The interaction between the microbial communities in the human body and the onset and progression of cancer has not been investigated until recently. The vast majority of the metagenomics research in this area has concentrated on the composition of microbiomes, attempting to link the overabundance or depletion of certain microorganisms to cancer proliferation, metastatic behaviour, and its resistance to therapies. However, studies elucidating the functional implications of the microbiome activity in cancer patients are still scarce; in particular, there is an overwhelming lack of studies assessing such implications directly, through analysis of the transcriptome of the bacterial community. This review summarises the contributions of metagenomics and metatranscriptomics to the knowledge of the microbial environment associated with several cancers; most importantly, it highlights all the advantages that metatranscriptomics has over metagenomics and suggests how such an approach can be leveraged to advance the knowledge of the cancer bacterial environment.

Competitive and naturally occurring yeast killer phenotype is governed by coinfection with dsRNA viruses. Long-term relationship between the host cell and viruses appear to be beneficial and co-adaptive; however, the impact of viral dsRNA on the host gene expression has barely been investigated. Here, we determined the transcriptomic profiles of the host Saccharomyces cerevisiae upon the loss of the M-2 dsRNA alone and the M-2 along with the L-A-lus dsRNAs. We provide a comprehensive study based on the high-throughput RNA-Seq data, Gene Ontology and the analysis of the interaction networks. We identified 486 genes differentially expressed after curing yeast cells of the M-2 dsRNA and 715 genes affected by the elimination of both M-2 and L-A-lus dsRNAs. We report that most of the transcriptional responses induced by viral dsRNAs are moderate. Differently expressed genes are related to ribosome biogenesis, mitochondrial functions, stress response, biosynthesis of lipids and amino acids. Our study also provided insight into the virus–host and virus–virus interplays.

Saccharomyces yeasts are widely distributed in the environment and microbiota of higher organisms. The killer phenotype of yeast, encoded by double-stranded RNA (dsRNA) virus systems, is a valuable trait for host survival. The mutual relationship between the different yet clearly defined LA and M virus pairs suggests complex fitting context. To define the basis of this compatibility, we established a system devoted to challenging inherent yeast viruses using viral proteins expressed in trans. Virus exclusion by abridged capsid proteins was found to be complete and nonspecific, indicating the presence of generic mechanisms of Totiviridae maintenance in yeast cells. Indications of specificity in both the exclusion of LA viruses and the maintenance of M viruses by viral capsid proteins expressed in trans were observed. This precise specificity was further established by demonstrating the importance of the satellite virus in the maintenance of LA virus, suggesting the selfish behavior of M dsRNA.