Metatrascriptomic Study of Microbes in Environment: A Community Function Based Approach

Abstract

Research on microbial ecology in recent years had shifted methodologically from traditional culture based techniques to culture independent molecular techniques. This is due to the fact that it has already been established that less than 1% of microbes in environmental samples are cultivable. In recent years, metagenomics research has developed into analyzing partial or complete genomes as well as other types of molecules in environmental samples, including RNA (transcripts), proteins (translated transcripts), and metabolites (metabolic intermediates and final products). While the analyses of DNA sequences in environmental samples can provide evidence about the diversity and function of specific groups of organisms in the analyzed ecological niches, the relative importance of those genes in environmental functions cannot be determined from DNA sequences alone. To understand which genes are expressed under a specific ecological condition, the analysis of transcripts from the communities is often needed.

Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota

“…Nevertheless, a number of recommendations can be made of which the most important is probably the necessity for ribodepletion in order to remove rRNAs from samples subjected to sequencing. This step remains critical and must be carefully controlled as the approaches used are not always successful (Barua, 2017). As with shotgun metagenomics, computer processing -in particular the assembly of the metatranscriptome, as well as the cost associated with sequencing remains an obstacle to the deployment of this approach on a large scale.…”