KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse Anti-mouse CD45.2 (104), APC-eFluor 780 | Invitrogen | Cat#47-0454-82; RRID: AB_1272175; Clone: 104 |
| Rat Anti-Mouse CD90.2 (30-H12), Brilliant Violet 605 | BD Biosciences | Cat#740334; RRID: AB_2740067; Clone: 30-H12 |
| Rat Anti-mouse CD3 molecular complex (17A2), PerCP-Cyanine5.5 | BD Biosciences | Cat#560527; RRID: AB_1727463; Clone: 17A2 |
| Hamster Anti-mouse TCR beta (H57-597), APC-eFluor 780 | Invitrogen | Cat# 47-5961-82; RRID: AB_1272173; H57-597 |
| Rat Anti-Mouse CD4 (RM4-5), Brilliant Violet 786 | BD Biosciences | Cat#563727; RRID: AB_2728707; Clone: RM4-5 |
| Rat Anti-mouse CD8b (H35-17.2), PE-Cyanine7 | Invitrogen | Cat#25-0083-82; RRID: AB_11218494; Clone H35-17.2 |
| Rat Anti-mouse CD44 (IM7), FITC | BD Biosciences | Cat#553133; RRID: AB_2076224; Clone: IM7 |
| Rat Anti-mouse CD44 (IM7), PerCP-Cyanine5.5 | Invitrogen | Cat#45-0441-82; RRID: AB_925746; Clone: IM7 |
| Rat Anti-mouse FOXP3 (FJK-16s), Alexa Fluor 488 | Invitrogen | Cat#53-5773-82; RRID: AB_763537; Clone: FJK-16s |
| Rat Anti-mouse FOXP3 (FJK-16s), eFluor 450 | Invitrogen | Cat#48-5773-82; RRID: AB_1518812; Clone: FJK-16s |
| Rat Anti-mouse CD304 (Neuropilin-1) (3E12), PE-Cyanine7 | Biolegend | Cat#145212; RRID: AB_2562360; Clone: 3E12 |
| Rat Anti-mouse ROR gamma (t) (B2D), PE | Invitrogen | Cat#12-6981-82; RRID: AB_10807092; Clone: B2D |
| Rat Anti-mouse Ki67 (16A8), FITC | Biolegend | Cat#652410; RRID: AB_2562141; Clone: 16A8 |
| Rat Anti-mouse CD39 (Duha59), PE-Dazzle™ 594 | Biolegend | Cat#143812; RRID: AB_2750322; Clone: Duha59 |
| Rat Anti-mouse CD73 (TY/11.8), Alexa Fluor 700 | Biolegend | Cat#127230; RRID: AB_2800625; Clone: TY/11.8 |
| Rat Anti-mouse CD11b (M1/70), PE-Cyanine7 | Invitrogen | Cat#25-0112-82; RRID: AB_469588; Clone: M1/70 |
| Hamster Anti-mouse CD11c (HL3), PerCP-Cyanine5.5 | BD Biosciences | Cat# 560584; RRID: AB_1727422; Clone: HL3 |
| Rat Anti-mouse Ly-6C (HK1.4), eFluor 450 | Invitrogen | Cat#48-5932-82; RRID: AB_10805519; Clone: HK1.4 |
| Rat Anti-mouse I-A/I-E (M5/114.15.2), Brilliant Violet 786 | BD Biosciences | Cat#742894; RRID: AB_2734759; Clone: M5/114.15.2 |
| Mouse Anti-mouse Cd64 (FcγRI) (X54-5/7.1), Brilliant Violet 605 | Biolegend | Cat#139323; RRID: AB_2629778; Clone: X54-5/7.1 |
| Rat Anti-mouse CD170 (Siglec F) (1RNM44N), eFluor 660 | Invitrogen | Cat#50-1702-82; RRID: AB_2574187; Clone: 1RNM44N |
| Rat Anti-mouse Ly-6G (1A8), PE-CF594 | BD Biosciences | Cat#562700; RRID: AB_2737730; Clone: 1A8 |
| Rat Anti-mouse CD19 (1D3), PE-CF594 | BD Biosciences | Cat#562291; RRID: AB_11154223; Clone: 1D3 |
| Rat Anti-mouse TER-119 (TER-119), PE-eFluor 610 | Invitrogen | Cat#61-5921-80; RRID: AB_2574637; Clone: TER-119 |
| Rat Anti-mouse CD11b (M1/70), PE-CF594 | BD Biosciences | Cat#562317; RRID: AB_11154422; Clone: M1/70 |
| Hamster Anti-mouse CD11c (HL3), PE-CF594 | BD Biosciences | Cat#562454; RRID: AB_2737617; Clone: HL3 |
| InVivoMAb anti-mouse CD4 (GK1.5) | BioXCell | Cat#BE0003-1; RRID: AB_1107636; Clone: GK1.5 |
| Goat Anti-Mouse IgA-HRP | SouthernBiotech | Cat#1040-05; RRID: AB_2714213 |
| Rat Anti-mouse CD16/32 (93) | Invitrogen | Cat#14-0161-86; RRID: AB_467135; Clone: 93 |
| Bacterial and virus strains | ||
| CUMT8 bacteria | (Craven et al., 2012; Dogan et al., 2014) | N/A |
| ECMB bacteria | (Molloy et al., 2013) | N/A |
| E coli 2A | Viladomiu et al., 2021) | N/A |
| ETEC KanaRes(jf876) | (Roy et al., 2011) | N/A |
| Biological samples | ||
| Stool samples and ileal contents from EED mice | This study | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Double mutant Labile Toxin (dmLT) from E. coli | Elizabeth Norton (Tulane) (Norton et al. 2011) | |
| Ionomycin | Millipore Sigma | Cat#I0634; CAS: 56092-82-1 |
| Phorbol 12-myristate 13-acetate | Millipore Sigma | Cat#P8139; CAS: 16561-29-8 |
| Brefeldin A | Invitrogen | Cat#00-514506-51 |
| Fluorescein isothiocyanate–dextran | Millipore Sigma | Cat#FD4; CAS: 60842-46-8 |
| LB Agar Plates, Kanamycin-50 | Teknova | Cat#L1025 |
| Metronidazole | Millipore Sigma | Cat#M1547; CAS: 443-48-1 |
| Ampicillin sodium salt | Millipore Sigma | Cat#A0166; CAS: 69-52-3 |
| Neomycin trisulfate salt hydrate | Millipore Sigma | Cat#N6386; CAS: 1405-10-3 |
| Vancomycin hydrochloride | Millipore Sigma | Cat#V1130; CAS: 1404-93-9 |
| Diphtheria Toxin | Millipore Sigma | Cat#D0564; MDL: MFCD00163490 |
| Tamoxifen | Millipore Sigma | Cat#T5648; CAS: 10540-29-1 |
| Corn oil | Millipore Sigma | CAS: 8001-30-7 |
| Fixable Live/Dead Aqua | Invitrogen | Cat#L34966 |
| Saccharin | Acros Organics | Cat#AC149005000 |
| Monomeric Avidin UltraLink− Resin | Thermo Scientific | Cat#53146 |
| Streptavidin-APC | Prozyme/Agilent | Cat#PJ27S-1 |
| Streptavidin-PE | Prozyme/Agilent | Cat#PJRS25-1 |
| Blasticidin | Invivogen | Cat#ant-bl-1 |
| Critical commercial assays | ||
| FoxP3/Transcription Factor Staining Buffer Set | Invitrogen | Cat#:00-5523-00 |
| Intracellular Fixation and and Permeabilization Buffer Set | Thermo Fisher Scientific | Cat#: 88-8824-00 |
| EasySep− APC Positive Selection Kit II | Stemcell Technologies | Cat#17681 |
| QIAamp Fast DNA Stool Mini Kit | Qiagen | Cat#51604 |
| MILLIPLEX MAP Mouse TH17 Magnetic Bead Panel - Immunology Multiplex Assay | Millipore Sigma | Cat#MTH17MAG-47K |
| SsoAdvanced Universal SYBR® Green Supermix | Bio-Rad | Cat#1725270 |
| Calcium Phosphate Transfection Kit | Invitrogen | Cat# K278001 |
| His-Tag Purification Kit | Millipore Sigma | Cat#70239-3 |
| Ultra-15 30kDa MWCO Centrifugal Filter Units | Millipore Sigma | Cat#UFC903024 |
| Deposited data | ||
| 16S rDNA amplicon sequencing of Stool samples and ileal contents from EED and control mice | This manuscript | PRJNA736663 |
| Experimental models: Cell lines | ||
| Drosophila S2 Cells in Schneider's Medium | Gibco | Cat#R69007 |
| Experimental models: Organisms/strains | ||
| Specific Pathogen Free C57BL/6NTac mice | Taconic Farms | MGI:5658006 |
| Foxp3DTR mice | Jackson Labs (Kim et al., 2007) | JAX stock #016958 |
| Foxp3eGFP-Cre-ERT2 mice | Jackson Labs Rubtsov et al., 2010). | JAX stock #016961 |
| Rorγtfl mice | Jackson Labs (Choi et al., 2016; . | JAX stock #008771 |
| Oligonucleotides | ||
| 16S primer Fwd 5'-ACTCCTACGGGAGGCAGCAGT-3' | IDT | N/A |
| 16S primer Rev 5'-ATTACCGCGGCTGCTGGC-3'. | IDT | N/A |
| ECMB OmpL Fwd 5’-TTCGGGTGGTGCAGTGTATC-3’ | IDT | N/A |
| ECMB OmpL Rev 5’-TGCTGCTATTAAAGTCATTTACGC-3’ | IDT | N/A |
| CUMT8 FliC Fwd 5’-CGACAGTGCCGGTATTTGTA-3’ | IDT | N/A |
| CUMT8 FliC Rev 5’-TGAGTACTGCGGATGGTTCA-3’ | IDT | N/A |
| LCN2 | Qiagen | PPMO3770A |
| Gapdh | Qiagen | PPM41731A |
| Recombinant DNA | ||
| Mouse I-Ab alpha chain on pRMHa-3 backbone | Jenkins lab, Moon et al | N/A |
| Mouse I-Ab beta chain with LT166-176 peptide DNA sequence on pRMHa-3 backbone | Jenkins lab, Moon et al | N/A |
| Software and algorithms | ||
| FlowJo X | BD Biosciences | N/A |
| FACSDiva | BD Biosciences | N/A |
| Prism 9 | GraphPad | 9.02 |
| R Studio | R Studio | N/A |
| Phyloseq | https://joey711.github.io/phyloseq/ | N/A |
| QIIME 2 2020.2 | (Bolyen et al., 2019). | N/A |
| DADA2 | (Callahan et al., 2016) | N/A |
| mafft | (Katoh et al., 2002) | N/A |
| fasttree2 | (Price et al., 2010) | N/A |
| Greengenes 13_8 99% OTUs reference sequences | (McDonald et al., 2012) | N/A |
| MicrobeR | J Bisanz, 2018 https://www.biorxiv.org/content/10.1101/304840v1 | N/A |
| LEfSe | https://huttenhower.sph.harvard.edu/galaxy/root | N/A |
| Other | ||
| Low protein/low fat diet (7% protein/7% fat) | Research Diets Brown et al., 2015 | D14071001 |
| Isocaloric diet (20% protein/15% fat) | Research Diets Brown et al., 2015 | D09051102 |