Microbiota studies in the bile duct strongly suggest a role for Helicobacter pylori in extrahepatic cholangiocarcinoma  F. Avilés-Jiménez, A. Guitron, F. Segura-López, A. Méndez-Tenorio, S. Iwai, A. Hernández-Guerrero, J. Torres  Clinical Microbiology and Infection  Volume 22, Issue 2, Pages 178.e11-178.e22 (February 2016) DOI: 10.1016/j.cmi.2015.10.008 Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 1 Phylum level composition of the microbiota in the biliary tract of patients with benign biliary pathology and extrahepatic cholangiocarcinoma. Proteobacteria dominated (over 60%) in all patients, and the top nine phyla represented on average 99.48% of the composition in all cases. Clinical Microbiology and Infection 2016 22, 178.e11-178.e22DOI: (10.1016/j.cmi.2015.10.008) Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 2 Two-dimensional principal components analysis plot based on Unweighted UniFrac distance between samples of patients with benign biliary pathology and extrahepatic cholangiocarcinoma, given presence/absence of 4002 taxa present in at least one sample. Axis 1 explained 13% of variation, and Axis 2 explained 10% of variation. A partial separation of microbiota composition between cancer and control patients was observed (p 0.01, Adonis test). Clinical Microbiology and Infection 2016 22, 178.e11-178.e22DOI: (10.1016/j.cmi.2015.10.008) Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 3 Hierarchical clustering based on Weighted UniFrac distance between samples of patients with benign biliary pathology and extrahepatic cholangiocarcinoma, given abundance of 21 taxa with significant differences across at least one of the categories. Analyses revealed a distinct cluster of control and cancer cases. Clinical Microbiology and Infection 2016 22, 178.e11-178.e22DOI: (10.1016/j.cmi.2015.10.008) Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. 4 Network of gene functions generated with Cytoscape and ARACNE (Mutual information algorithm, MI = 0.7). The node colour indicates association with extrahepatic cholangiocarcinoma in red, association with benign biliary pathology in green, and functions present in both groups in yellow. The group of functions encircled in blue was identified as ‘Epithelial cell signaling in Helicobacter pylori infection’. Clinical Microbiology and Infection 2016 22, 178.e11-178.e22DOI: (10.1016/j.cmi.2015.10.008) Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. S1 Bacterial genus richness in the bile duct of patients with benign biliary pathology and extrahepatic cholangiocarcinoma ranged from 100 to 219 genera. No significant changes were detected between cancer and control samples (non-paired, heteroskedastic Student's t-test). Clinical Microbiology and Infection 2016 22, 178.e11-178.e22DOI: (10.1016/j.cmi.2015.10.008) Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions

Fig. S3 Abundance of Helicobacter pylori operational taxonomic units (OTU) in the biliary tract of patients with extrahepatic cholangiocarcinoma (ca.) and benign biliary pathology (co.). Abundance of H. pylori was significantly higher in patients with extrahepatic cholangiocarcinoma (p 0.035 Mann–Whitney U test). Clinical Microbiology and Infection 2016 22, 178.e11-178.e22DOI: (10.1016/j.cmi.2015.10.008) Copyright © 2015 European Society of Clinical Microbiology and Infectious Diseases Terms and Conditions