Bacillus subtilis SC-8 (BSSC8) shows a narrow antimicrobial activity against the Bacillus cereus group. Previously, B. cereus-derived PapR as a signal peptide to stimulate PlcR, which plays a significant role in regulating the transcription of virulence factors, was assumed to stimulate antibiotic production in BSSC8. To better understand the functional role of PapR in the antibiotic production of BSSC8 and the interspecies interaction, the global transcriptomic profiling of BSSC8 was investigated using RNA-Seq in this study. Small peptides derived from B. cereus wild type (WTBC) and a papR-deleted mutant strain (MTBC) were individually supplied to BSSC8 cultures, and changes in global transcription levels were compared by RNA-Seq. In the presence of WTBC small peptides, more genes (80.9%) were significantly upregulated than in cells exposed to MTBC small peptides. Specifically, 48.8 and 83.4% of genes involved in glycolysis and the TCA cycle, respectively, showed changes in transcription levels in response to small peptides from both strains. Of the genes showing the alterations, 35.0% (glycolysis) and 60.0% (TCA cycle) of transcripts were significantly regulated only in response to WTBC-derived small peptides. Furthermore, the expression of biosynthetic genes encoding several known antibiotics in BSSC8 was further decreased in response to WTBC small peptides.