| Antibodies |
| Rat anti-IL-13 |
R &D Systems |
Cat#MAB413; RRID:AB_2124171 |
| Rat IgG2a isotype control |
R&D Systems |
Cat#MAB006; RRID:AB_357349 |
| Rabbit anti-Lysozyme |
BioGenex |
Cat#AR024-10R |
| Rabbit anti-Mucin 2 (Muc2) |
Santa Cruz Biotech |
Cat#sc-15334; RRID:AB_2146667 |
| Rabbit anti-DCLK1 |
Abcam |
Cat#ab37994; RRID:AB_873538 |
| Goat anti-MMP7 |
Santa Cruz Biotech |
Cat# sc-8832; RRID:AB_649337 |
| Mouse anti-E-Cadherin (E-Cad) |
BD Biosciences |
Cat#610404; RRID:AB_397786 |
| Mouse anti-Amphiregulin (Areg) |
Santa Cruz Biotech |
Cat# sc-74501; RRID:AB_1118939 |
| Rabbit anti-Arginase 1 |
Cell Signaling |
Cat#93668; RRID:AB_2800207 |
| Rabbit anti-phospho-Stat3 (pStat3) |
Cell Signaling |
Cat#9145; RRID:AB_2491009 |
| Rabbit anti-phospho-Stat6 (pStat6) |
Thermo Fisher Scientific |
Cat#700247; RRID:AB_2532305 |
| Donkey anti-mouse IgG, Alexa Fluor 488 |
Thermo Fisher Scientific |
Cat# A21202; RRID:AB_141607 |
| Donkey anti-rabbit IgG, Alexa Fluor 568 |
Thermo Fisher Scientific |
Cat# A10042; RRID:AB_2534017 |
| ImmPRESS HRP anti-rabbit IgG polymer |
Vector Labs |
Cat# MP-7401; RRID:AB_2336529 |
| ImmPRESS HRP anti-mouse IgG polymer |
Vector Labs |
Cat#MP-7402; RRID:AB_2336528 |
| Bacterial and Virus Strains |
| Akkermansia muciniphila |
DSMZ |
DSM-22959 |
| Bacteroides uniformis |
DSMZ |
DSM-6597 |
| Dorea formicigenerans |
DSMZ |
DSM-3992 |
| Ruminococcus gnavus |
DSMZ, ATCC |
FRE1, ATCC29149 |
| Lactobacillus rhamnosus GG |
ATCC |
ATCC53103 |
| Dorea longicatena |
DSMZ |
DSM-13814 |
| Biological Samples |
| UC colon biopsy samples |
Provided by Dr. Lanjing Zhang, Princeton University Hospital |
N/A |
| CD colon and ileum biopsy samples |
Provided by Dr. Lanjing Zhang, Princeton University Hospital |
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
| Recombinant IL-13 |
R&D Systems |
Cat#413-ML |
| Chicken egg white lysozyme |
Sigma |
Cat#L6876 |
| Dextran sulfate sodium (DSS, Colitis grade) |
MP Biologics |
SKU 0216011080 |
| Sodium cacodylate buffer, 0.2M, ph7.4 |
Electron Microscopy Sciences |
Cat# 11650 |
| 8% Glutaraldehyde (EM grade) |
Electron Microscopy Sciences |
Cat#16019 |
| 16% Paraformaldehyde (EM grade) |
Electron Microscopy Sciences |
Cat#15700 |
| 4% Osmium Tetroxide (OsO4) |
Electron Microscopy Sciences |
Cat#19150 |
| Proteinase Inhibitor cocktail |
Roche |
Cat#5892791001 |
| Phosphatase Inhibitor cocktail |
Roche |
Cat#4906845001 |
| Matrigel (growth factor reduced) |
Corning |
Cat#354230 |
| IntestiCult organoid culture medium |
StemCell Technologies |
Cat#06005 |
| Vector Nuclear Fast Red |
Vector Labs |
Cat# H-3403 |
| EMBed-812 kit |
Electron Microscopy Sciences |
Cat#14120 |
| Prolong Gold Antifade Mountant |
Thermo Fisher Scientific |
Cat# P36930
|
| Hematoxylin QS |
Vector Labs |
Cat# H-3404 |
| Cytoseal 60 |
Thermo Fisher Scientific |
Cat#8310-4 |
| 4’,6-Diamidino-2-Phenylindole (DAPI) |
Thermo Fisher Scientific |
Cat#D1306 |
| Critical Commercial Assays |
| Lysozyme activity assay kit |
Abcam |
Cat#ab211113 |
| QIAamp DNA Stool Mini Kit |
Qiagen |
Cat#51604 |
| PureLink Microbiome DNA purification kit |
Thermo Fisher Scientific |
Cat# A29789
|
| Ion 16s Metagenomics Kit |
Thermo Fisher Scientific |
Cat#A26216 |
| Cytokine array kit |
R&D Systems |
Cat# ARY006 |
| Maxima First Strand cDNA Synthesis Kit |
Thermo Fisher Scientific |
Cat# K1641 |
| AllPrep DNA/RNA Mini Kit |
Qiagen |
Cat#80204 |
| Deposited Data |
| Single-cell RNA-seq |
This paper |
GEO: GSE151152
|
| Bulk-cell RNA-seq |
This paper |
GEO: GSE151151
|
| Experimental Models: Organisms/Strains |
| Mouse: Lyz1H2BmCherry-IRES-CreERT2
|
Yu et al., 2018 |
N/A |
| Mouse: Villin-Lyz1TG transgenic
|
This study |
N/A |
| Mouse: B6.129S2(C)-Stat6tm1Gru/J (Stat6KO)
|
Kaplan et al., 1996 |
Jax #005977 |
| Mouse: BALB/c-Il4ratm1Sz/J (Il4RαKO) |
Noben-Trauth et al., 1997 |
Jax #003514 |
| Oligonucleotides |
| Primers for Dorea formicigenerans, see Table S7
|
Kurakawa et al., 2015 |
N/A |
| Primers for Ruminococcus gnavus, see Table S7
|
Png et al.,2010 |
N/A |
| Primers for Bacterial 16s rRNA, see Table S7
|
Randall et al., 2010 |
N/A |
| Primers for Tritrichomonas muris, see Table S7
|
Howitt et al., 2016 |
N/A |
| Primers for Mouse Lyz1, see Table S7
|
This paper |
N/A |
| Primers for Mouse Mucin 2 (Muc2), see Table S7
|
This paper |
N/A |
| Primers for Mouse Klf4, see Table S7
|
This paper |
N/A |
| Primers for Mouse Spdef, see Table S7
|
This paper |
N/A |
| Primers for Mouse Il4, see Table S7
|
This paper |
N/A |
| Primers for Mouse Il13, see Table S7
|
This paper |
N/A |
| Primers for Mouse Il17a, see Table S7
|
This paper |
N/A |
| Primers for Mouse Il17f, see Table S7
|
This paper |
N/A |
| Primers for Mouse Il25, see Table S7
|
This paper |
N/A |
| Primers for Mouse Il33, see Table S7
|
This paper |
N/A |
| Primers for Mouse Tslp, see Table S7
|
This paper |
N/A |
| Primers for Mouse Tnfa, see Table S7
|
This paper |
N/A |
| Primers for Mouse Pou2f3, see Table S7
|
This paper |
N/A |
| Primers for Mouse Gata3, see Table S7
|
This paper |
N/A |
| Primers for Mouse Tbx21 (Tbx), see Table S7
|
This paper |
N/A |
| Primers for Mouse Rorc (Rorγt), see Table S7
|
This paper |
N/A |
| Primers for Mouse Foxp3, see Table S7
|
This paper |
N/A |
| Primers for Mouse Tgfb1, see Table S7
|
This paper |
N/A |
| Primers for Mouse Amphiregulin (Areg), see Table S7
|
This paper |
N/A |
| Primers for Mouse Hprt, see Table S7
|
This paper |
N/A |
| Software and Algorithms |
| Metastats |
White et al., 2009 |
http://metastats.cbcb.umd.edu/detection.html |
| QIIME (v.1.9.1) |
Caporaso et al., 2010 |
https://qiime.org |
| LDA Effect size (LEfSe) analysis tool |
Afgan et al., 2018; Segeta et al., 2011 |
https://huttenhower.sph.harvard.edu/galaxy/ |
| Kallisto |
Bray et al., 2016 |
https://pachterlab.github.io/kallisto/ |
| nSolver Analysis software v4.0 with the nCounter Advanced Analysis module (v.2.0.115) |
NanoString Technologies |
https://www.nanostring.com/products/analysis-software/nsolver |
| GSEA |
Subramanian et al., 2005; Mootha et al., 2003
|
http://software.broadinstitute.org/gsea/index.jsp |
| GO Enrichment Analysis |
Ashburner et al., 2000; Mi et al., 2019
|
http://geneontology.org/ |
| Origin Pro 2019 |
OriginLab |
https://www.originlab.com/ |
| ImageJ |
NIH |
https://imagej.nih.gov/ij/ |
| Graphpad Prism (v.7.0) |
Graphpad |
https://www.graphpad.com/ |
| Cell Ranger Single Cell Software Suite (v3.0.1) |
10X Genomics |
https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| Partek Flow Software (v.9.0.20.0202) |
Partek |
In house license |
| Seurat (R toolkit) |
Butler et al., 2018 |
https://satijalab.org/seurat v.3.1.0 |
