title: Evaluation of 16SpathDB 2.0, an automated 16S rRNA gene sequence database, using 689 complete bacterial genomes.
abstract: Interpretation of 16S rRNA sequences is a difficult problem faced by clinical microbiologists and technicians. In this study, we evaluated the updated 16SpathDB 2.0 database, using 689 16S rRNA sequences from 689 complete genomes of medically important bacteria. Among these 689 16S rRNA sequences, none was wrongly identified, with 35.8% reported as a single bacterial species having >98% identity with the query sequence (category 1), 63.9% reported as more than 1 bacterial species having >98% identity with the query sequence (category 2), 0.3% reported to the genus level (category 3), and none reported as no match (category 4). For the 16S rRNA sequences of non-duplicated bacterial species reported as category 1 or 2, the percentage of bacterial species reported as category 1 was significantly higher for anaerobic Gram-positive/Gram-negative bacteria than aerobic/facultative anaerobic Gram-positive/Gram-negative bacteria. 16SpathDB 2.0 is a user-friendly and accurate database for 16S rRNA sequence interpretation in clinical laboratories.
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China.
authors.forename: Jade L L
authors.initials: JL
authors.lastname: Teng
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China.
authors.forename: Tom C C
authors.initials: TC
authors.lastname: Ho
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China; Department of Pathology, United Christian Hospital, Hong Kong, China.
authors.forename: Ronald S Y
authors.initials: RS
authors.lastname: Yeung
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China.
authors.forename: Annette Y P
authors.initials: AY
authors.lastname: Wong
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, 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, China.
authors.forename: Chen
authors.initials: C
authors.lastname: Chen
authors.affiliation: Department of Pathology, United Christian Hospital, Hong Kong, China.
authors.forename: Kitty S C
authors.initials: KS
authors.lastname: Fung
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China. Electronic address: skplau@hkucc.hku.hk.
authors.forename: Susanna K P
authors.initials: SK
authors.lastname: Lau
authors.affiliation: Department of Microbiology, The University of Hong Kong, Hong Kong, China; Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China; State Key Laboratory of Emerging Infectious Diseases, Hong Kong, China; Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China. Electronic address: pcywoo@hku.hk.
authors.forename: Patrick C Y
authors.initials: PC
authors.lastname: Woo
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics; D015373:Bacterial Typing Techniques; D030561:Databases, Nucleic Acid; D016680:Genome, Bacterial; D010802:Phylogeny; D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S; D064878:Web Browser
chemical_list: D012329:RNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: 16S rRNA; 16SpathDB; Automated; Bacteria; Database; Evaluation; Genome