MetaEdit: Computational Identification of RNA Editing in Microbiomes

RNA editing is a pivotal post-transcriptional mechanism that plays a critical role in the regulation of some genes by altering their mRNA sequences, thereby influencing the resulting protein sequence, structure, and the functional and cellular responses. While extensively studied in eukaryotes, its significance and prevalence in prokaryotic microbiomes remain underexplored. Given the crucial role of microbiomes in various biological processes and their potential impact on human health and disease, understanding RNA editing within these communities could reveal new insights into microbial gene regulation and adaptation. The lack of studies to detect RNA editing in microbiomes motivates the need for developing bioinformatic strategies to bridge this research gap. This study introduces MetaEdit, a computational tool designed to detect RNA editing in bacterial microbiomes. We apply MetaEdit to metatranscriptomic and metagenomic datasets to identify and characterize RNA editing events in the human gut microbiome. Our results demonstrate the presence of RNA editing in Escherichia coli and provide a foundation for future investigations into the functional implications of RNA editing in microbiomes. Our findings are supported by previously reported research but need validation with laboratory experiments. The developed pipeline is generic and can be applied to find RNA editing in any sequencing datasets containing both metagenomic and metatranscriptomic data.

Supplementary information: None.