Non-Intestinal Microbial Signatures in Stool as Predictors of Cancer Immunotherapy Outcome

Despite advances in immunotherapy, clinical responses remain heterogeneous, underscoring the need to elucidate the gut microbiome’s role in modulating therapeutic efficacy. We conducted a large-scale genome-resolved metagenomic analysis of 624 stool samples from 11 cohorts spanning five cancer types from three continents to identify conserved microbial biomarkers of immunotherapy response. Responders (R; n = 362) exhibited enrichment of Blautia species, linked to acetate production from CO ₂ via the Wood-Ljungdahl (WL) pathway, glycoside hydrolases (GH), and amino acid biosynthesis. Non-responders (NR; n = 262) showed increased oral (e.g. Veillonella parvula, Dialister invisus ) and food-derived taxa included opportunistic species e.g. Citrobacter freundii, Klebsiella spp., alongside depletion of gut-resident microbes and enriched lipopolysaccharide biosynthesis and flagellar assembly pathways. Interestingly, part of NR-associated microbes originated from non-intestinal niches (oral/food), which may correlate with reduced gut microbial load in the large intestine. These findings redefine dietary interventions as dual-edged: while carbon sources such as fiber processed by GH or CO ₂ processed by WL pathway supports beneficial taxa and immune system, pathogen-free food sourcing is critical to avoid introducing opportunistic microbes. Our work establishes the resident-to-transient microbial ratio as a novel predictive biomarker and positions Blautia as a keystone genus for next-generation probiotics targeting carbon metabolism-immune crosstalk. By integrating taxonomic, functional, and ecological axes, this study provides a roadmap for microbiome-guided precision nutrition to optimize immunotherapy outcomes. While immunotherapy non-responders exhibit gut microbiota enriched with food/oral commensals, Faecalibacterium prausnitzii - shows context-dependent associations, with strain-level variations potentially linked to A blood group antigen N-acetylgalactosamine utilization, highlighting its role as a conditional biomarker and the prognostic value of metagenomics in personalized therapy.