a method for metagenomics of helicobacter pylori from archived formalin-fixed gastric biopsies permitting longitudinal studies of carcinogenic risk幽门螺杆菌的宏基因组方法存档formalin-fixed胃活检允许纵向研究的致癌风险.pdfVIP

A Method for Metagenomics of Helicobacter pylori from Archived Formalin-Fixed Gastric Biopsies Permitting Longitudinal Studies of Carcinogenic Risk 1,2 3 1 ´ 1 2,4 2,4 Zongli Zheng , Anders F. Andersson , Weimin Ye , Olof Nyren , Staffan Normark , Lars Engstrand * 1 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden, 2 Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden, 3 Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden, 4 Swedish Institute for Communicable Disease Control, Solna, Sweden Abstract The human microbiota has come into focus in the search for component causes of chronic diseases, such as gastrointestinal cancers. Presumably long induction periods and altered local environments after disease onset call for the development of methods for characterization of microorganisms colonizing the host decades before disease onset. Sequencing of microbial genomes in old formalin-fixed and paraffin-embedded (FFPE) gastrointestinal biopsies provides a means for such studies but is still challenging. Here we report a method based on laser capture micro-dissection and modified Roche 454 high- throughput pyrosequencing to obtain metagenomic profiles of Helicobacter pylori. We applied this method to two 15 year old FFPE biopsies from two patients. Frozen homogenized biopsies from the same gastroscopy sessions were also available for comparison after re-culture of H. pylori. For both patients, H. pylori DNA dissected from FFPE sections had ,96.4% identity with culture DNA from the same patients, while only ,92.5% identity with GenBank