Fecal microbiota transplantation (FMT) has shown immunotherapeutic promise across multiple malignancies, yet its clinical efficacy in non-small-cell lung cancer (NSCLC) remains unexplored. Here, we report results from a single-arm trial demonstrating that FMT significantly enhances anti-PD-1 efficacy and prolongs progression-free survival in patients with advanced PD-L1-negative NSCLC. To understand the mechanistic basis of variable FMT outcomes, we developed a high-resolution strain-tracking framework and analyzed over 2,000 samples from FMT and longitudinal studies across NSCLC, melanoma, inflammatory bowel syndrome, recurrent Clostridioides difficile infection, type 2 diabetes, and healthy individuals.

Our analysis reveals that genetically distinct strains within the same bacterial species exert opposing therapeutic effects, explaining contradictory findings in previous reports. We discovered universal ecological principles governing strain persistence and engraftment that transcend disease contexts: engraftment success correlates with species-intrinsic fitness traits encoded in core metabolic and immune evasion pathways. Phylogenetic analysis revealed that key species segregate into functionally distinct clades with divergent clinical associations. Longitudinal tracking demonstrated that successful colonization by beneficial strain variants strongly associates with positive clinical outcomes. By integrating colonization dynamics with functional genomics, we identified 39 priority species exhibiting robust engraftment potential and strain-specific therapeutic effects as candidates for precision microbiome therapeutics. These findings establish a strain-function-efficacy paradigm that resolves inconsistent clinical outcomes in microbiome interventions and provides a framework for next-generation therapeutic development.

The authors have declared no competing interest.

CHiCTR2300076829

The project was funded by the National Natural Science Foundation of China (32170003, 32370099), the Provincial-level Talent Program for National Center of Technology Innovation for Biopharmaceuticals (NCTIB2024JS0101), the Natural Science Foundation of Jiangsu Province (BK20243008), the Suzhou Top-Notch Talent Groups (ZXD2022003).

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This study was approved by the Ethics Committee of The First Affiliated Hospital of Soochow University and the Ethics Committee of Soochow University, with approval numbers (2021) 026 and SUDA20250701H01, respectively.

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