Clinical Detection of Chronic Rhinosinusitis through Next-Generation Sequencing of the Oral Microbiota
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patient Recruitment
2.2. Saliva and Nasal Swab of DNA Extraction
2.3. PCR Amplification and 16S Sequencing
2.4. Bioinformatics Analysis
3. Results
3.1. CRS Patients Had a Lower Diversity of the Nasal Microbiome
3.2. Operational Taxonomic Units (OTUs) of the Phylum and Species Level among Different Groups
3.3. Specific Microbial Markers in CRS Patients
3.4. A Novel Microbial Ratio from Saliva to Distinguish CRS Patients from the Control Group
3.5. Microbiome-Related Functional Pathways in Chronic Rhinosinusitis
3.6. Comparison of Clinical Aerobic Culture and NGS Approaches
4. Discussion
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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SINNS1 | SINNS2 | SINNS3 | SINNS4 | SINNS5 | SINNS6 | SINNS7 | SINNS8 | SINNS9 | SINNS10 | SINNS11 | SINNS12 | SINNS13 | SINNS14 | SINNS15 | SINNS16 | SINNS17 | SINNS18 | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Common aerobic culture (Nasopharynx) | Staphylococcus aureus | No beta Streptococcus group A | No beta Streptococcus group A | No beta Streptococcus group A | Pseudomonas aeruginosa | No beta Streptococcus group A | No beta Streptococcus group A | No beta Streptococcus group A | No beta Streptococcus group A | No beta Streptococcus group A | Staphylococcus pneumoniae | No beta Streptococcus group A | No beta Streptococcus group A | Haemophilus influenzae | No beta Streptococcus group A | No beta Streptococcus group A | No beta Streptococcus group A | No beta Streptococcus group A |
NGS | 62.43% | 48.81% | 0.268% | 2.59% | ||||||||||||||
NGS: Aerobes | ||||||||||||||||||
Staphylococcus aureus | 62.43% | 0% | 0.006% | 0% | 0% | 0% | 0% | 0.006% | 0% | 0.341% | 0% | 0.005% | 0% | 0% | 0.003% | 0.105% | 0% | 40.028% |
Streptococcus pyogenes | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% |
Streptococcus pneumoniae | 0% | 0% | 0% | 0% | 0% | 0.011% | 0% | 0% | 0% | 0% | 0.268% | 0% | 0.001% | 0% | 0% | 0% | 0% | 0% |
Haemophilus influenza | 0% | 0% | 0% | 0% | 0% | 21.003% | 0% | 0% | 0% | 0.057% | 0% | 0.001% | 0.01% | 2.59% | 0% | 0% | 0% | 0% |
Moraxella catarrhalis | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0.001% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0% |
Pseudomonas aeruginosa | 0% | 0% | 0% | 0.001% | 48.81% | 0% | 0.003% | 0.003% | 0% | 0.118% | 0% | 0% | 0% | 0% | 0% | 0.012% | 0.002% | 0.117% |
NGS: Anaerobes- periodontopathogens | ||||||||||||||||||
Porphyromonas gingivalis | 0% | 0% | 0% | 0% | 0.001% (Saliva: 2.246%) | 0% | 0% | 0.228% (Saliva: 0.598%) | 0% | 0.042% (Saliva: 0.322%) | 0% | 0% | 0% | 0.023% (Saliva: 0.246%) | 0.001% (Saliva: 0.472%) | 0.001% (Saliva: 0%) | 0.2% (Saliva: 0.097%) | 0% |
Porphyromonas endodontalis | 0% | 3.352% (Saliva: 0.069%) | 43.814% (Saliva: 0.039%) | 0.008% (Saliva: 0.012%) | 0% | 0.001% (Saliva: 0.14%) | 0.002% (Saliva: 0.03%) | 2.33% (Saliva: 10.161%) | 21.005% (Saliva:0.254 %) | 44.197% (Saliva:0.355 %) | 0.003% (Saliva: 0.245%) | 11.3% (Saliva: 1.223%) | 19.587% (Saliva:0.002 %) | 15.89% (Saliva:0.834 %) | 0.286% (Saliva:0.468%) | 11.323% (Saliva: 0.856%) | 31.165% (Saliva: 1.186%) | 0.007% (Saliva: 0.015%) |
Fusobacterium nucleatum | 0% | 1.57% (Saliva: 0.133%) | 0.487% (Saliva: 0.089%) | 0% | 0% | 0% | 0% | 0.183% (Saliva: 0.789%) | 0.942% (Saliva: 0.031%) | 1.151% (Saliva: 0.214%) | 0.005% (Saliva: 0.125%) | 9.509% (Saliva: 1.027%) | 0.219% (Saliva: 0.026%) | 7.014% (Saliva: 0.383%) | 0.001% (Saliva: 0.284%) | 11.012% (Saliva: 0.154%) | 20.261% (Saliva: 2.068%) | 0% |
Prevotella oris | 0% | 27.092% (Saliva: 1.31%) | 28.478% (Saliva: 0.15%) | 0.014% (Saliva: 0.02%) | 0% | 0% | 0.001% (Saliva: 0.03%) | 0.986% (Saliva: 8.238%) | 0.004% (Saliva: 0.001%) | 11.349% (Saliva: 0.427%) | 0.003% (Saliva: 0.036%) | 6.93% (Saliva: 1.219%) | 0.004% (Saliva: 0.032%) | 0.003% (Saliva: 0.019%) | 0.256% (Saliva: 0.03%) | 0.001% (Saliva: 0.025%) | 0.001% (Saliva: 0.111%) | 0.002% (Saliva: 0.262%) |
Prevotella intermedia | 0% | 0.159% (Saliva: 0.024%) | 0.076% (Saliva: 0.022%) | 0.014% (Saliva: 0.02%) | 0% | 0% | 0.001% (Saliva: 0.288%) | 0% | 0% | 0% | 0% | 0.001% (Saliva: 0.223%) | 0.584% (Saliva: 0.001%) | 0.061% (Saliva: 0.17%) | 0.001% (Saliva: 0.753%) | 0.002% (Saliva: 0.002%) | 0% | 0% |
Treponema Denticola | 0% | 0% | 0% | 0% | 0% | 0% | 0% | 0.146% (Saliva: 0.469%) | 2.507% (Saliva: 0.012%) | 0.001% (Saliva: 0.07%) | 0% | 0% | 0% | 0.001% (Saliva: 0.073%) | 0% | 0.001% (Saliva: 0.002%) | 0.713% (Saliva: 0.42%) | 0% |
Tannerella Forsythia | 0% | (Saliva: 0.066%) | 0.001% (Saliva: 0.092%) | 0.001% (Saliva: 0.003%) | 0% | 0% | 0.001% (Saliva: 0.017%) | 0.038% (Saliva: 0.17%) | 0.007% (Saliva: 0.011%) | 0.015% (Saliva: 0.046%) | 0% | 0.247% (Saliva: 0.056%) | 0% | 0.016% (Saliva: 0.022%) | 0% | 0.002% (Saliva: 0.002%) | 0.733% (Saliva: 0.264%) | 0% |
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Yuan, B.-C.; Yeh, Y.-T.; Lin, C.-C.; Huang, C.-H.; Liu, H.-C.; Chiang, C.-P. Clinical Detection of Chronic Rhinosinusitis through Next-Generation Sequencing of the Oral Microbiota. Microorganisms 2020, 8, 959. https://doi.org/10.3390/microorganisms8060959
Yuan B-C, Yeh Y-T, Lin C-C, Huang C-H, Liu H-C, Chiang C-P. Clinical Detection of Chronic Rhinosinusitis through Next-Generation Sequencing of the Oral Microbiota. Microorganisms. 2020; 8(6):959. https://doi.org/10.3390/microorganisms8060959
Chicago/Turabian StyleYuan, Ben-Chih, Yao-Tsung Yeh, Ching-Chiang Lin, Cheng-Hsieh Huang, Hsueh-Chiao Liu, and Chih-Po Chiang. 2020. "Clinical Detection of Chronic Rhinosinusitis through Next-Generation Sequencing of the Oral Microbiota" Microorganisms 8, no. 6: 959. https://doi.org/10.3390/microorganisms8060959