Most abundant gene transcripts. Mean NPKM values of the most abundant gene transcripts are plotted against sampling points. Colored lines indicate classes of similarly abundant transcripts. Grey and black lines represent genes with high RNA abundances in all 15 samples (NPKM values 1000–5000); black lines additionally indicate genes referred to in the text. Green color marks those genes, whose transcripts are most abundant (NPKM values >5000) throughout all sampling points, whereas genes with highly abundant transcripts (NPKM values >5000) only at specific sampling points are shown in orange, red and blue. The most abundant transcript was assigned to lanA2 in sample R-III. This gene encodes a component of the two-peptide lantibiotic lichenicidin  and is transcribed with NPKM values >5000 at all sampling points. Accordingly high transcript abundance can also be observed for lanA1, which codes for the second prepeptide of this lantibiotic. Further genes with similar abundances are coding for the BsrG-like peptide (BLi05015) [25, 34], the sporulation protein SpoVG, the DNA-binding protein Hbsu, BLi01059 and Veg . The gene encoding the oxygen detoxification protein SodA, the cold shock responsive genes cspB and cspD, the gene for the elongation factor Tu, and genes coding for components of the translation machinery are transcribed with NPKM values >1000 at all sampling points. Transcripts which are highly abundant exclusively in the later, productive stages of the process are associated to spore formation, whereas transcripts which are highly abundant during the early stages of the process encode ribosomal proteins, proteins of the TCA cycle and ATP synthase subunits. For an illustration of highly abundant proteins please refer to Additional file 1: Figure S8.