KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Chemicals, peptides, and recombinant proteins | ||
| 12-keto Lithocholic Acid (12-oxo DCA) | Cayman Chemical | Cat# 29547 |
| 12-oxo-CA | Avanti | Cat# 700236P |
| 2,2′-dipyridyl disulfide | Alfa Aesar | Cat# A11118 |
| 2-hydrazinoquinol | TCI | Cat# H0178 |
| 3-oxo DCA (3-OH oxidized) | ChemCruz | Cat# sc-477977 |
| 3-oxo-CDCA | Avanti | Cat# 700255P |
| 3-Oxocholic Acid (3-oxo CA) | Cayman Chemical | Cat# 28403 |
| 3β-Cholic Acid-2,2,4,4-d4 (iso CA−-2,2,4,4-d4) | Cayman Chemical | Cat# 27376 |
| 7-Ketodeoxycholic acid (7-oxo CA) | Sigma | Cat# SMB00806 |
| Acetic acid | Fisher Chemical | Cat# A38-500 |
| Acetone | Fisher Chemical | Cat# A18-4 |
| Acetonitrile | Fisher Chemical | Cat# A21-4 |
| Ascorbic acid | Fisher Chemical | Cat# BP351500 |
| BBL™ Bacto Tryptone | BD | Cat# 211921 |
| Butyric acid | ACROS ORGANICS | Cat# 108111000 |
| CaCl2 | ACROS ORGANICS | Cat# 349615000 |
| Carbenicillin | GOLDBIO | Cat# C-103-25 |
| Chenodeoxycholic acid (CDCA) | Alfa Aesar | Cat# J60364 |
| Chloramphenicol | VWR | Cat# 0230 |
| Cholic acid (CA) | Alfa Aesar | Cat# A11257 |
| D-(−)-Fructose | VWR | Cat# 0226-1KG |
| D-(+)-Cellobiose | Alfa Aesar | Cat# A14553 |
| D-(+)-Glucose | VWR | Cat# BDH9230 |
| D-(+)-Maltose monohydrate | VWR | Cat# 1B1184 |
| D-cycloserine | TCI | Cat# C1189 |
| Deoxycholic acid (DCA) | Alfa Aesar | Cat# B20061 |
| Dextran sulfate sodium salt (DSS) | MP Biomedicals | Cat# 160110 |
| Difco™ Brain Heart Infusion Agar | BD | Cat# 241830 |
| Difco™ Columbia agar | BD | Cat# 279240 |
| Difco™ Columbia Broth | BD | Cat# 294420 |
| Difco™ Luria-Bertani (LB) broth | BD | Cat# BP1426-2 |
| Difco™ Tryptic Soy Agar | BD | Cat# 236950 |
| Difco™ Trypticase Peptone | BD | Cat# 211921 |
| Difco™ Yeast Extract | Fisher Bioreagents | Cat# BP1422-2 |
| DMSO | ACROS ORGANICS | Cat# 61097-1000 |
| Erythromycin | VWR | Cat# 0219 |
| Ethanol | Fisher Bioreagents | Cat# BP2818-4 |
| FeSO4 | ACROS ORGANICS | Cat# 423731000 |
| Formic acid | Fisher Chemical | Cat# A117-50 |
| Gentamicin | GOLDBIO | Cat# G-400-25 |
| Glycerol | Fisher Bioreagents | Cat# BP229-4 |
| Glycine | Alfa Aesar | Cat# J62407 |
| Ground beef (fat-free) | RESEARCH DIETS | Cat# D12451i |
| Horse blood | Hemostat Laboratories | Cat# 637291-1 |
| Isovalerate | ACROS ORGANICS | Cat# 156691000 |
| Isovaleric acid | ACROS ORGANICS | Cat# 156691000 |
| K2HPO4 | ACROS ORGANICS | Cat# 424195000 |
| Kanamycin | GOLDBIO | Cat# K-120-25 |
| KH2PO4 | ACROS ORGANICS | Cat# 42420-5000 |
| L-Cysteine hydrochloride | Fisher Bioreagents | Cat# BP376-100 |
| Lithocholic acid (LCA) | ICC | Cat# 123530 |
| Meat extract | Sigma | Cat# 70164 |
| Methanol | Fisher Chemical | Cat# A456-4 |
| MgSO4·7H2O | Fisher Chemical | Cat# M65-500 |
| Na2HPO4 | Alfa Aesar | Cat# 13437 |
| Na2SO4 | Fisher Chemical | Cat# S421-1 |
| NaCl | Fisher Chemical | Cat# S271-1 |
| Na-DL-lactate | Sigma | Cat# 71720 |
| NaH2PO4 | Fisher Bioreagents | Cat# BP329-500g |
| NaHCO3 | ACROS ORGANICS | Cat# 424270010 |
| Na-thioglycolate | TCI | Cat# M0053 |
| NH4Cl | Fisher Chemical | Cat# 12125-02-9 |
| PBS | Gibco | Cat# 10010-031 |
| Propionic acid | ACROS ORGANICS | Cat# 14930-0010 |
| Reinforced Clostridial Medium | BD | Cat# 218081 |
| Resazurin | ACROS ORGANICS | Cat# 418900250 |
| Soluble starch | ACROS ORGANICS | Cat# 177132500 |
| Spectinomycin | ENZO | Cat# BML-A281-0010 |
| Sucrose | Fisher Bioreagents | Cat# BP220-1 |
| Taurochenodeoxycholic Acid (sodium salt) (TCDCA) | Cayman Chemical | Cat# 20275 |
| Taurocholic Acid (sodium salt) (TCA) | Cayman Chemical | Cat# 16215 |
| Taurodeoxycholic acid (TDCA) | Cayman Chemical | Cat# 15935 |
| Tauroursodeoxycholic acid (TUDCA) | Cayman Chemical | Cat# 20277 |
| Tetracycline | GOLDBIO | Cat# T-101-25 |
| Thiamphenicol | ACROS ORGANICS | Cat# 455450250 |
| Triphenylphosphine | Alfa Aesar | Cat# L02502 |
| Tween 80 | VWR | Cat# 0442-1L |
| Ursocholic acid (UCA) (7-OH isomer) | Avanti | Cat# 700229 |
| Ursodeoxycholic acid (UDCA) (7-OH isomer) | Avanti | Cat# 700199 |
| Vitamin K1 | Alfa Aesar | Cat# L10575 |
| Vitamin K3 | MP | Cat# 102259 |
| Critical commercial assays | ||
| AscI restriction enzyme | NEB | Cat# R0558S |
| Blue sapphire DNA polymerase | TAKARA | Cat# RR350 |
| CpG (M. SssI) methyltransferases | NEB | Cat# M0226S |
| DNA Clean and Concentrator | Zymo Research | Cat# D4003 |
| Esp3I restriction enzyme | NEB | Cat# R0734S |
| FseI restriction enzyme | NEB | Cat# R0588S |
| Gibson Assembly Cloning Kit | NEB | Cat# E5510S |
| GpC (M.CviPI) methyltransferases | NEB | Cat# M0227S |
| Hemoccult II SENSA Dispensapak Plus kit | Backman Coulter | Cat# 61130 |
| Instant Sticky-end Ligase | NEB | Cat# M0370S |
| Mouse lipocalin-2/NGAL DuoSet ELISA | R&D Systems | Cat# DY1857-05 |
| NotI restriction enzyme | NEB | Cat# R3189S |
| Plasmid Midiprep Kit | Zymo Research | Cat# D4201 |
| Primer star DNA polymerase | TAKARA | Cat# R045 |
| PrimeScript™ RT Reagent Kit | Takara | Cat# RR047A |
| QIAamp Fast DNA Stool Mini Kit | Qiagen | Cat# 51604 |
| Qiagen Miniprep Kits | Qiagen | Cat# 27104 |
| Quant-iT™ dsDNA Assay Kit, high sensitivity | Invitrogen | Cat# Q33120 |
| Quick DNA fungal/bacterial kit | Zymo Research | Cat# D6005 |
| Quick RNA fungal/bacterial kit | Zymo Research | Cat# R2010 |
| SbfI restriction enzyme | NEB | Cat# R3642S |
| SYBR green chemistry | Applied Biosystems | Cat# 4368706 |
| T4 DNA Ligase (HC) | Promega | Cat# M1794 |
| XbaI restriction enzyme | NEB | Cat# R0145S |
| XhoI restriction enzyme | NEB | Cat# R0146S |
| Experimental models: Organisms/strains | ||
| Strains used in this study | Lab stock | Table S1 |
| Oligonucleotides | ||
| Primers used in this study | This study | Table S2 |
| Recombinant DNA | ||
| pDEST-hisMBP-AsCpf1-EC | Addgene | Cat# 79007 |
| pExchange | Lab stock | N/A |
| pGM-ABC1M_seq-opt | This study | N/A |
| pGM-ABCD | This study | N/A |
| pGM-ABCD-006 | This study | Table S2 |
| pGM-ABCD-008 | This study | Table S2 |
| pGM-ABCD-009 | This study | Table S2 |
| pGM-ABCD-013 | This study | Table S2 |
| pGM-ABCD-015 | This study | Table S2 |
| pGM-ABCD-019 | This study | Table S2 |
| pGM-ABCF | This study | N/A |
| pGM-ABCG | This study | N/A |
| pGM-ABCL | This study | N/A |
| pGM-ABCL1 | This study | N/A |
| pGM-ABCM | This study | N/A |
| pGM-BBCD | This study | N/A |
| pGM-BBCF | This study | N/A |
| pGM-BBCL | This study | N/A |
| pGM-BBCM | This study | N/A |
| pGM-CBC1M_seq-opt | This study | N/A |
| pGM-CBCD | This study | N/A |
| pGM-CBCD-017 | This study | Table S2 |
| pGM-CBCF | This study | N/A |
| pGM-CBCL | This study | N/A |
| pGM-CBCL1 | This study | N/A |
| pGM-CBCM | This study | N/A |
| pGM-DBC1M_seq-opt | This study | N/A |
| pGM-DBCD | This study | N/A |
| pGM-DBCD-012 | This study | Table S2 |
| pGM-DBCF | This study | N/A |
| pGM-DBCL | This study | N/A |
| pGM-DBCM | This study | N/A |
| pGM-EBC1M_seq-opt | This study | N/A |
| pGM-EBCD | This study | N/A |
| pGM-EBCD-014 | This study | Table S2 |
| pGM-EBCF | This study | N/A |
| pGM-EBCL | This study | N/A |
| pGM-EBCL1 | This study | N/A |
| pGM-EBCM | This study | N/A |
| pGM-FBC1M_seq-opt | This study | N/A |
| pGM-FBCD | This study | N/A |
| pGM-FBCD-007 | This study | Table S2 |
| pGM-FBCD-010 | This study | Table S2 |
| pGM-FBCD-011 | This study | Table S2 |
| pGM-FBCD-016 | This study | Table S2 |
| pGM-FBCD-020 | This study | Table S2 |
| pGM-FBCF | This study | N/A |
| pGM-FBCL | This study | N/A |
| pGM-FBCL1 | This study | N/A |
| pGM-FBCM | This study | N/A |
| pGM-FCAR-002 | This study | Table S2 |
| pGM-FCAR-003 | This study | Table S2 |
| pGM-GBC1M_seq-opt | This study | N/A |
| pGM-GBCD | This study | N/A |
| pGM-GBCF | This study | N/A |
| pGM-GBCL | This study | N/A |
| pGM-GBCM | This study | N/A |
| pGM-HBC1M_seq-opt | This study | N/A |
| pGM-HBCD | This study | N/A |
| pGM-HBCD-018 | This study | Table S2 |
| pGM-HBCF | This study | N/A |
| pGM-HBCL | This study | N/A |
| pGM-HBCL1 | This study | N/A |
| pGM-HBCM | This study | N/A |
| pGM-IBCD | This study | N/A |
| pGM-IBCF | This study | N/A |
| pGM-IBCL | This study | N/A |
| pGM-IBCM | This study | N/A |
| pGM-NAC2B | This study | N/A |
| pGM-NAC2P | This study | N/A |
| pGM-NACM-003 | This study | Table S2 |
| pGM-NACM-004 | This study | Table S2 |
| pGM-NACM-005 | This study | Table S2 |
| pGM-NACO1 | This study | N/A |
| pGM-NACO2 | This study | N/A |
| pGM-NACO4 | This study | N/A |
| pGM-NACO5 | This study | N/A |
| pGM-NACO6 | This study | N/A |
| pGM-NACO7 | This study | N/A |
| pGM-NAKO3 | This study | N/A |
| pGM-NBC2B | This study | N/A |
| pGM-NBCC | This study | N/A |
| pGM-NAEM-001 | This study | Table S2 |
| pGM-NAEM-002 | This study | Table S2 |
| synthetic Bacteroides Chi-16S rRNA | This study | Synthesized by Twist |
| synthetic Desulfovibrio Chi-16S rRNA | This study | Synthesized by Twist |
| synthetic fragment (gBlocks) | This study | Synthesized by IDT |
| synthetic Prevotella Chi-16S rRNA | This study | Synthesized by Twist |
| synthetic Proteus Chi-16S rRNA | This study | Synthesized by Twist |
| Software and algorithms | ||
| Adobe Illustrator | Adobe | N/A |
| Agilent Masshunter Workstation | Agilent | N/A |
| Agilent Qualitative analysis | Agilent | N/A |
| Blast | NCBI | https://blast.ncbi.nlm.nih.gov/Blast.cgi |
| Bowtie 2 (local, high sensitivity) | Johns Hopkins University | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| ChembioDraw Ultra 14.0 | PerkinElmer | N/A |
| ClosTron | ClosTron | http://www.clostron.com/pMTL80000.php |
| Clustal Omega | The European Bioinformatics Institute | https://www.ebi.ac.uk/Tools/msa/clustalo/ |
| Geneious | Geneious | http://www.geneious.com/ |
| GraphPad Prism version 8.0 | GraphPad | www.graphpad.com |
| Human Microbiome Project (HMP) | Human Microbiome Project | https://hmpdacc.org/ |
| iHMP-IBD | Human Microbiome Project | https://ibdmdb.org/ |
| Mega 7 | Mega | http://www.megasoftware.net/ |
| Microsoft excel | Microsoft | N/A |
| Microsoft word | Microsoft | N/A |
| MultiGeneBlast | Medema et al., 2013 | http://multigeneblast.sourceforge.net/ |
| NEB Tm Calculator | NEB | https://tmcalculator.neb.com/#!/main |
| NEBaseChanger | NEB | http://nebasechanger.neb.com/ |
| Prokka (v1.12) | Victorian Bioinformatics Consortium | https://vicbioinformatics.com/software.prokka.shtml |
| REBASE | The Restriction Enzyme Database | http://rebase.neb.com/rebase/rebase.html |
| Scifinder | The American Chemical Society | https://scifinder.cas.org/ |
| Silva database | Max Planck Institute | https://www.arb-silva.de/ |
| SnapGene Viewer | SnapGene | http://www.snapgene.com/products/snapgene_viewer/ |
| XCMS online | The Scripps Research Institute | https://xcmsonline.scripps.edu/landing_page.php?pgcontent=mainPage |
| Other | ||
| ACQUITY UPLC BEH C18 column, 130Å, 1.7 μm, 2.1 mm × 100 mm | Waters | N/A |
| Agilent 6530 Q-TOF LC/MS equipment | Agilent | N/A |
| Anaerobic chamber | Coy Laboratory Products | N/A |
| Electroporation cuvette | USA Scientific | Cat. #9104-1050 |
| Electroporation System | BTX | N/A |
| Emulsiflex homogenizer | Avestin | N/A |
| 50 mL Tube Top Vacuum Filter System (0.22 μm) | Corning Life Sciences | Cat. #430320 |
| Kinetex C18 column, 1.7 μm, 2.1 mm × 100 mm | Phenomenex | N/A |
| Multiskan Sky Microplate Spectrophotometer | Thermo Fisher Scientific | N/A |
| Real-time quantitative PCR system (ABI 7500) | Applied Biosystems | N/A |
| Thermo Scientific Nanodrop 2000 | Thermo Scientific | N/A |