| Antibodies |
| Rat anti-Human Reg1A antibody |
R&D Systems |
Cat#: MAB4937; RRID: AB_2102139; Clone: 431202 |
| Mouse anti-Human Reg3A antibody |
R&D Systems |
Cat#: 62257S; RRID: AB_1964697; Clone: 512124 |
| Rabbit anti-REG3G antibody |
Abcam |
Cat#: ab233480 |
| Rabbit anti-REG4 antibody |
Abcam |
Cat#: ab255820; Clone: EPR22810-327 |
| Rabbit anti-SagA antibody |
Dr. Hang (Scripps Research Institutes)41
|
|
| Mouse anti-IL-22 antibody |
R&D Systems |
Cat#: MAB782; RRID: AB_2295882; Clone: 142938 |
| Mouse anti-NOD2 antibody |
Invitrogen |
Cat#: MA1-16611; RRID: AB_568643; Clone: 2D9 |
| Mouse anti-β-Actin antibody |
Sigma |
Cat#: A5441; RRID: AB_476744; Clone: AC-15 |
| IRDye 680RD Goat anti-Rabbit IgG Secondary Antibody |
LI-COR |
Cat# 925-68071; RRID: AB_2721181; |
| IRDye 800CW Goat anti-Mouse IgG Secondary Antibody |
LI-COR |
Cat#: 925-32210; RRID: AB_2687825; |
| IRDye 800CW Goat anti-Rat IgG Secondary Antibody |
LI-COR |
Cat#: 925-32219; RRID: AB_2721932; |
| PerCP/Cyanine5.5 anti-mouse/human CD11b Antibody |
Biolegend |
Cat#: 101228; RRID: AB_893232; Clone: M1/70 |
| PerCP/Cyanine5.5 anti-mouse CD11c Antibody |
Biolegend |
Cat#: 117328; RRID: AB_2129641; Clone: N418 |
| PerCP/Cyanine5.5 anti-mouse Ly-6G/Ly-6C (Gr-1) Antibody |
Biolegend |
Cat#: 108428; RRID: AB_893558; Clone: RB6-8C5 |
| PerCP/Cyanine5.5 anti-mouse TER-119/Erythroid Cells Antibody |
Biolegend |
Cat#: 116228; RRID: AB_893636; Clone: TER-119 |
| PerCP/Cyanine5.5 anti-mouse NK-1.1 Antibody |
Biolegend |
Cat#: 108728; RRID: AB_2132705; Clone: PK136 |
| PE anti-T-bet Antibody |
Biolegend |
Cat#: 644810; RRID: AB_2200542; Clone: 4B10 |
| PE- Cyanine7 anti-mouse/human CD44 antibody |
Biolegend |
Cat#: 103030; RRID: AB_830787; Clone: IM7 |
| APC/Cyanine7 anti-mouse CD4 Antibody |
Biolegend |
Cat#: 100414; RRID: AB_312699; Clone: GK1.5 |
| Brilliant Violet 570 anti-mouse CD62L Antibody |
Biolegend |
Cat#: 104433; RRID: AB_10900262; Clone: MEL-14 |
| Brilliant Violet 605 anti-mouse CD127 (IL-7Ra) Antibody |
Biolegend |
Cat#: 135041; RRID: AB_2572047; Clone: A7R34 |
| Brilliant Violet 650 anti-mouse NK-1.1 Antibody |
Biolegend |
Cat#: 108736; RRID: AB_2563159; Clone: PK136 |
| Alexa Fluor 700 anti-mouse CD8a Antibody |
Biolegend |
Cat#: 100730; RRID: AB_493703; Clone: 53-6.7 |
| Brilliant Violet 711 anti-mouse TCR β chain Antibody |
Biolegend |
Cat#: 109243; RRID: AB_2629564; Clone: H57-597 |
| PerCP/Cyanine5.5 anti-mouse CD19 |
eBioscience |
Cat#: 45-0193-82; RRID: AB_1106999; Clone: 1D3 |
| PE anti-mouse IL-22 Antibody |
eBioscience |
Cat#: 12-7221-82; RRID: AB_10597428; Clone: 1H8PWSR |
| APC anti-mouse FOXP3 Antibody |
eBioscience |
Cat#: 17-5773-82; RRID: AB_469457; Clone: FJK-16s |
| PE-CF594 anti-mouse γδ T-Cell Receptor Antibody |
BD Bioscience |
Cat#: 563532; RRID: AB_2661844; Clone: GL3 |
| BUV395 anti-mouse CD45 Antibody |
BD Bioscience |
Cat#: 564279; RRID: AB_2651134; Clone: 30-F11 |
| BV421 anti-mouse RORgt Antibody |
BD Bioscience |
Cat#: 562894; RRID: AB_2687545; Clone: Q31-378 |
| BV421 anti-mouse IL-10 Antibody |
BD Bioscience |
Cat#: 566295; RRID: AB_2739668; Clone: JES5-16E3 |
| Alexa Fluor 488 anti-mouse GATA3 Antibody |
BD Bioscience |
Cat#: 560163; RRID: AB_1645302; Clone: L50-823 |
| Bacterial strains |
|
Enterococcus faecalis OG1RF |
Dr. Hang (Scripps Research Institutes), originally acquired from ATCC 47077. |
N/A |
|
Enterococcus faecium Com15 |
Dr. Hang (Scripps Research Institutes), originally acquired Dr. Gilmore (Harvard Medical School). |
N/A |
|
Salmonella Typhimurium SL1344 |
Gift from Dr. Littman (NYU) |
N/A |
|
Lactococcus lactis thyA auxotroph |
Dr. Hang (Scripps Research Institutes)50, generated in collaboration with Rise Therapeutics |
N/A |
|
Lactococcus lactis thyA expressing wild-type SagA |
Dr. Hang (Scripps Research Institutes)50, generated in collaboration with Rise Therapeutics |
N/A |
|
Lactococcus lactis thyA expressing catalytic mutant SagA |
Dr. Hang (Scripps Research Institutes)50, generated in collaboration with Rise Therapeutics |
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
| Bacto brain heart infusion |
BD |
Cat#: 237500 |
| Sabouraud dextrose broth |
Millipore |
Cat#: S3306 |
| Nutrient Broth |
Millipore |
Cat#: 70122 |
| BsaHI |
NEB |
Cat#: R0556S |
| Dulbecco’s Modified Eagle’s Medium |
Corning |
Cat#: 10-017-CV |
| Fetal bovine serum |
Peak Serum |
Cat#: PS-FB2 |
| Penicillin-Streptomycin Solution |
Corning |
Cat#: 30-002-CI |
| Normicin |
InvivoGen |
Cat#: ant-nr |
| Zeocin |
InvivoGen |
Cat#: ant-zn |
| Blastocidin |
InvivoGen |
Cat#: ant-bl |
| Trypsin-EDTA |
Gibco |
Cat#: 25200056 |
| M17 Broth |
BD |
Cat#: 218561 |
| M17 Agar |
BD |
Cat#: 218571 |
| Bile esculin azide agar |
Millipore |
Cat#: 06105 |
| HiCrome Enterococcus faecium Agar Base |
HIMEDIA |
Cat#: M1580 |
| Enterococcus faecium Selective Supplement |
HIMEDIA |
Cat#: FD226 |
| Lactose |
Sigma-Aldrich |
Cat#: 17814 |
| Thymidine |
Sigma-Aldrich |
Cat#: T9250 |
| Phosphate-buffer saline |
Corning |
Cat#: 21040CV |
| Triton X-100 |
Sigma-Aldrich |
Cat#: T8787 |
| Glycerol |
Sigma-Aldrich |
Cat#: G5516 |
| Halt Protease and Phosphatase Inhibitor Cocktail |
Thermo Fisher |
Cat#: 78440 |
| Bolt 4-12% Bis-Tris Plus Gels |
Invitrogen |
Cat#: NW04120BOX |
| Intercept (TBS) Blocking Buffer |
LI-COR |
Cat#: 927-60003 |
| Trypticase soy agar with 5% sheep blood |
Henry Schein |
Cat#: 9873908 |
| HEK-Blue detection medium |
InvivoGen |
Cat#: hb-det2 |
| Dextran sulfate sodium |
TdB Consultancy |
Cat#: DB001 |
| Ampicillin |
Amercian Bioanalytical |
Cat#: 69-52-3 |
| Streptomycin |
Sigma-Aldrich |
Cat#: S6501 |
| Low melting point agar |
Promega |
Cat#: V2111 |
| 10% Formalin |
Thermo Fisher |
Cat#: SF99-4 |
| Roswell Park Memorial Institute 1640 Medium |
Gibco |
Cat#: 61870127 |
| L-glutamine |
Corning |
Cat#: 25-005-CI |
| HEPES |
Corning |
Cat#: 25-060-CI |
| Minimum Essential Medium Nonessential Amino Acids |
Corning |
Cat#: 25-025-CI |
| Sodium pyruvate |
Corning |
Cat#: 25-000-CI |
| β-mercaptoethanol |
Gibco |
Cat#: 21985023 |
| Hank’s Balanced Salt Solution |
Gibco |
Cat#: 14175103 |
| DL-dithiothreitol |
Sigma Aldrich |
Cat#: D0632 |
| Collagenase |
Sigma Aldrich |
Cat#: C2139 |
| Deoxyribonuclease I |
Sigma Aldrich |
Cat#: DN25 |
| Percoll |
Sigma-Aldrich |
Cat#: P1644 |
| Cell Stimulation Cocktail (plus protein transport inhibitors) |
eBioscience |
Cat#: 00-4975-93 |
| Bovine Serum Albumin |
Thermo Fisher |
Cat#: BP1600-100 |
| Fixation Buffer |
Biolegend |
Cat#: 420801 |
| Intracellular Staining Permeabilization Wash Buffer |
Biolegend |
Cat#: 421002 |
| Foxp3 / Transcription Factor Staining Buffer Set |
Thermo Fisher |
Cat#: 00-5523-00 |
| Zombie UV Fixable Viability Kit |
Biolegend |
Cat#: 423108 |
| Critical commercial assays |
| 10 ml syringe |
BD |
Cat#: 302995 |
| Gauze pad |
4MD Medical |
Cat#: PROP157025 |
| Millex-GS Syringe Filter Unit, 0.22 μm |
Millipore |
Cat#: SLGL0250S |
| Nalgene Rapid-Flow Sterile Disposable Filter Units with PES Membranes |
Thermo Fisher |
Cat#: 567-0020 |
| Human Reg3A DuoSet ELISA |
R&D systems |
Cat#: DY5940-05 |
| Mouse Lipocalin-2/NGAL DuoSet ELISA |
R&D systems |
Cat#: DY1857-05 |
| Mouse IL-22 DuoSet ELISA |
R&D systems |
Cat#: DY582-05 |
| Mouse IL-18 DuoSet ELISA |
R&D systems |
Cat#: DY7625-05 |
| Mouse IL-1 beta/IL-1 F2 DuoSet ELISA |
R&D systems |
Cat#: DY401-05 |
| DNeasy PowerSoil Pro Kit |
Qiagen |
Cat#: 47016 |
| MagMAX DNA Multi-Sample Ultra 2.0 kit |
Thermo Fisher |
Cat#: A36570
|
| RNeasy Mini Kit |
Qiagen |
Cat#: 74106 |
| RNase-Free DNase Set |
Qiagen |
Cat#: 79256 |
| 70 μm nylon mesh |
ELKO Filtering |
Cat#: 03-70/33 |
| High-Capacity cDNA Reverse Transcription Kit |
Thermo Fisher |
Cat#: 4368814 |
| LightCycler 480 SYBR Green I Master |
Roche |
Cat#: 04707516001 |
| TOPO TA Cloning Kit |
Invitrogen |
Cat#: 450002 |
| Experimental Models: Organisms/Strains |
| Mouse: Nod2−/−
|
Jackson Laboratory |
Cat#: 005763 |
| Mouse Nod2fl/fl
|
Dr. Keestra-Gounder (University of Colorado Anschutz Medical Campus) |
N/A |
| Mouse: Il22ra1fl/fl
|
Dr. Sergei Koralov (New York University Grossman school of medicine), originally acquired from Jackson Laboratory (Cat#: 031003) |
N/A |
| Mouse: LysM-Cre
|
Jackson Laboratory |
Cat#: 004781 |
| Mouse: Villin-Cre
|
Jackson Laboratory |
Cat#: 004586 |
| Mouse: Il1r1
|
Jackson Laboratory |
Cat#: 003245 |
| Mouse Nlrp3
|
Jackson Laboratory |
Cat#: 021302 |
| Mouse: Nod2Q675W/Q675W
|
This study |
N/A |
| Cell line: HEK-Blue Null2 |
InvivoGen |
Cat#: hkb-hnod2 |
| Cell line: HEK-Blue NOD2 |
InvivoGen |
Cat#: hkb-null2 |
| Deposited data |
| 16S rRNA sequencing data related to Figure 2
|
This study |
BioProject: PRJNA915760 |
| Whole genome sequencing data related to Figure S1
|
This study |
BioProject: PRJNA978059 |
| 16S rRNA sequencing data related to Figure S6
|
This study |
BioProject: PRJNA977252 |
| Software and Algorithms |
| Prism 9 |
GraphPad Software |
https://www.graphpad.com/scientific-software/prism/
|
| FlowJo |
BD |
https://www.flowjo.com
|
| NCBI Gene and Protein Data Base |
NCBI |
http://www.ncbi.nlm.nih.gov
|
| Nucleotide blast |
NCBI |
https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
| Blastx |
NCBI |
https://blast.ncbi.nlm.nih.gov/Blast.cgi
|
| Fiji/ImageJ |
NIH |
https://fiji.sc
|
