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. Author manuscript; available in PMC: 2024 Nov 23.
Published in final edited form as: Cell Host Microbe. 2024 Oct 28;32(11):1887–1896.e8. doi: 10.1016/j.chom.2024.10.002

Key resources table.

REAGENT or RESOURCE SOURCE IDENTIFIER
Bacterial and virus strains
Gordonibacter pamelaeae 3C Prof. Peter Turnbaugh N/A
Gordonibacter sp. 28C Prof. Peter Turnbaugh N/A
Paraeggerthella hongkongensis RC2/2A Prof. Peter Turnbaugh N/A
Eggerthella lenta A2 Prof. Peter Turnbaugh N/A
Eggerthella Sinensis DSM 16107 Prof. Peter Turnbaugh N/A
Adlercreutzia equolifaciens DSM 19450 DSMZ N/A
Adlercreutzia equolifaciens subsp. celatus DSM 18785 DSMZ N/A
Slackia heliotrinireducens DSM 20476 DSMZ N/A
Senegalimassilia anaerobia DSM 25959 DSMZ N/A
Gordonibacter urolithinfaciens DSM 27213 DSMZ N/A
Gordonibacter pamelaeae 7-10-1b DSMZ N/A
Raoultibacter massiliensis DSM 103407 DSMZ N/A
Gordonibacter urolithinfaciens DSM 27213 hcdh K/O This paper N/A
Gordonibacter sp. 28C Prof. Peter Turnbaugh N/A
Paraeggerthella hongkongensis RC2/2A Prof. Peter Turnbaugh N/A
Eggerthella lenta A2 Prof. Peter Turnbaugh N/A
Eggerthella Sinensis DSM 16107 Prof. Peter Turnbaugh N/A
Adlercreutzia equolifaciens DSM 19450 DSMZ N/A
Adlercreutzia equolifaciens subsp. celatus DSM 18785 DSMZ N/A
Slackia heliotrinireducens DSM 20476 DSMZ N/A
Senegalimassilia anaerobia DSM 25959 DSMZ N/A
Gordonibacter urolithinfaciens DSM 27213 DSMZ N/A
Gordonibacter pamelaeae 7-10-1b DSMZ N/A
Raoultibacter massiliensis DSM 103407 DSMZ N/A
Gordonibacter urolithinfaciens DSM 27213 hcdh K/O This paper N/A
Chemicals, peptides, and recombinant proteins
3,4-dihydroxyhydrocinnamic acid (hydrocaffeic acid; HCA) Sigma-Aldrich Cat#102601-10G
3-(3-hydroxyphenyl)propionic acid (mHPPA) Toronto Research Chemicals Cat#H940090-1g
Caffeic acid Millipore Sigma Cat#C0625-2G
3,4-dihydroxyphenylacetic acid (DOPAC) Millipore Sigma Cat#850217-1G
Dopamine Sigma-Aldrich Cat#PHR1090-1G
Chlorogenic acid Ambeed Cat#A163338
trans-ferulic acid Sigma-Aldrich Cat#128708-5G
trans-isoferulic acid Sigma-Aldrich Cat#PHL89717-100MG
DL-3,4-dihydroxymandelic acid Sigma-Aldrich Cat#151610-500MG
Rosmarinic acid Astatech Cat#44324
L-arginine monohydrochloride Sigma-Aldrich Cat#A5131-500G
L-cysteine hydrochloride monohydrate Sigma-Aldrich Cat#C7880-100G
Sodium formate Sigma-Aldrich Cat#247596-100G
Methyl viologen Sigma-Aldrich Cat#856177-1g
Sodium dithionite Sigma-Aldrich Cat#157953-5G
Ammonium sulfate Sigma-Aldrich Cat#157953-5G
Sodium molybdate Sigma-Aldrich Cat#243655-100G
Sodium nitrite Sigma-Aldrich Cat#237213-100G
SIGMAFAST protease inhibitor tablets Sigma-Aldrich Cat#S8830
DNase Sigma-Aldrich Cat#DN25-1G
Lysozyme Sigma-Aldrich Cat#L6876-5G
Brain–Heart Infusion (BHI) Becton Dickinson Cat#211060
TRIzol Invitrogen Cat#15596026
3-(3-hydroxyphenyl)propionic acid (mHPPA) Toronto Research Chemicals Cat#H940090-1g
Caffeic acid Millipore Sigma Cat#C0625-2G
3,4-dihydroxyphenylacetic acid (DOPAC) Millipore Sigma Cat#850217-1G
Dopamine Sigma-Aldrich Cat#PHR1090-1G
Chlorogenic acid Ambeed Cat#A163338
trans-ferulic acid Sigma-Aldrich Cat#128708-5G
trans-isoferulic acid Sigma-Aldrich Cat#PHL89717-100MG
DL-3,4-dihydroxymandelic acid Sigma-Aldrich Cat#151610-500MG
Rosmarinic acid Astatech Cat#44324
L-arginine monohydrochloride Sigma-Aldrich Cat#A5131-500G
L-cysteine hydrochloride monohydrate Sigma-Aldrich Cat#C7880-100G
Sodium formate Sigma-Aldrich Cat#247596-100G
Methyl viologen Sigma-Aldrich Cat#856177-1g
Sodium dithionite Sigma-Aldrich Cat#157953-5G
Ammonium sulfate Sigma-Aldrich Cat#157953-5G
Sodium molybdate Sigma-Aldrich Cat#243655-100G
Sodium nitrite Sigma-Aldrich Cat#237213-100G
SIGMAFAST protease inhibitor tablets Sigma-Aldrich Cat#S8830
DNase Sigma-Aldrich Cat#DN25-1G
Lysozyme Sigma-Aldrich Cat#L6876-5G
Brain–Heart Infusion (BHI) Becton Dickinson Cat#211060
TRIzol Invitrogen Cat#15596026
Critical commercial assays
Direct-Zol RNA MiniPrep Plus Kit Zymo Research Cat#R2070
RQ1 RNase-free DNase kit Promega Cat#M6101
Luna® Universal One-Step RT-qPCR Kit New England Biolabs Cat#E3005S
BacTiter-Glo Promega Cat#8230
RQ1 RNase-free DNase kit Promega Cat#M6101
Luna® Universal One-Step RT-qPCR Kit New England Biolabs Cat#E3005S
BacTiter-Glo Promega Cat#8230
Deposited data
Gordonibacter urolithinfaciens DSM 27213 hcdh K/O genome This work BioProject PRJNA1150218
Metagenome-assembled genomes from human-associated microbiome Pasolli et al. N/A
Gordonibacter pamelaeae 3C RNA-seq raw data Bess et al. BioProject PRJNA450120
Men’s Lifestyle Validation Study (MLVS) Mehta et al. BioProject PRJNA354235
Human Microbiome Project 2 (HMP2) Lloyd-Price et al. BioProject PRJNA398089
Recombinant DNA
pXD71Cas10RFP Addgene Plasmid #192273
pXD68Kan2 Addgene Plasmid #191248
pXD80GuCas3.1 This work N/A
Software and algorithms
GraphPad Prism 9 and 10 GraphPad Software N/A
tblastn Altschul et al. N/A
PhyloPhlAn 3.0 Asnicar et al. https://github.com/biobakery/phylophlan
iTOL v6.5.8 Letunic and Bork https://github.com/iBiology/iTOL
Enzyme Function Initiative’s Enzyme Similarity Tool (EFI-EST) Zallot et al. https://efi.igb.illinois.edu/efi-est/
Cytoscape v3.9.1 Shannon et al. https://github.com/cytoscape
KneadData v0.10.0 N/A https://github.com/biobakery/kneaddata
ShortBRED Kaminski et al. https://github.com/biobakery/shortbred
DIAMOND Buchfink et al. https://github.com/bbuchfink/diamond
MicrobeCensus Nayfach and Pollard https://github.com/snayfach/MicrobeCensus
Bowtie2 v2.4.2 Langmead and Salzberg https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
HTseq-count v0.13.5 Anders et al. https://htseq.readthedocs.io/en/release_0.11.1/index.html
Salmon v1.9.0 Patro et al. https://combine-lab.github.io/salmon/
MaAsLin2 1.0.0 Mallick et al. https://github.com/biobakery/Maaslin2
MAFFT-linsi v7.505 Katoh and Standley https://mafft.cbrc.jp/alignment/software/
trimAl v1.4.1 Capella-Gutiérrez et al. https://vicfero.github.io/trimal/
iqtree2 v2.1.3 Minh et al. https://github.com/iqtree/iqtree2
Diet and MTX analysis pipeline This paper https://zenodo.org/records/13390717