TCR clone numbers and reduced diversity posttransplantation. (A) Schematic diagram of hematopoietic transplantation and sampling of gut tissues and T cells for TCR repertoire analysis. Four different mice strains (C57BL/6, BALB.B, B10.BR, and BALB/c) received hematopoietic stem cell transplantation from the same donor graft (C57BL/6) to evaluate T-cell reconstitution. Donor GI tract tissues and graft T cells were harvested on pretransplant day 0, and recipient tissues were sampled on posttransplant days 9 to 11 (Phase I) and days 18 to 32 (Phase II). (B) TCRA and TCRB repertoire capture. Total and distinct productive clonal sequence counts for all GI samples from all experiments are shown. (C) General trend of TCRA and TCRB diversity across all transplant and recipient groups. Significantly decreased diversity was observed in the GI tract after transplantation, which increased over time (95% confidence interval, ANOVA). (D) Diversity of the TCRA and TCRB repertoire according to mismatch recipient group. Although syngeneic recipients and minor mismatch recipients trended toward decreased diversity over time, major mismatch recipients exhibited statistically decreased diversity (pooled from 5 separate experiments, 2-tailed Student t test). Recip, recipient; tx, transplantation.