Analyzing proteins from gut bacteria in 1,967 Chinese adults revealed aging drives specific functional shifts in carbon metabolism and energy production across four major bacterial phyla. Metabolic diseases consistently showed depletion of Bacillota species and their proteins responsible for carbohydrate metabolism, energy production, and short-chain fatty acid synthesis. Megasphaera elsdenii emerged as a key species in type 2 diabetes, with experimental validation showing antidiabetic drugs promote its growth while it regulates glucose through butyrate production. This metaproteomic approach moves beyond traditional DNA sequencing to examine actual bacterial protein function, offering unprecedented insight into how gut microbes contribute to metabolic health. The findings suggest aging fundamentally rewires gut bacterial metabolism, creating conditions that predispose to disease. The consistent protein depletion patterns across diabetes, hypertension, and dyslipidemia indicate shared microbial mechanisms underlying metabolic syndrome. While the study's Chinese population limits generalizability, the protein-level evidence provides concrete therapeutic targets. This represents a methodological advance that could reshape how we understand and treat age-related metabolic decline through targeted microbiome interventions.