Supplementary Table 1. Monoclonal antibodies (mAb) used in this study

Antibody Target Clone Conjugate Supplier

CD3 UCHT1 AF700 BD Pharmingen

CD8α SK1 APC-H7 BD Pharmingen

CD4 RPA-T4 BV605 BD Pharmingen

CD45 HI30 PE-Cy7 BD Pharmingen

V 7.2α 3C10 FITC BioLegend

CD161 DX12 APC BD Pharmingen

CD19 HIB19 PerCP-Cy5.5 BD Pharmingen

CD69 FN50 PE BD Pharmingen

CD45RA HI100 PerCP-Cy5.5 BD Pharmingen

CD62L Dreg56 APC-Cy7 BioLegend

Supplementary Table 2. Sample identifiers and barcodes used for GI microbial species 16s rRNA

sequencing

Participant ID Heme Sample Matched Pyro Sample ID

Plate Barcode

m-2000 m-2000_21.blood.flow j30tr11 j30 TTGTACm-2000 m-2000_35.blood.flow j30tr17 j30 TATCACm-2000 m-2000_62.blood.flow j30tr23 j30 TACCTCm-2000 m-2000_103.blood.flow j30tr29 j30 TCTAGCm-2000 m-2000_-6.blood.flow j30tr8 j30 TTCAGTm-2000 m-2000_12.blood.flow j30tr9 j30 TTCCTTm-2001 m-2001_-10.blood.flow j14tr18 j14 TATGCCm-2001 m-2001_11.blood.flow j14tr22 j14 TACTACm-2001 m-2001_19.blood.flow j14tr23 j14 TACCTCm-2001 m-2001_29.blood.flow j14tr9 j14 TTCCTTm-2001 m-2001_61.blood.flow j29tr33 j29 TCGTCTm-2001 m-2001_99.blood.flow j29tr40 j29 TGACACm-2002 m-2002_-4.blood.flow j28tr41 j28 TGCATTm-2002 m-2002_13.blood.flow j28tr45 j28 ATGGATm-2002 m-2002_20.blood.flow j28tr45 j28 ATGGATm-2008 m-2008_12.blood.flow j14tr12 j14 TTGTGTm-2008 m-2008_-8.blood.flow j14tr32 j14 TCACTCm-2008 m-2008_21.blood.flow j14tr34 j14 TCGGTTm-2008 m-2008_32.blood.flow j29tr49 j29 AACTTCm-2008 m-2008_62.blood.flow j29tr53 j29 AAGTCTm-2031 m-2031_20.blood.flow j50tr12 j50 TTGTGTm-2031 m-2031_31.blood.flow j50tr18 j50 TATGCCm-2031 m-2031_62.blood.flow j50tr24 j50 TACGTTm-2031 m-2031_-11.blood.flow j50tr7 j50 TTCTCCm-2035 m-2035_10.blood.flow j50tr39 j50 TGACTTm-2035 m-2035_21.blood.flow j50tr40 j50 TGACACm-2035 m-2035_63.blood.flow j50tr41 j50 TGCATTm-2040 m-2040_-1.blood.flow j50tr45 j50 ATGGATm-2040 m-2040_32.blood.flow j50tr49 j50 AACTTCm-2041 m-2041_32.blood.flow j49tr11 j49 TTGTACm-2041 m-2041_63.blood.flow j49tr19 j49 TAATCCm-2041 m-2041_-14.blood.flow j49tr4 j49 TTACGCm-2041 m-2041_12.blood.flow j49tr7 j49 TTCTCCm-2041 m-2041_21.blood.flow j49tr7 j49 TTCTCCm-2045 m-2045_-9.blood.flow j49tr34 j49 TCGGTT

m-2045 m-2045_14.blood.flow j49tr38 j49 TGAAGTm-2045 m-2045_21.blood.flow j49tr39 j49 TGACTTm-2045 m-2045_32.blood.flow j49tr41 j49 TGCATTm-2051 m-2051_-8.blood.flow j51tr17 j51 TATCACm-2051 m-2051_20.blood.flow j51tr19 j51 TAATCCm-2059 m-2059_7.blood.flow j51tr24 j51 TACGTTm-2059 m-2059_18.blood.flow j51tr27 j51 TCTTACm-2059 m-2059_27.blood.flow j51tr31 j51 TCAACCm-2059 m-2059_39.blood.flow j51tr32 j51 TCACTCm-2062 m-2062_-22.blood.flow j50tr51 j50 AACACCm-2062 m-2062_1.blood.flow j50tr52 j50 AACCGTm-2062 m-2062_20.blood.flow j50tr55 j50 AAGGTTm-2062 m-2062_21.blood.flow j50tr55 j50 AAGGTTm-2064 m-2064_10.blood.flow j51tr42 j51 TGGAACm-2064 m-2064_32.blood.flow j51tr45 j51 ATGGATm-2066 m-2066_-6.blood.flow j51tr48 j51 AATAGCm-2066 m-2066_9.blood.flow j51tr49 j51 AACTTCm-2069 m-2069_11.blood.flow j67tr60 j67 ACAGACm-2069 m-2069_19.blood.flow j67tr60 j67 ACAGACm-2069 m-2069_34.blood.flow j67tr61 j67 ACCTATm-2069 m-2069_62.blood.flow j67tr62 j67 ACCAAC

Supplementary Table 3. Patient and Transplant Characteristics

PBSCT Haploidentical Cord BloodN 107 6 6Median Age, N(Range) 56(21-76) 49(27-68) 50(30-67)Conditioning Intensity, N(%)

Myeloablative 41(38) 0 3TBI 15No TBI 26

Non-myeloablative 66(62) 6 3Donor, N(%)

Related 44(41)Unrelated 63(59)

HLA Match, N(%)10/10 101(94)9/10 6(6)

Indication, N(%)AML 31(29) 1 2ALL 12(11)MDS 21(20) 3MPN 13(12)Lymphoma 22(21) 5 1Myeloma 7(6)Other 1(1)

Acute GVHD, N(%)None 35(34) 1Grades 1,2 61(59) 3 6Grades 3,4 8(7) 1

Chronic GVHD, N(%) 43(44) 1 0Died, N(%)* 32(30) 2 2Unless contraindicated, patients undergoing transplantation received fluoroquinolone (e.g. levofloxacin)

and anti-fungal (e.g. fluconazole) prophylaxis until recovery from neutropenia (ANC ≥ 1000 cells/L), and

trimethoprim/sulfamethoxazole or dapsone prophylaxis after stable engraftment. Anti-viral prophylaxis

is continued for approximately one year after transplant. Gut decontamination is not routinely

prescribed. Patients received daily iron-free multivitamin supplementation. PBSCT=Peripheral Blood

Stem Cell Transplant; TBI=Total Body Irradiation as part of myeloablative conditioning; HLA=Human

Leucocyte Antigen; AML=Acute Myeloid Leukemia; ALL=Acute Lymphoblastic Leukemia;

MDS=Myelodysplastic Syndrome; MPN=Myeloproliferative Neoplasm; GVHD=Graft versus Host Disease;

*Median days post HCT for death=187 days (Range: 21 days-2 years)

Supplementary Figure 1. MAIT cell reconstitution.

Absolute MAIT cell counts in blood for HCT recipients receiving (A) TBI (Total Body Irradiation, n=15) or

chemotherapy only (n=26) myeloablative conditioning, (B) unrelated (n=63) or related donor (n=44)

transplants, (C) 10/10 HLA (n=101) matched or 9/10 HLA (n=6) matched transplants and (D) transplants

for Acute Leukemia (n=41) or other diagnoses (n=66).

Supplementary Figure 2. MAIT cell reconstitution does not correlate with CD19 recovery after HCT.

(A-B) Absence of correlation between MAIT cells and CD19+ B cell counts in blood on day 10 (A; n=42) or

day 30 (B; n=65) after allogeneic HCT. Log-log linear regression Pearson correlation coefficient r and p

values are shown.

Supplementary Figure 3. TCR stimulation and inflammatory cytokines are required for upregulation of

Ki67 in MAIT cells.

Representative flow cytometric analysis of Ki67 expression on MAIT cells. MAIT cells were isolated from

healthy donors (n = 2) and Ki67 expression was evaluated after 4 days of incubation with anti-CD3

stimulation alone, inflammatory cytokine (IL-1β, IL-12, IL-18 or IL-23) stimulation alone, or anti-CD3 with

inflammatory cytokine stimulation.

Supplementary Figure 4. MAIT cell suppression of CD4+ T cell proliferation.

CD4+ CD25- responder T cells, MAIT cells, CD8+ T cells, and CD4+ CD25+ regulatory T cells were isolated

from the peripheral blood of 3 healthy donors. CFSE-labeled CD4+ responder T cells were stimulated

with αCD3/28 beads for 4 days in the presence of MAIT cells, CD8+ T cells, regulatory T cells, or CD4+

responder T cells at a ratio of 1:1. Representative flow cytometric analysis of CFSE dilution in CD4+

responder T cells is shown.