Metagenomic Sequencing of the Gut Microbiome Identifies Specific Short-Chain Fatty Acid Producing Taxa Correlated with Response to Anti-PD-1 Immunotherapy in Melanoma Patients

Immune checkpoint inhibitors targeting Programmed Cell Death Protein 1 (Anti-PD-1) have revolutionized the therapeutic landscape for advanced melanoma, yet primary resistance remains a major clinical challenge. Emerging evidence underscores the gut microbiome as a pivotal regulator of systemic anti-tumor immunity. In this prospective observational study, shotgun metagenomic sequencing was performed on baseline fecal samples from 68 patients with metastatic melanoma prior to initiating anti-PD-1 therapy (pembrolizumab or nivolumab). Taxonomic and functional profiling revealed that objective clinical responders possessed significantly higher gut alpha-diversity and an enrichment of short-chain fatty acid (SCFA)-producing species, notably Faecalibacterium prausnitzii, Roseburia intestinalis, and Eubacterium rectale. Metabolic pathway reconstruction demonstrated enriched genes involved in pyruvate fermentation to butyrate and acetate in responders. Targeted serum and fecal metabolomics confirmed elevated concentrations of butyrate in responding patients, which correlated positively with peripheral blood CD8+ effector memory T cell activation and prolonged progression-free survival (hazard ratio 0.42, 90% CI 0.23-0.76, p = 0.004). Conversely, non-responders exhibited an overrepresentation of Bacteroides thetaiotaomicron and pathways associated with lipopolysaccharide biosynthesis. These findings establish specific SCFA-producing taxa and their metabolic output as key determinants of anti-PD-1 efficacy, presenting candidate biomarkers and actionable targets for microbiome-targeted therapeutic interventions in melanoma.