749-5-2 DO - 10.1186/1757-4749-5-2 ID - Geng2013 ER - TY - JOUR AU - Gong, H. -. L. AU - Shi, Y. AU - Zhou, L. AU - Wu, C. -. P. AU - Cao, P. -. Y. AU - Tao, L. PY - 2013 DA - 2013// TI - The composition of microbiome in larynx and the throat biodiversity between laryngeal squamous cell carcinoma patients and control population JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0066476 DO - 10.1371/journal.pone.0066476 ID - Gong2013 ER - TY - JOUR AU - Seo, S. -. S. AU - Oh, H. Y. AU - Lee, J. -. K. AU - Kong, J. -. S. AU - Lee, D. O. AU - Kim, M. K. PY - 2016 DA - 2016// TI - Combined effect of diet and cervical microbiome on the risk of cervical intraepithelial neoplasia JO - Clin Nutr VL - 35 UR - https://doi.org/10.1016/j.clnu.2016.03.019 DO - 10.1016/j.clnu.2016.03.019 ID - Seo2016 ER - TY - JOUR AU - Allali, I. AU - Delgado, S. AU - Marron, P. I. AU - Astudillo, A. AU - Yeh, J. J. AU - Ghazal, H. PY - 2015 DA - 2015// TI - Gut microbiome compositional and functional differences between tumor and non-tumor adjacent tissues from cohorts from the US and Spain JO - Gut Microbes VL - 6 UR - https://doi.org/10.1080/19490976.2015.1039223 DO - 10.1080/19490976.2015.1039223 ID - Allali2015 ER - TY - JOUR AU - Nasrollahzadeh, D. AU - Malekzadeh, R. AU - Ploner, A. AU - Shakeri, R. AU - Sotoudeh, M. AU - Fahimi, S. PY - 2015 DA - 2015// TI - Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia JO - Sci Rep VL - 5 UR - https://doi.org/10.1038/srep08820 DO - 10.1038/srep08820 ID - Nasrollahzadeh2015 ER - TY - JOUR AU - Guerrero-Preston, R. AU - Godoy-Vitorino, F. AU - Jedlicka, A. AU - Rodríguez-Hilario, A. AU - González, H. AU - Bondy, J. PY - 2016 DA - 2016// TI - 16S rRNA amplicon sequencing identifies microbiota associated with oral cancer, human papilloma virus infection and surgical treatment JO - Oncotarget. VL - 7 UR - https://doi.org/10.18632/oncotarget.9710 DO - 10.18632/oncotarget.9710 ID - Guerrero-Preston2016 ER - TY - JOUR AU - Wang, H. AU - Altemus, J. AU - Niazi, F. AU - Green, H. AU - Calhoun, B. C. AU - Sturgis, C. PY - 2017 DA - 2017// TI - Breast tissue, oral and urinary microbiomes in breast cancer JO - Oncotarget. VL - 8 UR - https://doi.org/10.18632/oncotarget.21490 DO - 10.18632/oncotarget.21490 ID - Wang2017 ER - TY - JOUR AU - Li, T. H. AU - Qin, Y. AU - Sham, P. C. AU - Lau, K. S. AU - Chu, K. -. M. AU - Leung, W. K. PY - 2017 DA - 2017// TI - Alterations in gastric microbiota after H. pylori eradication and in different histological stages of gastric carcinogenesis JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/srep44935 DO - 10.1038/srep44935 ID - Li2017 ER - TY - JOUR AU - Yoon, H. AU - Kim, N. AU - Park, J. H. AU - Kim, Y. S. AU - Lee, J. AU - Kim, H. W. PY - 2017 DA - 2017// TI - Comparisons of gut microbiota among healthy control, patients with conventional adenoma, sessile serrated adenoma, and colorectal cancer JO - J Cancer Prev VL - 22 UR - https://doi.org/10.15430/JCP.2017.22.2.108 DO - 10.15430/JCP.2017.22.2.108 ID - Yoon2017 ER - TY - STD TI - Flemer B, Herlihy M, O’Riordain M, Shanahan F, O’Toole PW. Tumour-associated and non-tumour-associated microbiota: addendum. Gut Microbes. 2018;9:369-73. ID - ref179 ER - TY - JOUR AU - Kinross, J. AU - Mirnezami, R. AU - Alexander, J. AU - Brown, R. AU - Scott, A. AU - Galea, D. PY - 2017 DA - 2017// TI - A prospective analysis of mucosal microbiome-metabonome interactions in colorectal cancer using a combined MAS 1HNMR and metataxonomic strategy JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/s41598-017-08150-3 DO - 10.1038/s41598-017-08150-3 ID - Kinross2017 ER - TY - JOUR AU - Xuan, C. AU - Shamonki, J. M. AU - Chung, A. AU - Dinome, M. L. AU - Chung, M. AU - Sieling, P. A. PY - 2014 DA - 2014// TI - Microbial dysbiosis is associated with human breast cancer JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0083744 DO - 10.1371/journal.pone.0083744 ID - Xuan2014 ER - TY - JOUR AU - Schmidt, B. L. AU - Kuczynski, J. AU - Bhattacharya, A. AU - Huey, B. AU - Corby, P. M. AU - Queiroz, E. L. S. PY - 2014 DA - 2014// TI - Changes in abundance of oral microbiota associated with oral cancer JO - PLoS One VL - 9 UR - https://doi.org/10.1371/journal.pone.0098741 DO - 10.1371/journal.pone.0098741 ID - Schmidt2014 ER - TY - JOUR AU - Oh, H. Y. AU - Kim, B. -. S. AU - Seo, S. -. S. AU - Kong, J. -. S. AU - Lee, J. -. K. AU - Park, S. -. Y. PY - 2015 DA - 2015// TI - The association of uterine cervical microbiota with an increased risk for cervical intraepithelial neoplasia in Korea JO - Clin Microbiol Infect VL - 21 UR - https://doi.org/10.1016/j.cmi.2015.02.026 DO - 10.1016/j.cmi.2015.02.026 ID - Oh2015 ER - TY - JOUR AU - Zeller, G. AU - Tap, J. AU - Voigt, A. Y. AU - Sunagawa, S. AU - Kultima, J. R. AU - Costea, P. I. PY - 2014 DA - 2014// TI - Potential of fecal microbiota for early-stage detection of colorectal cancer JO - Mol Syst Biol VL - 10 UR - https://doi.org/10.15252/msb.20145645 DO - 10.15252/msb.20145645 ID - Zeller2014 ER - TY - JOUR AU - Gong, H. AU - Shi, Y. AU - Zhou, X. AU - Wu, C. AU - Cao, P. AU - Xu, C. PY - 2014 DA - 2014// TI - Microbiota in the throat and risk factors for laryngeal carcinoma JO - Appl Environ Microbiol Am Soc Microbiol VL - 80 UR - https://doi.org/10.1128/AEM.02329-14 DO - 10.1128/AEM.02329-14 ID - Gong2014 ER - TY - JOUR AU - Eun, C. S. AU - Kim, B. K. AU - Han, D. S. AU - Kim, S. Y. AU - Kim, K. M. AU - Choi, B. Y. PY - 2014 DA - 2014// TI - Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods JO - Helicobacter. VL - 19 UR - https://doi.org/10.1111/hel.12145 DO - 10.1111/hel.12145 ID - Eun2014 ER - TY - JOUR AU - Gao, Z. AU - Guo, B. AU - Gao, R. AU - Zhu, Q. AU - Wu, W. AU - Qin, H. PY - 2015 DA - 2015// TI - Probiotics modify human intestinal mucosa-associated microbiota in patients with colorectal cancer JO - Mol Med Rep VL - 12 UR - https://doi.org/10.3892/mmr.2015.4124 DO - 10.3892/mmr.2015.4124 ID - Gao2015 ER - TY - JOUR AU - Dejea, C. M. AU - Wick, E. C. AU - Hechenbleikner, E. M. AU - White, J. R. AU - Mark Welch, J. L. AU - Rossetti, B. J. PY - 2014 DA - 2014// TI - Microbiota organization is a distinct feature of proximal colorectal cancers JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1406199111 DO - 10.1073/pnas.1406199111 ID - Dejea2014 ER - TY - JOUR AU - Jo, H. J. AU - Kim, J. AU - Kim, N. AU - Park, J. H. AU - Nam, R. H. AU - Seok, Y. -. J. PY - 2016 DA - 2016// TI - Analysis of gastric microbiota by pyrosequencing: minor role of bacteria other than Helicobacter pylori in the gastric carcinogenesis JO - Helicobacter. VL - 21 UR - https://doi.org/10.1111/hel.12293 DO - 10.1111/hel.12293 ID - Jo2016 ER - TY - JOUR AU - Al-Hebshi, N. N. AU - Nasher, A. T. AU - Idris, A. M. AU - Chen, T. PY - 2015 DA - 2015// TI - Robust species taxonomy assignment algorithm for 16S rRNA NGS reads: application to oral carcinoma samples JO - J Oral Microbiol VL - 7 UR - https://doi.org/10.3402/jom.v7.28934 DO - 10.3402/jom.v7.28934 ID - Al-Hebshi2015 ER - TY - JOUR AU - Nakatsu, G. AU - Li, X. AU - Zhou, H. AU - Sheng, J. AU - Wong, S. H. AU - Wu, W. K. K. PY - 2015 DA - 2015// TI - Gut mucosal microbiome across stages of colorectal carcinogenesis JO - Nat Commun VL - 6 UR - https://doi.org/10.1038/ncomms9727 DO - 10.1038/ncomms9727 ID - Nakatsu2015 ER - TY - JOUR AU - Burns, M. AU - Lynch, J. AU - Starr, T. AU - Knights, D. AU - Blekhman, R. PY - 2015 DA - 2015// TI - Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment JO - Genome Med VL - 7 UR - https://doi.org/10.1186/s13073-015-0177-8 DO - 10.1186/s13073-015-0177-8 ID - Burns2015 ER - TY - JOUR AU - Wang, L. AU - Zhou, J. AU - Xin, Y. AU - Geng, C. AU - Tian, Z. AU - Yu, X. PY - 2016 DA - 2016// TI - Bacterial overgrowth and diversification of microbiota in gastric cancer JO - Eur J Gastroenterol Hepatol VL - 28 UR - https://doi.org/10.1097/MEG.0000000000000542 DO - 10.1097/MEG.0000000000000542 ID - Wang2016 ER - TY - JOUR AU - Chng, K. R. AU - Chan, S. H. AU - Ng, A. H. Q. AU - Li, C. AU - Jusakul, A. AU - Bertrand, D. PY - 2016 DA - 2016// TI - Tissue microbiome profiling identifies an enrichment of specific enteric bacteria in Opisthorchis viverrini associated cholangiocarcinoma JO - EBioMedicine. VL - 8 UR - https://doi.org/10.1016/j.ebiom.2016.04.034 DO - 10.1016/j.ebiom.2016.04.034 ID - Chng2016 ER - TY - JOUR AU - Lu, Y. AU - Chen, J. AU - Zheng, J. AU - Hu, G. AU - Wang, J. AU - Huang, C. PY - 2016 DA - 2016// TI - Mucosal adherent bacterial dysbiosis in patients with colorectal adenomas JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep26337 DO - 10.1038/srep26337 ID - Lu2016 ER - TY - JOUR AU - Audirac-Chalifour, A. AU - Torres-Poveda, K. AU - Bahena-Román, M. AU - Téllez-Sosa, J. AU - Martínez-Barnetche, J. AU - Cortina-Ceballos, B. PY - 2016 DA - 2016// TI - Cervical microbiome and cytokine profile at various stages of cervical cancer: a pilot study JO - PLoS One VL - 11 UR - https://doi.org/10.1371/journal.pone.0153274 DO - 10.1371/journal.pone.0153274 ID - Audirac-Chalifour2016 ER - TY - JOUR AU - Zhang, C. AU - Liu, Y. AU - Gao, W. AU - Pan, Y. AU - Gao, Y. AU - Shen, J. PY - 2018 DA - 2018// TI - The direct and indirect association of cervical microbiota with the risk of cervical intraepithelial neoplasia JO - Cancer Med VL - 7 UR - https://doi.org/10.1002/cam4.1471 DO - 10.1002/cam4.1471 ID - Zhang2018 ER - TY - JOUR AU - Drewes, J. L. AU - White, J. R. AU - Dejea, C. M. AU - Fathi, P. AU - Iyadorai, T. AU - Vadivelu, J. PY - 2017 DA - 2017// TI - High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia JO - NPJ Biofilms Microbiomes VL - 3 UR - https://doi.org/10.1038/s41522-017-0040-3 DO - 10.1038/s41522-017-0040-3 ID - Drewes2017 ER - TY - JOUR AU - Thomas, A. M. AU - Jesus, E. C. AU - Lopes, A. AU - Aguiar, S. AU - Begnami, M. D. AU - Rocha, R. M. PY - 2016 DA - 2016// TI - Tissue-associated bacterial alterations in rectal carcinoma patients revealed by 16S rRNA community profiling JO - Front Cell Infect Microbiol VL - 6 UR - https://doi.org/10.3389/fcimb.2016.00179 DO - 10.3389/fcimb.2016.00179 ID - Thomas2016 ER - TY - JOUR AU - Zhao, H. AU - Chu, M. AU - Huang, Z. AU - Yang, X. AU - Ran, S. AU - Hu, B. PY - 2017 DA - 2017// TI - Variations in oral microbiota associated with oral cancer JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/s41598-017-11779-9 DO - 10.1038/s41598-017-11779-9 ID - Zhao2017 ER - TY - STD TI - Gao R, Kong C, Huang L, Li H, Qu X, Liu Z, et al. Mucosa-associated microbiota signature in colorectal cancer. Eur J Clin Microbiol Infect Dis. 2017;36:2073-83. ID - ref201 ER - TY - JOUR AU - Sanapareddy, N. AU - Legge, R. M. AU - Jovov, B. AU - McCoy, A. AU - Burcal, L. AU - Araujo-Perez, F. PY - 2012 DA - 2012// TI - Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans JO - ISME J VL - 6 UR - https://doi.org/10.1038/ismej.2012.43 DO - 10.1038/ismej.2012.43 ID - Sanapareddy2012 ER - TY - JOUR AU - Chen, W. AU - Liu, F. AU - Ling, Z. AU - Tong, X. AU - Xiang, C. PY - 2012 DA - 2012// TI - Human intestinal lumen and mucosa-associated microbiota in patients with colorectal cancer JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0039743 DO - 10.1371/journal.pone.0039743 ID - Chen2012 ER - TY - JOUR AU - Mangul, S. AU - Martin, L. S. AU - Eskin, E. AU - Blekhman, R. PY - 2019 DA - 2019// TI - Improving the usability and archival stability of bioinformatics software JO - Genome Biol VL - 20 UR - https://doi.org/10.1186/s13059-019-1649-8 DO - 10.1186/s13059-019-1649-8 ID - Mangul2019 ER - TY - JOUR AU - Bolyen, E. AU - Rideout, J. R. AU - Dillon, M. R. AU - Bokulich, N. A. AU - Abnet, C. C. AU - Al-Ghalith, G. A. PY - 2019 DA - 2019// TI - Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 JO - Nat Biotechnol VL - 37 UR - https://doi.org/10.1038/s41587-019-0209-9 DO - 10.1038/s41587-019-0209-9 ID - Bolyen2019 ER - TY - JOUR AU - List, M. AU - Ebert, P. AU - Albrecht, F. PY - 2017 DA - 2017// TI - Ten simple rules for developing usable software in computational biology JO - PLoS Comput Biol VL - 13 UR - https://doi.org/10.1371/journal.pcbi.1005265 DO - 10.1371/journal.pcbi.1005265 ID - List2017 ER - TY - JOUR AU - Stupple, A. AU - Singerman, D. AU - Celi, L. A. PY - 2019 DA - 2019// TI - The reproducibility crisis in the age of digital medicine JO - NPJ Digit Med VL - 2 UR - https://doi.org/10.1038/s41746-019-0079-z DO - 10.1038/s41746-019-0079-z ID - Stupple2019 ER - TY - JOUR AU - Yilmaz, P. AU - Kottmann, R. AU - Field, D. AU - Knight, R. AU - Cole, J. R. AU - Amaral-Zettler, L. PY - 2011 DA - 2011// TI - Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications JO - Nat Biotechnol VL - 29 UR - https://doi.org/10.1038/nbt.1823 DO - 10.1038/nbt.1823 ID - Yilmaz2011 ER - TY - JOUR AU - Bowers, R. M. AU - Kyrpides, N. C. AU - Stepanauskas, R. AU - Harmon-Smith, M. AU - Doud, D. AU - Reddy, T. B. K. PY - 2017 DA - 2017// TI - Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea JO - Nat Biotechnol VL - 35 UR - https://doi.org/10.1038/nbt.3893 DO - 10.1038/nbt.3893 ID - Bowers2017 ER - TY - JOUR AU - Elm, E. AU - Altman, D. G. AU - Egger, M. AU - Pocock, S. J. AU - Gøtzsche, P. C. AU - Vandenbroucke, J. P. PY - 2007 DA - 2007// TI - The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) statement: guidelines for reporting observational studies JO - PLoS Med VL - 4 UR - https://doi.org/10.1371/journal.pmed.0040296 DO - 10.1371/journal.pmed.0040296 ID - Elm2007 ER - TY - JOUR AU - Field, N. AU - Cohen, T. AU - Struelens, M. J. AU - Palm, D. AU - Cookson, B. AU - Glynn, J. R. PY - 2014 DA - 2014// TI - Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement JO - Lancet Infect Dis VL - 14 UR - https://doi.org/10.1016/S1473-3099(13)70324-4 DO - 10.1016/S1473-3099(13)70324-4 ID - Field2014 ER - TY - JOUR AU - Altman, D. G. AU - McShane, L. M. AU - Sauerbrei, W. AU - Taube, S. E. PY - 2012 DA - 2012// TI - Reporting recommendations for tumor marker prognostic studies (REMARK): explanation and elaboration JO - PLoS Med VL - 9 UR - https://doi.org/10.1371/journal.pmed.1001216 DO - 10.1371/journal.pmed.1001216 ID - Altman2012 ER - TY - JOUR AU - Sauerbrei, W. AU - Taube, S. E. AU - McShane, L. M. AU - Cavenagh, M. M. AU - Altman, D. G. PY - 2018 DA - 2018// TI - Reporting recommendations for tumor marker prognostic studies (REMARK): an abridged explanation and elaboration JO - J Natl Cancer Inst VL - 110 UR - https://doi.org/10.1093/jnci/djy088 DO - 10.1093/jnci/djy088 ID - Sauerbrei2018 ER - TY - JOUR AU - Marques, F. Z. AU - Jama, H. A. AU - Tsyganov, K. AU - Gill, P. A. AU - Rhys-Jones, D. AU - Muralitharan, R. R. PY - 2019 DA - 2019// TI - Guidelines for transparency on gut microbiome studies in essential and experimental hypertension JO - Hypertension. VL - 74 UR - https://doi.org/10.1161/HYPERTENSIONAHA.119.13079 DO - 10.1161/HYPERTENSIONAHA.119.13079 ID - Marques2019 ER - TY - JOUR AU - Laukens, D. AU - Brinkman, B. M. AU - Raes, J. AU - Vos, M. AU - Vandenabeele, P. PY - 2016 DA - 2016// TI - Heterogeneity of the gut microbiome in mice: guidelines for optimizing experimental design JO - FEMS Microbiol Rev VL - 40 UR - https://doi.org/10.1093/femsre/fuv036 DO - 10.1093/femsre/fuv036 ID - Laukens2016 ER - TY - STD TI - Raising standards in microbiome research. Nat Microbiol. 2016;1:16112. ID - ref216 ER - TY - JOUR AU - Duvallet, C. AU - Gibbons, S. M. AU - Gurry, T. AU - Irizarry, R. A. AU - Alm, E. J. PY - 2017 DA - 2017// TI - Meta-analysis of gut microbiome studies identifies disease-specific and shared responses JO - Nat Commun VL - 8 UR - https://doi.org/10.1038/s41467-017-01973-8 DO - 10.1038/s41467-017-01973-8 ID - Duvallet2017 ER - TY - JOUR AU - Shah, M. S. AU - DeSantis, T. Z. AU - Weinmaier, T. AU - McMurdie, P. J. AU - Cope, J. L. AU - Altrichter, A. PY - 2018 DA - 2018// TI - Leveraging sequence-based faecal microbial community survey data to identify a composite biomarker for colorectal cancer JO - Gut. VL - 67 UR - https://doi.org/10.1136/gutjnl-2016-313189 DO - 10.1136/gutjnl-2016-313189 ID - Shah2018 ER - TY - STD TI - Sze MA, Schloss PD. Leveraging existing 16S rRNA gene surveys to identify reproducible biomarkers in individuals with colorectal tumors. MBio. 2018;9. Available from: https://doi.org/10.1128/mBio.00630-18. ID - ref219 ER - TY - JOUR AU - Pevsner-Fischer, M. AU - Tuganbaev, T. AU - Meijer, M. AU - Zhang, S. -. H. AU - Zeng, Z. -. R. AU - Chen, M. -. H. PY - 2016 DA - 2016// TI - Role of the microbiome in non-gastrointestinal cancers JO - World J Clin Oncol VL - 7 UR - https://doi.org/10.5306/wjco.v7.i2.200 DO - 10.5306/wjco.v7.i2.200 ID - Pevsner-Fischer2016 ER -