KEY RESOURCES TABLE
| REAGENT or RESOURCE Antibodies | SOURCE | IDENTIFIER |
|---|---|---|
| mouse anti-CD4 (1:200; IHC) | eBioscience from Thermo Fisher Scientific | Cat#14–0041-86; RRID: AB_467063 |
| rat anti-CD8 (1:200; IHC) | Abcam | Cat#ab22378; RRID: AB_447033 |
| rabbit anti-Lgr5 (1:200; IHC) | Abcam | Cat#ab75732; RRID: AB_1310281 |
| mouse anti-Sox9 (1 mg/ml; IHC). | eBioscience from Thermo Fisher Scientific | Cat#14–9765-80; RRID: AB_2573005 |
| Alexafluor 488 anti-mouse/human CD11b (1:200; IHC) | BioLegend | Cat#101219; RRID: AB_493545 |
| donkey anti-rabbit Alexafluor 594 (1:300; IHC), | Thermo Fisher Scientific | Cat#A21207; RRID: AB_141637 |
| donkey anti-mouse Alexafluor 488 (1:300; IHC) | Thermo Fisher Scientific | Cat#A21202; RRID: AB_141607 |
| donkey anti-rat Alexafluor 594 (1:300; IHC) | Thermo Fisher Scientific | Cat#A21209; RRID: AB_2535795 |
| CD3 Alexa700 (0.25 mg/test; FACS) | eBioscience from Thermo Fisher Scientific | Cat#56–0032-82; RRID: AB_529507 |
| CD4 PE-Cy5 (0.06 mg/test; FACS) | eBioscience from Thermo Fisher Scientific | Cat#15–0041-82; RRID: AB_468695 |
| CD8 Alexa488 (0.5 mg/test; FACS) | eBioscience from Thermo Fisher Scientific | Cat#53–0081-82; RRID: AB_469897 |
| CD44 APC (0.06 mg/test; FACS) | eBioscience from Thermo Fisher Scientific | Cat#17–0441-82; RRID: AB_469390 |
| CD62L PE-Cy7 (0.25 mg/test; FACS) | eBioscience from Thermo Fisher Scientific | Cat#25–0621-82; RRID: AB_469633 |
| CD19 PE (0.125 mg/test; FACS) | eBioscience from Thermo Fisher Scientific | Cat#12–0193-82; RRID: AB_657661 |
| CD11b PE-eFluor 610 (0.25 mg/test; FACS) | eBioscience from Thermo Fisher Scientific | Cat#61–0112-82; RRID: AB_2574528 |
| F4/80 PE-Cy5 (0.25 mg/test; FACS) | eBioscience from Thermo Fisher Scientific | Cat#15–4801-82; RRID: AB_468798 |
| Ly-6G(ar-1) APC (0.5 mg/test; FACS) | eBioscience from Thermo Fisher Scientific | Cat#17–9668-82; RRID: AB_2573307 |
| CD45 APC-eFluor 780 (0.125 mg/test; FACS) | eBioscience from Thermo Fisher Scientific | Cat#47–0451-82; RRID: AB_1548781 |
| Bacterial and Virus Strains | ||
| Lactobacillus rhamnosus GG (LGG) | ATCC | ATCC 53103 |
| Biological Samples | ||
| Human serum | Clinical Trial | NCT02158897 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Dextran sulfate sodium salt (DSS) | Alfa Aesar by Thermo Fisher Scientific | Cat#J14489–22; CAS:9011–18-1 |
| Paraformaldehyde | Sigma-Aldrich | Cat#158127; CAS:30525–89-4 |
| 5-Bromo-2’-deoxyuridine (BrdU) | Sigma-Aldrich | Cat#B002; CAS:59–14-3 |
| Normal Donkey Serum | Jackson ImmunoResearch | Cat#017–000-121 |
| Polyvinyl alcohol mounting medium with DABCO, antifading | Sigma-Aldrich | Cat#10981 |
| Fluorescein isothiocyanate-dextran | Sigma-Aldrich | Cat# FD4; CAS: 60842–46-8 |
| Hoechst 33342 Solution | Thermo Fisher Scientific | Cat#62249 |
| Critical Commercial Assays | ||
| Hematoxylin & Eosin Stain Kit | Vector Laboratories | Cat#H-3502 |
| BrdU In Situ Detection Kit | 3D Biosciences | Cat#550803 |
| Mouse TNF-alpha Quantikine ELISA Kit | R&D Systems | Cat#MTA00B |
| Mouse IFN-gamma Quantikine ELISA Kit | R&D Systems | Cat#MIF00 |
| Mouse IL-17 Quantikine ELISA Kit | R&D Systems | Cat#M1700 |
| ProcartaPlex Custom Multiplex Panel | Thermo Fisher Scientific | Cat#PPX-11; Design ID: MX9HH77 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | JAX:000664 |
| Software and Algorithms | ||
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| GraphPad Prism v.7 | Graphpad | https://www.graphpad.com/ |
| cellSens Standard | Olympus | https://www.olympus-lifescience.com/en/software/cellsens/ |
| BD FACSDiva | BD Biosciences | http://www.bdbiosciences.com/us/instruments/research/software/flowcytometry-acquisition/bd-facsdivasoftware/m/111112/overview |
| FloJo Software | BD Biosciences | https://www.flowjo.com/solutions/flowjo/downloads |
| Other | ||
| Mouse diet: Fasting mimicking diet (FMD) | Cheng et al., 2017 | N/A |
| Human diet: Fasting mimicking diet (FMD) | Propriety formulation belonging to L-Nutra | http://www.l-nutra.com/prolon/ |
| Control Diet: PicoLab Rodent Diet 20 | LabDiet | Cat#5053 |
| Irradiated Sterile Diet: Pico-Vac Lab Rodent Diet | LabDiet | Cat#5061 |
| HydroGel | ClearH2O | N/A |
| Hemoccult II SENSA Fecal Occult Blood Test Systems | Beckman Coulter | Cat# 10012–018 |
| Hemavet 950 System | Drew Scientific | N/A |
| Bead Ruptor 12 | Omni International | Cat#19–050A |
| CO2 pouch system | BD Diagnostics | Cat#260684/90003–650 |
| Lactobacilli MRS Agar | BD Diagnostics | Cat#288210 |
| Lactobacilli MRS Broth | BD Diagnostics | Cat#288130 |
| Microbiome sequencing: V4 16S rRNA gene sequencing (Illumina MiSeq platform) | Second Genome Solutions; South San Francisco, CA, USA | N/A |
| EVOS FL Imaging System | Thermo Fisher Scientific | Cat# AMF4300 |
| All-in-One Fluorescence Microscope | Keyence | Cat# BZ-X710 |
| Olympus BX50 Microscope | Olympus | N/A |
| Olympus DP73 Camera | Olympus | N/A |
| BD LSR II | BD Biosciences | N/A |
| Bio-Plex Suspension Array System | BioRad | N/A |
| SoectraMax M2 MicroDlate Reader | Molecular Devices | N/A |