Role of Gut Microbiome Composition in Modulating Host Response to Immunotherapy

Abstract

Response to immune checkpoint inhibitor therapy varies substantially among patients with advanced melanoma
even after accounting for established clinical and tumour-intrinsic predictors, and a growing body of evidence
implicates gut microbiome composition as an independent modulator of anti-tumour immune response, though the
specific taxa and mechanisms involved remain incompletely resolved and existing cohorts have been criticised for
taxonomic and geographic heterogeneity that complicates cross-study comparison. We performed shotgun
metagenomic sequencing of pre-treatment stool samples from 156 patients with advanced melanoma initiating
anti-PD-1 monotherapy across two clinical centres, paired with prospective response assessment by RECIST
criteria at twelve weeks, and complemented this observational analysis with a gnotobiotic mouse experiment
testing whether fecal microbiota transplantation from responder and non-responder patients causally influences
anti-PD-1 efficacy in a syngeneic melanoma model. Responders showed significantly higher relative abundance of
Akkermansia muciniphila and Faecalibacterium prausnitzii and higher overall species richness than
non-responders (Wilcoxon rank-sum, both P<0.001), and a random-forest classifier trained on species-level
relative abundance achieved an area under the receiver operating characteristic curve of 0.79 in cross-validation,
with Akkermansia muciniphila abundance the single most important predictive feature. Germ-free mice colonised
with responder-derived stool and subsequently challenged with anti-PD-1 therapy showed significantly reduced
tumour growth and higher intratumoural CD8+ T cell infiltration compared with mice colonised with non-responder
stool (P=0.003 and P=0.008 respectively), and this causal effect was substantially attenuated, though not fully
abolished, by selective depletion of Akkermansia muciniphila from responder-derived inoculum prior to
transplantation. These results provide converging observational and causal evidence that gut microbiome
composition, and Akkermansia muciniphila abundance specifically, contributes mechanistically to anti-PD-1
response in melanoma, supporting continued clinical development of microbiome-based biomarkers and
adjunctive interventions in this setting.