Intratumoral Microbiome of Metastatic Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal oncological diseases, with a 5-year survival rate of approximately 13%—among the lowest in oncology. Poor survival is driven by aggressive tumor progression and metastasis, which may be influenced by the tumor microbiome. This study aimed to evaluate the role of microbiome in PDAC progression and metastasis. First, we assessed the microbial composition of control samples (surface swabs, empty paraffin, extraction controls, and sequencing controls) and removed contaminant taxa. Overall bacterial biomass was extremely low, with no significant differences in alpha or beta-diversity between tumor and normal tissue. Kocuria rosea was significantly enriched in tumors compared to normal tissue, and this difference persisted after decontamination. Metastatic tumors showed altered abundance of K. rosea and Herbaspirillum huttiense, whereas non-metastatic tumors differed in Lysobacter bugurensis, Caulobacter ginsengisoli, and H. huttiense relative to normal tissue. No global compositional differences were observed between KRAS-mutant and wild-type tumors; however, KRAS-mutant tumors exhibited differential enrichment of K. rosea and L. bugurensis relative to adjacent normal tissue. The PDAC microbiome harbors very low bacterial biomass and does not robustly distinguish tumor from normal tissue at the community level. Nonetheless, K. rosea emerges as a candidate taxon differentially enriched in PDAC, with potential stage- and KRAS-associated patterns. These findings highlight the need for orthogonal validation (qPCR, FISH, culture) and larger prospective cohorts to differentiate true biological associations from residual contamination or stochastic noise in low-biomass settings.