Weber J, Mandala M, Del Vecchio M, Gogas HJ, Arance AM, Cowey CL, et al. Adjuvant nivolumab versus ipilimumab in resected stage III or IV melanoma. The New England journal of medicine. 2017;377(19):1824–35. https://doi.org/10.1056/NEJMoa1709030.
Article
CAS
PubMed
Google Scholar
Michot JM, Bigenwald C, Champiat S, Collins M, Carbonnel F, Postel-Vinay S, et al. Immune-related adverse events with immune checkpoint blockade: a comprehensive review. European Journal of Cancer (Oxford, England: 1990). 2016;54:139–48.
Article
CAS
Google Scholar
Kau AL, Ahern PP, Griffin NW, Goodman AL, Gordon JI. Human nutrition, the gut microbiome and the immune system. Nature. 2011;474(7351):327–36. https://doi.org/10.1038/nature10213.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peters BA, Wilson M, Moran U, Pavlick A, Izsak A, Wechter T, et al. Relating the gut metagenome and metatranscriptome to immunotherapy responses in melanoma patients. Genome medicine. 2019;11(1):61. https://doi.org/10.1186/s13073-019-0672-4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gopalakrishnan V, Spencer CN, Nezi L, Reuben A, Andrews M, Karpinets T, et al. Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients. Science. 2018;359(6371):97–103. https://doi.org/10.1126/science.aan4236.
Article
CAS
PubMed
Google Scholar
Li Y, Tinoco R, Elmén L, Segota I, Xian Y, Fujita Y, et al. Gut microbiota dependent anti-tumor immunity restricts melanoma growth in Rnf5−/− mice. Nature Communications. 2019;10(1):1–16. https://doi.org/10.1038/s41467-019-09525-y.
Article
CAS
Google Scholar
Wargo JA, Gopalakrishnan V, Spencer C, Karpinets T, Reuben A, Andrews MC, et al. Association of the diversity and composition of the gut microbiome with responses and survival (PFS) in metastatic melanoma (MM) patients (pts) on anti-PD-1 therapy. In: Association of the diversity and composition of the gut microbiome with responses and survival (PFS) in metastatic melanoma (MM) patients (pts) on anti-PD-1 therapy. American Society of Clinical Oncology; 2017.
Chapter
Google Scholar
Rausch MP, Hastings KT. Immune checkpoint inhibitors in the treatment of melanoma: from basic science to clinical application. Exon Publications. 2017:121–42. https://doi.org/10.15586/codon.cutaneousmelanoma.2017.ch9.
Wang Y, Wiesnoski DH, Helmink BA, Gopalakrishnan V, Choi K, DuPont HL, et al. Fecal microbiota transplantation for refractory immune checkpoint inhibitor-associated colitis. Nature Medicine. 2018;24(12):1804–8. https://doi.org/10.1038/s41591-018-0238-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pezo RC, Wong M, Martin A. Impact of the gut microbiota on immune checkpoint inhibitor-associated toxicities. Therapeutic Advances in Gastroenterology. 2019;12:1756284819870911. https://doi.org/10.1177/1756284819870911.
Article
CAS
PubMed
PubMed Central
Google Scholar
Atkinson TM, Ryan SJ, Bennett AV, Stover AM, Saracino RM, Rogak LJ, et al. The association between clinician-based common terminology criteria for adverse events (CTCAE) and patient-reported outcomes (PRO): a systematic review. Supportive Care in Cancer. 2016;24(8):3669–76. https://doi.org/10.1007/s00520-016-3297-9.
Article
PubMed
PubMed Central
Google Scholar
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Lozupone CA, Turnbaugh PJ, et al. Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample. Proceedings of the National Academy of Sciences. 2011;108(Supplement 1):4516–22.
Article
CAS
Google Scholar
Caporaso JG, Lauber CL, Walters WA, Berg-Lyons D, Huntley J, Fierer N, et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. The ISME Journal. 2012;6(8):1621–4. https://doi.org/10.1038/ismej.2012.8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolyen E, Rideout JR, Dillon MR, Bokulich NA, Abnet C, Al-Ghalith GA, et al. QIIME 2: reproducible, interactive, scalable, and extensible microbiome data science. PeerJ Preprints; 2018. Report No.: 2167-9843.
Schmieder R, Edwards R. Quality control and preprocessing of metagenomic datasets. Bioinformatics. 2011;27(6):863–4. https://doi.org/10.1093/bioinformatics/btr026.
Article
CAS
PubMed
PubMed Central
Google Scholar
Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD. PANDAseq: paired-end assembler for Illumina sequences. BMC Bioinformatics. 2012;13(1):31. https://doi.org/10.1186/1471-2105-13-31.
Article
CAS
PubMed
PubMed Central
Google Scholar
Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: high-resolution sample inference from Illumina amplicon data. Nature Methods. 2016;13(7):581–3. https://doi.org/10.1038/nmeth.3869.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang Q, Garrity GM, Tiedje JM, Cole JR. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Applied and Environmental Microbiology. 2007;73(16):5261–7. https://doi.org/10.1128/AEM.00062-07.
Article
CAS
PubMed
PubMed Central
Google Scholar
DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K, et al. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol. 2006;72(7):5069–72. https://doi.org/10.1128/AEM.03006-05.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20. https://doi.org/10.1093/bioinformatics/btu170.
Article
CAS
PubMed
PubMed Central
Google Scholar
Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012;9(4):357–9. https://doi.org/10.1038/nmeth.1923.
Article
CAS
PubMed
PubMed Central
Google Scholar
Segata N, Waldron L, Ballarini A, Narasimhan V, Jousson O, Huttenhower C. Metagenomic microbial community profiling using unique clade-specific marker genes. Nature Methods. 2012;9(8):811–4. https://doi.org/10.1038/nmeth.2066.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology. 2012;19(5):455–77. https://doi.org/10.1089/cmb.2012.0021.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Research. 2014;42(D1):D581–D91. https://doi.org/10.1093/nar/gkt1099.
Article
CAS
PubMed
Google Scholar
Team RC. R: a language and environment for statistical computing; 2013.
Google Scholar
Fuglede B, Topsoe F, editors. Jensen-Shannon divergence and Hilbert space embedding. International Symposium on Information Theory, 2004 ISIT 2004 Proceedings; 2004: IEEE.
Ward JH Jr. Hierarchical grouping to optimize an objective function. Journal of the American Statistical Association. 1963;58(301):236–44. https://doi.org/10.1080/01621459.1963.10500845.
Article
Google Scholar
Jacobs JP, Goudarzi M, Singh N, Tong M, McHardy IH, Ruegger P, et al. A disease-associated microbial and metabolomics state in relatives of pediatric inflammatory bowel disease patients. Cellular and Molecular Gastroenterology and Hepatology. 2016;2(6):750–66. https://doi.org/10.1016/j.jcmgh.2016.06.004.
Article
PubMed
PubMed Central
Google Scholar
Oksanen J, Kindt R, Legendre P, O’Hara B, Stevens MHH, Oksanen MJ, et al. The vegan package. Community Ecology Package. 2007;10(631-637):719.
Google Scholar
Zhao N, Chen J, Carroll IM, Ringel-Kulka T, Epstein MP, Zhou H, et al. Testing in microbiome-profiling studies with MiRKAT, the microbiome regression-based kernel association test. The American Journal of Human Genetics. 2015;96(5):797–807. https://doi.org/10.1016/j.ajhg.2015.04.003.
Article
CAS
PubMed
Google Scholar
Mandal S, Van Treuren W, White RA, Eggesbø M, Knight R, Peddada SD. Analysis of composition of microbiomes: a novel method for studying microbial composition. Microbial Ecology in Health and Disease. 2015;26(1):27663. https://doi.org/10.3402/mehd.v26.27663.
Article
PubMed
Google Scholar
Eun Y, Kim IY, Sun J-M, Lee J, Cha H-S, Koh E-M, et al. Risk factors for immune-related adverse events associated with anti-PD-1 pembrolizumab. Scientific Reports. 2019;9(1):1–8.
CAS
Google Scholar
Frankel AE, Coughlin LA, Kim J, Froehlich TW, Xie Y, Frenkel EP, et al. Metagenomic shotgun sequencing and unbiased metabolomic profiling identify specific human gut microbiota and metabolites associated with immune checkpoint therapy efficacy in melanoma patients. Neoplasia. 2017;19(10):848–55. https://doi.org/10.1016/j.neo.2017.08.004.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dubin K, Callahan MK, Ren B, Khanin R, Viale A, Ling L, et al. Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nature Communications. 2016;7(1):10391. https://doi.org/10.1038/ncomms10391.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pitt JM, Vétizou M, Daillère R, Roberti MP, Yamazaki T, Routy B, et al. Resistance mechanisms to immune-checkpoint blockade in cancer: tumor-intrinsic and-extrinsic factors. Immunity. 2016;44(6):1255–69. https://doi.org/10.1016/j.immuni.2016.06.001.
Article
CAS
PubMed
Google Scholar
Iida N, Dzutsev A, Stewart CA, Smith L, Bouladoux N, Weingarten RA, et al. Commensal bacteria control cancer response to therapy by modulating the tumor microenvironment. Science. 2013;342(6161):967–70. https://doi.org/10.1126/science.1240527.
Article
CAS
PubMed
PubMed Central
Google Scholar
Vétizou M, Pitt JM, Daillère R, Lepage P, Waldschmitt N, Flament C, et al. Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota. Science. 2015;350(6264):1079–84. https://doi.org/10.1126/science.aad1329.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chaput N, Lepage P, Coutzac C, Soularue E, Le Roux K, Monot C, et al. Baseline gut microbiota predicts clinical response and colitis in metastatic melanoma patients treated with ipilimumab. Annals of Oncology. 2017;28(6):1368–79. https://doi.org/10.1093/annonc/mdx108.
Article
CAS
PubMed
Google Scholar
Davis-Richardson AG, Ardissone AN, Dias R, Simell V, Leonard MT, Kemppainen KM, et al. Bacteroides dorei dominates gut microbiome prior to autoimmunity in Finnish children at high risk for type 1 diabetes. Frontiers in Microbiology. 2014;5:678. https://doi.org/10.3389/fmicb.2014.00678.
Article
PubMed
PubMed Central
Google Scholar
Pedersen RM, Marmolin ES, Justesen US. Species differentiation of Bacteroides dorei from Bacteroides vulgatus and Bacteroides ovatus from Bacteroides xylanisolvens–back to basics. Anaerobe. 2013;24:1–3. https://doi.org/10.1016/j.anaerobe.2013.08.004.
Article
CAS
PubMed
Google Scholar
Huang J, Liu D, Wang Y, Liu L, Li J, Yuan J, et al. Ginseng polysaccharides alter the gut microbiota and kynurenine/tryptophan ratio, potentiating the antitumour effect of antiprogrammed cell death 1/programmed cell death ligand 1 (anti-PD-1/PD-L1) immunotherapy. Gut. 2021:gutjnl-2020-321031. https://doi.org/10.1136/gutjnl-2020-321031.
Zhang F, Ferrero M, Dong N, D’Auria G, Reyes-Prieto M, Herreros-Pomares A, et al. Analysis of the gut microbiota: an emerging source of biomarkers for immune checkpoint blockade therapy in non-small cell lung cancer. Cancers. 2021;13(11):2514. https://doi.org/10.3390/cancers13112514.
Article
PubMed
PubMed Central
Google Scholar
Atarashi K, Tanoue T, Shima T, Imaoka A, Kuwahara T, Momose Y, et al. Induction of colonic regulatory T cells by indigenous Clostridium species. Science. 2011;331(6015):337–41. https://doi.org/10.1126/science.1198469.
Article
CAS
PubMed
Google Scholar
Round JL, Mazmanian SK. Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota. Proceedings of the National Academy of Sciences. 2010;107(27):12204–9. https://doi.org/10.1073/pnas.0909122107.
Article
Google Scholar
Frankel AE, Deshmukh S, Reddy A, Lightcap J, Hayes M, McClellan S, et al. Cancer immune checkpoint inhibitor therapy and the gut microbiota. Integrative Cancer Therapies. 2019;18:1534735419846379. https://doi.org/10.1177/1534735419846379.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hopkins AM, Rowland A, Kichenadasse G, Wiese MD, Gurney H, McKinnon RA, et al. Predicting response and toxicity to immune checkpoint inhibitors using routinely available blood and clinical markers. British Journal of Cancer. 2017;117(7):913–20. https://doi.org/10.1038/bjc.2017.274.
Article
PubMed
PubMed Central
Google Scholar
Nigro G, Rossi R, Commere P-H, Jay P, Sansonetti PJ. The cytosolic bacterial peptidoglycan sensor Nod2 affords stem cell protection and links microbes to gut epithelial regeneration. Cell Host & Microbe. 2014;15(6):792–8. https://doi.org/10.1016/j.chom.2014.05.003.
Article
CAS
Google Scholar
Ramanan D, San Tang M, Bowcutt R, Cadwell K. Bacterial sensor Nod2 prevents inflammation of the small intestine by restricting the expansion of the commensal Bacteroides vulgatus. Immunity. 2014;41(2):311–24. https://doi.org/10.1016/j.immuni.2014.06.015.
Article
CAS
PubMed
PubMed Central
Google Scholar
Higuchi BS, Rodrigues N, Gonzaga MI, Paiolo JCC, Stefanutto N, Omori WP, et al. Intestinal dysbiosis in autoimmune diabetes is correlated with poor glycemic control and increased interleukin-6: a pilot study. Frontiers in Immunology. 2018;9:1689. https://doi.org/10.3389/fimmu.2018.01689.
Article
CAS
PubMed
PubMed Central
Google Scholar
He Y, Wu W, Zheng H-M, Li P, McDonald D, Sheng H-F, et al. Regional variation limits applications of healthy gut microbiome reference ranges and disease models. Nature medicine. 2018;24(10):1532–5. https://doi.org/10.1038/s41591-018-0164-x.
Article
CAS
PubMed
Google Scholar
Costea PI, Hildebrand F, Arumugam M, Bäckhed F, Blaser MJ, Bushman FD, et al. Enterotypes in the landscape of gut microbial community composition. Nature Microbiology. 2018;3(1):8–16. https://doi.org/10.1038/s41564-017-0072-8.
Article
CAS
PubMed
Google Scholar
Morgan XC, Segata N, Huttenhower C. Biodiversity and functional genomics in the human microbiome. Trends in Genetics. 2013;29(1):51–8. https://doi.org/10.1016/j.tig.2012.09.005.
Article
CAS
PubMed
Google Scholar
Leone RD, Emens LA. Targeting adenosine for cancer immunotherapy. Journal for Immunotherapy of Cancer. 2018;6(1):57. https://doi.org/10.1186/s40425-018-0360-8.
Article
PubMed
PubMed Central
Google Scholar
Leone RD, Emens LA. Targeting adenosine for cancer immunotherapy. Journal for Immunotherapy of Cancer. 2018;6(1):1–9.
Article
Google Scholar
Vujkovic-Cvijin I, Sklar J, Jiang L, Natarajan L, Knight R, Belkaid Y. Host variables confound gut microbiota studies of human disease. Nature. 2020;587(7834):448–54. https://doi.org/10.1038/s41586-020-2881-9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma [Internet]. 2021. Available from: https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA541981.