title: Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population.
abstract: BACKGROUND
  Reports on the composition of oral bacteriome in Arabs are lacking. In addition, the majority of previous studies on other ethnic groups have been limited by low-resolution taxonomic assignment of next-generation sequencing reads. Furthermore, there has been a conflict about the existence of a 'core' bacteriome.
  
  
  OBJECTIVE
  The objective of this study was to characterize the healthy core oral bacteriome in a young Arab population at the species level.
  
  
  METHODS
  Oral rinse DNA samples obtained from 12 stringently selected healthy young subjects of Arab origin were pyrosequenced (454's FLX chemistry) for the bacterial 16S V1-V3 hypervariable region at an average depth of 11,500 reads. High-quality, non-chimeric reads ≥380 bp were classified to the species level using the recently described, prioritized, multistage assignment algorithm. A core bacteriome was defined as taxa present in at least 11 samples. The Chao2, abundance-based coverage estimator (ACE), and Shannon indices were computed to assess species richness and diversity.
  
  
  RESULTS
  Overall, 557 species-level taxa (211±42 per subject) were identified, representing 122 genera and 13 phyla. The core bacteriome comprised 55 species-level taxa belonging to 30 genera and 7 phyla, namely Firmicutes, Proteobacteria, Actinobacteria, Bacteroidetes, Fusobacteria, Saccharibacteria, and SR1. The core species constituted between 67 and 87% of the individual bacteriomes. However, the abundances differed by up to three orders of magnitude among the study subjects. On average, Streptococcus mitis, Rothia mucilaginosa, Haemophilus parainfluenzae, Neisseria flavescence/subflava group, Prevotella melaninogenica, and Veillonella parvula group were the most abundant. Streptococcus sp. C300, a taxon never reported in the oral cavity, was identified as a core species. Species richness was estimated at 586 (Chao2) and 614 (ACE) species, whereas diversity (Shannon index) averaged at 3.99.
  
  
  CONCLUSIONS
  A species-level core oral bacteriome representing the majority of reads was identified, which can serve as a reference for comparison with oral bacteriomes of other populations as well as those associated with disease.
authors.affiliation: Department of Preventive Dentistry, College of Dentistry, Jazan University, Jazan, Saudi Arabia; nazhebshi@yahoo.com.
authors.forename: Nezar Noor
authors.initials: NN
authors.lastname: Al-Hebshi
authors.affiliation: Unit of Medical Microbiology, Department Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Abdulhaq
authors.affiliation: Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia.
authors.forename: Ahmed
authors.initials: A
authors.lastname: Albarrag
authors.affiliation: Unit of Medical Microbiology, Department Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.
authors.forename: Vinod Kumar
authors.initials: VK
authors.lastname: Basode
authors.affiliation: Department of Microbiology, Forsyth Institute, Cambridge, MA, USA.
authors.forename: Tsute
authors.initials: T
authors.lastname: Chen
keywords: core; high-throughput nucleotide sequencing; human; micgrobiome; mouth; pyrosequencing