## 2 Materials and Methods  
Study Participants  
Caucasian subjects participating in the sleep cohort [18] (\(n\) = 142, 48 monozygotic, MZ and 23 dizygotic, DZ twin pairs, mean age 51 \(\pm\) 15 years) of the voluntary-based Hungarian Twin Registry [19; 20] who was diagnosed with OSA, underwent a carotid ultrasound examination and provided a stool sample for microbiome analysis were included. On the left and right common carotid artery (CCA) and the proximal segment of the internal carotid artery (ICA), the mean and maximal IMT, in addition to the presence of the plaques, were measured and detected. Based on the ultrasound examination, two groups were formed: OSA patients with and without atherosclerosis. Atherosclerosis was defined as if one person had at least one plaque either on the left, right, or both sides. Prior to the study, none of the subjects had been diagnosed with OSA or received any sort of OSA treatment. Pregnancy, prior carotid surgery, acute infection within three weeks of the study, underlying oncologic disease, inflammatory bowel disease, and acute respiratory, cardiac, and renal failure were among the exclusion criteria. Among patients with OSA, 16 subjects with atherosclerosis (aged 46-74 years, mean age 63 \(\pm\) 8.8 years, 56% female) and 6 subjects without atherosclerosis (aged 23-67 years, mean age 47 \(\pm\) 18.6 years, 50% female) met these criteria and classified into the two groups. Laboratory tests, blood pressure measurements, questionnaires  
Venous blood was collected by a professional nurse to measure triglycerides, total cholesterol, high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), and C-reactive protein (CRP). Blood pressure was also measured, in the morning. Self-report questionnaires were used to assess the presence of comorbidities such as hypertension, cardiovascular disease, diabetes, dyslipidemia, and other important influencing factors like smoking. Along with measuring body weight and height, BMI was also computed. Sleep Studies  
The sleep study was executed as published previously [9] using the Sommocreen Plus Tele PSG and the Sommocreen RC devices (Sommoctides GmbH, Randersacker, Germany). A 90% reduction in nasal airflow that lasts at least 10 s is referred to as apnoea. A nasal airflow reduction of 30% or more that lasts for at least 10 s accompanied by either arousal (on PSG) or a decrease in oxygen saturation of at least 3% (on both the PG and PSG) was referred to as hypopnoea. The proportion of the total sleep time that was below 90% of saturation (TST90%), the oxygen desaturation index (ODI), and the apnea-hypopnea index (AHI) were all calculated. If the AHI was 5/h or more, OSA was identified. Carotid Ultrasound  
The ultrasound scan used a high-resolution linear LM4-15B (15 MHz) transducer and a Samsung RS85 device in accordance with the previously described technique [4]. Plaque presence was detected along the CCA and the proximal segment of ICA, and semi-automated IMT measurements on the distal wall of the CCA distal segment were made at a distance of 0.5-2 cm from the bifurcation using the Arterial Analysis software. During the measurement, the software displays the specific vessel wall segment it detects and uses for the analysis on the screen of the ultrasound machine, which the examiner has the opportunity to override and modify, avoiding possible erroneous data and results from the fully automatic measurement. Stool Sample Collection and Procession, Bioinformatics and Statistical Analysis  
The procedure described in earlier publications [4; 21] was followed for the collection and processing of the stool samples and for the bioinformatics and statistical analysis. The participants received a detailed instruction manual, with a flow chart, for the purpose of standardized sampling, in which the importance of the short time between sampling and return, the prevention of external contamination, the quantity, proper storage, and packaging of the sample were highlighted.