Gut Microbiota and Immunotherapy: Baseline 16S rRNA Profiling as a Pragmatic Tool for Clinical Stratification

The gut microbiota is a complex and dynamic ecosystem involved in the modulation of host immune responses. Accumulating evidence links gut microbial composition to the efficacy and toxicity of immune checkpoint inhibitors (ICIs), although most evidence supporting microbiota-based biomarkers remains observational. Higher baseline alpha-diversity has been associated with favorable outcomes in several cohorts, but these associations are not uniform, and individual taxonomic signatures show substantial inter-study variability. In this perspective, we discuss baseline microbiota profiling as a promising investigational approach to patient stratification in immuno-oncology. Despite its methodological limitations, 16S rRNA sequencing remains a scalable, reproducible, and clinically feasible approach compared with more complex techniques such as shotgun metagenomics. Standardization of sampling procedures, sequencing methodologies, and bioinformatic pipelines is essential for the reliable implementation of microbiota-based biomarkers in routine clinical care. Integrating gut microbiota assessment into pre-treatment evaluation may improve patient selection and support a more biologically informed approach to immunotherapy.