RESEARCH I REPORTS ed ruminococcaceae hascolarctobadterun Faecalibacterium Scoresland dasses Mean Decrease Accuracy B n=18 B。 bacterium mpnwsolate groi of Bamesiella inp, CCUG 39913 意人8盒A家 Stools Before After ipilimumab cluster B Cluster C 2001 Clister A Cluster B Cluster C Days after treatment Bacteroides Prevotella B. fragilis B. thetaiotaomicron Cluster C 寸69月85885 Fg.4. cal significance of ipilimumab-induced dysbiosis in patients. ipilimumab from eight patents falling into each of the three clusters(stool selec- 3 k means clustering algorithm was applied on the basis of genus composition tion for fecal microbial transplantation marked with an asterisk*in fig. S20A) into Calinski-Harabasz index(14) and showed good performance in recovering three SEM of tumor sizes depicted for each cluster over time. (D)QPCR analyses of feces clusters before and after therapy(interclass PCA): (A)(left)(Monte-Carlo test, DNA of the recipient before(2 weeks postcolonization) and 2 weeks after ipi, P=0.000199)(A)(right) Random Forest analysis was applied to decipher the targeting Bacteroidales and Bacteroides spp. Results are represented as 2-aCtx nain genera responsible for this significant clustering( B)(right) The relative 10, normalized to 16S rDNA No significant difference in the relative abundance of abundance of main Bacteroides spp significantly differed between clusters b Bf was detectable in the donors of cluster B versus c before colonization(not d C(B)(left) The proportions of patients falling into each cluster were ana- shown ).(E) Spearman correlations between the amount of Bf in stools 15 days lyzed in a nonpaired manner before versus after ipi injections regardless of the after treatment with 9D9 Ab and tumor sizes across cluster B-and C-recipient time point(fig. S20A).(C) Fecal microbial transplantation after introduction of mice. *P <0.05: **P<0.01; ***P<0.001 REFERENCES AND NOTES 13. 1. Qin et al, Nature 464, 59-65(2010 supported by La Ligue contre le cancer and ARC, respectively. L2 1. K.S. Peggs, S. A. Quezada, A.J. Korman, J. P. Allison 14. A. Cebula et al, Nature 497. 258-262(2013) received a special prize from the Swiss Bridge Foundation and ISREC. Curr. Opin. Immunol 18, 206-213(2006). 15.IL Sonnenburg.C. T.Chen, 1.L.Gordon. PLOS Biol. 4, e413 GK and L.Z. were supported by the Ligue Nationale contre le Cancer 2. F.S. Hodi et al, N. Engl. I. Med. 363. 711-723(2010). (2006) 16. W. Lam et al., Sci. Trans. Med. 2, 45ra59(2010) 5. S Viaud et a, Science 342, 971-976(2013) 11Hx知时乱,N加m51.237-2402041.casm1/ uropean Research Council Advanced Investigator Grant(oGK 18. M Mimee, A. C. Tucker, C. A. Voigt, T.K. Fondation pour la Recherche Medicale(FRM). Institut National du 62-71(2015) Methods421.8-95(2015) ridge Foundation. the LabEx 7. S Dasgupta, D.Erturk-Hlasderni, 1. O0choa-Reparaz,HC. Reinecke.ACKNOWLEDGMENTS D L Kasper, Cel Host Microbe 15. 413-423(2014). We are grateful to the staff of the 8. S K Mazmanian, C H. Liu, A 0. Tzianabos, D L Kasper, Cell and Institut Pasteur. The data pre 122107-118(2005) aper and in 9.F. Stingele et at.mno.172.1483-1490(2004) LZ, MV, and PL have filed patent 二 asy Oncology Cell DNA Repair and Tumor the SIRIC Cancer Research and Personal zed Medicine(CARPEM), an supported by NIH(RO1 CA161879, as Principal Investigator).MC was aA.0. Tzianabos et af. 1. Biol. Chem. 267. 18230-18235(1992) that relates to the following: Methods and products for modulating Fondation l1.1YHargSM.Lee,SK. Mazmarian, Anaerobe 17, 137-141(201). microbiota composition for improving the efficacy of a car ARC pour la recherche sur le cancer, and Institut Nationale du Cancer. 12. M. Arumugam ef al. Nature 473, 174-180(2011) treatment with an immune checkpoint blocker M.V. and JMP.were N.W. is a recipient of a postdoctoral Fellowship from the Agence SCIENCE sciencemag. org 27 NOVEMBER 2015. VOL 350 ISSUE 6264 1083REFERENCES AND NOTES 1. K. S. Peggs, S. A. Quezada, A. J. Korman, J. P. Allison, Curr. Opin. Immunol. 18, 206–213 (2006). 2. F. S. Hodi et al., N. Engl. J. Med. 363, 711–723 (2010). 3. K. E. Beck et al., J. Clin. Oncol. 24, 2283–2289 (2006). 4. D. Berman et al., Cancer Immun. 10, 11 (2010). 5. S. Viaud et al., Science 342, 971–976 (2013). 6. A. Rogoz, B. S. Reis, R. A. Karssemeijer, D. Mucida, J. Immunol. Methods 421, 89–95 (2015). 7. S. Dasgupta, D. Erturk-Hasdemir, J. Ochoa-Reparaz, H. C. Reinecker, D. L. Kasper, Cell Host Microbe 15, 413–423 (2014). 8. S. K. Mazmanian, C. H. Liu, A. O. Tzianabos, D. L. Kasper, Cell 122, 107–118 (2005). 9. F. Stingele et al., J. Immunol. 172, 1483–1490 (2004). 10. A. O. Tzianabos et al., J. Biol. Chem. 267, 18230–18235 (1992). 11. J. Y. Huang, S. M. Lee, S. K. Mazmanian, Anaerobe 17, 137–141 (2011). 12. M. Arumugam et al., Nature 473, 174–180 (2011). 13. J. Qin et al., Nature 464, 59–65 (2010). 14. A. Cebula et al., Nature 497, 258–262 (2013). 15. J. L. Sonnenburg, C. T. Chen, J. I. Gordon, PLOS Biol. 4, e413 (2006). 16. W. Lam et al., Sci. Transl. Med. 2, 45ra59 (2010). 17. H. Xu et al., Nature 513, 237–241 (2014). 18. M. Mimee, A. C. Tucker, C. A. Voigt, T. K. Lu, Cell Systems 1, 62–71 (2015). ACKNOWLEDGMENTS We are grateful to the staff of the animal facility of Gustave Roussy and Institut Pasteur. The data presented in this manuscript are tabulated in the main paper and in the supplementary materials. L.Z., M.V., and P.L. have filed patent application no. EP 14190167 that relates to the following: Methods and products for modulating microbiota composition for improving the efficacy of a cancer treatment with an immune checkpoint blocker. M.V. and J.M.P. were supported by La Ligue contre le cancer and ARC, respectively. L.Z. received a special prize from the Swiss Bridge Foundation and ISREC. G.K. and L.Z. were supported by the Ligue Nationale contre le Cancer (Equipes labelisées), Agence Nationale pour la Recherche (ANR AUTOPH, ANR Emergence), European Commission (ArtForce), European Research Council Advanced Investigator Grant (to G.K.), Fondation pour la Recherche Médicale (FRM), Institut National du Cancer (INCa), Fondation de France, Cancéropôle Ile-de-France, Fondation Bettencourt-Schueller, Swiss Bridge Foundation, the LabEx Immuno-Oncology, the Institut national du cancer (SIRIC) Stratified Oncology Cell DNA Repair and Tumor Immune Elimination (SOCRATE); the SIRIC Cancer Research and Personalized Medicine (CARPEM), and the Paris Alliance of Cancer Research Institutes (PACRI). S.M. was supported by NIH (R01 CA161879, as Principal Investigator). M.C. was supported by the Fondation pour la Recherche Médicale, the Fondation ARC pour la recherche sur le cancer, and Institut Nationale du Cancer. N.W. is a recipient of a Postdoctoral Fellowship from the Agence SCIENCE sciencemag.org 27 NOVEMBER 2015 • VOL 350 ISSUE 6264 1083 Fig. 4. Biological significance of ipilimumab-induced dysbiosis in patients. The k means clustering algorithm was applied on the basis of genus composition before and during ipilimumab treatment in 25 MM patients, validated using the Calinski-Harabasz index (14), and showed good performance in recovering three clusters before and after therapy (interclass PCA); (A) (left) (Monte-Carlo test, P = 0.000199). (A) (right) Random Forest analysis was applied to decipher the main genera responsible for this significant clustering. (B) (right) The relative abundance of main Bacteroides spp. significantly differed between clusters B and C. (B) (left) The proportions of patients falling into each cluster were ana￾lyzed in a nonpaired manner before versus after ipi injections regardless of the time point (fig. S20A). (C) Fecal microbial transplantation after introduction of ipilimumab from eight patients falling into each of the three clusters (stool selec￾tion for fecal microbial transplantation marked with an asterisk * in fig. S20A) into GF animals. One representative experiment out of three is shown with means ± SEM of tumor sizes depicted for each cluster over time. (D) QPCR analyses of feces DNA of the recipient before (2 weeks postcolonization) and 2 weeks after ipi, targeting Bacteroidales and Bacteroides spp. Results are represented as 2–DCt x 103 , normalized to 16S rDNA. No significant difference in the relative abundance of Bf was detectable in the donors of cluster B versus C before colonization (not shown). (E) Spearman correlations between the amount of Bf in stools 15 days after treatment with 9D9 Ab and tumor sizes across cluster B- and C-recipient mice. *P < 0.05; **P < 0.01; ***P < 0.001. RESEARCH | REPORTS on June 24, 2016 http://science.sciencemag.org/ Downloaded from