| Bacterial and virus strains |
|
| Ruminococcus gnavus strain VPI C7-9 |
ATCC |
Cat #29149 |
| Clostridium scindens strain VPI 13733 |
ATCC |
Cat #35704 |
| Ileibacterium valens strain NYU-BL-A3 |
ATCC |
Cat #TSD-63 |
| Lactobacillus acidophilus strain VPI 11091 |
ATCC |
Cat # 9224 |
| Lactobacillus reuteri strain IDCC3701 |
ATCC |
Cat # BAA-2837 |
|
| Chemicals, peptides, and recombinant proteins |
|
| Tauro-chenodeoxycholic acid (T-CDCA) |
Caymen Chemical |
Item# 20275 |
| Glyco-chenodeoxycholic acid (G-CDCA) |
Caymen Chemical |
Item# 16942 |
| Chenodeoxycholic acid (CDCA) |
Steraloids |
Cat# C0940-000 |
| Tauro-β-muricholic acid (T-βMCA) |
Steraloids |
Cat# C1899-000 |
| β-muricholic acid (βMCA) |
Steraloids |
Cat#C1895-000 |
| α-muricholic acid (αMCA) |
Steraloids |
Cat#C1890-000 |
| Tauro-cholic acid (T-CA) |
Caymen Chemical |
Item# 16215 |
| Glyco-cholic acid (G-CA) |
Caymen Chemical |
Item# 20276 |
| Cholic acid (CA) |
Caymen Chemical |
Item# 20253 |
| Tauro-deoxycholic acid (T-DCA) |
Caymen Chemical |
Item# 15935 |
| Glyco-deoxycholic acid (G-DCA) |
Caymen Chemical |
Item# 20274 |
| Deoxycholic acid (DCA) |
Steraloids |
Cat# C1070-015 |
| Lithocholic acid (LCA) |
Steraloids |
Cat# C1420-000 |
| Tauro-lithocholic acid (T-LCA) |
Caymen Chemical |
Item# 17275 |
| Glyco-lithocholic acid (G-LCA) |
Caymen Chemical |
Item# 21723 |
| ω-muricholic acid (ωMCA) |
Steraloids |
Cat#C1888-000 |
| γ -muricholic acid (γ-MCA) |
Steraloids |
Cat# C1850-000 |
| Tauro-hyodeoxycholic Acid (T-HDCA) |
Caymen Chemical |
Item# 21956 |
| Glyco-hyodeoxycholic Acid (G-HDCA) |
Caymen Chemical |
Item# 22643 |
| Hyodeoxycholic Acid (HDCA) |
Steraloids |
Cat# C0885-000 |
| Tauro-Ursodeoxycholic Acid (T-UDCA) |
Caymen Chemical |
Item# 20277 |
| Glyco-ursodeoxycholic Acid (G-UDCA) |
Caymen Chemical |
Item# 21698 |
| Ursodeoxycholic Acid (UDCA) |
Caymen Chemical |
Item# 15121 |
| Cholic-2,2,4,4-d4 acid |
C/D/N Isotopes |
D-2452 |
| Chenodeoxycholic-2,2,4,4-d4 acid |
C/D/N Isotopes |
D-2772 |
| Lithocholic-2,2,4,4-d4 acid |
C/D/N Isotopes |
D-3742 |
| Fexaramine D |
WUXI |
Custom order |
| Serine conjugated cholic acid (Ser-CA) |
WUXI |
Custom order |
| Alanine conjugated cholic acid (Ala-CA) |
WUXI |
Custom order |
| Phenyalanine conjugated cholic acid (Phe-CA) |
WUXI |
Custom order |
| Tyrosine conjugated cholic acid (Tyr-CA) |
WUXI |
Custom order |
| Leucine conjugated cholic acid (Leu-CA) |
WUXI |
Custom order |
| Glutamate conjugated cholic acid (Glu-CA) |
WUXI |
Custom order |
| Tryptophan conjugated cholic acid (Trp-CA) |
WUXI |
Custom order |
| INT-777 |
Caymen Chemical |
Item# 17678 |
| pre-reduced anaerobic transport media (ATM) |
Anaerobe System Inc |
Cat #AS-911 |
| Anaerobic Enrichment Broth (MTGE BROTH) |
Anaerobe System Inc |
Cat # AS-778 |
| Yeast Casitone Fatty Acids Agar with Carbohydrates without blood (YCFAC) plates |
Anaerobe System Inc |
Cat # AS-675 |
| Yeast Casitone Fatty Acids Agar with Carbohydrates with blood (YCFAC-B) plates |
Anaerobe System Inc |
Cat # AS-677 |
| Brucella Blood Agar |
Anaerobe System Inc |
Cat # AS-141 |
| ATCC 260 Tryptic Soy Broth |
Fisher scientific |
BD 211825 |
| ATCC 260 Tryptic Soy Agar |
Fisher scientific |
BD 236950 |
| ATCC 416 MRS broth medium |
Fisher scientific |
BD 288130 |
| Water |
Fisher scientific |
W64 |
| Acetonitrile |
Fisher scientific |
A9554 |
| Methanol |
Fisher scientific |
A4564 |
| Formic acid |
Fisher scientific |
A117-50 |
|
| Critical commercial assays |
|
| Total bile acid assay kit |
Diazyme laboratories |
Cat #DZ042A-K |
| CellTiter-Glo Luminescent Cell Viability Assay Kit |
Promega Corporation |
Cat #G7572 |
| CellTiter-Glo Luminescent 3D Cell Viability Assay Kit |
Promega Corporation |
Cat #G9683 |
| Dual-Luciferase reporter kit |
Promega Corporation |
Cat #PRE1910 |
| Cignal TCF/LEF Reporter (luc) Kit |
Qiagen |
Cat#CCS-018L |
| RNeasy Mini Kit |
Qiagen |
Cat #74106 |
| RNeasy Micro Kit |
Qiagen |
Cat #74004 |
| Bio-Rad iScript Reverse Transcription supermix |
Bio-rad |
Cat #1708841 |
| Advanced Universal SyBr Green Supermix |
Bio-rad |
Cat #725271 |
| Matrigel, growth factor reduced |
Corning |
Cat #354230 |
| Gentle cell dissociation buffer |
Stem Cell Inc |
Cat #7174 |
| Intesticult organoid growth medium |
Stem Cell Inc |
Cat #6005 |
| PBS (Mg2+/Ca2+) solution |
Corning |
Cat # 21-031-CM |
| FBS |
Gemini Bio-products |
Cat #900-208 |
| Antibiotic-Antimycotic solution |
Gibco |
Cat #15240062 |
| Penicillin-Streptomycin |
Gibco |
Cat #15070063 |
|
| Deposited data |
|
| Microbiome 16S rRNA gene amplicon and shotgun sequencing data |
Illumina HiSeq4000 platform |
Qiita study ID 10955 |
| Serum and Cecum Metabolites profiling data |
Bruker Impact II™ UHR-QqTOF (Ultra-High Resolution Qq-Time-Of-Flight) mass spectrometer coupled with the Agilent 1290 Infinity™ II LC system |
MetaboLights (www.ebi.ac.uk/metabolights/MTBLS5765) |
|
| Experimental models: Cell lines |
|
| HT29 |
ATCC |
Cat# HTB-38, RRID:CVCL_0320 |
| CACO2 |
ATCC |
Cat# HTB-37, RRID:CVCL_0025 |
| HEK293 |
ATCC |
Cat# PTA-4488, RRID:CVCL_0045 |
|
| Experimental models: Organisms/strains |
|
| Mouse: C57BL/6J |
The Jackson Laboratory |
Cat# JAX:000664, RRID:IMSR_JAX:000664 |
| Mouse: C57BL/6J-ApcMin/J |
The Jackson Laboratory |
Cat# JAX:002020, RRID:IMSR_JAX:002020 |
|
| Oligonucleotides |
|
| Primers for RT-qPCR, see Table S2. |
IDT |
Designed using Primer 3 software |
|
| Software and algorithms |
|
| STAR |
Dobin et al.32; https://github.com/alexdobin/STAR
|
|
| RSEM |
https://deweylab.github.io/RSEM/
|
N/A |
| rsem-generate-data-matrix and rsem-run-ebseq commands |
https://deweylab.github.io/RSEM/rsem-run-ebseq.html
|
N/A |
| GSEA |
https://www.gsea-msigdb.org/gsea/index.jsp
|
N/A |
| Emperor |
https://biocore.github.io/emperor/
|
N/A |
| SurvExpress |
https://ngdc.cncb.ac.cn/databasecommons/database/id/1097
|
N/A |
| Homer |
http://homer.ucsd.edu/homer/
|
N/A |
| CASAVA-1.8.2 |
https://www.illumina.com/
|
Illumina |
| Fiji |
https://fiji.sc/
|
|
| FreeStyle |
Thermo Fisher Scientific |
|
