ww.nature.com/scientificreports/ 46. Grivennikov, S L et aL. Adenoma-linked barrier defects and microbial products drive IL-23/IL-17-mediated tumour growth. Nature 491,254-258,doi:10.1038/ nature11465(2012) 47. Yabuuchi, E. et al. Proposals of Sphingomonas paucimobilis gen nov and comb. nov. Sphingomonas parapaucimobilis sp. nov. comb, nov, and Two Genospecies Visvanathan, K. ef aL. The Reliability of Nipple ate and ductal e in Women at Increased Risk for Breast Cancer-a otential Tool for Breast Cancer Risk Assessment and Biomarker Evaluation. Cancer Epidemiology Biomarkers d- Prevention 16, 950-955,doi:10.1158/1055-99651-06-0974(2007 ut microbial community analysis on the Illumina HiSeq and MiSe platforms. ISMEJ 1-1624,doi10.038/sme120128(2012 50.AndrewsS.faStqc:aqualitycontroltoolforhighthroughputsequencedataUrlhttp://www.bioinformatics.babraham.ac.uk 51. Schloss, P D et al. Introducing mothur: Open-Source, Platform-Independent, Cor Comparing Microbial Communities. Applied and Environmental Microbiology 75, 7537-7541, doi: 10 52. Quast, C. ef al. The SILVA rib Research4,D590-D596,do10.1093/nar/gks219(2013) B ], Clemente, J C, Quince, C.& Knight, R. UCHIME improves sensitivity and speed of chimera detection. ,2194-2200,do:10.1093/ bioinformatics/btr381(2011) 54. Cole J. R et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42, D633-D642, i:10.1093/nar/gkt244(2014) 55.Oksanen,J.etal.veganCommunityEcologyPackageRpackageversion2.3-5.Urlhttp:/ LR-project. org/package=vegan (201 56. R Core Team R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria. UrlHttpS://www.r-project.org/(2015). orkbench Compatible with ARB. Appli ivironmental Microbiology 72, 5069-5072, doi: 10. 1128/aem.03006-05(2006) 58. Kanehisa, M.& Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28, 27-30, doi: 10.1093/nar/27. 1.2 Acknowledgements This study was supported by the Avon Breast Cancer Crusade. We are grateful to the members of the Army of Women who participated in this study. Many thanks to Drs Caiyun Xuan and Eva Gordon who participated in the planning and early stages of this project. Dr. Xuan also extracted the DNA. Thank you to Dr lan Hutchinson helpful discussion and review of manuscript. D J. L is supported by the Joseph B. Gould Foundation, Maria c Clay Foundation, Fashion Footwear Association of New York(FFANY), and Associates for Breast and Prostat Cancer Studies(ABCs). Part of the work was carried out at the Jet Propulsion Laboratory, California Institute of Technology, who has a contract with the National Aeronautics and Space Administration. M.B. is funded by the doctoral college of molecular inflammation(DK- MOLIN) and the Bank Austria Visiting Scientist program. Author Contributions S L., P.A. V and D. .L contributed equally jointly supervising the work Designed project: S L and D. . L. Collected the samples: S.L. and K D. Performed wet or computational experiments: A.A. C and M. B. Analyzed the data M B, A.A.C, MNR, P.A. S, D J.L. and P.A. V. Generated figures and tables: A.A. C, M.B. and M.N.R. wrote the anuscript: A.A. C, M B, M N.R. and D J. L Critically reviewed the manuscript: A. A C, M.B., MNR,KD Additional Information Supplementaryinformationaccompaniesthispaperathttp://www.nature.com/srep Competing financial interests: The authors declare no competing financial interests. How to cite this article: Chan, A.A.et al. Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors. Sci. Rep. 6, 28061; doi: 10.1038/srep28061 (2016) ceO This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license unless indicated otherwise in the credit line if the material is not included under the Creative Commons license users will need to obtain permission from the license holder to reproduce the material. To view a copy of th license,visithttp://creativecommons.org/licenses/by/4.0/ SCIENTIFIC REPORTS 6: 28061 DO1: 10.1038/srep28061www.nature.com/scientificreports/ Scientific Reports | 6:28061 | DOI: 10.1038/srep28061 1 1 46. Grivennikov, S. I. et al. Adenoma-linked barrier defects and microbial products drive IL-23/IL-17-mediated tumour growth. Nature 491, 254–258, doi: 10.1038/nature11465 (2012). 47. Yabuuchi, E. et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb, nov., and Two Genospecies of the Genus Sphingomonas. Microbiology and Immunology 34, 99–119, doi: 10.1111/j.1348-0421.1990.tb00996.x (1990). 48. Visvanathan, K. et al. The Reliability of Nipple Aspirate and Ductal Lavage in Women at Increased Risk for Breast Cancer—a Potential Tool for Breast Cancer Risk Assessment and Biomarker Evaluation. Cancer Epidemiology Biomarkers & Prevention 16, 950–955, doi: 10.1158/1055-9965.epi-06-0974 (2007). 49. Caporaso, J. G. et al. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6, 1621–1624, doi: 10.1038/ismej.2012.8 (2012). 50. Andrews, S. FASTQC : a quality control tool for high throughput sequence data. URL http://www.bioinformatics.babraham.ac.uk/ projects/fastqc (2010). 51. Schloss, P. D. et al. Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities. Applied and Environmental Microbiology 75, 7537–7541, doi: 10.1128/aem.01541-09 (2009). 52. Quast, C. et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41, D590–D596, doi: 10.1093/nar/gks1219 (2013). 53. Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C. & Knight, R. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27, 2194–2200, doi: 10.1093/bioinformatics/btr381 (2011). 54. Cole J. R. et al. Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42, D633–D642, doi: 10.1093/nar/gkt1244 (2014). 55. Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.3-5. URL http://CRAN.R-project.org/package=vegan (2016). 56. R Core Team R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Vienna, Austria. URL https://www.R-project.org/(2015). 57. DeSantis, T. Z. et al. Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB. Applied and Environmental Microbiology 72, 5069–5072, doi: 10.1128/aem.03006-05 (2006). 58. Kanehisa, M. & Goto, S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28, 27–30, doi: 10.1093/nar/27.1.29 (2000). Acknowledgements This study was supported by the Avon Breast Cancer Crusade. We are grateful to the members of the Army of Women who participated in this study. Many thanks to Drs. Caiyun Xuan and Eva Gordon who participated in the planning and early stages of this project. Dr. Xuan also extracted the DNA. Thank you to Dr. Ian Hutchinson for helpful discussion and review of manuscript. D.J.L. is supported by the Joseph B. Gould Foundation, Maria McClay Foundation, Fashion Footwear Association of New York (FFANY), and Associates for Breast and Prostate Cancer Studies (ABCs). Part of the work was carried out at the Jet Propulsion Laboratory, California Institute of Technology, who has a contract with the National Aeronautics and Space Administration. M.B. is funded by the doctoral college of molecular inflammation (DK-MOLIN) and the Bank Austria Visiting Scientist program. Author Contributions S.L., P.A.V. and D.J.L. contributed equally jointly supervising the work. Designed project: S.L. and D.J.L. Collected the samples: S.L. and K.D. Performed wet or computational experiments: A.A.C. and M.B. Analyzed the data: M.B, A.A.C, M.N.R, P.A.S., D.J.L. and P.A.V. Generated figures and tables: A.A.C., M.B. and M.N.R. Wrote the manuscript: A.A.C., M.B., M.N.R. and D.J.L. Critically reviewed the manuscript: A.A.C., M.B., M.N.R, K.D., P.A.S., T.R.P., P.A.V., S.L. and D.J.L. Additional Information Supplementary information accompanies this paper at http://www.nature.com/srep Competing financial interests: The authors declare no competing financial interests. How to cite this article: Chan, A. A. et al. Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors. Sci. Rep. 6, 28061; doi: 10.1038/srep28061 (2016). This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/