Oral microbiota study of the patients after hospitalisation for COVID-19, considering selected dental indices and antibiotic therapy using the next generation sequencing method (NGS)

Figures & data

Table 1. The result of one-way analysis of variance (ANOVA) for age and seed dental indices between the study groups.

Study parameters	Total (n = 60)	Group I (n = 17)	Group II (n = 23)	Group III (n = 20)	P
Age [years]; M ± SD	53.03 ± 14.28	54.06 ± 11.83	54.65 ± 16.68	50.30 ± 13.47	0.580
DMFT index; M ± SD	53.12 ± 20.07	60.29 ± 15.41^b	60.29 ± 15.10^a	33.90 ± 10.72^a,b	<0.001*
PI index [%]; M ± SD	18.48 ± 7.52	20.00 ± 3.08^a	18.61 ± 6.06	15.40 ± 5.42^a	0.011*
D number; M ± SD	3.12 ± 4.10	3.65 ± 2.60^b	5.35 ± 5.14^a	0.10 ± 0.31^a,b	<0.001*

DMFT – Decayed, Missing and Filled Teeth, PI – Plaque Index simplified, D Decayed, n – number of people in the study group; M – mean; SD – standard deviation; P -significance level; means marked with the same letter in the superscript differ from each other at the level of *P < 0.05.

Table 2. Alpha diversity (assessed by richness Chao1, Shannon and Simpson), and beta diversity indices (estimated by the Bray-Curtis, Jensen-Shannon and Jaccard indices) in the studied groups (group I vs. Group II vs. Group III).

Clinical materials	Alpha diversity indices P-values			Beta diversity indices P-values
	Chao1	Shannon	Simpson	Bray-Curtis	Jensen-Shannon	Jaccard
Saliva	<0.001	<0.009	0.06	0.001	0.001	0.001
Subgingival plaque	<0.001	<0.001	0.001	0.001	0.001	0.001
Supragingival plaque	0.004	0.003	0.009	0.001	0.001	0.001
Tongue ridge	0.001	<0.001	0.003	0.001	0.001	0.001

P < 0.05 the significance level.

Figure 1. Relative percentage distribution of bacteria from the mouth on COVID-19 infection and taking antimicrobials at the phylum level (L2) depending on clinical material: saliva (Figure 1a), tongue ridge (Figure 1b), subgingival plaque (Figure 1c) and supragingival plaque (Figure 1d), respectively.

All taxa with relative percentages below 1% are shown as “other”. Logarithmic scale (log base 10).

Figure 1. (Continued).

Figure 2. Relative percentage distribution of bacteria from the mouth on COVID-19 infection and taking antimicrobials at the genus level (L6) depending on clinical material: saliva (Figure 2a), tongue ridge (Figure 2b), subgingival plaque (Figure 2c) and supragingival plaque (Figure 2d), respectively.

All taxa with relative percentages below 1% are shown as “other”. Logarithmic scale (log base 10).

Figure 2. (Continued).

Figure 3. Increase and decrease the number of studied bacteria at the phylum (L2) and genus (L6) level in COVID-19 convalescents who received antibiotics during hospitalization compared to the control (left side of figure) and COVID-19 infection without antimicrobial treatment compared to the control group (right side of the figure) taking antimicrobials depending on clinical material: saliva, tongue ridge, subgingival plaque, supragingival plaque, respectively.

Table 3. Correlations between selected dental indices and types of bacteria in the examined clinical materials for the groups of patients included in the study.

Groups	Investigated factors	Bacteria genus	Clinical materials
			Saliva		Tongue ridge		Subgingival plaque		Supragingival plaque
			Spearman’s Rho	P-value	Spearman’s Rho	P-value	Spearman’s Rho	P-value	Spearman’s Rho	P-value
I	D	Cardiobacterium	−0.347	0.172	−0.283	0.272	−0.168	0.518	−0.527	0.030*
	D	Fusobacterium	0.601	0.011*	0.489	0.047*	0.002	0.992	0.117	0.655
	D	Leptotrichia	0.516	0.034*	0.354	0.163	0.370	0.144	0.207	0.426
	PI	Eikenella	0.028	0.916	−0.557	0.020*	−0.034	0.897	−0.121	0.644
	PI	Prevotella	0.333	0.192	0.498	0.042*	0.472	0.056	0.383	0.129
	PI	Selenomonas	0.297	0.247	0.320	0.211	0.564	0.018*	0.305	0.233
	DMFT	Corynebacterium	−0.379	0.133	−0.295	0.250	−0.664	0.005*	−0.478	0.052
	DMFT	Fusobacterium	−0.142	0.587	−0.054	0.838	−0.324	0.204	−0.528	0.029*
	DMFT	Leptotrichia	−0.714	0.001*	−0.802	0.001*	−0.616	0.009*	−0.566	0.018*
	DMFT	Rothia	−0.376	0.137	−0.291	0.257	−0.497	0.042*	−0.326	0.202
II	D	Cardiobacterium	−0.413	0.05*	−0.527	0.012*	−0.327	0.128	−0.412	0.051
	D	Prevotella	−0.389	0.067	−0.006	0.978	0.322	0.133	0.610	0.02*
	D	Rothia	−0.050	0.822	0.144	0.522	−0.286	0.186	−0.448	0.032*
	PI	Fusobacterium	0.302	0.161	0.042	0.853	0.414	0.05*	−0.168	0.443
	PI	Selenomonas	0.316	0.142	0.124	0.582	0.416	0.048*	0.314	0.145
	DMFT	Prevotella	−0.419	0.047*	0.034	0.881	0.114	0.604	0.391	0.065
	DMFT	Rothia	−0.165	0.452	0.068	0.764	−0.169	0.440	−0.486	0.019*
	DMFT	Selenomonas	0.092	0.677	−0.133	0.555	0.392	0.064	0.475	0.022*
	DMFT	Veillonella	−0.244	0.261	0.075	0.739	−0.610	0.02*	−0.294	0.173
III	D	Eikenella	0.528	0.017*	−0.033	0.894	0.130	0.585	0.174	0.464
	D	Rothia	−0.202	0.392	−0.501	0.029*	−0.202	0.392	−0.029	0.904
	D	Selenomonas	0.463	0.040*	0.189	0.440	0.260	0.268	0.173	0.465
	PI	Corynebacterium	−0.565	0.009*	−0.218	0.370	−0.211	0.372	−0.281	0.231
	DMFT	Aggregatibacter	−0.257	0.274	−0.506	0.027*	−0.025	0.917	−0.059	0.806
	DMFT	Akkermansia	0.142	0.549	0.177	0.470	0.499	0.025*	0.553	0.011*
	DMFT	Corynebacterium	−0.526	0.017*	−0.004	0.989	0.044	0.855	0.023	0.925
	DMFT	Fusobacterium	−0.412	0.071	−0.520	0.023*	−0.099	0.678	−0.315	0.176
	DMFT	Haemophilus	−0.415	0.069	−0.465	0.045*	−0.323	0.165	−0.376	0.102
	DMFT	Porphyromonas	−0.435	0.055	−0.481	0.037*	−0.109	0.647	−0.331	0.154

Group I – patients after COVID-19 disease, subjected to antibiotic therapy during treatment; Group II – patients after COVID-19 disease, not subjected to antibiotic therapy during treatment; Group III – healthy patients who have not been infected with the SARS-CoV-2 virus and have not been treated with antibiotics (control group); DMFT – Decayed, Missing and Filled Teeth; PI -Plaque Index simplified; D – Decayed; P < 0.05 the significance level, correlation power (Spearman’s Rho): 0.0–0.3 – weak, 0.3–0.5 – moderate, 0.5–1.0 – strong.