Interspecies interactions mediated by arginine metabolism enhance the stress tolerance of <i>Fusobacterium nucleatum</i> against <i>Bifidobacterium animalis</i>

Colorectal cancer (CRC) is a common cancer accompanied by microbiome dysbiosis. Exploration of probiotics against oncogenic microorganisms is promising for CRC treatment. Here, differential microorganisms between CRC and healthy control were analyzed. Antibacterial experiments, whole-genome sequencing, and metabolic network reconstruction were combined to reveal the anti-<i>Fusobacterium nucleatum</i> mechanism, which was verified by co-culture assay and mendelian randomization analysis. Sequencing results showed that <i>F. nucleatum</i> was enriched in CRC, yet <i>Bifidobacterium animalis</i> decreased gradually from healthy to CRC. Additionally, <i>F. nucleatum</i> could be inhibited by <i>B. animalis</i>. Whole-genome sequencing of <i>B. animalis</i> showed high phylogenetic similarity with known probiotic strains and highlighted its functions for amino acid and carbohydrate metabolism. Metabolic network reconstruction demonstrated that cross-feeding and specific metabolites (acidic molecules, arginine) had a great influence on the coexistence relationship. Finally, the arginine supplement enhanced the competitive ability of <i>F. nucleatum</i> against <i>B. animalis</i>, and the mendelian randomization and metagenomic sequencing analysis confirmed the positive relationship among <i>F. nucleatum</i>, arginine metabolism, and CRC. Thus, whole-genome sequencing and metabolic network reconstruction are valuable for probiotic mining and patient dietary guidance.IMPORTANCEUsing probiotics to inhibit oncogenic microorganisms (<i>Fusobacterium nucleatum</i>) is promising for colorectal cancer (CRC) treatment. In this study, whole-genome sequencing and metabolic network reconstruction were combined to reveal the anti-<i>F. nucleatum</i> mechanism of <i>Bifidobacterium animalis</i>, which was verified by co-culture assay and mendelian randomization analysis. The result indicated that the arginine supplement enhanced the competitive ability of <i>F. nucleatum</i>, which may be harmful to <i>F. nucleatum</i>-infected CRC patients. <i>B. animalis</i> is a potential probiotic to relieve this dilemma. Thus, using in silico simulation methods based on flux balance analysis, such as genome-scale metabolic reconstruction, provides valuable insights for probiotic mining and dietary guidance for cancer patients.