title: Comparative analysis of microbiome between accurately identified 16S rDNA and quantified bacteria in simulated samples.
abstract: Although 16S rRNA gene (rDNA) sequencing is the gold standard for categorizing bacteria or characterizing microbial communities its clinical utility is limited by bias in metagenomic studies, in either the experiments or the data analyses. To evaluate the efficiency of current metagenomic methods, we sequenced seven simulated samples of ten bacterial species mixed at different concentrations. The V3 region of 16S rDNA was targeted and used to determine the distribution of bacterial species. The number of target sequences in individual simulated samples was in the range 1-1000 to provide a better reflection of natural microbial communities. However, for a given bacterial species present in the same proportion but at different concentrations, the observed percentage of 16S rDNAs was similar, except at very low concentrations that cannot be detected by real-time PCR. These results confirmed that the comparative microbiome in a sample characterized by 16S rDNA sequencing is sufficient to detect not only potential infectious pathogens, but also the relative proportion of 16S rDNA in the sample.
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, PR China.
authors.forename: Haiyin
authors.initials: H
authors.lastname: Wang
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, PR China.
authors.forename: Pengcheng
authors.initials: P
authors.lastname: Du
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, PR China.
authors.forename: Juan
authors.initials: J
authors.lastname: Li
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, PR China.
authors.forename: Yuanyuan
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, PR China.
authors.forename: Wen
authors.initials: W
authors.lastname: Zhang
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, PR China.
authors.forename: Na
authors.initials: N
authors.lastname: Han
authors.affiliation: Carol Yu Centre for Infection, University of Hong Kong, PR China.|State Key Laboratory of Emerging Infectious Diseases, Research Centre of Infection and Immunology, Department of Microbiology, University of Hong Kong, Hong Kong, PR China.
authors.forename: Patrick C Y
authors.initials: PCY
authors.lastname: Woo
authors.affiliation: National Institute for Communicable Disease Control and Prevention, Center for Disease Control and Prevention, State Key Laboratory for Infectious Disease Prevention and Control, Beijing 102206, PR China.
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
mesh_terms: D000333:Aeromonas / Q000145:classification* / Q000235:genetics; D001483:Base Sequence; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D004755:Enterobacteriaceae / Q000145:classification* / Q000235:genetics; D006801:Humans; D054892:Metagenome; D064307:Microbiota; D012329:RNA, Bacterial / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013211:Staphylococcus aureus / Q000145:classification* / Q000235:genetics
chemical_list: D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S