KEY RESOURCE TABLE
| Reagent or resource | Source | Identifier |
|---|---|---|
| Antibodies | ||
| Rabbit VIP | Abcam | Cat# ab22736; RRID:AB_447294 |
| β-tubulin3 Alexa Fluor 488 | Thermo Fisher Scientific | Cat# 53-4510-82; RRID:AB_2574421 |
| Hu C/D Alexa Fluor 647 | Abcam | Cat# ab237235 |
| EpCAM-APC | Invitrogen | Cat# 17-5791-82; RRID:AB_2716944 |
| Rabbit Erk1/2 | Cell Signaling Technology | Cat# 4695S |
| Rabbit pErk1/2 | Cell Signaling Technology | Cat# 4370S |
| Rabbit C-fos | Cell Signaling Technology | Cat# 2250S |
| Mouse Muc2 | Abcam | Cat# ab11197; RRID:AB_297837 |
| Rabbit Muc2 | Abcam | Cat# ab272692; RRID:AB_2888616 |
| Mouse Anti-6x His | Thermo Fisher Scientific | Cat# MA1-21315; RRID:AB_557403 |
| Gr-1-PE | Invitrogen | Cat# 12-5931-83; RRID:AB_466046 |
| CD11b-APC | Invitrogen | Cat# 17-0012-83 |
| Goat anti-Rabbit Alexa Fluor 594 | Thermo Fisher Scientific | Cat# A32740; RRID:AB_2762824 |
| Goat anti-Rabbit Alexa Fluor 680 | Thermo Fisher Scientific | Cat# A32734; AB_2633283 |
| Goat anti-Mouse Alexa Fluor 488 | Thermo Fisher Scientific | Cat# A32723; RRID:AB_2633275 |
| IRDye 800CW Goat anti-Mouse | LI-COR Biosciences | Cat# 926-32210; RRID:AB_621842 |
| IRDye 800CW Goat anti-Rabbit | LI-COR Biosciences | Cat# 926-32211; RRID:AB_621843 |
| IRDye® 800CW Streptavidin | LI-COR Biosciences | Cat# 926-32230 |
| UEA-1 Rhodamine | Vector Laboratories | Cat# RL-1062; RRID:AB_2336769 |
| UEA-1 Biotin | Vector Laboratories | Cat# B-1065; RRID:AB_2336766 |
| UEA-1 Unconjugated | Vector Laboratories | Cat# L-1060; RRID:AB_2336768 |
| Bacterial strains | ||
| Bifidobacterium bifidum | ATCC | Cat# 29521 |
| Bifidobacterium longum subsp. longum 105A | (Sakanaka et al., 2019) | N/A |
| Enterococcus faecalis | ATCC | Cat# 29212 |
| E. coli Top10 | Invitrogen | Cat# C404006 |
| E. coli BL21 (DE3) | Invitrogen | Cat# C600003 |
| Chemicals, peptides, and recombinant proteins | ||
| Difco™ Lactobacilli MRS Broth | Becton Dickinson | Cat# 288130 |
| BBL™ Brain Heart Infusion | Becton Dickinson | Cat# 221778 |
| BBL™ Enterococcosel™ Broth | Becton Dickinson | Cat# 212207 |
| LB Broth (Miller) | Sigma | Cat# L3522-250G |
| RNAprotect Bacteria Reagent | Qiagen | Cat#76506 |
| Ni-NTA Agarose | Thermo Fisher Scientific | Cat# R90101 |
| Dynabeads™ M-270 Streptavidin | Invitrogen | Cat# 65305 |
| SuperScript™ IV First-Strand Synthesis System | Invitrogen | Cat# 18091050 |
| RNase-free DNase І | New England Biolabs | Cat# M0303S |
| Kanamycin | Sigma | Cat# K1876 |
| Chloramphenicol | Sigma | Cat# C0378 |
| Erythromycin | Sigma | Cat# E5389 |
| Ampicillin | Sigma | Cat# A9393 |
| 2’-Fucosyllactose (2’-FL) | Sigma | Cat# 41263-94-9 |
| VIP | Tocris Bioscience | Cat# 1911 |
| [D-p-Cl-Phe6,Leu17]-VIP (VIPx) | Tocris Bioscience | Cat# 3054 |
| Clozapine N Oxide (CNO) | Tocris Bioscience | Cat# 4936 |
| 4-methylumbelliferyl-alpha-l-fucopyranoside (4-MUF) | GoldBio | Cat# M-580-50 |
| FR180204 | Cayman Chemical | Cat# 15544 |
| Oil Red O | Sigma | Cat# O0625 |
| Gill™ Hematoxylin | Thermo Fisher Scientific | Cat# 6765007 |
| Shandon™ Eosin-Y | Thermo Fisher Scientific | Cat# 6766007 |
| B-27 Supplement | Gibco | Cat# 17504044 |
| N-2 Supplement | Gibco | Cat# 17502001 |
| Complete™ Protease Inhibitor Cocktail | Sigma | Cat# 11697498001 |
| Phosphatase Inhibitor Cocktail | Sigma | Cat# P2850 |
| Q5® Hot Start HiFi PCR Master Mix | New England Biolabs | Cat# M0543S |
| Critical Commercial Assays | ||
| RNeasy Mini Kit | Qiagen | Cat# 74104 |
| Nunc™ Lab-Tek™ II Chamber Slide™ System | Thermo Scientific | Cat# 154453 |
| RiboPure RNA Purification Kit, bacteria | Invitrogen | Cat# AM1925 |
| PowerUP™ SYBR™ Green Master Mix | Qiagen | Cat# 204143 |
| HiScribe T7 Quick High Yield RNA Synthesis Kit | New England Biolabs | Cat# E2050S |
| QIAamp@ Fast DNA Stool Mini Kit | Qiagen | Cat# 51604 |
| IntestiCult™ Organoid Growth Medium | Stem Cell Biotechnology | Cat# 06005 |
| Luciferase Reporter Gene Detection Kit | Sigma | Cat# LUC1-1KT |
| NEBuilder® HiFi DNA Assembly Master Mix | New England Biolabs | Cat# E2621S |
| Deposited data | ||
| Next generation 16s rRNA sequencing | Sequence Read Archive | PRJNA870429; SRR21103243-SRR21103252 |
| Next generation Poly(A) RNA sequencing | Sequence Read Archive | PRJNA870429; SRR21102741-SRR21102746 |
| Experimental Models: Organisms/Strains Mouse | ||
| C57BL/6 | Jackson Laboratory Stock | Cat# 000664 |
| VIPR1−/− | Jackson Laboratory Stock | Cat# 034744 |
| Fut2−/− | Jackson Laboratory Stock | Cat# 006262 |
| hM3Dq fl-stop-fl | Jackson Laboratory Stock | Cat# 026220 |
| hM4Di fl-stop-fl | Jackson Laboratory Stock | Cat# 026219 |
| Vip IRES-cre | Jackson Laboratory Stock | Cat# 031628 |
| oligos | ||
| Primers see table S1 | Sigma | N/A |
| Recombinant DNA | ||
| pET28b-MBP-TEV | (Currinn et al., 2016) | RRID: Addgene_69929 |
| pET28b-AfcA | This paper | N/A |
| pET28b-UK | This paper | N/A |
| pET28b-FUC | This paper | N/A |
| pBFS38 | (Sakanaka et al., 2014) | N/A |
| pBFS38-AfcA | This paper | N/A |
| pBFS38-Erm | This paper | N/A |
| pBFS38-UK | This paper | N/A |
| p16337 | (Gu et al., 2005) | RRID: Addgene_16337 |
| p16337-fut2p-Naive | This paper | N/A |
| p16337-fut2p-Mutant | This paper | N/A |
| pFUW-tetO-fos | (Pereira et al., 2013) | RRID: Addgene_131593 |
| Software and algorithms | ||
| Prism (GraphPad Software) | GraphPad | https://www.graphpad.com |
| Bugbase | (Ward et al., 2017) | https://bugbase.cs.umn.edu/ |
| Qiime2 | (Hall and Beiko, 2018) | https://qiime2.org/ |
| Bioedit | (Hall, 1999) | https://www.bioedit.com/ |
| SnapGene | SnapGene | https://www.snapgene.com/ |