Gut microbiota (GM) alterations and related metabolic outputs have been implicated in metabolic syndrome (MetS) and early cardiometabolic risk. However, the associations between GM alterations and MetS, and their relationship with the marked interindividual variability in cardiovascular risk, remain incompletely defined. We conducted a cross-sectional study in individuals with obesity (n = 176) to evaluate associations between GM features and MetS clinical traits using 16S amplicon profiling data. Prevalence of individual MetS traits was 37.4% for hyperglycemia, 23.4% for hypertriglyceridemia, 54.0% for hypertension, and 52.1% for low HDL cholesterol, with 51.1% of participants meeting criteria for MetS overall. Comparative analysis of 16S rRNA amplicon sequencing data identified a shared gut microbial signature comprising 45 ASVs across MetS clinical components. Members of Prevotellaceae and Ruminococcaceae were consistently reduced in MetS, whereas Veillonella and Streptococcus were enriched. Reduced microbial alpha diversity was observed in individuals with MetS. PICRUSt2-based functional inference indicated lower representation of pathways related to complex carbohydrate utilization and short-chain fatty acid (SCFA) metabolism in MetS-positive individuals. Our results, derived from two independent datasets, indicate that MetS is associated with a depletion of bacterial taxa involved in complex carbohydrate metabolism and SCFA production.