Emerging technologies and current challenges in intratumoral microbiota research

Intratumoral microbiota are now recognized as an integral component of the tumor microenvironment, affecting tumor initiation, metastatic potential, immune modulation, and treatment response. However, their extremely low biomass poses significant challenges for accurate detection, functional interpretation, and reproducibility, largely because the detection process is highly susceptible to environmental contamination. Standardization of analytical procedures has not yet been established; consequently, variability in sampling protocols, sequencing workflows, and bioinformatic pipelines further complicates cross-study comparisons and hampers the consolidation of robust evidence in this field. Recent advances in technology have begun to provide opportunities to overcome these barriers. Improved contamination-control strategies and more sophisticated decontamination algorithms have enhanced the reliability of microbial detection in low-biomass tissues. High-resolution approaches, such as single-cell RNA sequencing, spatial transcriptomics and optimized anaerobic cultivation, enable the sensitive identification, spatial localization, and mechanistic study of tumor associated microbes. Parallel developments in genome-resolved and enzyme-level analysis reveal microbial metabolic pathways that shape immune responses, drug resistance, and tumor progression. Organoid-based co-culture models further provide physiologically relevant platforms to dissect host-microbe-immune interactions and interpret microbiota-driven modulation of therapeutic responses. Integrating microbiome data with clinical and multi-omics profiles, assisted by artificial intelligence, is accelerating biomarker discovery and informing microbe-guided therapeutic strategies. Taken together, the standardization of research strategies, combined with the application of advanced detection technologies, is propelling the field beyond descriptive profiling toward mechanistic understanding and clinical translation, thereby unlocking the potential of intratumoral microbiota for precision oncology.