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Oral microbiome of deep and shallow dental pockets in chronic periodontitis.

Ge X, Rodriguez R, Trinh M, Gunsolley J, Xu P - PLoS ONE (2013)

Bottom Line: Fifty-one of 170 genera and 200 of 746 species were found significantly different in abundances between shallow and deep sites.Besides previously identified periodontal disease-associated bacterial species, additional species were found markedly changed in diseased sites.Cluster analysis revealed that the microbiome difference between deep and shallow sites was influenced by patient-level effects such as clinic location, race and smoking.

View Article: PubMed Central - PubMed

Affiliation: VCU Philips Institute of Oral and Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America.

ABSTRACT
We examined the subgingival bacterial biodiversity in untreated chronic periodontitis patients by sequencing 16S rRNA genes. The primary purpose of the study was to compare the oral microbiome in deep (diseased) and shallow (healthy) sites. A secondary purpose was to evaluate the influences of smoking, race and dental caries on this relationship. A total of 88 subjects from two clinics were recruited. Paired subgingival plaque samples were taken from each subject, one from a probing site depth >5 mm (deep site) and the other from a probing site depth ≤3mm (shallow site). A universal primer set was designed to amplify the V4-V6 region for oral microbial 16S rRNA sequences. Differences in genera and species attributable to deep and shallow sites were determined by statistical analysis using a two-part model and false discovery rate. Fifty-one of 170 genera and 200 of 746 species were found significantly different in abundances between shallow and deep sites. Besides previously identified periodontal disease-associated bacterial species, additional species were found markedly changed in diseased sites. Cluster analysis revealed that the microbiome difference between deep and shallow sites was influenced by patient-level effects such as clinic location, race and smoking. The differences between clinic locations may be influenced by racial distribution, in that all of the African Americans subjects were seen at the same clinic. Our results suggested that there were influences from the microbiome for caries and periodontal disease and these influences are independent.

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Related in: MedlinePlus

Genus-level OTUs with >1.0% of abundance in at least one patient in deep and/or shallow sites.Colors reflect the abundance of OTUs from high (red) to low (black); gray, OTU missing.
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pone-0065520-g002: Genus-level OTUs with >1.0% of abundance in at least one patient in deep and/or shallow sites.Colors reflect the abundance of OTUs from high (red) to low (black); gray, OTU missing.

Mentions: We collected a total of 2,299,090 sequences, 1,790,237 of which qualified sequences were considered (as defined as described in Materials and Methods) and were analyzed further. All raw sequences were deposited in the NCBI Sequence Read Archive (access number SRA061999). The average was about 10,000 sequences per sample. Sequence barcoding indexes were associated with patient samples for analysis. Sequences were grouped for genera by operational taxonomic units (OTUs) using Ribosomal Database Project (RDP) Classifier 2.2. Microbial species were classified using BLAST search against HOMD 16S rRNA database. A total of 170 and 746 independent microbial genera and species were identified within the samples analyzed. For every deep and shallow site sampled, the percentage of each individual genus and species from the overall microbial abundance was calculated. The richness and diversity of OTUs at both genus and species levels were analyzed by the Shannon diversity index [26] and paired t-test (Figure 1). The results indicated that the microbiome in deep sites had higher numbers of both genera and species and a greater range of diversity values than shallow sites, and this difference was statistically significant (P<0.05). Based on genus-level OTUs, the dominant genera (average abundance >1.0% of the total per subjects) included Streptococcus, Prevotella, Fusobacterium, Actinomyces, Porphyromonas, Leptotrichia, Veillonella, Corynebacterium, Treponema, Capnocytophaga, Selenomonas, Lactobacillus, Rothia, Tannerella, and Parvimonas in both deep and shallow sites (Figure 2). There were 35 other genera present at an abundance >1.0% of the population in at least one patient each (Figure 2).


Oral microbiome of deep and shallow dental pockets in chronic periodontitis.

Ge X, Rodriguez R, Trinh M, Gunsolley J, Xu P - PLoS ONE (2013)

Genus-level OTUs with >1.0% of abundance in at least one patient in deep and/or shallow sites.Colors reflect the abundance of OTUs from high (red) to low (black); gray, OTU missing.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3675156&req=5

pone-0065520-g002: Genus-level OTUs with >1.0% of abundance in at least one patient in deep and/or shallow sites.Colors reflect the abundance of OTUs from high (red) to low (black); gray, OTU missing.
Mentions: We collected a total of 2,299,090 sequences, 1,790,237 of which qualified sequences were considered (as defined as described in Materials and Methods) and were analyzed further. All raw sequences were deposited in the NCBI Sequence Read Archive (access number SRA061999). The average was about 10,000 sequences per sample. Sequence barcoding indexes were associated with patient samples for analysis. Sequences were grouped for genera by operational taxonomic units (OTUs) using Ribosomal Database Project (RDP) Classifier 2.2. Microbial species were classified using BLAST search against HOMD 16S rRNA database. A total of 170 and 746 independent microbial genera and species were identified within the samples analyzed. For every deep and shallow site sampled, the percentage of each individual genus and species from the overall microbial abundance was calculated. The richness and diversity of OTUs at both genus and species levels were analyzed by the Shannon diversity index [26] and paired t-test (Figure 1). The results indicated that the microbiome in deep sites had higher numbers of both genera and species and a greater range of diversity values than shallow sites, and this difference was statistically significant (P<0.05). Based on genus-level OTUs, the dominant genera (average abundance >1.0% of the total per subjects) included Streptococcus, Prevotella, Fusobacterium, Actinomyces, Porphyromonas, Leptotrichia, Veillonella, Corynebacterium, Treponema, Capnocytophaga, Selenomonas, Lactobacillus, Rothia, Tannerella, and Parvimonas in both deep and shallow sites (Figure 2). There were 35 other genera present at an abundance >1.0% of the population in at least one patient each (Figure 2).

Bottom Line: Fifty-one of 170 genera and 200 of 746 species were found significantly different in abundances between shallow and deep sites.Besides previously identified periodontal disease-associated bacterial species, additional species were found markedly changed in diseased sites.Cluster analysis revealed that the microbiome difference between deep and shallow sites was influenced by patient-level effects such as clinic location, race and smoking.

View Article: PubMed Central - PubMed

Affiliation: VCU Philips Institute of Oral and Craniofacial Molecular Biology, Virginia Commonwealth University, Richmond, Virginia, United States of America.

ABSTRACT
We examined the subgingival bacterial biodiversity in untreated chronic periodontitis patients by sequencing 16S rRNA genes. The primary purpose of the study was to compare the oral microbiome in deep (diseased) and shallow (healthy) sites. A secondary purpose was to evaluate the influences of smoking, race and dental caries on this relationship. A total of 88 subjects from two clinics were recruited. Paired subgingival plaque samples were taken from each subject, one from a probing site depth >5 mm (deep site) and the other from a probing site depth ≤3mm (shallow site). A universal primer set was designed to amplify the V4-V6 region for oral microbial 16S rRNA sequences. Differences in genera and species attributable to deep and shallow sites were determined by statistical analysis using a two-part model and false discovery rate. Fifty-one of 170 genera and 200 of 746 species were found significantly different in abundances between shallow and deep sites. Besides previously identified periodontal disease-associated bacterial species, additional species were found markedly changed in diseased sites. Cluster analysis revealed that the microbiome difference between deep and shallow sites was influenced by patient-level effects such as clinic location, race and smoking. The differences between clinic locations may be influenced by racial distribution, in that all of the African Americans subjects were seen at the same clinic. Our results suggested that there were influences from the microbiome for caries and periodontal disease and these influences are independent.

Show MeSH
Related in: MedlinePlus