KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-CD16 and anti-CD32 (clone 2.4G2) | BD Biosciences | Cat# 553142; RRID:AB_394657 |
| anti-Mouse CD4 monoclonal antibody (Rat, Clone GK1.5), Brilliant Violet 650 conjugated | BD Biosciences | Cat# 563232; RRID:AB_2738083 |
| anti-Mouse CD8 monoclonal antibody (Rat, Clone 53-6.7), Brilliant Violet 570 conjugated | Biolegend | Cat# 100740; RRID:AB_2563055 |
| anti-Mouse IFN-gamma monoclonal antibody (Rat, Clone XMG1.2), Brilliant Violet 605 conjugated | BioLegend | Cat# 505839; RRID:AB_2561438 |
| anti-Mouse CD45 monoclonal antibody (Rat, Clone 30-F11), Brilliant Violet 480 conjugated | BD Biosciences | Cat# 566095; RRID:AB_2739499 |
| anti-Mouse TCR β monoclonal antibody (armenian hamster, Clone H57-597), Alexa Fluor® 700 conjugated | BD Biosciences | Cat# 560705; RRID:AB_1727573 |
| anti-Mouse FOXP3 monoclonal antibody (Rat, Clone FJK-16s), FITC conjugated | Thermo Fisher Scientific | Cat# 11-5773-82; RRID:AB_465243 |
| anti-Mouse CD45 monoclonal antibody (Rat, 30-F11), APC-Cy™7 conjugated | BD Biosciences | Cat# 557659; RRID:AB_396774 |
| anti-Mouse CD4 monoclonal antibody (Rat, GK1.5), BUV395 conjugated | BD Biosciences | Cat# 563790; RRID:AB_2738426 |
| anti-Mouse CD8 monoclonal antibody (Rat, 53-6.7), BUV737 conjugated | BD Biosciences | Cat# 612759; RRID:AB_2870090 |
| anti-Mouse CD19 monoclonal antibody (Rat, Clone 1D3/CD19), PerCP/Cyanine5.5 conjugated | BioLegend | Cat# 152406; RRID:AB_2629815 |
| anti-Mouse F4/80 monoclonal antibody (Rat, Clone BM8), PE-Cyanine5 conjugated | eBioscience™ | Cat# 15-4801-82; RRID:AB_468798 |
| anti-Mouse CD11c monoclonal antibody (Armenian hamster, Clone N418), Brilliant Violet 421 conjugated | BD Biosciences | Cat# 565451; RRID:AB_2744278 |
| anti-Mouse IL-17A monoclonal antibody (Rat, Clone TC11-18H10.1), Alexa Fluor(R) 647 conjugated | BioLegend | Cat# 506912; RRID:AB_536014 |
| anti-Mouse NK-1.1 monoclonal antibody (Mouse, Clone PK136), Brilliant Violet 786 conjugated | BD Biosciences | Cat# 740853; RRID:AB_2740506 |
| anti-Mouse CD44 monoclonal antibody (Rat, IM7), APC conjugated | BD Biosciences | Cat# 559250; RRID:AB_398661 |
| anti-Mouse CD62L monoclonal antibody (Rat, Clone MEL-14), PE conjugated | Thermo Fisher Scientific | Cat# 12-0621-81; RRID:AB_465720 |
| anti-Mouse NK1.1 monoclonal antibody (Rat, Clone PK136), FITC conjugated | BioLegend | Cat# 108706; RRID:AB_313393 |
| anti-Mouse MHC II monoclonal antibody (Rat, Clone M5/114.15.2), FITC conjugated | Thermo Fisher Scientific | Cat# 11-5321-82; RRID:AB_465232 |
| anti-Mouse TCR γ/δ monoclonal antibody (Rat, Clone UC7-13D5), FITC conjugated | BioLegend | Cat# 107504; RRID:AB_313313 |
| anti-Mouse CD11b monoclonal antibody (Rat, Clone M1/70), APC-eFluor 780 conjugated | Thermo Fisher Scientific | Cat# 47-0112-82; RRID:AB_1603193 |
| anti-Mouse Ly-6G/Ly-6C (Gr-1) monoclonal antibody (Rat, Clone RB6-8C5), Alexa Fluor(R) 700 conjugated | BioLegend | Cat# 108422; RRID:AB_2137487 |
| anti-Mouse Ly-6G/Ly-6C monoclonal Antibody (Rat, Clone RB6-8C5), PerCP-Cyanine5.5 conjugated | Thermo Fisher Scientific | Cat# 45-5931-80; RRID:AB_906247 |
| anti-Mouse CD11b Monoclonal Antibody (Rat, Clone M1/70), PE-Cyanine7 conjugated | Thermo Fisher Scientific | Cat# 25-0112-82; RRID:AB_469588 |
| anti-Mouse IL-12/IL-23 p40 Monoclonal Antibody (Rat, Clone C17.8), PE conjugated | eBioscience™ | Cat# 12-7123-82; RRID:AB_466185 |
| anti-Mouse IFNγ monoclonal Antibody (Rat, Clone XMG1.2) unconjugated | Bio X Cell | Cat# BE0055; RRID:AB_1107694 |
| IgG1 isotype control (anti-HRP) monoclonal antibody (Rat, Clone, HRPN) unconjugated | Bio X Cell | Cat# BE0088; RRID:AB_1107775 |
| anti-Mouse CD3e monoclonal antibody (Armenian hamster, 145-2C11) unconjugated | BD Biosciences | Cat# 553057; RRID:AB_394590 |
| anti-Mouse CD28 monoclonal antibody (Syrian hamster, 37.51) unconjugated | BD Biosciences | Cat# 553294; RRID:AB_394763 |
| anti-Mouse CD138 Monoclonal Antibody (Rat, Clone 281-2), PE conjugated | BioLegend | Cat# 142504; RRID:AB_10916119 |
| anti-Mouse IFN gamma Receptor 1 Monoclonal Antibody (Armenian hamster, Clone 2E2), PE conjugated | Thermo Fisher Scientific | Cat# 12-1191-82; RRID:AB_1210730 |
| anti-Human/Mouse IL-12 R beta 2 Monoclonal Antibody (Mouse IgG1, Clone 305719), APC conjugated | R & D Systems | Cat# FAB1959A; RRID: AB_2124049 |
| anti-Mouse STAT1 Monoclonal Antibody (Mouse, Clone A15158B), PE conjugated | BioLegend | Cat# 686404; RRID:AB_2616939 |
| Goat Anti-Mouse IgG, Human ads-UNLB antibody unconjugated | SouthernBiotech | Cat# 1030-01, RRID:AB_2794290 |
| goat anti-Mouse IgG, Human ads-HRP antibody unconjugated | SouthernBiotech | Cat# 1030-05, RRID:AB_2619742 |
| goat anti-Mouse IgG, Human ads-FITC antibody unconjugated | SouthernBiotech | Cat# 1030-02, RRID:AB_2794291 |
| anti-mouse IFN-gamma Monoclonal Antibody (Rat, Clone AN 18), unconjugated | BD Biosciences | Cat# 551309, RRID:AB_394145 |
| anti-mouse IFN-gamma Monoclonal Antibody (Rat, Clone XMG1.2), biotin conjugated | BD Biosciences | Cat# 554410, RRID:AB_395374 |
| Peroxidase-Streptavidin antibody | Jackson ImmunoResearch | Cat# 016-030-084, RRID:AB_2337238 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Recombinant Mouse IFN-gamma | R & D Systems | Cat# 485-MI-100 |
| Zombie NIR™ Fixable Viability Kit | BioLegend | Cat# 423106 |
| LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit | Invitrogen | Cat# L34957 |
| Super Bright Complete Staining Buffer | eBioscience | Cat# SB-4401-75 |
| Proteinase K Solution | Invitrogen | Cat# 25530049 |
| ExoSAP-IT™ PCR Product Cleanup Reagent | Applied Biosystems | Cat# 78201.1.ML |
| iTaq™ Universal SYBR® Green Supermix | Bio-Rad | Cat# 1725125 |
| GolgiStop™ | BD Biosciences | Cat# 554724 |
| GolgiPlug™ | BD Biosciences | Cat# 555029 |
| PMA | Sigma-Aldrich | Cat# P1585 |
| Ionomycin calcium salt | Sigma-Aldrich | Cat# I0634 |
| Mouse Erythrocyte Lysing Kit | R & D Systems | Cat# WL2000 |
| Percoll™ | Thermo Fisher Scientific | Cat# 45-001-747 |
| RPMI 1640 | Thermo Fisher Scientific | Cat# MT10040CV |
| DMEM | Gibco™ | Cat# 11-995-065 |
| Penicillin-Streptomycin-Glutamine | Gibco™ | Cat# 10-378-016 |
| L-Tryptophan | Sigma-Aldrich | Cat# T0254 |
| Peptone | Sigma | Cat# 70173 |
| Tryptone | Sigma | Cat# T7293 |
| Sodium chloride | Sigma | Cat# S3014 |
| Indole-3-aldehyde (carboxyaldehyde) | Sigma-Aldrich | Cat# 129445 |
| AHR inhibitor (CH-223191) | Sigma-Aldrich | Cat# C8124 |
| DNase I | Roche | Cat# 10104159001 |
| BBL™ Fluid Thioglycollate | BD Biosciences | Cat# BB21196 |
| BBL™ Brucella Agar with 5% Sheep Blood, Hemin and Vitamin K1 Prepared Media | Midland Scientific | Cat# 297848 |
| Lactobacillus spp. MRS Broth | BD Biosciences | Cat# DF0881-17-5 |
| Vancomycin | Sigma-Aldrich | Cat# V2002 |
| Kanamycin | Sigma-Aldrich | Cat# 60615 |
| Metronidazole | Sigma-Aldrich | Cat# M3761 |
| Colistin | Sigma-Aldrich | Cat# C4461 |
| Gentamycin | Sigma-Aldrich | Cat# G1914 |
| ALT /GPT Reagent; Infinity | Fisher Scientific | Cat# TR71121 |
| Normocin | InvivoGen | ant-nr-1 |
| Zeocin | InvivoGen | ant-zn-05 |
| QUANTI-Luc™ | InvivoGen | rep-qlc1 |
| Recombinant Mouse IL-12 (p70) | BioLegend | Cat#577002 |
| Concanavalin A | Sigma-Aldrich | Cat# C5275 |
| Carbon tetrachloride | Sigma-Aldrich | Cat# 319961 |
| Critical Commercial Assays | ||
| FoxP3 Transcription Factor Staining Kit | eBioscience | Cat# 00-5523-00 |
| Cytofix/Cytoperm™ Fixation/Permeablization Kit | BD Biosciences | Cat# 554714 |
| In Situ Cell Death Detection Kit, TMR red | Sigma-Aldrich | Cat# 12156792910 |
| EasySep™ Mouse Naïve CD8+ T Cell Isolation Kit | STEMCELL Technologies | Cat# 19858 |
| EasySep™ Mouse Naïve CD4+ T Cell Isolation Kit | STEMCELL Technologies | Cat# 19765 |
| Mouse Anti-nuclear antibody (ANA) ELISA Kit | MyBioSource | Cat# MBS261480 |
| TMB Substrate Kit | Thermo Fisher Scientific | Cat# 34021 |
| iScript™ cDNA Synthesis Kit | Bio-Rad | Cat# #1708891BUN |
| SuperScript™ VILO™ cDNA Synthesis Kit | Invitrogen | Cat# 11754050 |
| RNeasy Plus Mini Kit | Qiagen | Cat# 74136 |
| DNA Microbiome Kit | Qiagen | Cat# 51704 |
| RNeasy Plus Micro Kit | Qiagen | Cat# 74034 |
| QIAamp Fast DNA Stool Mini Kit | Qiagen | Cat# 51604 |
| Phosflow Lyse/Fix Buffer | BD Biosciences | Cat# 558049 |
| True-Phos™ Perm Buffer | BioLegend | Cat#425401 |
| Mouse Liver Kidney Microsome Autoantibody (Anti-LKM) ELISA Kit | MyBioSource | Cat# MBS3807100 |
| Mouse soluble liverantigen antibody (SLA) ELISA Kit | MyBioSource | Cat# MBS266348 |
| Kallestad HEp-2 Slides | Bio-Rad | Cat# 26103 |
| Invitrogen™ Fluoromount-G™ Mounting Medium | Fisher Scientific | Cat# 00-4958-02 |
| Deposited Data | ||
| Raw and analyzed 16S rRNA-Seq data | This paper | NCBI Sequence Read Archive, SRA: PRJNA830441 |
| Raw and analyzed hepatic RNA-seq data | This paper | NCBI: GSE201459 |
| Experimental Models: Organisms/Strains | ||
| Mouse: B6.Tet2−/− | Meisel et al. (2018) | N/A |
| Mouse: B6. Tet2f (B6;129S-Tet2tm1.1Iaai/J) | Meisel et al. (2018) | N/A |
| Mouse: B6. Vav-cre line (B6.Cg-Tg(Vav1-icre)A2Kio/J) | Jackson Laboratory | Stock No: 008610 |
| Mouse: B6. LysM-cre line (Lyz2tm1(cre)Ifo)) | Jackson Laboratory | Stock No: 004781 |
| Mouse: B6. Tg(CD2-cre)1Lov/J | Jackson Laboratory | Stock No: 027406 |
| Mouse: B6. Albumin-cre (B6.Cg-Speer6-ps1Tg(Alb-cre)21Mgn/J) | Jackson Laboratory | Stock no.: 003574 |
| Mouse: B6. Ifng−/− (B6.129S7-Ifngtm1Ts/J) | Jackson Laboratory | Stock no.: 002287 |
| CD8α-Cre (C57BL/6-Tg(Cd8a-cre)1Itan/J) | Jackson Laboratory | Stock no.: 008766 |
| Mouse: B6. Rag−/− | Provided by M. Shlomchik | N/A |
| Germ free B6. Tet2−/− and B6.Tet2+/+ | Meisel et al. (2018) | N/A |
| L. reuteri | ATCC | Cat# BAA-2837 |
| L. johnsonii | ATCC | Cat# BAA-3147 |
| ΔArAT L. reuteri | Dr. Cervantes-Barragan | N/A |
| AhR reporter cell line | Invivogen | Cat# ht2l-ahr |
| Blautia producta | ATCC | 27340D-5 |
| Oligonucleotides | ||
| (mouse) see Table S8 | ||
| Software and Algorithms | ||
| GraphPad Prism 9 | GraphPad Software | N/A |
| FlowJo 10.7.1 | Tree Star | https://www.flowjo.com/solutions/flowjo/downloads |
| ImageJ | Open source | https://imagej.nih.gov/ij/index.html |
| BioRender | BioRender Company | N/A |