Altered composition of the oral microbiome in integrin beta 6-deficient mouse

Figures & data

Figure 1. The micro-CT images and analysis of 3- and 6-month-old Itgb6^−/− and WT mouse molar teeth.

a-d, Micro-CT scan of the maxillary molar region of 3- and 6-month-old Itgb6^−/− and WT mice. a, 3-month-old WT mouse; b, 3-month-old Itgb6^−/− mouse; c, 6-month-old WT mouse; d, 6-month-old Itgb6^−/− mouse. e, the analysis of vertical distance between the ridge of bone and CEJ in mesial and distal of 2nd molar of 3- and 6-month-old Itgb6^−/− and WT mice. n = 6 animals per group; Mean ± SEM; *, p < 0.05; **, p < 0.01; ***, p < 0.001. Scale bars = 500 μm.

Figure 2. The histological view of periodontal tissues in 3- and 6-month-old Itgb6^−/− and WT mice.

a-h, Representative images of H&E staining of the maxillary 2nd molar region of 3- and 6-month-old Itgb6^−/− and WT mice. a and c, 3-month-old WT mouse; b and d, 3-month-old Itgb6^−/− mouse; eand g, 6-month-old WT mouse; f and h, 6-month-old Itgb6^−/− mouse. a, b, e and f, original magnification ×4; Scale bars = 20 μm; c, d, g and h, show mesial of the maxillary 2nd molar, original magnification ×20; Scale bars = 100 μm.

Figure 3. The alpha diversity measurements of the oral microbiome in 3- and 6-month-old Itgb6^−/− and WT mice.

a, Scatter dot plot comparing total observed features in the 3- and 6-month-oldItgb6^−/− (KO) mice (KO_3M and KO_6M, respectively) and wide-type (WT) mice (WT_3M and WT_6M); b, Good’s coverage; c, Chao1 diversity index; d, ACE diversity index; e, Shannon diversity index; f, Simpson diversity index. n = 6 animals per group; Mean ± SEM is presented. Significances for diversity measurements: A; WT_3M vs WT_6M p<0.05; vs KO_3M p<0.001; vs KO_6M <0.01; C; WT3 vs KO3 p<0.001; vs KO6 <0.01; D; WT3 vs KO3 p<0.001; WT3 vs KO6 <0.01; E; KO_3M vs all the others p<0.001; F; WT3 vs all the others p<0.001.

Figure 4. The beta diversity patterns of Principal Coordinate Analysis (PCoA).

A, The PCoA of unweighted UniFrac distances of oral microbiomes in 3- and 6-month-old Itgb6^−/− and WT mice; B, The PCoA of weighted UniFrac distances of oral microbiomes in 3- and 6-month-old Itgb6^−/− and WT mice. Each dot represents an individual mouse, and each mouse group is represented by different colors. n = 6 animals per group.

Figure 5. The taxonomic composition of the oral microbiome in 3- and 6-month-old Itgb6^−/− and WT mice.

The genus level analysis in bacterial composition using the QIIME 2 database between the Itgb6^−/− (KO) and wide-type (WT) mice at ages of 3 and 6 months. Left, Taxonomic composition alterations of individual samples of oral microbiome in 3- and 6-month-oldItgb6^−/− (KO_3M and KO_6M) and WT mice (WT_3M and WT_6M); Right, The mean of taxonomic composition alterations of oral microbiome in groups of 3- and 6-month-oldItgb6^−/− and WT mice. n = 6 animals per group.

Table 1. The ANCOM results and percentile abundances of features in each group.

The ANCOM results and percentile abundances of features in each group	Median Percentile Abundance				Max Percentile Abundance				W
	WT3M	WT 6M	KO 3M	KO 6M	WT 3M	WT 6M	KO 3M	KO 6M
k_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Rikenellaceae;g_Alistipes	73	88	8.5	1	103	299	16	1	84
k_Bacteria;p_Bacteroidota;c_Bacteroidia;o_Bacteroidales;f_Tannerellaceae;g_Parabacteroides	184.5	1	1	187	264	9	1	266	84
k_Bacteria;p_Campilobacterota;c_Campylobacteria;o_Campylobacterales;f_Helicobacteraceae;g_Helicobacter	1	1	1	60.5	1	1	1	84	83
k_Bacteria;p_Desulfobacterota;c_Desulfovibrionia;o_Desulfovibrionales;f_Desulfovibrionaceae;g_uncultured	351.5	34.5	1	26	443	62	1	38	71
k_Bacteria;p_Firmicutes;c_Clostridia;o_Lachnospirales;f_Lachnospiraceae;g_Lachnospiraceae_NK4A136_group	371.5	7.5	1	1	644	62	1	7	68
k_Bacteria;p_Proteobacteria;c_Gammaproteobacteria;o_Enterobacterales;f_Enterobacteriaceae;g_Escherichia-Shigella	98	1	1	1	167	32	1	1	64

Figure 6. The Linear Discriminant Analysis Effect Size (LEfSe) of 3- and 6-month-old Itgb6^−/−and WT mice.

LEfSe analysis was used to compare the differences of bacterial profiles at taxonomic levels from phylum to genus in percent abundance among 3- and 6-month-oldItgb6^−/− (KO3 and KO6) and WT mice (WT3 and WT6). a, The bar graph of LEfSe analysis among 3- and 6-month-oldItgb6^−/− and WT mice. Linear discriminant analysis (LDA) scores > 4. n = 6 animals per group; b, The cladogram of LEfSe analysis among 3- and 6-month-oldItgb6^−/− and WT mice. Linear discriminant analysis (LDA) scores > 4. n = 6 animals per group.

Figure 7. LEfSe analysis of oral microbiomes in 3- and 6-month-old Itgb6^−/− and WT mice.

LEfSe analysis was used to compare the differences of bacterial profiles at taxonomic levels from phylum to genus in percent abundance between 3- and 6-month-oldItgb6^−/− (KO3 and KO6) and WT mice (WT3 and WT6). a and b, LEfSe analysis between 3- and 6-month-old WT mice; c and d, LEfSe analysis between 3- and 6-month-oldItgb6^−/− mice; e and f, LEfSe analysis between 3-month-oldItgb6^−/− and WT mice; g and h, LEfSe analysis between 6-month-oldItgb6^−/− and WT mice. All linear discriminant analysis (LDA) scores > 4. n = 6 animals per group.