| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD317 (BSTII) APC (clone 927) | BioLegend | Cat# 127016; RRID:AB_1967127 |
| CD317 (BSTII) BV421 (clone 927) | BioLegend | Cat# 127023; RRID:AB_2687109 |
| CCR7 PE (clone 4B12) | BioLegend | Cat# 120106; RRID:AB_389358 |
| CCR7 PECy5 (clone 4B12) | BioLegend | Cat# 120113; RRID:AB_493571 |
| CD11b BV786 (clone M1/70) | BioLegend | Cat# 101243; RRID:AB_2561373 |
| CD11c PE Cy7(clone N418) | BioLegend | Cat# 117318; RRID:AB_493568 |
| CD11c BUV737 (clone N418) | BD Biosciences | Cat# 749039; RRID:AB_2873433 |
| CD45 APC-R700 (clone 30-F11) | BD Biosciences | Cat# 565478; RRID:AB_2739257 |
| CD45 R718 (clone 30-F11) | BD Biosciences | Cat# 567075 |
| CD64 PE Dazzle 594 (clone X54-5/7.1) | BioLegend | Cat# 139319; RRID:AB_2566558 |
| CD172a (SIRPa) APC (clone P84) | BioLegend | Cat# 144014; RRID:AB_2564061 |
| CD172a (SIRPa) FITC (clone P84) | BioLegend | Cat# 144006; RRID:AB_11204425 |
| I-A/I-E (MHCII) BV510 (clone M5/114.15.2) | BioLegend | Cat# 107635; RRID:AB_2561397 |
| RORgt PE (clone B2D) | Thermo Fisher Scientific | Cat# 12-6981-82; RRID:AB_10807092 |
| XCR1 BV650 (clone ZET) | BioLegend | Cat# 148220; RRID:AB_2566410 |
| XCR1 BV421 (clone ZET) | BioLegend | Cat# 148216; RRID:AB_2565230 |
| CD74 APC (clone In1/CD74) | BioLegend | Cat# 151003; RRID:AB_2632608 |
| CD86 APC (clone GL-1) | BioLegend | Cat# 105011; RRID:AB_493343 |
| IgA PE (clone mA-6E1) | Thermo Fisher Scientific | Cat# 12-4204-81; RRID:AB_465916 |
| IgG1 FITC (clone RG11/39.4) | BD Biosciences | Cat# 553892; RRID:AB_395120 |
| CD4 BV510 (clone RM4-5) | BioLegend | Cat# 100559; RRID:AB_2562608 |
| CD8a BV711 (clone 53-6.7) | BioLegend | Cat# 100748; RRID:AB_2562100 |
| CD44 BV785 (clone IM7) | BioLegend | Cat# 103059; RRID:AB_2571953 |
| CD45.1 BUV 737 (clone A20) | BD Biosciences | Cat# 612811; RRID:AB_2870136 |
| CD45.1 FITC (clone A20) | BioLegend | Cat# 110706; RRID:AB_313495 |
| CD45.2 AF700 (clone 104) | BioLegend | Cat# 109822; RRID:AB_493731 |
| CD69 PE Cy7 (clone H1.2F3) | BioLegend | Cat# 104512; RRID:AB_493564 |
| Va2 BV421 (clone B20.1) | BD Biosciences | Cat# 562944; RRID:AB_2737910 |
| TCRb APC Cy7 (clone H57-597) | BioLegend | Cat# 109220; RRID:AB_893624 |
| GL7 PerCP-Cy5.5 (clone GL7) | BioLegend | Cat# 144609; RRID:AB_2562978 |
| B220 (CD45R) PE/Fire 700 (clone RA3-6B2) | BioLegend | Cat# 103279; RRID:AB_2876408 |
| CD19 Spark NIR 685 (clone 6D5) | BioLegend | Cat# 115568; RRID:AB_2819829 |
| CD3 APC/Fire 810 (clone 17A2) | BioLegend | Cat# 100267; RRID:AB_2876392 |
| IgM eF450 (clone II/41) | Thermo Fisher Scientific | Cat# 48-5790-80; RRID:AB_2574072 |
| IgD BV480 (clone 11-26c.2a) | BD Biosciences | Cat# 566199; RRID:AB_2739590 |
| CD64 (FcγRI) BV605 (clone X54-5/7.1) | BioLegend | Cat# 139323; RRID:AB_2629778 |
| CD45 BUV 395 (clone 30-F11) | BD Biosciences | Cat# 564279; RRID:AB_2651134 |
| CD95 BUV 563 (clone Jo2) | BD OptiBuild | Cat# 741292; RRID:AB_2870823 |
| Chicken anti-GFP unlabeled | Aves Labs | Cat# GFP-1020; RRID:AB_2307313 |
| Hamster anti-mouse CD11c unlabeled (clone N418) | Biolegend | Cat# 117302; RRID:AB_313771 |
| Rabbit anti-mouse IRF8 unlabeled | Bethyl Laboratories | Cat#A304-028A-T; RRID:AB_2620376 |
| Rabbit anti-lysozyme unlabeled | Agilent | Cat# A0099; RRID:AB_2341230 |
| Rat anti-mouse TLR3 unlabeled (clone 11F8) | Bio-Rad | Cat#MCA5891GA |
| Rat anti-mouse SIRPa unlabeled (clone P84) | Biolegend | Cat# 144002; RRID:AB_11203711 |
| Rat anti-ROR gamma (t) unlabeled (clone AFKJS-9) | Thermo Fisher Scientific | Cat# 14-6988-82; RRID:AB_1834475 |
| Rat anti-mouse GP2 unlabeled (clone 2F11-C3) | MBL International | Cat# D278-3; RRID:AB_10598188 |
| Rat anti-mouse CD45 unlabeled (clone 30F11) | Biolegend | Cat# 103101; RRID:AB_312966 |
| Rat anti-mouse CD4-eFluor 450 (clone RM4-5) | Thermo Fisher Scientific | Cat# 48-0042-82; RRID:AB_1272194 |
| Rat anti-mouse Ep-CAM-Alexa Fluor 647 (clone G8.8) | Biolegend | Cat# 118211; RRID:AB_1134104 |
| Donkey anti-chicken IgG- Alexa Fluor 488 | Jackson ImmunoResearch | Cat# 703-545-155; RRID:AB_2340375 |
| Donkey anti-rat IgG-Cy3 | Jackson ImmunoResearch | Cat# 712-165-153; RRID:AB_2340667 |
| Goat anti-Armenian hamster IgG-Alexa Fluor 594 | Jackson ImmunoResearch | Cat# 127-585-160; RRID:AB_2338999 |
| Goat anti-rabbit IgG- Alexa Fluor 514 | Thermo Fisher Scientific | Cat# A-31558; RRID:AB_2536173 |
| Bacterial and virus strains | ||
| Bacteroides fragilis | Clavel Lab | CLA-KB-H83 and CLA-JM-H48 |
| Salmonella Typhiumurium | N/A | SL1344 |
| Biological samples | ||
| E.coli OMVs | Gerkara Lab, Erttmann et al.41 | N/A |
| PAA Salmonella Typhiumurium | Moor et al.44 | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| R848 | Invivogen | TLRL-R848 |
| Ovalbumin | Sigma | A5253-500G |
| Ultrapure flagellin from S. typhimurium | Invivogen | tlrl-epstfla-5 |
| RANKL | Biomol | RP0437M-100 |
| Fluoresbrite® YG Microspheres 0.10μm | Polysciences | 17150-10 |
| Liberase TH | Sigma Aldrich | 5401135001 |
| DNAse I | Sigma Aldrich | 11284932001 |
| Critical commercial assays | ||
| LEGENDplex™ Mouse Anti-Virus Response Panel (13-plex) with V-bottom Plate | Biolegend | 740622 |
| LEGENDplex™ MU Th Cytokine Panel (12-plex) w/ VbP V03 | Biolegend | 741044 |
| Chromium Single Cell 3’ v2 kit | 10xGenomics | PN-120267 |
| Deposited data | ||
| scRNAseq data | this manusript | GSE188714 |
| Metagenomic data | this manusript | BioProject # PRJNA794356 |
| Experimental models: Organisms/strains | ||
| C57BL/6J (B6) | N/A | The Jackson Laboratory |
| B6.Cg-Tg(TcraTcrb)425Cbn Rag1tm1Mom/J (OTII) | Barnden et al.89 | The Jackson Laboratory |
| C57BL/6-Tg(TcraTcrb)1100Mjb/J (OTI) | Hogquist et al.90 | The Jackson Laboratory |
| B6.129P2(SJL)-Myd88tm1DefrCg-Tg(Itgax-cre)1-1Reiz/J (MyD88DCD11c) | Caton et al.91 and Hou et al.92 | The Jackson Laboratory |
| B6.SJL-PtprcaPepcb/Boy/J (CD45.1) | Shen et al.93 | The Jackson Laboratory |
| C57BL/6-pIgR™/J (pIgR-/-) | Shimada et al.94 | The Jackson Laboratory |
| B6.Cg-Tnfrsf11atm1.1Irw/J-Tg(Vil1-cre)997Gum/J (RANKDIEC) | Rios et al.45 | The Jackson Laboratory |
| B6(Cg)-Ifnar1™/J-Tg(Itgax-cre)1-1Reiz/J (IFNARDCD11c) | Caton et al.91 and Kamphuis et al.95 | The Jackson Laboratory |
| B6.129P2(Cg)-Cx3cr1tm1Litt/J (CX3CR1-GFP) | Jung et al.96 | The Jackson Laboratory |
| Oligonucleotides | ||
| 5′-GCTGCCTCCCGTAGGAGT-3′ | IDT | Eub338 3′ and 5′ AF647 labeled |
| 5′-CCTACGGGNGGCWGCAG-3′ (16S_341_F) | Klindworth et al.97 | 16S_341_F |
| 5′-GACTACHVGGGTATCTAATCC-3′ (16S_805_R) | Klindworth et al.97 | 16S_805_R |
| Ccl9 | Thermofisher Scientific | Mm00441260_m1 |
| Spib | Thermofisher Scientific | Mm03048233_m1 |
| Gp2 | Thermofisher Scientific | Mm00482557_m1 |
| Intronic GAPDH | Thermofisher Scientific | Mm05724508-g1 |
| Hprt | Thermofisher Scientific | Mm00446968_m1 |
| Software and algorithms | ||
| FlowJo v10 | BD | RRID: SCR_008520 |
| Seurat v3.1.0 | Satija et al.98 | https://satijalab.org/seurat/ |
| Prism v9 | GraphPad Software | RRID: SCR_002798 |
| Cell Ranger v2.1.1 | 10x Genomicx | https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/2-1 |
| DeqMS v1.8.0 | N/A | https://github.com/yafeng/DEqMS |
| Monocle v2.12.0 | Trapnell et al.99 | https://www.bioconductor.org/packages/release/bioc/html/monocle.html |
| BOTA v0.1.0 | Graham et al.35 | N/A |
| MEGAhit v1.2.9 | Li et al.100 | https://kbase.us/applist/apps/MEGAHIT/run_megahit/release |
| PROKKA v1.13 | Seemann et al.101 | https://github.com/tseemann/prokka/releases |
| Kofamscan v1.3.0 | Aramaki et al.102 | https://github.com/takaram/kofam_scan |
| Trimmomatic v0.36 | Bolger et al.103 | http://www.usadellab.org/cms/?page=trimmomatic |
| BBmap 11-06-2018 | Bushnell104 | https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbmap-guide/ |
| BBsplit 11-06-2018 | Bushnell104 | https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh |
| iTOL v6.5 | Letunic et al.105 | https://itol.embl.de/ |
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