Multi-omics analysis of the gut microbiome and carotid artery atherosclerosis in men with and without HIV

Figures

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  Fig. 1. Overview of the study design. The MACS/WIHS Combined Cohort Study (MWCCS) is a multicenter cohort of individuals living with or at risk for HIV infection. In this study, we included a total of 359 eligible participants (MACS men; 60.5% living with HIV) who underwent B-mode carotid artery ultrasound for atherosclerotic plaque assessment and provided fecal samples for gut microbiome profiling via shotgun metagenomics sequencing. In addition, we measured circulating metabolites using liquid chromatography–mass spectrometry (LC-MS), and proteomic inflammatory markers using the Olink Explore 3072/384 platform. We performed integrated multi-omics analyses to examine associations of gut microbial features, circulating metabolomic profiles, and proteomic inflammatory markers with carotid artery plaque, in the context of HIV infection.

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  Fig. 2. Associations between microbial taxa and carotid artery plaque status (n=359). (A) Associations between species and plaque status (multivariable logistic regression). Results are odds ratios (ORs) and 95% confidence intervals (CIs) for carotid artery plaque per standard deviation increment of CLR transformed abundance of gut microbial species, adjusted for age, race/ethnicity, study site, antibiotic use, income, education, BMI, current smoking, alcohol, HIV status and ART use. (B) Integrated phylogenetic tree. Taxa from inner to outer circle represent bacterial kingdom to species level. Blue and red fonts represent positive and negative associations between species and carotid artery plaque, respectively. (C) Partial Spearman correlations between plaque-associated bacterial species and traditional CVD risk factors, adjusted for the aforementioned covariates (∗P < 0.05, partial Spearman correlation). Abbreviations: BMI, body mass index; SBP, Systolic blood pressure; DBP, Diastolic blood pressure; HDL, high-density lipoprotein; LDL, low-density lipoprotein; HbA1C, haemoglobin A1c.

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  Fig. 3. Gut microbiota, circulating metabolites, proteomic inflammatory markers, and carotid artery plaque status (n=359). Associations of identified plaque-associated bacterial species with (A) host circulating metabolites and (B) proteomic inflammatory markers. Partial Spearman correlations were performed with adjustment for age, race/ethnicity, study site, antibiotic use, income, education, body mass index, alcohol use, smoking, and HIV status. (C) Associations of microbial-associated circulating metabolites and proteomic inflammatory markers with plaque status, adjusted for the aforementioned covariates. Results are odds ratios and 95% confidence intervals (CIs) for carotid artery plaque per standard deviation change in the CLR transformed abundance of each metabolite, metabolite module, or inflammatory marker. The complete lists of metabolites comprising the PC and SM modules, together with their inter-metabolite correlation structure, are provided in Fig. S6. PCs, phosphatidylcholines; SMs, sphingomyelins.

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  Fig. 4. Associations between microbial species and plaque status, with and without adjustment for microbial-related metabolites and/or microbial-related proteomic inflammatory markers (n=359). Data are odds ratios (ORs) and 95% confidence intervals (CIs) for carotid artery plaque per standard deviation increment of CLR-transformed abundance of each gut microbial species. Model 1: adjusted for age, race/ethnicity, study site, antibiotic use, income, education, body mass index, current smoking, alcohol, HIV status and antiretroviral therapy use. Model 2: adjusted for covariates in Model 1 + circulating metabolites relevant to each specific species. Model 3: adjusted for covariates in Model 1 + proteomic inflammatory markers relevant to each specific species. Model 4: adjusted for covariates in Model 1 + circulating metabolites and proteomic inflammatory markers relevant to each specific species.