NDLI: Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population

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Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population

Content Provider	Taylor & Francis Online
Author	Albarrag, Ahmed Basode, Vinod Kumar Al-hebshi, Nezar Noor Chen, Tsute Abdulhaq, Ahmed
Abstract	BackgroundReports 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.ObjectiveThe objective of this study was to characterize the healthy core oral bacteriome in a young Arab population at the species level.MethodsOral 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.ResultsOverall, 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.ConclusionsA 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.
File Format	PDF HTM / HTML
ISSN	20002297
DOI	10.3402/jom.v8.31444
Journal	Journal of Oral Microbiology
Volume Number	8
Issue Number	1
Language	English
Publisher	Taylor & Francis
Publisher Date	2016-05-17
Access Restriction	Open
Subject Keyword	Core Human High-throughput nucleotide sequencing Microbiome Mouth Pyrosequencing
Content Type	Text
Resource Type	Article
Subject	Microbiology (medical) Dentistry Infectious Diseases 3500/3501

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