comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine焦磷酸测序和系统发育的比较分析微阵列为探索人类远端肠道微生物群落结构.pdfVIP

Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine 1,2 3 4 ¨ 5 1,2¤ Marcus J. Claesson *, Orla O’Sullivan , Qiong Wang , Janne Nikkila , Julian R. Marchesi , Hauke Smidt6, Willem M. de Vos5,6, R. Paul Ross2,3, Paul W. O’Toole1,2 1 Department of Microbiology, University College Cork, Cork, Ireland, 2 Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland, 3 Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland, 4 Center for Microbial Ecology and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America, 5 Department of Basic Veterinary Medicine, Division of Microbiology and Epidemiology, University of Helsinki, Helsinki, Finland, 6 Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands Abstract Background: Variations in the composition of the human intestinal microbiota are linked to diverse health conditions. High- throughput molecular technologies have recently elucidated microbial community structure at much higher resolution than was previously possible. Here we compare two such methods, pyrosequencing and a phylogenetic array, and evaluate classifications based on two variable 16S rRNA gene regions. Methods and Findings: Over 1.75 million amplicon sequences were generated from the V4 and V6 regions of 16S rRNA genes in bacterial DNA extracted from four fecal samples of elderly individuals. The phylotype richness, for individual samples, was 1,400–1,800 for V4 reads and 12,500 for V6 reads, and 5,200 unique phylotypes when combining V4 reads from all samples.