Metatranscriptomic Profiling of Host-Microbiome Interactions in the Telencephalon and Liver of Carollia perspicillata

RNA-seq data provide valuable insights into both host transcriptomes and microbial transcripts from active microbiota within host tissues. The presence of microbial transcripts within specific tissues indicates the replication and transcriptional activity of microorganisms. Integrative analyses of the host transcriptome and the meta-transcriptome allow for the characterization of microbial gene expression and the interactive response of the host to the microbiome in each sample. In this study, we employed metatranscriptomics to explore microbial communities in the telencephalon and liver of Carollia perspicillata. By combining host and microbial RNA-seq data, we identified 287 microbial species in the liver and 283 in the telencephalon, revealing tissue-specific microbial diversity. Bacteria were the most abundant taxa in both tissues, followed by notable eukaryotic, archaeal, and viral populations. Using the Metatranscriptome Detector pipeline and NCBI databases, we identified species of potential epidemiological relevance and characterized the host’s transcriptional response to the microbiome. Functional analyses indicated differential expression of microbial and host genes across tissues, with enriched metabolic pathways and Gene Ontology (GO) terms aligning with hepatic and neural functions. This research underscores the tissue-specific adaptation of the microbiome to host physiology, offering new insights into host-microbiome dynamics in the telencephalon and liver of this frugivorous bat species.