REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD122 (Mik-β)	BD Biosciences	Cat#564688; RRID:AB_2738895
Perforin (dG9)	Biolegend	Cat#308114; RRID:AB_2284280
Granzyme B (GB11)	BD Biosciences	Cat#563389; RRID:AB_2738175
CD3 (UCHT1)	Biolegend	Cat#300436; RRID:AB_2562124
CD31 (WM59)	BD Biosciences	Cat#562855; RRID:AB_2737841
CD127 (HIL-7R-M21)	BD Biosciences	Cat#563225; RRID:AB_2738081
CD45RO (UCHL1)	BD Biosciences	Cat#563722; RRID:AB_2744413
CD8a (RPA-T8)	Biolegend	Cat#301045; RRID:AB_11219195
KLRG1 (13F12F2)	eBioscience	Cat#17-9488-42; RRID:AB_2573303
CD185 (RF8B2)	BD Biosciences	Cat#565191; RRID:AB_2739103
CD197 (G043H7)	Biolegend	Cat#353212; RRID:AB_10916390
Foxp3 (236A/E7)	eBioscience	Cat#12-4777-42; RRID:AB_1944444
CD4 (S3.5)	Invitrogen	Cat#MHCD0417; RRID:AB_10371766
CD28 (CD28.2)	BD Biosciences	Cat#561791; RRID:AB_10898345
CD57 (TB01)	eBioscience	Cat#25-0577-42; RRID:AB_2573354
IL-8 (E8N1)	BioLegend	Cat#511406; RRID:AB_893462
IL-17 (BL168)	BioLegend	Cat#512312; RRID:AB_961392
CD14 (MΦP9)	BD Biosciences	Cat#563079; RRID:AB_2737993
IL-2 (MQ1-17H12)	BD Biosciences	Cat#564165; RRID:AB_2738636
CD45RA (HI100)	BD Biosciences	Cat#563963; RRID:AB_2738514
IL-10 (JES3-9D7)	BD Biosciences	Cat#564050; RRID:AB_2738564
TNFa (Mab11)	BioLegend	Cat#502948; RRID:AB_2565858
IL-6 (MQ2-13A5)	BD Biosciences	Cat#561441; RRID:AB_10679121
CD69 (FN50)	BioLegend	Cat#310914; RRID:AB_314849
CD107a (H4A3)	BD Biosciences	Cat#562628; RRID:AB_2737686
IFN-g (B27)	BD Biosciences	Cat#557643; RRID:AB_396760
Chemicals, peptides, and recombinant proteins
Enterotoxin Type B from Staphylococcus aureus	List Biological Laboratories	Cat#122
Phusion High-Fidelity PCR Master Mix with HF Buffer	New England Biolabs	Cat#M0531L
Critical commercial assays
Quant-IT PicoGreen dsDNA Assay	Thermo Fisher	Cat#P7589
SequalPrepTM Normalization Plate Kit	Invitrogen	Cat#A1051001
Quick-DNA Fecal/Soil Microbe MiniPrep Kit	Zymo Research	Cat#D6010
Fixable Aqua Dead Cell Stain Kit, for 405 nm excitation	Thermo Fisher	Cat#L34957
eBioscience Foxp3/Transcription Factor Staining Buffer Set	Thermo Fisher	Cat#00-5523-00
BD Cytofix/Cytoperm Kit	BD Biosciences	Cat#554714; RRID: AB_2869008
BD GolgiPlug	BD Biosciences	Cat#555029; RRID: AB_2869014
BD GolgiStop	BD Biosciences	Cat#554724; RRID: AB_2869012
Rainbow Calibration Particles, 6th peak from the 8 peak set	Spherotech	Cat#RCP-30-5A-6
AgPath-ID™ One-Step RT-PCR Reagents	Applied Biosystems	Cat#4387424
Black Hole Quencher-1	Biosearch Technologies	3'-BHQ-1 CPG
Deposited data
Annotated datasets for:-16S gene sequencing-flow cytometry results	dbGaP	phs001347
Oligonucleotides
Forward primer V3-V4 rRNA sequencing (319F): 5'-ACT CCT ACG GGA GGC AGC AG-3'	Grier et al. (2018)	N/A
Reverse primer V3-V4 rRNA sequencing(806R): 5'-GGA CTA CHV GGG TWT CTA AT-3'	Grier et al. (2018)	N/A
Forward primer V1-V3 rRNA sequencing(8F): 5'-AGA GTT TGA TCC TGG CTC AG-3'	Grier et al. (2018)	N/A
Reverse primer V1-V3 rRNA sequencing(534R): 5'-ATT ACC GCG GCT GCT GG-3'	Grier et al. (2018)	N/A
Forward primer, UL55: 5'-TGG GCG AGG ACA ACG AA	Boeckh et al. (2004)	N/A
Reverse primer, UL55: 5'-TGA GGC TGG GAA GCT GAC AT	Boeckh et al. (2004)	N/A
Forward primer, UL123-exon4: 5'-TCC CGC TTA TCC TCR GGT ACA	Boeckh et al. (2004)	N/A
Reverse primer, UL123-exon4: 5'-TGA GCC TTT CGA GGA SAT GAA	Boeckh et al. (2004)	N/A
Software and algorithms
Code and interim data	github (zenodo)	https://doi.org/10.5281/zenodo.5786917