Fig. 1

Differentially abundant species according to carotid artery plaque status. A Taxonomic linear discriminative analysis (LDA) effect size (LefSe) analysis by carotid artery plaque status. B Integrated phylogenetic tree. Taxa from inner to outer circle represent bacteria kingdom to species level. Blue and red font represent positive and negative associations between species and plaque, respectively. C Associations between species and plaque status. Data are odds ratios (ORs) and 95% confidence intervals (CIs) for carotid artery plaque per standard deviation increment of CLR transformed abundance of gut bacterial species, adjusted for age, race, study site, antibiotics use, income, education, BMI, alcohol, smoking status, HIV status, and ART use (model 1) and further adjusted for blood pressure, total cholesterol, high-density lipoprotein cholesterol, antihypertensive medication use, and lipid-lowering medication use (model 2). In addition, we also show ANCOM2 detection level of each species, adjusting for aforementioned covariates in model 1. D Associations between gut microbiota functional enzymes, plaque-associated bacteria species, and carotid artery plaque status. The Spearman correlation heatmap include 11 microbial functional enzymes under carbon–nitrogen ligases category and the 6 plaque-associated bacterial species. Associations between the 11 microbial functional enzymes and carotid artery plaque status were estimated by linear regression models after adjustment for age, race, study site, antibiotics use, income, education, BMI, alcohol, smoking status, HIV status, and ART use