Short-term Bacillus clausii administration remodels the peripheral T-cell receptor repertoire through convergent CDR3 sequence architectures

Background The intestinal microbiota is a major regulator of systemic immunity, yet its influence on the structural organization of the T-cell receptor (TCR) repertoire remains poorly understood. While probiotic administration has been shown to modulate immune function through changes in cytokine production and immune-cell activity, whether these interventions reshape the architecture of the circulating T-cell repertoire at single-clonotype resolution has not been established. We therefore investigated the longitudinal impact of short-term Bacillus clausii administration on the peripheral TCRβ repertoire using ultra-deep immune repertoire sequencing. Methods Peripheral blood mononuclear cells were collected from a healthy individual immediately before and after completion of a 10-day oral Bacillus clausii regimen. TCRβ repertoires were analyzed using complementary nucleotide- and amino acid-based clonotype definitions. Repertoire richness, diversity, clonal evenness, V(D)J gene usage, repertoire overlap, differential clonotype abundance, CDR3 sequence composition, motif enrichment, and hierarchical sequence clustering were evaluated to characterize quantitative and structural changes induced by probiotic administration. Results Short-term probiotic administration was associated with marked quantitative remodeling of the peripheral TCRβ repertoire. Repertoire richness and diversity decreased substantially, accompanied by increased clonal focusing and expansion of dominant clonotypes. Despite this contraction of the low-frequency clonotype compartment, the overall structural organization of the repertoire remained remarkably stable. CDR3 length distribution, TRBV/TRBJ gene usage, and dominant V-J rearrangements were largely preserved, while abundance-weighted repertoire similarity remained exceptionally high, indicating conservation of the principal antigen-experienced T-cell populations. Differential abundance analysis demonstrated that repertoire remodeling was driven predominantly by expansion of pre-existing clonotypes rather than widespread emergence of new clones. Moreover, expanded clonotypes segregated into multiple clusters sharing conserved CDR3 sequence motifs despite heterogeneous TRBV and TRBJ usage, revealing convergent receptor architectures that were independent of germline gene composition. Conclusions These findings demonstrate that short-term Bacillus clausii administration does not induce wholesale restructuring of the peripheral T-cell repertoire but instead promotes selective quantitative remodeling within a preserved structural framework. Expansion of pre-existing clonotypes together with the emergence of convergent CDR3 sequence architectures suggests that microbiota-directed interventions fine-tune the organization of the adaptive immune repertoire rather than replacing it. This study establishes ultra-deep immune repertoire sequencing as a powerful approach for investigating the systemic immunological effects of probiotics and provides a conceptual framework for understanding how microbiota-targeted interventions shape adaptive immunity.