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7 protocols using lysogeny broth medium

1

Bacterial Culture and DNA Extraction

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All the samples were cultured on Mueller–Hinton agar plates at 33°C overnight. Then, a single bacterial colony was suspended onto 3 mL of sterile lysogeny broth medium (Oxoid, Hampshire, UK) and subsequently incubated at 33°C with vigorous shaking for 8 hours. Then, DNA was extracted using Hipure bacterial DNA kit (Magen, Guangzhou, China) according to the manufacturer’s instructions.
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2

Culturing Gut Microbiome Isolates

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A. muciniphila (Akk) was obtained from American Type Culture Collection (ATCC, No. BAA835) and cultured in brain heart infusion medium (BHI; Oxoid) at 37 °C under anaerobic conditions. D. newyorkensis (Dab) and C. innocuum were purchased from the German collection of microorganisms (DSMZ, DSM103457 and DSM1286-1213-001) and cultured in chopped meat carbohydrate broth (CMC, Hopebio) at 37 °C under anaerobic conditions. E. faecalis (EF) was purchased from the China Center for Type Culture Collection (CCTCC, AB 2018154) and cultured in Lysogeny broth medium (Oxoid) at 37 °C. The concentration of each bacterial species was estimated based on the optical density at 600 nm (OD600).
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3

Bacterial Culture and Antibiotic Selection

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Bacterial strains and plasmids used throughout this study are listed in Key Resources Table. Bacteria were cultured in Lysogeny Broth (LB) medium (Fisher) unless differently specified. Cultures were grown at 37°C under well-aerated conditions. As relevant, the following chemicals (Sigma-Aldrich) were added to the growth medium to the indicated final concentrations: ampicillin (100 μg/mL; Ap100), chloramphenicol (30 μg/mL; Cm30), kanamycin (50 μg/mL; Km50), L-arabinose (0.2%) and IPTG (1 mM).
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4

Yeast and Bacterial Culture Conditions

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A haploid CENPK2.1D (MATα; his3D;1 leu2-3_112; ura3-52; trp1-289; MAL2-8c; SUC2) was used in this work. Yeast strains were cultured at 30 o C in complex yeast extract peptone dextrose (YPD, all components from BD Diagnostics) medium or synthetic defined medium (SDM) containing yeast nitrogen base (YNB) (BD Diagnostics), ammonium sulfate (Fisher Scientific), 2% (w/v) unless specified and the appropriate dropout (Takara Bio) solution for selection. E. coli strain TOP10 was used in the inhibition assay, and cultured at 37 °C in lysogeny broth (LB) medium (Fisher Scientific).
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5

Protein Purification Protocol using ÄKTA FPLC

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Lysogeny broth (LB) medium was purchased from Oxoid Limited (Hampshire, U.K.). Methanol and acetonitrile used for liquid chromatography-mass spectrometry (LC-MS) were high-purity solvents from Concord Technology (Minnesota, U.S.A.). Water used in this work was ultrapure deionized water from Millipore Direct-Q. Chemicals were purchased from Sigma–Aldrich, Geneview, J&K, Amresco or Solarbio. Oligonucleotide primers were synthesized by Tsingke Biological Technology (Beijing, China). DNA plasmid Mini prep, fragment gel extraction and restriction endonucleases clean up kits were from Tiangen (Beijing, China). Talon Cobalt resins were purchased from Clonetech (California, U.S.A.). All protein purification chromatographic experiments were performed on an ‘ÄKTA pure’ or ‘ÄKTA prime plusFPLC machine equipped with appropriate columns (GE Healthcare). Protein concentrations were determined according to the method of Bradford [12 (link)] using bovine serum albumin (BSA) as a standard, or using NanoDrop One (Thermo Fisher Scientific). The extinction coefficient for each protein was obtained using the ExPASy ProtParam tool.
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6

Antimicrobial Preservative Preparation Protocol

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Tryptone soya medium (agar, TSA; broth, TSB) and Lysogeny Broth (LB) medium were obtained from Oxoid Ltd. Tetracycline (Tc) and ciprofloxacin (CIP) antibiotics were supplied by Sigma-Aldrich; dimethyl sulfoxide (DMSO) and other analytical grade chemicals were supplied by Fisher Scientific. A minimal basal salts growth medium (BSM) was prepared as described by Rushton et al. [21 (link)] without casamino acids. A 3 : 1 cosmetics grade blend of chloromethylisothiazolinone and methylisothiazolinone (CMIT/MIT), and methylisothiazolinone (MIT) were obtained from Dow Chemical Company, USA; dimethyl dimethylol hydantoin (DMDMH) from Lonza, UK; benzisothiazolinone (BIT) and phenoxyethanol (PH) from Clariant International Ltd, Switzerland. Preservative stock solutions were prepared (in sterile distilled water or DMSO for PH) on the day of use and diluted as required.
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7

Engineered E. coli for Uric Acid Degradation

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The strains and plasmids used in this study are listed in Table S1. All the primers are listed in Table S2. E. coli XL1-Blue MRF’ was used for plasmid construction, and E. coli Nissle1917 was used to construct engineered strain for UA degradation. They were cultured at 37°C in Lysogeny broth (LB medium)(#10855001, Oxoid). Kanamycin (A506636, Sangon Biotech), spectinomycin (A600901, Sangon Biotech), and ampicillin (A610028, Sangon Biotech) were used at 50 μg/mL, 50 μg/mL, and 100 μg/mL, respectively.
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