Metabolic Biosynthesis Pathways Identified from Fecal Microbiome Associated with Prostate Cancer

Wong, 2016, Global incidence and mortality for prostate cancer: analysis of temporal patterns and trends in 36 countries, Eur Urol, 70, 862, 10.1016/j.eururo.2016.05.043 Amirian, 2013, Potential role of gastrointestinal microbiota composition in prostate cancer risk, Infect Agent Cancer, 8, 42, 10.1186/1750-9378-8-42 Cavarretta, 2017, The microbiome of the prostate tumor microenvironment, Eur Urol, 72, 625, 10.1016/j.eururo.2017.03.029 Sfanos, 2018, The inflammatory microenvironment and microbiome in prostate cancer development, Nat Rev Urol, 15, 11, 10.1038/nrurol.2017.167 Shrestha, 2018, Profiling the urinary microbiome in men with positive versus negative biopsies for prostate cancer, J Urol, 199, 161, 10.1016/j.juro.2017.08.001 Hullar, 2014, Gut microbes, diet, and cancer, Cancer Treat Res, 159, 377, 10.1007/978-3-642-38007-5_22 Schwabe, 2013, The microbiome and cancer, Nat Rev Cancer, 13, 800, 10.1038/nrc3610 Golombos, 2018, The role of gut microbiome in the pathogenesis of prostate cancer: a prospective, pilot study, Urology, 111, 122, 10.1016/j.urology.2017.08.039 Magoc, 2011, FLASH: fast length adjustment of short reads to improve genome assemblies, Bioinformatics, 27, 2957, 10.1093/bioinformatics/btr507 Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170 Kuczynski, 2012, Using QIIME to analyze 16S rRNA gene sequences from microbial communities, Curr Protoc Bioinformatics Caporaso, 2010, PyNAST: a flexible tool for aligning sequences to a template alignment, Bioinformatics, 26, 266, 10.1093/bioinformatics/btp636 Edgar, 2011, UCHIME improves sensitivity and speed of chimera detection, Bioinformatics, 27, 2194, 10.1093/bioinformatics/btr381 Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat Methods, 9, 357, 10.1038/nmeth.1923 McDonald, 2012, An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea, ISME J, 6, 610, 10.1038/ismej.2011.139 Wang, 2007, Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy, Appl Environ Microbiol, 73, 5261, 10.1128/AEM.00062-07 Grim, 2017, High-resolution microbiome profiling for detection and tracking of Salmonella enterica, Front Microbiol, 8, 1587, 10.3389/fmicb.2017.01587 Ottesen, 2016, Enrichment dynamics of Listeria monocytogenes and the associated microbiome from naturally contaminated ice cream linked to a listeriosis outbreak, BMC Microbiol, 16, 275, 10.1186/s12866-016-0894-1 Abernethy, 2017, Urinary microbiome and cytokine levels in women with interstitial cystitis, Obstet Gynecol, 129, 500, 10.1097/AOG.0000000000001892 Drewes, 2017, High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia, NPJ Biofilms Microbiomes, 3, 34, 10.1038/s41522-017-0040-3 Daquigan, 2017, High-resolution profiling of the gut microbiome reveals the extent of Clostridium difficile burden, NPJ Biofilms Microbiomes, 3, 35, 10.1038/s41522-017-0043-0 Langille, 2013, Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences, Nat Biotechnol, 31, 814, 10.1038/nbt.2676 Anders, 2010, Differential expression analysis for sequence count data, Genome Biol, 11, R106, 10.1186/gb-2010-11-10-r106 Benjamini, 2001, Controlling the false discovery rate in behavior genetics research, Behav Brain Res, 125, 279, 10.1016/S0166-4328(01)00297-2 Paul, 2015, Influences of diet and the gut microbiome on epigenetic modulation in cancer and other diseases, Clin Epigenetics, 7, 112, 10.1186/s13148-015-0144-7 Price, 2016, Circulating folate and vitamin B12 and risk of prostate cancer: a collaborative analysis of individual participant data from six cohorts including 6875 cases and 8104 controls, Eur Urol, 70, 941, 10.1016/j.eururo.2016.03.029 Wang, 2014, Folate intake, serum folate levels, and prostate cancer risk: a meta-analysis of prospective studies, BMC Public Health, 14, 1326, 10.1186/1471-2458-14-1326 Figueiredo, 2009, Folic acid and risk of prostate cancer: results from a randomized clinical trial, J Natl Cancer Inst, 101, 432, 10.1093/jnci/djp019 Pompei, 2007, Folate production by bifidobacteria as a potential probiotic property, Appl Environ Microbiol, 73, 179, 10.1128/AEM.01763-06 Powers, 2005, Interaction among folate, riboflavin, genotype, and cancer, with reference to colorectal and cervical cancer, J Nutr, 135, 2960S, 10.1093/jn/135.12.2960S Bassett, 2012, Dietary intake of B vitamins and methionine and prostate cancer incidence and mortality, Cancer Causes Control, 23, 855, 10.1007/s10552-012-9954-5 Hsueh, 2012, Deprivation of arginine by recombinant human arginase in prostate cancer cells, J Hematol Oncol, 5, 17, 10.1186/1756-8722-5-17 Plun-Favreau, 2010, Cancer and neurodegeneration: between the devil and the deep blue sea, PLoS Genet, 6, e1001257, 10.1371/journal.pgen.1001257 Rodriguez-Melendez, 2004, Biotin supplementation increases expression of the cytochrome P450 1B1 gene in Jurkat cells, increasing the occurrence of single-stranded DNA breaks, J Nutr, 134, 2222, 10.1093/jn/134.9.2222