Spatial atlas highlights contribution of C. difficile in early-stage colorectal cancer

作者：Nicholas O. Markham, Julia L. Drewes, Emily H. Green, William E Ball, Hannah M. Lunnemann, Alan J Simmons, Harsimran Kaur, Jessica Queen, Abby L. Geis, Maryam Pourmaleki, Bryan R. Helm, Erik Storrs, Marisol Ramirez-Solano, Xiang Li, Zhicheng Ma, PhD Frank Revetta, Annika Windon, M Kay Washington, Jane W. Wanyiri, Thevambiga Iyadorai, April C. Roslani, Jamuna Vadivelu, Jonathan Coggin, Leslie M. Meenderink, D Borden Lacy, C. Curtis, Siyuan Ma, Li Ding, Qi Liu, Martha J. Shrubsole, Ken S. Lau, Cynthia L Sears, Robert J. Coffey · 发表于：bioRxiv (Cold Spring Harbor Laboratory) · 年份：2026 · DOI：10.64898/2026.06.18.733268 · 研究领域：Clostridium difficile and Clostridium perfringens research、Cancer Research and Treatments、Gut microbiota and health

Abstract Background and Aims Intratumoral heterogeneity with respect to both host and microbial components has emerged as an important contributor to colorectal cancer (CRC) biology. Although the overall taxonomy and abundance of the CRC tumor microbiome have become well characterized, much less is known about bacterial niches within the tumor microenvironment (TME). Escherichia coli and Fusobacterium nucleatum are highly prevalent and abundant species linked to CRC. Less abundant organisms, like Clostridioides difficile and Enterocloster aldenensis , are emerging as potentially important CRC-associated bacteria. Additionally, many studies are confounded by preoperative oral antibiotics or the inclusion of late-stage cancers, both of which may alter the gut microbiome. To better understand the spatial relationships between bacteria and CRC, we generated a molecular atlas based on surgically resected tissue specimens collected from a unique cohort of early-stage CRC patients in whom oral antibiotics were not administered preoperatively. Methods From 20 CRC specimens, we performed matched histopathological analysis, fluorescence in situ hybridization (FISH), whole exome sequencing (WES), 16S rRNA amplicon bacterial DNA sequencing, codetection by indexing (CODEX) multiplex immunofluorescence, and spatial transcriptomics of 756 regions among the specimens. We used 16S rRNA amplicon sequencing data to design and experimentally validate custom bacterial probes that were applied to ...