Thrilled to share that our lab’s paper regarding tumor microbiome is out in Nature Methods today —nearly two years in the making it happen! Congratulations to the lead author, Yingjie Li, MD, M, S, and all the coauthors!
The tumor microbiome - microbial genomes detected within tumors and adjacent normal tissues – has drawn intense interest in cancer research in the recent couple of years. Yet low biomass in many tumor types and debates around profiling microbes from human tumor sequencing have raised valid concerns. These motivated us to ask: Why does this matter? What are the key challenges? How can we do better? In this work, we:
✔︎ Clarify terminology used in tumor-microbiome research.
✔︎ Survey and visualize state-of-the-art evidence from human and animal studies, along with notable technologies.
✔︎ Map current challenges and propose practical, methodological recommendations—what tends to work (and what doesn’t) for computational analysis.
✔︎ Outline promising downstream analyses to illuminate microbial roles in cancer.
✔︎ We emphasize the importance of microbe-targeted sequencing, rigorous, reproducible pipelines, and solid validation to maximize the reliability of discovery and association studies.
This was a truly multi-institutional effort spanning The Ohio State University & Pelotonia Institution of Immuno-Oncology (PIIO), Rutgers University, Case Western Reserve University, Beth Israel Deaconess Medical Center, and Dana-Farber Cancer Institute.
Grateful to all collaborators, Anjun Ma, Ph.D. W. Evan Johnson, Charis Eng, Subhajyoti De, Sizun Jiang, Zihai Li, MD, PhD, and my co-corresponding author, Daniel Spakowicz, for their insights and great support in this project. We hope this serves as a roadmap for advancing tumor-microbiome research and supports the computational community.
Read more: https://lnkd.in/gYy7WC7a