Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis
Abstract
1. Introduction
2. Results
2.1. Sequence Overview of Plaque Samples
2.2. Taxonomic Composition Analysis
2.3. Functional Gene Category Analysis
3. Discussion
4. Materials and Methods
4.1. Sample Collection
4.2. DNA Extraction, Library Preparation and Sequencing
4.3. Sequencing Data Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample Name | Indiv. No. | Status of Individual | Sampling Site and Status | Age | Sex 1 | Raw Reads | Reads for Metagenomic Analysis |
---|---|---|---|---|---|---|---|
HH1 | 1 | Healthy | 46, Healthy | 29 | M | 5,775,202 | 1,402,887 |
HH2 | 2 | Healthy | 46, Healthy | 43 | M | 3,831,266 | 204,308 |
HH3 | 3 | Healthy | 46, Healthy | 37 | M | 5,422,140 | 995,685 |
HH4 | 4 | Healthy | 46, Healthy | 41 | F | 4,866,418 | 1,100,826 |
HH5 | 5 | Healthy | 46, Healthy | 31 | F | 4,247,496 | 1,089,164 |
HH6 | 6 | Healthy | 46, Healthy | 27 | M | 4,265,064 | 663,850 |
PH11_2 | 11 | Periodontitis | 43, Healthy | 48 | M | 2,624,566 | 548,873 |
PH12_1 | 12 | Periodontitis | 23, Healthy | 69 | M | 1,205,826 | 695,215 |
PH12_2 | 12 | Periodontitis | 25, Healthy | 69 | M | 2,697,604 | 1,750,204 |
PH14 | 14 | Periodontitis | 43, Healthy | 48 | F | 8,165,844 | 239,717 |
PH15 | 15 | Periodontitis | 12, Healthy | 79 | M | 7,358,454 | 366,238 |
PH17 | 17 | Periodontitis | 24, Healthy | 56 | F | 2,125,774 | 278,004 |
PH23_1 | 23 | Periodontitis | 23, Healthy | 42 | M | 2,340,430 | 463,933 |
PH25_1 | 25 | Periodontitis | 41, Healthy | 43 | M | 5,952,692 | 1,716,829 |
PH25_2 | 25 | Periodontitis | 41, Healthy | 43 | M | 4,593,914 | 1,556,673 |
PH26_2 | 26 | Periodontitis | 31, Healthy | 60 | M | 4,678,568 | 225,769 |
PH29 | 29 | Periodontitis | 27, Healthy | 58 | F | 5,253,782 | 516,845 |
PH30 | 30 | Periodontitis | 13, Healthy | 76 | M | 6,012,650 | 390,445 |
PH31 | 31 | Periodontitis | 23, Healthy | 46 | F | 4,890,982 | 213,660 |
PP12_2 | 12 | Periodontitis | 25, Periodontal pocket | 69 | M | 2,398,604 | 1,894,262 |
PP13_1 | 13 | Periodontitis | 26, Periodontal pocket | 47 | F | 327,016 | 245,066 |
PP13_2 | 13 | Periodontitis | 25, Periodontal pocket | 47 | F | 309,300 | 306,024 |
PP14_1 | 14 | Periodontitis | 16, Periodontal pocket | 48 | F | 7,440,288 | 535,904 |
PP14_2 | 14 | Periodontitis | 27, Periodontal pocket | 48 | F | 7,213,688 | 630,156 |
PP15_1 | 15 | Periodontitis | 11, Periodontal pocket | 79 | M | 7,346,724 | 414,834 |
PP15_2 | 15 | Periodontitis | 47, Periodontal pocket | 79 | M | 6,530,194 | 350,097 |
PP16_1 | 16 | Periodontitis | 24, Periodontal pocket | 55 | F | 1,904,568 | 452,740 |
PP16_2 | 16 | Periodontitis | 26, Periodontal pocket | 55 | F | 3,093,452 | 226,275 |
PP17 | 17 | Periodontitis | 47, Periodontal pocket | 56 | F | 3,646,976 | 297,839 |
PP18_1 | 18 | Periodontitis | 16, Periodontal pocket | 36 | F | 1,604,552 | 439,199 |
PP18_2 | 18 | Periodontitis | 25, Periodontal pocket | 36 | F | 3,920,256 | 912,649 |
PP21_1 | 21 | Periodontitis | 27, Periodontal pocket | 50 | M | 1,099,140 | 998,367 |
PP21_2 | 21 | Periodontitis | 13, Periodontal pocket | 50 | M | 2,426,890 | 987,197 |
PP22 | 22 | Periodontitis | 37, Periodontal pocket | 48 | F | 7,794,000 | 1,322,677 |
PP23 | 23 | Periodontitis | 35, Periodontal pocket | 42 | M | 8,557,728 | 1,484,973 |
PP24_1 | 24 | Periodontitis | 13, Periodontal pocket | 59 | F | 5,485,608 | 262,343 |
PP24_2 | 24 | Periodontitis | 16, Periodontal pocket | 59 | F | 8,658,802 | 768,780 |
PP25_1 | 25 | Periodontitis | 27, Periodontal pocket | 43 | M | 9,030,826 | 2,508,972 |
PP25_2 | 25 | Periodontitis | 47, Periodontal pocket | 43 | M | 6,575,378 | 817,066 |
PP26_1 | 26 | Periodontitis | 18, Periodontal pocket | 60 | M | 1,427,528 | 1,008,404 |
PP26_2 | 26 | Periodontitis | 37, Periodontal pocket | 60 | M | 11,622,702 | 440,551 |
PP27 | 27 | Periodontitis | 24, Periodontal pocket | 56 | F | 8,580,870 | 3,233,325 |
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Izawa, K.; Okamoto-Shibayama, K.; Kita, D.; Tomita, S.; Saito, A.; Ishida, T.; Ohue, M.; Akiyama, Y.; Ishihara, K. Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis. Int. J. Mol. Sci. 2021, 22, 5298. https://doi.org/10.3390/ijms22105298
Izawa K, Okamoto-Shibayama K, Kita D, Tomita S, Saito A, Ishida T, Ohue M, Akiyama Y, Ishihara K. Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis. International Journal of Molecular Sciences. 2021; 22(10):5298. https://doi.org/10.3390/ijms22105298
Chicago/Turabian StyleIzawa, Kazuki, Kazuko Okamoto-Shibayama, Daichi Kita, Sachiyo Tomita, Atsushi Saito, Takashi Ishida, Masahito Ohue, Yutaka Akiyama, and Kazuyuki Ishihara. 2021. "Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis" International Journal of Molecular Sciences 22, no. 10: 5298. https://doi.org/10.3390/ijms22105298
APA StyleIzawa, K., Okamoto-Shibayama, K., Kita, D., Tomita, S., Saito, A., Ishida, T., Ohue, M., Akiyama, Y., & Ishihara, K. (2021). Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis. International Journal of Molecular Sciences, 22(10), 5298. https://doi.org/10.3390/ijms22105298