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Background: Neutralizing antibody level wanes with time after COVID-19 vaccination. We aimed to study the relationship between baseline gut microbiota and immunogenicity after three doses of CoronaVac. Methods: This was a prospective cohort study recruiting three-dose CoronaVac recipients from two centers in Hong Kong. Blood samples were collected at baseline and one year post-first dose for virus microneutralization (vMN) assays to determine neutralization titers. The primary outcome was high immune response (defined as with vMN titer ≥ 40). Shotgun DNA metagenomic sequencing of baseline fecal samples identified potential bacterial species and metabolic pathways using Linear Discriminant Analysis Effect Size (LEfSe) analysis. Univariate and multivariable logistic regression models were used to identify high response predictors. Results: In total, 36 subjects were recruited (median age: 52.7 years [IQR: 47.9–56.4]; male: 14 [38.9%]), and 18 had low immune response at one year post-first dose vaccination. <i>Eubacterium rectale</i> (log₁₀LDA score = 4.15, <i>p</i> = 0.001; relative abundance of 1.4% vs. 0, <i>p</i> = 0.002), <i>Collinsella aerofaciens</i> (log₁₀LDA score = 3.31, <i>p</i> = 0.037; 0.39% vs. 0.18%, <i>p</i> = 0.038), and <i>Streptococcus salivarius</i> (log₁₀LDA score = 2.79, <i>p</i> = 0.021; 0.05% vs. 0.02%, <i>p</i> = 0.022) were enriched in low responders. The aOR of high immune response with <i>E. rectale, C. aerofaciens</i>, and <i>S. salivarius</i> was 0.03 (95% CI: 9.56 × 10⁻⁴–0.32), 0.03 (95% CI: 4.47 × 10⁻⁴–0.59), and 10.19 (95% CI: 0.81–323.88), respectively. <i>S. salivarius</i> had a positive correlation with pathways enriched in high responders like incomplete reductive TCA cycle (log₁₀LDA score = 2.23). <i>C. aerofaciens</i> similarly correlated with amino acid biosynthesis-related pathways. These pathways all showed anti-inflammation functions. Conclusion: <i>E. rectale,</i><i>C. aerofaciens</i>, and <i>S. salivarius</i> correlated with poorer long-term immunogenicity following three doses of CoronaVac.