KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
|
| ||
| Rabbit E. coli O 152 antiserum | Denka Seiken | 295774 |
| Goat anti-Rabbit IgG (H + L) Cross-Adsorbed Secondary Antibody, Alexa Fluor™ 488 | ThermoFisher | A-11008; RRID:AB_2633280 |
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| ||
| Bacterial and virus strains | ||
|
| ||
| Citrobacter rodentium strain ICC169 | Sara K Linden | N/A |
| Escherichia coli K12 strain W3110 | Fredrik Bäckhed | N/A |
|
| ||
| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Autoclavable Mouse Breeder Diet | LabDiet | 5021 |
| Fat adjusted diet | Envigo | TD.96132 |
| Ampicillin | Merck | A9518-100G |
| Metronidazole | Merck | M3761-5G |
| Vancomycin | Merck | V2002-5G |
| Neomycin | Merck | N6386-100G |
| Isoflurane | Kronans apotek | N01AB06 |
| SYTO™ 9 Green Fluorescent Nucleic Acid Stain | ThermoFisher | S34854 |
| FluoSpheres™ Carboxylate-Modified Microspheres | ThermoFisher | F8816 |
| Lysing matrix E | MPBio | 116914100 |
| cOmplete Protease Inhibitor Cocktail | Roche | 11873580001 |
| GuHCl 8M | ThermoFisher | 24115 |
| DTT | Merck | D9163 |
| Iodoacetamide | Merck | I6125 |
| LysC | Wako | 125-05061 |
| Trypsin | Promega | V5111 |
| Ulex Europaeus Agglutinin I (UEA I), DyLight™ 649 | Vectorlabs | DL-1068-1 |
| Wheat Germ Agglutinin (WGA), Rhodamine | Vectorlabs | RL-1022 |
| MacConkey Agar | ThermoFisher | CM0007B |
| Luria Broth Base | ThermoFisher | 12795027 |
| Nalidixic acid | Merck | N8878-5G |
| Xylene Substitute | Merck | A5597 |
| Hoechst 34580 | Merck | 63493 |
| cOmplete™ Protease Inhibitor Cocktail | Merck | 11697498001 |
| SYTOX™ Green Nucleic Acid Stain | ThermoFisher | S7020 |
| Polymyxin B Sulfate | Millipore | 5291 |
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| ||
| Critical commercial assays | ||
|
| ||
| Five Prime Hot Master Mix | Quantabio | 733-2474 |
| NucleoSpin Gel and PCR Clean-up kit | Macherey-Nagel | 740609 |
| Quant-iT PicoGreen dsDNA kit | ThermoFisher | P11496 |
| Agencourt AMPure XP | Beckman Coulter | A63880 |
| QIAamp PowerFecal Pro DNA Kit | Qiagen | 51804 |
| SsoFast™ EvaGreen® Supermix | Bio-Rad | 1725203 |
| Pierce™ BCA Protein Assay Kit | ThermoFisher | 23225 |
|
| ||
| Deposited data | ||
|
| ||
| Silva v.138 reference sequence database | Quast et al.37 | N/A |
| Mass spectrometry proteomics data | PRIDEpartner repository | PXD028613 |
| 16S DNA sequencing data | ENA sequence read archive | PRJEB47610 |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| C57BL/6J | In house | N/A |
| C57BL/6J | Charles River | 000664 |Black 6 |
| Muc2tm1Avel | Velcich et al.17 | N/A |
| Tgm2tm1Gml | Laurenzi & Melino38 | N/A |
|
| ||
| Oligonucleotides | ||
|
| ||
| V4 region 515F and 806R primers | Kozich et al.39 | N/A |
| EUB338 16S FISH probe (Alexa Fluor™ 555 conjugated) | Amann et al.40 | N/A |
|
| ||
| Software and algorithms | ||
|
| ||
| Zen (version 2.3) | Carl Zeiss | http://www.zeiss.com |
| Imaris ×64 (version 9.5.0) | Oxford Instruments | http://imaris.oxinst.com/ |
| Prism (version 9.4.1) | GraphPad | http://www.graphpad.com/ |
| QIIME 2 (version 2020.11) | Bolyen et al.41 | N/A |
| DADA2 | Callahan et al.42 | N/A |
| MAFFT (version 7.407) | Katoh et al.43 | N/A |
| FastTree 2 | Price et al.44 | N/A |
| q2-feature-classifier | Bokulich et al.45 | N/A |
| LEfSe | Segata et al.46 | N/A |
| MaxQuant (v1.5.7.4) | Cox & Mann47 | N/A |
| Perseus (v1.6.2.2) | Tyanova et al.48 | N/A |
| StavroX (version 3.6.6) | Gotze et al.49 | N/A |
| R (v4.1.1) | The R Project for Statistical Computing | https://www.r-project.org/ |
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| ||
| Other | ||
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| ||
| Laser scanning confocal imaging system | Carl Zeiss | LSM 700 |
| Illumina MiSeq | Illumina | http://www.illumina.com/systems/sequencing-platforms/miseq.html |
| Nanosep 10K Omega | Pall Life Sciences | OD010C35 |
| EASY-nLC system 1000 | ThermoFisher | LC120 |
| reverse-phase column (150 × 0.075 µm inner diameter, C18-AQ 3 µm | In-house | N/A |
| QExactive Hybrid Quadrupole-Orbitrap Mass Spectrometer | ThermoFisher | IQLAAEGAAPFALGMAZR |
| T 10 basic ULTRA-TURRAX® | IKA | 0003737000 |
| RapidFISH Slide Hybridizer | Boekel Scientific | 240200 |
| FastPrep-24™ | MP Biomedicals | 116004500 |
| CFX96 Touch Real-Time PCR Detection System | Bio-Rad | 1845097 |
| SpectraMax® M2 Multimode microplate reader | Molecular Devices | https://www.moleculardevices.com/products/microplate-readers/multi-mode-readers/spectramax-m-series-readers |