Optimizing mouse metatranscriptome profiling by selective removal of redundant nucleic acid sequences

Metatranscriptome (MetaT) sequencing is a critical tool for profiling the dynamic metabolic functions of microbiomes. In addition to taxonomic information, MetaT also provides real-time gene expression data of both host and microbial populations, thus permitting authentic quantification of the functional (enzymatic) output of the microbiome and its host. The main challenge to effective and accurate MetaT analysis is the removal of highly abundant rRNA transcripts from these complex mixtures of microbes, which can number in the thousands of individual species. Regardless of the methodology for rRNA depletion, the design of rRNA removal probes based solely upon the taxonomic content of the microbiome typically requires very large numbers of individual probes, making this approach complex to commercially manufacture, costly, and frequently technically infeasible. In previous work (A. Tan, S. Murugapiran, A. Mikalauskas, J. Koble, et al., BMC Microbiol 23:299, 2023, https://doi.org/10.1186/s12866-023-03037-y), we designed a set of depletion probes for human stool samples using a design strategy based solely on sequence abundance, completely agnostic of the microbiomal species present. Here, we show that human-based probes are less effective when used with mouse cecal samples. However, adapting additional rRNA depletion probes specifically to cecal content provides both greater efficiency and consistency for MetaT analysis of mouse samples.IMPORTANCESequencing total RNA from microbiome samples is seriously impaired by the overwhelming proportion of rRNA to mRNA content. As much as 99% of sequencing reads can be assigned to the rRNA content, thus removal of these abundant transcripts is critical to metatranscriptome (MetaT) analysis. The use of Ribo Zero Plus rRNA depletion probes designed for human gut microbiomes proved to be less effective and more inconsistent across mouse cecal donor samples, a common experimental system for microbiome studies. In the present work, we have extended and refined a taxonomically neutral probe design method for mouse cecal content. The additional probes were carefully chosen to limit the number needed for effective depletion to reduce both the cost and risk of introducing bias to MetaT analysis. Our results demonstrate this method as efficient and consistent for rRNA removal in mouse cecal samples, thus providing a significant increase in the number of mRNA-rich sequencing reads for MetaT analysis.