From enrollment to sequencing: cancer microbiome methods reporting is inconsistent and incomplete

Reproducibility in microbiome research depends on transparent reporting of sample sizes and sequence counts both before and after quality control (QC) processes. This is an expectation formalized in the STORMS (Strengthening The Organization and Reporting of Microbiome Studies) checklist published in November 2021. Whether cancer microbiome studies comply with the STORMS items governing sample size, sequencing and quality control, however, remains largely unexamined. Here, we audited 67 clinical cancer microbiome studies against ten STORMS items that apply to every microbiome study, spanning participant and sample counts, laboratory processing, sequencing, bioinformatic processing and experimental controls. Nearly all studies reported their number of participants (96%) and final number of samples analyzed (97%). However, STORMS items beyond sample sizes were largely underreported, ranging from 9% to 36%. The median study reported two of these eight methods items, and 16 studies reported none. Reporting did not change measurably after STORMS was published and was unrelated to journal impact factor. Because aspects like read normalization, quality-control filtering, taxa removal, and contamination handling directly affect the end result of a cancer microbiome study, differences in how these are implemented can have critical implications for the field’s reproducibility as well as rigor at large. Resolving this issue will require buy-in from scientists, funding institutions, and journals to work together to enforce stricter standards for cancer microbiome methodology reporting.