Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population
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 existenc...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2016-05-01
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| Series: | Journal of Oral Microbiology |
| Subjects: | |
| Online Access: | http://www.journaloforalmicrobiology.net/index.php/jom/article/view/31444/46703 |
| _version_ | 1828192363258839040 |
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| author | Nezar Noor Al-hebshi Ahmed Abdulhaq Ahmed Albarrag Vinod Kumar Basode Tsute chen |
| author_facet | Nezar Noor Al-hebshi Ahmed Abdulhaq Ahmed Albarrag Vinod Kumar Basode Tsute chen |
| author_sort | Nezar Noor Al-hebshi |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T08:53:38Z |
| format | Article |
| id | doaj.art-38ad17f848a0497c833ca9d26430ee92 |
| institution | Directory Open Access Journal |
| issn | 2000-2297 |
| language | English |
| last_indexed | 2024-04-12T08:53:38Z |
| publishDate | 2016-05-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Journal of Oral Microbiology |
| spelling | doaj.art-38ad17f848a0497c833ca9d26430ee922022-12-22T03:39:27ZengTaylor & Francis GroupJournal of Oral Microbiology2000-22972016-05-01801910.3402/jom.v8.3144431444Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab populationNezar Noor Al-hebshi0Ahmed Abdulhaq1Ahmed Albarrag2Vinod Kumar Basode3Tsute chen4 Department of Preventive Dentistry, College of Dentistry, Jazan University, Jazan, Saudi Arabia Unit of Medical Microbiology, Department Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia Unit of Medical Microbiology, Department Medical Laboratory Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia Department of Microbiology, Forsyth Institute, Cambridge, MA, USABackground: 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.http://www.journaloforalmicrobiology.net/index.php/jom/article/view/31444/46703corehumanhigh-throughput nucleotide sequencingmicrobiomemouthpyrosequencing |
| spellingShingle | Nezar Noor Al-hebshi Ahmed Abdulhaq Ahmed Albarrag Vinod Kumar Basode Tsute chen Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population Journal of Oral Microbiology core human high-throughput nucleotide sequencing microbiome mouth pyrosequencing |
| title | Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population |
| title_full | Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population |
| title_fullStr | Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population |
| title_full_unstemmed | Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population |
| title_short | Species-level core oral bacteriome identified by 16S rRNA pyrosequencing in a healthy young Arab population |
| title_sort | species level core oral bacteriome identified by 16s rrna pyrosequencing in a healthy young arab population |
| topic | core human high-throughput nucleotide sequencing microbiome mouth pyrosequencing |
| url | http://www.journaloforalmicrobiology.net/index.php/jom/article/view/31444/46703 |
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