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5 protocols using sterile filtered fetal bovine serum

1

Cell Culture of Common Cancer Cell Lines

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MCF-7 (HTB-22, oestrogen receptor-positive human breast adenocarcinoma cells), HepG2 (HB-8065, human hepatocellular carcinoma cells) and HT-29 (HTB-38, human colon adenocarcinoma cells) were obtained from American Type Culture Collection (ATCC, Manassas, VA, USA). The MCF-7 and HepG2 cells were maintained in RPMI-1640 medium (Sigma-Aldrich, Munich, Germany), supplemented with 10% sterile-filtered fetal bovine serum (FBS) (Sigma-Aldrich, Germany) and 1% antibiotic (l-glutamine-penicillin-streptomycin) (Sigma-Aldrich, Germany) solution. HT-29 cells were maintained in DMEM medium (Sigma-Aldrich, Germany), supplemented with 10% sterile-filtered fetal bovine serum (FBS) (Sigma-Aldrich, Germany) and 1% antibiotic (l-glutamine-penicillin-streptomycin) (Sigma-Aldrich, Germany) solution. Cells were grown at 37 °C in a humidified incubator containing 5% CO2.
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2

Transcriptomic Analysis of B. thetaiotaomicron

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Cultures of B. thetaiotaomicron VPI-5482 Δtdk and Δtdk Δspt were diluted 1:100 from overnight cultures into 5 mL of BHI medium, supplemented with 1% Vitamin K1-hemin (Becton Dickinson) or minimal medium [1× M9 salts (Teknova), 1% sterile-filtered fetal bovine serum (Sigma-Aldrich), 1% vitamin K1-hemin solution (Becton Dickinson), 1% trace mineral supplement (ATCC), 1% trace vitamin supplement (ATCC), 1 g/L D-(+)-cellobiose (Sigma-Aldrich), 1 g/L D-(+)-maltose (Sigma-Aldrich), 1 g/L D-(+)-fructose (Sigma-Aldrich) and 0.5 g/L L-cysteine (Sigma-Aldrich)] and grown to exponential phase (OD600 ~0.4) in anaerobic conditions. Each culture was pelleted in the anaerobic chamber, supernatants were decanted, and pellets were resuspended in 500 μL Trizol. Trizol suspensions underwent a step of bead-beating using ~500 μL of 0.1 mm silica beads (BioSpec). RNA was extracted with the Direct-Zol RNA MiniPrep Plus (Zymo Research) according to manufacturer’s instructions.
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3

Anaerobic Growth of Ruminococcus gnavus

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We grew R. gnavus ATCC 29149 in BHI medium (37 g/L) containing: 5% sterile-filtered fetal bovine serum (Sigma-Aldrich), 1% vitamin K1-hemin solution (BD Biosciene), 1% trace mineral supplement (ATCC), 1% vitamin supplement (ATCC), 1 g/L D-(+)-cellobiose (Sigma-Aldrich), 1 g/L D-(+)-maltose (Sigma-Aldrich), 1 g/L D-(+)-fructose (Sigma-Aldrich) and 0.5 g/L L-cysteine (Sigma-Aldrich). Growth occurred under anaerobic conditions (atmosphere 5% H2, 20% CO2, 75% N2) in a soft-sided vinyl chamber (Coy Laboratory Products, Michigan, USA). We sterilized the media using a Corning filter unit (0.22 µm pore diameter). All metabolite standards (Sigma-Aldrich) were brought to 100 mM in DMSO (Sigma-Aldrich, D2438) prior to dilution for dose assays. Overnight bacterial cultures were diluted 100-fold in appropriate media and 40 µL were dispensed per well in 384-well plates (low evaporation lid, Costar 3680) containing metabolites or DMSO control. The plates were shaken to ensure homogeneity and bacterial growth was monitored anaerobically (absorbance at 600 nm) in a microplate reader (PowerWave HT Microplate Spectrophotometer, BioTek) for 24 hours at 37°C without shaking. Values recorded for DMSO controls and metabolite-treated triplicates were averaged.
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4

Anaerobic Growth of Ruminococcus gnavus

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We grew R. gnavus ATCC 29149 in BHI medium (37 g/L) containing: 5% sterile-filtered fetal bovine serum (Sigma-Aldrich), 1% vitamin K1-hemin solution (BD Biosciene), 1% trace mineral supplement (ATCC), 1% vitamin supplement (ATCC), 1 g/L D-(+)-cellobiose (Sigma-Aldrich), 1 g/L D-(+)-maltose (Sigma-Aldrich), 1 g/L D-(+)-fructose (Sigma-Aldrich) and 0.5 g/L L-cysteine (Sigma-Aldrich). Growth occurred under anaerobic conditions (atmosphere 5% H2, 20% CO2, 75% N2) in a soft-sided vinyl chamber (Coy Laboratory Products, Michigan, USA). We sterilized the media using a Corning filter unit (0.22 μm pore diameter). All metabolite standards (Sigma-Aldrich) were brought to 100 mM in DMSO (Sigma-Aldrich, D2438) prior to dilution for dose assays. Overnight bacterial cultures were diluted 100-fold in appropriate media and 40 μL were dispensed per well in 384-well plates (low evaporation lid, Costar 3680) containing metabolites or DMSO control. The plates were shaken to ensure homogeneity and bacterial growth was monitored anaerobically (absorbance at 600 nm) in a microplate reader (PowerWave HT Microplate Spectrophotometer, BioTek) for 24 hours at 37°C without shaking. Values recorded for DMSO controls and metabolite-treated triplicates were averaged.
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5

HepG2 and MCF-7 Cell Culture

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HepG2 (HB-8065, human hepatocellular carcinoma cells) and MCF-7 (HTB-22, oestrogen receptor-positive human breast adenocarcinoma cells), were obtained from American Type Culture Collection (ATCC, Manassas, VA, USA). The HepG2 and MCF-7 cells were routinely maintained and incubated at 37 °C with 5% CO2 in RPMI-1640 medium (Sigma-Aldrich, Munich, Germany), supplemented with 10% sterile-filtered fetal bovine serum (FBS) (Sigma-Aldrich, Germany) and 1% antibiotic (penicillin-streptomycin) (Sigma-Aldrich, Germany).
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