Gut microbiota is associated with persistence of longer-term vaccine immunogenicity after two doses of BNT162b2

Ho Yu Ng ¹ YUNSHI LIAO ² Ching-Lung Cheung ³ Ruiqi Zhang ⁴ Kwok Hung Chan ⁵ Wai-Kay Seto ⁴ Wai K Leung ⁴ Ivan FN Hung ⁴ Tommy Tsan-Yuk Lam ^2,6,7 Ka Shing Cheung ^4*

• ¹ LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, SAR China
• ² State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, SAR China
• ³ Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, SAR China
• ⁴ Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, SAR China
• ⁵ Department of Microbiology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, SAR China
• ⁶ Centre for Immunology & Infection Limited, Hong Kong, Hong Kong, SAR China
• ⁷ Laboratory of Data Discovery for Health Limited, Hong Kong, Hong Kong, SAR China

Introduction: BNT162b2 immunogenicity wanes with time and we investigated association between gut microbiota and longer-term immunogenicity. Methods: This cohort study prospectively recruited adult BNT162b2 two-dose recipients from three vaccination centers in Hong Kong. Blood samples were collected at baseline and day180 after first dose, and tested for neutralising antibodies (NAb) against receptor-binding domain (RBD) of wild type SARS-CoV-2 virus using chemiluminescence immunoassay. Shotgun DNA metagenomic sequencing was performed to characterize baseline stool microbiome. Baseline metabolites were measured by gas and liquid chromatography-tandem mass spectrometry (GC-MS/MS and LC-MS/MS). Primary outcome was persistent high NAb response (defined as top 25% of NAb level) at day180. Putative bacterial species and metabolic pathways were identified using linear discriminant analysis [LDA] effect size analysis. Multivariable logistic regression adjusting for clinical factors was used to derive adjusted odds ratio (aOR) of outcome with bacterial species and metabolites. Results: Of 242 subjects (median age:50.2years[IQR:42.5-55.6];male:85[35.1%]), 61(25.2%) were high-responders while 33(13.6%) were extreme-high responders (defined as NAb≥200AU/mL). None had COVID-19 at end of study. Ruminococcus bicirculans (log10LDA score=3.65), Parasutterella excrementihominis (score=2.82) and Streptococcus salivarius (score=2.31) were enriched in high-responders, while Bacteroides thetaiotaomicron was enriched in low-responders (score=-3.70). On multivariable analysis, bacterial species (R. bicirculans–aOR:1.87,95%CI:1.02-3.51;P. excrementihominis–aOR: 2.2,95%CI:1.18-4.18;S. salivarius–aOR:2.09,95%CI:1.13-3.94) but not clinical factors associated with high response. R. bicirculans positively correlated with most metabolic pathways enriched in high-responders, including superpathway of L-cysteine biosynthesis (score=2.25) and L-isoleucine biosynthesis I pathway (score=2.16) known to benefit immune system. Baseline serum butyrate (aOR:10.00,95%CI:1.81-107.2) and isoleucine (aOR:1.17,95%CI:1.04-1.35) significantly associated with extreme-high vaccine response. Conclusion: Certain gut bacterial species, metabolic pathways and metabolites associate with longer-term COVID-19 vaccine immunogenicity.