## 3 Results  
Table 1 displays basic patient data in groups with and without atherosclerosis. No significant difference was found between the two groups. Figure 1 shows the result of the LEFse analysis. 25 taxonomic groups were significant. Figure 1: Discriminant features between the two groups based on the LEFse method. Red bars represent taxa more abundant in the atherosclerotic group, green bars represent taxa more abundant in the non-atherosclerotic group. \begin{table}
\begin{tabular}{l c c c} \hline \hline  & **OSA + Atherosclerosis** & **OSA – Atherosclerosis** & \(p\) \\  & **(\(n=16\))** & **(\(n=6\))** & **(\(p\)** \\ \hline Age (years) & 63 (9) & 47 (19) & 0.09 \\ Gender (males \%) & 44 & 50 & 0.81 \\ BMI (kg/m\({}^{2}\)) & 28.1 (6.2) & 26.3 (3.3) & 0.39 \\ Smoking (\%) & 19 & 33 & 0.55 \\ Hypertension (\%) & 63 & 33 & 0.27 \\ Cardiovascular disease (\%) & 13 & 0 & 0.16 \\ Diabetes (\%) & 13 & 0 & 0.16 \\ Dyslipidemia (\%) & 44 & 50 & 0.81 \\ SBP (mmHg) & 131 (22) & 123 (15) & 0.35 \\ DBP (mmHg) & 81 (10) & 78 (10) & 0.48 \\ CRP (mg/L) & 33 (2.4) & 15.(1.3) & 0.09 \\ Total cholesterol (mmol/L) & 5.6 (1.3) & 5.7 (1.5) & 0.85 \\ LDL-C (mmol/L) & 3.1 (1.2) & 3.6 (1.4) & 0.56 \\ HDL-C (mmol/L) & 1.8 (1.6) & 14.(0.5) & 0.44 \\ Triglyceride (mmol/L) & 1.5 (0.5) & 1.6 (0.8) & 0.79 \\ AHI (1/h) & 14.1 (10.2) & 118.(7.6) & 0.58 \\ OOI (1/h) & 10.9 (7.1) & 7.4 (7) & 0.33 \\ TSP0\% & 2.9 (4) & 2.5 (4.4) & 0.87 \\ \hline AHI: a-pnoea-hypropnoea index; BMI: body mass index; CRP: C-reactive protein; DBP: diastolic blood pressure; HDL-C: high-density lipoprotein-cholesterol; LDL: low-density lipoprotein-cholesterol; ODI: oxygen desaturation index; OSA: obstructive sleep apnoea; SBP: systolic blood pressure; TST90%: percentage of total sleep time spent with saturation below 90%. & \\ \hline \end{tabular}
\end{table} 
Table 1: Descriptive analysis in the two groups. Figures 2 and 3 show the results of alpha diversity analyses at 2 taxonomic levels (phylum and genus); and Figures 4-7 show the results of beta diversity analyses at 4 taxonomic levels (phylum, class, family, and genus). Wilcoxon rank sum test between the genus level Shannon indexes of the groups: \(p\) = 0.1970, no significant difference between the groups (with alpha = 0.05). Figure 4: Beta diversity analyses at the phylum level: PCoA based on Bray–Curtis distance measure. Green: OSA – atherosclerosis. Red: OSA + atherosclerosis. Figure 5: Beta diversity analyses at the class level: PCoA based on Bray–Curtis distance measure. Green: OSA – atherosclerosis. Red: OSA + atherosclerosis. Figure 6: Beta diversity analyses at the family level: PCoA based on Bray–Curtis distance measure. Green: OSA – atherosclerosis. Red: OSA + atherosclerosis. Figure 7: Beta diversity analyses at the genus level: PCoA based on Bray–Curtis distance measure. Green: OSA – atherosclerosis. Red: OSA + atherosclerosis. There was no visible clustering in the PCoA space. Atherosclerosis positive group seemed to be more variable (of note, its sample size is much bigger than the other group, 16 vs. 6 samples). Next, we performed 2 linear regressions on the bilateral mean of maximal CCA IMT at 2 taxonomic levels, where the predictor variables were gender, age, and the Shannon index at the taxonomic levels of phylum and genus, respectively (Table 2.). Maximal CCA IMT is significantly associated with phylum-level diversity: a decrease in diversity correlates with an increase in IMT. As age and gender are included in the regression, the correlation is considered to be corrected. The effect of age also appears in regression. The correlation between Shannon index at the phylum taxonomic level and maximal CCA IMT is shown in Figure 8 as an effect plot based on regression. The results of PCAs are shown in Figures 9-12. Figure 11: The results of PCA at the family level. Green: OSA – atherosclerosis. Red: OSA + atherosclerosis. Figure 10: The results of PCA at the class level. Green: OSA – atherosclerosis. Red: OSA + atherosclerosis. Figure 9: The results of PCA at the phylum level.