title: Improving the microbial community reconstruction at the genus level by multiple 16S rRNA regions.
abstract: 16S rRNA genes have been widely used for phylogenetic reconstruction and the quantification of microbial diversity through the application of next-generation sequencing technology. However, long-read sequencing is still costly, while short-read sequencing carries less information for complex microbial community profiling; therefore, the applications of high throughput sequencing platforms still remain challenging in microbial community reconstruction analysis.
  
  
  
  Here, we developed a method to investigate the profile of aligned 16S rRNA gene sequences and to measure the proper region for microbial community reconstruction, as a step in creating a more efficient way to detect microorganism at the genus level. Finally, we found that each genus has its own preferential genus-specific amplicons for a genus assignment, which are not always located in hyper variable regions (HVRs). It was also noted that the rare genera should contribute less than dominant ones to the common profile of the aligned 16S rRNA sequences and have lower affinity to the common universal primer.
  
  
  
  Therefore, using multiple 16S rRNA regions rather than one "universal" region can significantly improve the ability of microbial community reconstruction. In addition, we found that a short fragment is suitable for most genera identifications, and the proper conserved regions used for primer design are larger than before.
authors.affiliation: College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
authors.forename: Shengqin
authors.initials: S
authors.lastname: Wang
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
authors.forename: Beili
authors.initials: B
authors.lastname: Sun
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
authors.forename: Jing
authors.initials: J
authors.lastname: Tu
authors.affiliation: State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100781, China. Electronic address: zhlu@seu.edu.cn.
authors.forename: Zuhong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D001483:Base Sequence; D017124:Conserved Sequence / Q000235:genetics; D064307:Microbiota / Q000235:genetics*; D009690:Nucleic Acid Conformation; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics*
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: Genus-specific fragment; High throughput sequencing; Hyper-variable region