2025/10/14 by Weiwei Zhou, Qingyi Yang, Jiyu Guo +9 · 1 voice
Biochemistry, Genetics and Molecular Biology · Immunology and Microbiology · #Single-cell and spatial transcriptomics #Immune cells in cancer #Gut microbiota and health
paper · pdf · doi:10.1093/molbev/msaf263
openalex publication_date 2025/10/14 · openalex created_date 2025/10/15 · openalex updated_date 2026/07/31
Microorganisms have been detected in various tumors, and research on the tumor microbiome has received increasing attention. However, the investigation of the cancer microbiome at the spatial resolution level remains a challenging issue. The emergence of spatially resolved transcriptomics technology has enabled to map transcripts at the single-cell resolution in various cancer types. Here, we constructed a comprehensive spatial meta-transcriptome resource by manually curating 203 fresh frozen slices from 20 cancer types encompassing 334,253 spots and 1,908,646 cells. A spatial meta-transcriptome database (SMTdb; http://bio-bigdata.hrbmu.edu.cn/SMTdb/) was constructed to provide detailed insights into the abundance, distribution, and enriched tumor microenvironment (TME) regions of 1,218 microbiota in spatial tissue slices. SMTdb enables to explore the vast interactive data of spatial distribution and expression of microbiota, provides host gene modules associated with certain microbiota, and contains data on the co-occurrence between the microbiota and immune cells within the TME. The atlas resource serves as a comprehensive and structured platform to investigate the interactions between microbial ecosystems and hosts in cancer.