The application of next-generation sequencing (NGS) technologies to RNAs directly extracted from a community of organisms yields a mixture of fragments characterizing both coding and non-coding types of RNAs. The task to distinguish among these and to further categorize the families of messenger RNAs and ribosomal RNAs (rRNAs) is an important step for examining gene expression patterns of an interactive environment and the phylogenetic classification of the constituting species.