metatranscriptomica

Metatranscriptomica, known in English as metatranscriptomics, is the study of the collective RNA transcripts produced by all organisms within a mixed microbial community. It aims to measure which genes are actively expressed in a given environment or host-associated microbiome, providing a functional snapshot that complements DNA-based studies of potential capabilities.

Typical workflow involves stabilizing and extracting total RNA from an environmental or biological sample, depleting ribosomal RNA to enrich messenger RNA, and constructing cDNA libraries for high-throughput sequencing. Data analysis includes quality control, removal of adapters and rRNA reads, taxonomic and functional annotation, and quantification of transcript abundance. Transcripts are often mapped to reference genomes or assembled into transcripts to infer active pathways, with differential expression analyses used to compare conditions or time points.

Applications span environmental microbiology (soil, water, sediments), human and animal microbiomes, industrial bioprocesses, and studies of host-microbe interactions. Metatranscriptomics can illuminate active processes such as nutrient cycling, pollutant degradation, stress responses, and expression of virulence factors or symbiotic functions, offering insight into how communities respond to environmental changes or perturbations.

Challenges include RNA instability and contamination with host or environmental RNAs, biases introduced during RNA extraction or ribosomal depletion, the difficulty of assembling transcripts from diverse, low-abundance taxa, and limited reference genomes for many organisms. Computational demands and the dependence on reference databases can complicate interpretation and reproducibility.

Future directions emphasize integration with metagenomics and metaproteomics for a holistic view of structure and function, improvements in rRNA depletion and sequencing technologies, and development of standardized, scalable analysis pipelines to handle complex communities.