Comparative Analysis of Indole Derivative Production Among Clinical Isolates of Fusobacterium nucleatum

Pathogenic bacteria adapt to distinct disease environments, but whether these adaptations create therapeutic vulnerabilities remains unclear. Fusobacterium nucleatum has emerged as a key microbial player in colorectal cancer (CRC), yet the molecular mechanisms underlying its niche-specific virulence remain poorly defined. In this study, we investigated whether F. nucleatum displays disease-specific vulnerabilities to indole derivatives across 16 clinical isolates from CRC (n=6), Crohns disease (n=6), healthy individuals (n=3), and an oral lesion (n=1). Using HPLC, we found that CRC-associated isolates produced a 3-4-fold higher level of endogenous indole compared to healthy isolates (p < 0.05), including indole, indole-3-acetic acid (IAA), and indole-3-carboxylic acid (I3CA), which is a metabolite enriched in CRC patient samples. Exogenous indole derivatives (0.25-2 mM) selectively suppressed CRC isolates, exhibiting 40-50% reductions in biofilm formation (*p < 0.001) and bacterial invasion of colon cancer cells, while non-CRC isolates displayed minimal or no response. Mechanistically, indole derivatives triggered distinct, disease-specific changes in virulence gene expression, with naive Bayes classifier achieving 90% accuracy in disease association (AUC = 0.90-0.92; accuracy = 0.74-0.75; p < 2 x 10-16). This disease-adapted vulnerability was independent of subspecies identity, suggesting niche-specific phenotypes. Furthermore, exogenous indole derivatives, I3A and indole, strengthened epithelial tight junction gene expression while inhibiting bacterial invasion, demonstrating dual host-protective and pathogen-suppressive effects. These findings establish a key disease-adapted indole sensitivity that could enable selective suppression of pathogenic populations of F. nucleatum while preserving beneficial commensals.