KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial strains | ||
| Clostridium sporogenes | ATCC | ATCC 15579 |
| Bacteroides caccae | ATCC | ATCC 43185 |
| Bacteroides cellulosilyticus | DSMZ | DSM 14838 |
| Bacteroides ovatus | ATCC | ATCC 8483 |
| Bacteroides thetaiotaomicron | ATCC | VPI-5482 |
| Bacteroides uniformis | ATCC | ATCC 8492 |
| Alistipes indistinctus | DSMZ | YIT 12060 |
| Lachnoclostridium (Clostridium) asparagiforme | DSMZ | DSM 15981 |
| Hungatella (Clostridium) hathewayi | DSMZ | DSM 13479 |
| Collinsella aerofaciens | ATCC | ATCC 25986 |
| Akkermansia muciniphila | ATCC | ATCC BAA-835 |
| Collinsella intestinalis | DSMZ | DSM 13280 |
| Lachnoclostridium (Clostridium) symbiosum | ATCC | ATCC 14940 |
| Eubacterium rectale | ATCC | ATCC 33656 |
| Bifidobacterium dentium | ATCC | ATCC 27678 |
| Escherichia fergusonii | ATCC | ATCC 35469 |
| Klebsiella pneumoniae | BEI Resources | WGLW1 |
| Staphylococcus aureus | BEI Resources | HI022 |
| Proteus mirabilis | ATCC | ATCC 29906 |
| Acinetobacter baumannii | ATCC | ATCC 19606 |
| Escherichia coli S17-1 λ pir | Yale CGSC | S17–1 λ pir |
| Escherichia coli BL21 (DE3) | Yale CGSC | BL21 (DE3) |
| Escherichia coli MP1 | Dr. Mark Goulian at University of Pennsylvania | MP1 |
| Proteus mirabilisΔ HMPREF0693_2975 | This study | N/A |
| E. coli ppdc + | This study | N/A |
| E. coli ppfor + | This study | N/A |
| B. thetaiotaomicron Δtdk | Koropatkin et al., 200868 | N/A |
| B. thetaiotaomicron ΔtdkΔBT0331 | This study | N/A |
| B. thetaiotaomicron ΔtdkΔBT2826 | This study | N/A |
| B. thetaiotaomicron ΔtdkΔBT0430 | This study | N/A |
| B. thetaiotaomicron ΔtdkΔBT0430ΔBT0331ΔBT0430 | This study | N/A |
| Clostridium sporogenes ΔfldH | Dodd et al., 201719 | |
| Biological samples | ||
| Human fecal samples | Wilcox et al., 202162 | (NCT03039023; http://www.clinicaltrials.gov) |
| Chemicals | ||
| Natural ingredient rodent diet | Envigo | Cat# TD.130104 |
| Gluten-free Egg white (For murine NTZ challenge) | Judes | N/A |
| Methyl viologen (MV) | Sigma-Aldrich | Cat# 856177 |
| Phenylalanine (Phe) | Sigma-Aldrich | Cat# P5030 |
| Phenylpyruvic acid (PPY) | Sigma-Aldrich | Cat# 286958 |
| Thiamine pyrophosphate (TPP) | Sigma-Aldrich | Cat# C8754 |
| 5-Fluoro-2′-deoxyuridine | Sigma-Aldrich | Cat# SIAL-F0503 |
| Coenzyme A (CoA) sodium salt | Sigma-Aldrich | Cat# SIAL-C3144 |
| 2,4-dinitrophenylhydrazine (DNPH) | Sigma-Aldrich | Cat#D199303 |
| 2-Phenylpropionaldehyde | Sigma-Aldrich | Cat#241369 |
| Phenylacetaldehyde | Sigma-Aldrich | Cat#107395 |
| Phenylacetyl coenzyme A lithium salt | Sigma-Aldrich | Cat# P2153 |
| isopropyl-β-d-thiogalactopyranoside (IPTG) | Bio Basic | Cat# C9H18O5S |
| 13C2-Phenylacetic acid (13C2-PAA) | Chem Cruz | Cat# SC-236371 |
| D3-Creatinine | CDN Isotopes | Cat# D-3689 |
| p-Cresol sulfate potassium salt | Toronto Research Chemicals (TRC) | Cat# T536805 |
| D7-p-cresol sulfate potassium salt | Cambridge Isotopes Laboratories | Cat# DLM-9786–0.01 |
| D5-Phenylacetylglutamine (D5-PAgln) | CDN Isotopes | Cat# D-6900 |
| L-13C9 15N-Phenylalaine | Sigma-Aldrich | Cat# 608017 |
| L-13C6-Phenylalaine | Cambridge isotope | Cat# CLM-1055-PK |
| Phenylacetylglycine (PAGly) | Bachem | Cat# 4016439.0001 |
| Phenylacetylglutamine (PAGln) | Santa Cruz | Cat# SC-212551A |
| Nicotinamide adenine dinucleotide sodium salt | Sigma-Aldrich | Cat# N0632 |
| Alcohol dehydrogenase from Saccharomyces cerevisiae | Sigma-Aldrich | Cat# A7011 |
| Nitazoxanide (NTZ) | Sigma-Aldrich | Cat# N0290 |
| Pyruvic acid | Sigma-Aldrich | Cat# 107360 |
| Indole-3-pyruvic acid (I3PY) | Sigma-Aldrich | Cat# I7017 |
| 4-hydroxy-phenylpyruvic Acid (4-OH-PPY) | Sigma-Aldrich | Cat# 114286 |
| 3-methyl-2-oxovaleric acid | Santa Cruz | Cat# sc-214140 |
| Benzoylformic acid | Sigma-Aldrich | Cat# B13055 |
| Ethyl 2-oxo-4-phenylbutanoate | Sigma-Aldrich | Cat# 375322 |
| 2-oxobutanoic acid | Sigma-Aldrich | Cat# K401 |
| Methyl 2-oxopropanoate | Sigma-Aldrich | Cat# 371173 |
| Ethyl thiophene-2-glyoxylate | Sigma-Aldrich | Cat# CDS001215 |
| 4-methylthio-2-oxobutanoic acid | Sigma-Aldrich | Cat# K6000 |
| Ethyl pyruvate | Sigma-Aldrich | Cat# W245712 |
| Brain Heart Infusion (BHI) powder | Millipore | Cat# VM929593 024 |
| Reinforced Clostridial Media (RCM) powder | Difco | Cat# 218081 |
| Luria Bertani broth (LB) powder | Difco | Cat# 244620 |
| Agar powder | Difco | Cat# 281230 |
| Hematin | ChemCruz | Cat# SSC-207729 |
| L-Histidine | TCI | Cat# H0149 |
| L-Cysteine | J.T.Baker | Cat# 2071-05 |
| Tryptone | MP | Cat# 1010817 |
| Yeast extract | Alfa Aesar | Cat# J60287 |
| Glycerol | Fisher Bio reagents | Cat# BP229-1 |
| Sodium chloride | Fisher Chemical | Cat# S271-500 |
| Sucrose | Sigma-Aldrich | Cat# S0389 |
| D-glucose | Acros Organics | Cat# 41095-0010 |
| Potassium Phosphate | MP | Cat# 191431 |
| Magnesium sulfate | Macron Fine Chemicals | Cat# 6070-12 |
| Sodium bicarbonate | J.T.Baker | Cat# 3509-01 |
| Calcium chloride | J.T.Baker | Cat# 1313-01 |
| Ferrous sulfate heptahydrate | MP | Cat# 194663 |
| Tween 80 | Fisher Chemical | Cat# T164-500 |
| Sodium Acetate trihydrate | Fisher Scientific | Cat# S220-1 |
| Meat Extract | Sigma-Aldrich | Cat# 70164 |
| ATCC Vitamin Mix | ATCC | Cat# MD-VS |
| ATCC Trace Mineral Mix | ATCC | Cat# MD-TMS |
| chow diet | LabDiet | Cat# 5010 |
| Experimental models: Organisms/strains | ||
| Mouse: Swiss Webster female | Taconic | SW-F |
| Mouse: Germ Free mice (C57BL/6) | Raised in in the gnotobiotic facility at Cleveland Clinic foundation | N/A |
| Recombinant DNA | ||
| pExchange-tdk | Koropatkin et al., 200868 | N/A |
| pK18mobsacB | Schafer et al., 199473 | N/A |
| pExSacB-2975::Kan | This study | N/A |
| pKEx-MP-PPDC | This study | N/A |
| pKEx-MP-PPFOR | This study | N/A |
| pET16-PPDC | chemically synthesized by GenScript | N/A |
| pET16-PPFOR | chemically synthesized by GenScript | N/A |
| Critical commercial assays | ||
| Bradford Protein Assay | Bio-Rad | Cat# 5000201 |
| Software and Algorithms | ||
| MultiQuant | Sciex | https://sciex.com/products/software/multiquant-software |
| GraphPad Prism (version 9.4) | GraphPad | https://www.graphpad.com/ |
| Lab Solutions (version 5.89) | Shimadzu | https://www.shimadzu.com/an/products/software-informatics/labsolutions-series/index.html |
| Megahit (version 1.2.9) | Li et al., 201575 | https://github.com/voutcn/megahit |
| Vsearch (Version 2.21.1) | Rognes et al., 201677 | https://github.com/torognes/vsearch |
| Nesoni (Version 0.134) | Paul Harrison | https://github.com/Victorian-Bioinformatics-Consortium/nesoni |
| Khmer (Version 2.1.2) | Crusoe et al., 201574 | https://github.com/dib-lab/khmer |
| E_utils (Version 0.6.0) | https://github.com/biocommons/eutils | |
| R (version 4.1.3) | RStudio | https://www.rstudio.com/ |
| Human Microbiome Project (HMP) genomes in The Integrated Microbial Genomes and Metagenomes (IMG/M-HMP) | The Joint Genome Institute | http://www.hmpdacc-resources.org/imgm_hmp/. |
| Clustal Omega for Multiple sequence alignment | Sievers et al., 201169 | https://www.ebi.ac.uk/Tools/msa/clustalo/ |
| Deposited data | ||
| Metagenomics data (For data in Figure 6) | Jie et al., 201750 | European Bioinformatics Institute (EBI) accession code ERP023788 |
| Pyruvate decarboxylase isozyme 1 (PDC1) from S. cerevisiae | Vuralhan et al., 200341 | NCBI Accession: CAA97573.1 |
| Pyruvate decarboxylase isozyme 2 (PDC5) from S. cerevisiae | Vuralhan et al., 200341 | NCBI Accession: CAA97705.1 |
| pyruvate decarboxylase (PDC) from Zymomonas mobilis | Zverlov et al., 198970 | NCBI Accession: AHJ73198.1 |
| Branched-chain keto acid decarboxylase from Lactococcus lactis (KDC) | Smit et al., 200571 | NCBI Accession: AY548760.1 |
| Indolepyruvate decarboxylase (IPDC) from Enterobacter cloacae | Schutz et al., 200372 | NCBI Accession: WP_013098183 |
| Others | ||
| In-Fusion® HD Cloning kit | Takara | Cat# 638910 |