Journal of Prevention and Treatment for Stomatological Diseases ›› 2021, Vol. 29 ›› Issue (3): 157-165.DOI: 10.12016/j.issn.2096-1456.2021.03.003
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Received:
2020-04-24
Revised:
2020-05-30
Online:
2021-03-20
Published:
2021-01-12
Contact:
Jie XU
Supported by:
通讯作者:
徐杰
作者简介:
杨万娟,住院医师,硕士研究生在读,Emai:基金资助:
CLC Number:
YANG Wanjuan,XU Jie. High-throughput sequencing analysis of the microbiota of subgingival plaque in patients with periodontitis[J]. Journal of Prevention and Treatment for Stomatological Diseases, 2021, 29(3): 157-165.
杨万娟,徐杰. 牙周炎患者龈下菌斑菌群的高通量测序分析[J]. 口腔疾病防治, 2021, 29(3): 157-165.
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Figure 1 Histogram of relative abundance of dominant bacteria in each group at different classification levels a: phylum; b: genus; c: species; GAgP: generalized aggressive periodontitis; SCP: severe chronic periodontitis; QA: GAgP baseline; MA: SCP baseline; QB: GAgP after treatment; MB: SCP after treatment
Figure 2 Relative abundance heatmap in genus level in GAgP group and SCP group before and after treatment The color represents the relative abundance value, the redder the color is, the higher the relative abundance is, the bluer the color is, the lower the relative abundance is; GAgP: generalized aggressive periodontitis; SCP: severe chronic periodontitis; QA: GAgP baseline; MA: SCP baseline; QB: GAgP after treatment; MB: SCP after treatment
GAgP | SCP | t | P | |
---|---|---|---|---|
Shannon index | 5.69 ± 0.46 | 5.67 ± 0.46 | 0.080 | 0.937 |
Simpson index | 0.94 ± 0.02 | 0.94 ± 0.25 | 0.280 | 0.782 |
Table 1 The α diversity index of GAgP and SCP at baseline
GAgP | SCP | t | P | |
---|---|---|---|---|
Shannon index | 5.69 ± 0.46 | 5.67 ± 0.46 | 0.080 | 0.937 |
Simpson index | 0.94 ± 0.02 | 0.94 ± 0.25 | 0.280 | 0.782 |
α diversity index | Shannon index | Simpson index | ||
---|---|---|---|---|
GAgP | SCP | GAgP | SCP | |
Baseline | 5.69 ± 0.46 | 5.67 ± 0.46 | 0.94 ± 0.02 | 0.94 ± 0.25 |
6th week after initial therapy | 5.07 ± 0.76 | 5.32 ± 0.44 | 0.91 ± 0.05 | 0.93 ± 0.22 |
t | 2.146 | 2.356 | 1.883 | 1.088 |
P | 0.057 | 0.035 | 0.089 | 0.296 |
Table 2 The α diversity index of GAgP and SCP before and after initial therapy
α diversity index | Shannon index | Simpson index | ||
---|---|---|---|---|
GAgP | SCP | GAgP | SCP | |
Baseline | 5.69 ± 0.46 | 5.67 ± 0.46 | 0.94 ± 0.02 | 0.94 ± 0.25 |
6th week after initial therapy | 5.07 ± 0.76 | 5.32 ± 0.44 | 0.91 ± 0.05 | 0.93 ± 0.22 |
t | 2.146 | 2.356 | 1.883 | 1.088 |
P | 0.057 | 0.035 | 0.089 | 0.296 |
Figure 3 Rarefaction curve a: shannon index curve; b: simpson index curve; with the increase of sequencing depth, when the sequence number is more than 50 000, it indicates that the sequencing quantity is enough to cover all strains
Figure 4 PCoA figure of the microbiota of subgingival plaque in each group before and after treatment a: PC1 vs. PC2 plot; b: PC3 vs. PC2 plot; c: PC1 vs. PC3 plot; GAgP: generalized aggressive periodontitis; SCP: severe chronic periodontitis; QA: GAgP baseline; MA: SCP baseline; QB: GAgP after treatment; MB: SCP after treatment; PC: principal coordinates; PCoA: principal coordinates analysis.
Figure 5 LEfSe analysis of the changes of subgingival microbiota in GAgP group before and after treatment In LEfSe, non parametric factorial Kruskal Wallis sum rank test was used to count the groups with significant difference in abundance, and then LDA was used to estimate the impact of species richness on the difference effect, but the effect of QA species richness on the difference effect cannot be calculated; a-b: phylum; c-d: class; e-f: order; GAgP: generalized aggressive periodontitis; SCP: severe chronic periodontitis; LEfSe: linear discriminant analysis effect size; LDA: linear discriminant analysis; QA: GAgP baseline; QB: GAgP after treatment
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