Characterization of Peptide Utilization by <i>Bifidobacterium bifidum</i> : Insights From Computer Simulations and In Vitro Verification to Enhance Nitrogen Source Utilization

<i>Bifidobacterium bifidum</i> (<i>B. bifidum</i>) exhibits limited efficiency in utilizing nitrogen sources, posing challenges for its industrial production. Preliminary investigations indicate that <i>B. bifidum</i> preferentially utilizes peptides over amino acids and proteins during its growth. Understanding the specific peptide utilization characteristics of <i>B. bifidum</i> is essential for addressing these production challenges. In this study, we hydrolyzed casein using various enzymes to prepare peptides, which were then used to culture <i>B. bifidum</i> strains. We identified peptides that are preferentially utilized by <i>B. bifidum</i> and analyzed their characteristics. The results demonstrated that <i>B. bifidum</i> favors peptides with molecular weights below 2000 Da, particularly those rich in proline, glutamic acid/glutamine, and leucine. Subsequently, we employed CDOCKER to dock the key peptide transport protein OppA with 2098 peptides. The docking results revealed that OppA binds peptides ranging from 2 to 15 residues in length, with molecular weights less than 2000 Da and containing proline or leucine, which is consistent with in vitro experimental results. Further analysis indicated that the length of transportable peptides correlates with the size of the OppA-binding cavity. The presence of proline and leucine enhances interactions with OppA, thereby increasing affinity and preference for these amino acids in peptides. This study elucidates the peptide utilization characteristics of <i>B. bifidum</i> and explores the relationship between the OppA protein and peptide transport properties, providing theoretical insights for improving the growth and industrial production of <i>B. bifidum</i>.