Our results show that in this model, cancer cells with enhanced aggressivity acquire a supplementary pathway of pre-rRNA processing.
Therefore, utilizing organic substances is probably only a supplementary pathway when ammonium or nitrite is in short supply in the environments.
However, recent studies have shown that activin alone may not produce homogeneous differentiation and additional factors must be used to modulate supplementary signaling pathways along with the nodal pathway activated by activin [ 1, 4].
In contrast, distributed genomes constitute to the species diversity and might encode supplementary biochemical pathways and functions not essential for bacterial growth but which confer selective advantages, such as adaptation to different niches and antimicrobial resistance.
Results of bioinformatic analysis of the mRNA and miRNA transcriptomic data are shown in additional supplementary tables (pathway analysis - Additional file 3: Table S3; gene ontology enrichment analysis Additional file 4: Table S4; DEG miRNA Additional file 5: Table S5).
These proteins are primarily involved in the autophagic and cell growth-related pathways (Supplementary Information, Supplementary Table S3).
Microbes involved in both processes are potential consumers of available organic acids and fermentation products35 and we found that the LC polygons were enriched with genes involved in degradation of simpler carbohydrates (i.e., sugars) and mixed acid fermentation pathways (Supplementary Fig. 15, Supplementary Fig. 16) that could be linked to these processes.
These strains also differentially regulated NCR genes at different positions in the proline and arginine utilization pathways (supplementary fig. S8 b and c, Supplementary Material online).
A broad range of biological processes, molecular functions, cell cycle pathways (Supplementary Table S5) and gene sets from the MSigDB (Supplementary Table S6) was enriched across these different modules.
Furthermore, we also found that the upregulated gene entities were significantly (corrected p < 0.05) enriched in 53 KEGG pathways (Supplementary Table S4) and the downregulated gene entities in 1 KEGG pathway (Supplementary Table S5).
Of these, 88 mutations affect previously described or putative antimicrobial resistance-associated genes, gene-regions, or pathways (Supplementary Data 1–4).
