Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| BUV395 anti-mouse CD45 | BD Biosciences | Cat# 564279, RRID AB_2651134 |
| BV785 anti-mouse CD326 (EpCAM) | BioLegend | Cat# 118245, RRID AB_2860639 |
| Pacific Blue anti-mouse I-A/I-E | BioLegend | Cat# 107620, RRID AB_493527 |
| Pacific Blue Rat IgG2b, κ Isotype control | BioLegend | Cat# 400627, RRID AB_493561 |
| Brilliant Violet 650 rat anti-mouse CD19 | BD Bioscience | Cat# 563235, RRID AB_2738085 |
| PE/Cyanine5 anti-mouse CD19 Antibody | BioLegend | Cat# 115510, RRIDAB_313645 |
| PE/Dazzle™ 594 anti-mouse CD3ε Antibody | BioLegend | Cat# 100348, RRID AB_2564029 |
| Brilliant Violet 510™ anti-mouse CD90.2 (Thy-1.2) Antibody | BioLegend | Cat# 140319, RRID AB_2561395 |
| BUV805 Mouse Anti-Rat CD90/Mouse CD90.1 | BD Bioscience | Cat# 741974, RRID AB_2871278 |
| BUV496 Rat Anti-Mouse CD4 | BD Bioscience | Cat# 612952 |
| Brilliant Violet 785™ anti-mouse CD4 Antibody | BioLegend | Cat# 100453, RRID AB_2565843 |
| BUV805 Rat Anti-Mouse CD8a | BD Bioscience | Cat# 612898, RRID AB_2870186 |
| Brilliant Violet 650™ anti-mouse CD8a Antibody | BioLegend | Cat# 100742, RRID AB_2563056 |
| BUV661 Rat Anti-Mouse CD8b | BD Bioscience | Cat# 741585, RRID AB_2870998 |
| Brilliant Violet 711™ anti-mouse CD317 (BST2, PDCA-1) Antibody | BioLegend | Cat# 127039, RRID AB_2832459 |
| BUV737 Rat Anti-Mouse Siglec-H | BD Bioscience | Cat# 748293, RRID AB_2872719 |
| Biotin Rat Anti-Mouse CD119 | BD Bioscience | Cat# 558771, RRID AB_397115 |
| Biotin Rat IgG2a, κ Isotype Ctrl Antibody | Biolegend | Cat# 400503, RRID AB_2783537 |
| PE Streptavidin | Biolegend | Cat# 405203 |
| Foxp3 PE-Cyanine5 | eBioscence | Cat# 15-5773-82, RRID AB_468806 |
| Brilliant Violet 711™ anti-mouse Ly-6G Antibody | BioLegend | Cat# 127643, RRID AB_2565971 |
| APC/Cy7 anti-mouse Ly-6G | BioLegend | Cat# 127624, RRID AB_10640819 |
| Brilliant Violet 605 anti-mouse CD11c | BioLegend | Cat# 117334, RRID AB_2562415 |
| PE/Cy7 anti-mouse CD64 (FcγRI) | BioLegend | Cat# 139314, RRID AB_2563904 |
| PerCP/Cyanine5.5 anti-mouse/human CD11b | BioLegend | Cat# 101228, RRID AB_893232 |
| CD200 Receptor Monoclonal Antibody (OX110), APC | eBioscience | Cat# 17-5201-82, RRID AB_10717289 |
| APC Rat IgG2a, κ Isotype Ctrl Antibody | BioLegend | Cat# 400512, RRID AB_2814702 |
| FITC Rat Anti-Mouse Vβ 6 T-Cell Receptor | BD Biosciences | Cat# 553193, RRID AB_394700 |
| Alexa Fluor® 700 anti-mouse Ly-6C | BD Biosciences | Cat# 128024, RRID AB_10643270 |
| BUV563 Hamster Anti-Mouse CD49b | BD Bioscience | Cat# 741280, RRID AB_2870819 |
| FITC anti-mouse NK-1.1 Antibody | BioLegend | Cat# 108706, RRID AB_313393 |
| APC/Cyanine7 anti-mouse NK-1.1 Antibody | BioLegend | Cat# 108724, RRID AB_830871 |
| Purified Rat Anti-Mouse CD16/CD32 (Mouse BD Fc Block™) | BD Bioscience | Cat# 553142, RRID AB_394656 |
| Alexa Fluor® 488 anti-human CD326 (EpCAM) Antibody | BioLegend | Cat# 324210, RRID AB_756084 |
| Brilliant Violet 510™ anti-human CD45 Antibody | BioLegend | Cat# 304036, RRID AB_2561940 |
| PE Anti-HLA DR + DP + DQ antibody [WR18] | Abcam | Cat# ab23901 |
| Purified anti-human CD326 (EpCAM) Antibody | BioLegend | Cat# 32402, RRID AB_756076 |
| CD45, Leucocyte Common Antigen (Concentrate) | DAKO | PartNumber: M070101-2 Code Number: M0701 |
| Anti-HLA DR + DP + DQ antibody [CR3/43] | Abcam | Cat# ab7856 |
| Mouse IgG1 Isotype Control | R&D systems | Cat# MAB002 |
| PowerVision+ Poly-HRP IHC Detection System | Leica Biosystems | Cat# PV6107 |
| 1X OPAL ANTI-MS + RB HRP (Formerly Opal Polymer HRP Ms + Rb) | Akoya Bioscences | SKU: ARH1001EA |
| Akoya Opal 570 reagent | Akoya Bioscences | Cat# FP1488001KT |
| Akoya Opal 520 reagent Pack | Akoya Bioscences | Cat# FP1487001KT |
| Akoya Opal 690 reagent | Akoya Bioscences | Cat$ FP1497001KT |
| Purified CD25 (clone PC-61.5.3) | BioXcell | Cat# BE0012 |
| Bacterial and virus strains | ||
| Bacteroides thetaiotaomicron (VPI 5482) | ATCC | Cat# 29148 |
| Clostridium sporogenes | ATCC | Cat# 15579 |
| Biological samples | ||
| Human ileal and colonic biopsy tissues from healthy donors and pre, post transplant patients | Fred Hutchinson Cancer Center (FHCC) | N/A |
| Human fecal samples | Memorial Sloan Kettering Cancer Center | N/A |
| Chemicals, reagents, peptides, and recombinant proteins | ||
| 7-Aminoactinomycin D (7AAD) | Sigma Aldrich | Cat# A9400-5MG |
| Phorbol 12-myristate 13-acetate (PMA) | Sigma Aldrich | Cat#P1585-1MG |
| Ionomycin | Sigma Aldrich | Cat#I0634-1MG |
| BD Horizon™ Fixable Viability Stain 440UV | BD Biosciences | Cat# 566332, RRID AB_2869748 |
| Tamoxifen | MP Biomedicals | CAS#10540-29-1 |
| NaHCO3 | Sigma | Cat# S4019 |
| MgSO4.7H2O | Sigma | Cat# M63-500 |
| NaCl | Sigma | Cat# S3014 |
| CaCl2 | Sigma | Cat# C7902 |
| FeSO4 | Sigma | Cat# F8048 |
| BBL™ Trypticase Peptone | BD Biosciences | Cat# 211921 |
| Bacto Yeast extract | Gibco | Cat# 212750 |
| Glucose | Sigma | Cat# G8270 |
| Cysteine (free base) | Sigma | Cat# C1276 |
| KH2PO4 | Sigma | Cat# P0662 |
| K2HPO4 | Sigma | Cat# P3786 |
| meat extract | Sigma | Cat# 70164 |
| Menadione (Vitamin K) | Sigma | Cat# M5625 |
| Hematin | Sigma | Cat# H3281 |
| ATCC Viotamin mix | ATCC | Cat# MD-VS |
| ATCC Mineral mix | ATCC | Cat# MD-TMS |
| Tween 80 | Sigma | Cat# P1754 |
| cellobiose | Sigma | Cat# C7252 |
| maltose | Sigma | Cat# M5885 |
| fructose | Sigma | Cat# F0127 |
| sodium acetate | Fisher (Fluka) | Cat# BP333-500 |
| sodium sulfate | Sigma | Cat# S9627 |
| malic acid | Sigma | Cat# M7937 |
| Collagenase type I | Gibco | Cat# 17100017 |
| Deoxyribonuclease I from bovine pancreas | Sigma | SKU: DN25-1G |
| HEPES 1M | Gibco | Cat# 15630080 |
| Pen Strep | Gibco | Cat# 15140122 |
| L-glutamine | Gibco | Cat# 25030081 |
| MgCl2 | Sigma | SKU: M8266-100G |
| CaCl2 | Sigma | SKU: C1016-100G |
| TaqMan 1000RXN Gold/Buffer Pkg Kit; custom order | ThermoFisher Scientific | Cat# A26028 |
| AmpliTaq Gold DNA polymerase, LD | ThermoFisher Scientific | Cat# 4338856 |
| Custom Taqman Probe | ThermoFisher Scientific | Cat# 450024 |
| Nextera® XT Index Kit v2 Set A (96 Indices, 384 Samples) | Illumina | Cat# FC-131-2001 |
| Nextera® XT Index Kit v2 Set B (96 Indices, 384 Samples) | Illumina | Cat# FC-131-2002 |
| Nextera® XT Index Kit v2 Set C (96 Indices, 384 Samples) | Illumina | Cat# FC-131-2003 |
| Nextera® XT Index Kit v2 Set D (96 Indices, 384 Samples) | Illumina | Cat# FC-131-2004 |
| KAPA HotStart ReadyMix, 500 x 25 μL reactions | Roche | Cat# KK2602 |
| Magnetic Bead, Agencourt® AMPure® XP, 5 mL | Beckman Coulter | Cat# A63880 |
| PhiX Control v3 | Illumina | Cat# FC-110-3001 |
| AccuPrime™ Taq DNA Polymerase High Fidelity | ThermoFisher Scientific | Cat# 12346086 |
| Quant-iT™ dsDNA Assay Kit, high sensitivity | ThermoFisher Scientific | Cat# Q33120 |
| MiSeq Reagent Kit v3 | Illumina | Cat# MS-102-3003 |
| ATCC 20 Strain Staggered Mix Genomic Material | ATCC | Cat# MSA-1003 |
| Critical commercial assays | ||
| eBioscience™ Foxp3 / Transcription Factor Staining Buffer Set | eBioscience | Cat# 00-5523-00 |
| Cytometric Bead Array; IFNγ, IL-6, TNF, IL-17A | BD Biosciences | Cat#560485 |
| Lamina Propria Dissociation Kit, mouse | MACS Miltenyi Biotec | Cat#130-097-410 |
| QIAamp BiOstic Bacteremia DNA Isolation Kit | QIAGEN | Cat#12240-50 |
| MiSeq Reagent Kit v3 (600-cycle) | Illumina | Cat# MS-102-3003 |
| QIAamp PowerFecal Pro DNA Kit | QIAGEN | Cat# 51804 |
| DNeasy PowerClean Pro Cleanup Kit | QIAGEN | Cat# 12997-50 |
| Deposited data | ||
| Murine fecal and ileal 16S RNA gene sequence | This article | Accession: Bioproject PRJNA980199 |
| Human pre-transplant patients fecal 16S RNA gene sequence | MSKCC | Accession: Listed in Table S6 |
| Experimental models: Cell lines | ||
| (Bacteria described in ”Bacterial and virus strains”) | ||
| Experimental models: Organisms/strains | ||
| Mouse: B6J ARC: C57BL/6JArc | The Animal Resources Centre (ARC), Perth, AU | Cat# 000664 |
| Mouse: B6J JAX: C57BL/6J | The Jackson Laboratory | RRID:IMSR_JAX:000664 |
| Mouse: B6N JAX: C57BL/6NJ | The Jackson Laboratory | RRID:IMSR_JAX:005304 |
| Mouse: B6N CR: C57BL/6NCrl | Charles River | Strain Code: 027 |
| Mouse: B6N TAC: C57BL/6NTac | Taconic | Model#: B6-F, B6-M |
| Mouse: B6N ADFH: C57BL/6N | Maintained at FHCC | N/A |
| Mouse: BALB/c: BALB/cJ | The Jackson Laboratory | RRID:IMSR_JAX:000651 |
| Mouse: B6.I-Ab−/−: H2-Ab−/− | Australian National University, Canberra, AU | Grusby M.J., et al. 1991 |
| Mouse: Villin Cre-ERT2 | Dr R Blumberg, Harvard Medical School, Boston, MA, USA | El Marjou F., et al. 2004 |
| Mouse: I-Ab-fl/fl: B6.129X1-H2-Ab1tm1Koni/J | The Jackson Laboratory | RRID:IMSR_JAX:013181 |
| Mouse: B6.Ifnγ-YFP: B6.129S4-Ifngtm3.1Lky/J (GREAT) | The Jackson Laboratory | RRID:IMSR_JAX:017581 |
| Mouse: B6.Ifnγ-YFP: B6.129S4-Ifngtm3.1Lky/J (GREAT) | Maintained at QIMR Berghofer, then FHCC | RRID:IMSR_JAX:017581 |
| Mouse: B6.Ifngr−/− : B6.129S7-Ifngr1tm1Agt/J | The Jackson Laboratory | RRID:IMSR_JAX:003288 |
| Mouse: C57BL/6N-Ifngr1tm1.1Rds/J | The Jackson Laboratory | RRID:IMSR_JAX:025394 |
| Mouse: Marilynluc+: Rag2−/− Marilyn mice were backcrossed onto a B6 β-actin-luciferase background | QIMR Berghofer, Brisbane, AU | N/A |
| Villin-Cre-ERT2 strain and I-Ab -fl/fl or Ifngr1 l/fl strains were intercrossed to generate: | N/A | N/A |
| Mouse: Villin-Cre-ERT2 I-Ab-fl/fl | FHCC | N/A |
| Mouse: Villin-Cre-ERT2 Ifngr1 fl/fl | FHCC | N/A |
| Oligonucleotides | ||
| N/A | ||
| Recombinant DNA | ||
| N/A | ||
| Software and algorithms | ||
| BD FACSDiva software version 9.1 | BD Bioscience | https://www.bdbiosciences.com/in/instruments/software/facsdiva/ |
| FlowJo v10 | Tree Star | https://www.flowjo.com/ |
| GraphPad Prism (ver. 9.4.0) | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ |
| R (ver. 4.0.3) | R Foundation for Statistical Computing | https://www.r-project.org/ |
| HALO Link image analysis software | Indica Labs | https://indicalab.com/halo/ |
| barcodecop v0.41 | Dr. Noah Hoffman | https://github.com/nhoffman/barcodecop |
| DADA2 package | Callahan et al. Nat. Methods. PMID 27214047 | https://benjjneb.github.io/dada2/index.html |
| ya16sdb pipeline | Dr. Noah Hoffman | https://github.com/nhoffman/ya16sdb. |
| cmalign | Nawrocki and Eddy. PMID 24008419 | http://eddylab.org/infernal/ |
| pplacer | Matsen et al. BMC Bioinform. PMID 21034504 | https://matsen.fhcrc.org/pplacer/ |
| Other | ||
| BD Symphony A3 | BD Biosciences | https://www.bdbiosciences.com/en-us/products/instruments/flow-cytometers/research-cell-analyzers/bd-facsymphony-a3 |
| Vectra Polaris Quantitative Pathology Imaging System | Akoya Biosciences | https://www.akoyabio.com/wp-content/uploads/2021/11/Vectra_Polaris_Product_Note_with_MOTiF_Akoya.pdf |