Nature Microbiology, Published online: 10 August 2026; doi:10.1038/s41564-026-02442-z Metastrand integrates strand-aware metatranscriptomic and metagenomic data to distinguish microbial sense from antisense transcription at gene-level resolution, and a use case study highlights the importance of antisense RNAs in understanding the microbial dynamics in inflammatory bowel disease.