Gut microbiome alterations in high-fat-diet-fed mice are associated with antibiotic tolerance
Description
Raw Metabolomics data, the data set is related to figure 3d, Extended Data Fig. 5 and 6.
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Fecal samples (about 50 mg) from standard and high-fat diet-fed mice after 64 days of feeding were mixed with 400 μL extraction solution (methanol: water = 4:1), and were homogenized using high-throughput tissue disruptor at -20 °C for 6 min. Samples were mixed using a vortex for 30 s and extracted by low-temperature ultrasonic extraction for 30 min (5 °C, 40 KHz), then the samples were kept at -20 °C for 30 min. The tubes containing samples were then centrifuged (13,000 g, 15 min, 4 °C) and the supernatants were obtained for following LC-MS analysis. The metabolite extracts from mice fecal samples were analyzed using an UPLC-Q-Exactive Orbitrap mass spectrometer (Thermo Fisher Scientific, MA, USA). Chromatographic separation was performed on a BEH C18 column (100 mm × 2.1 mm, 1.7 μm, Waters, Milford, USA). The autosampler and column were maintained at 4 °C and 40 °C, respectively. Water with 0.1% formic acid (A) and acetonitrile/isopropanol (1:1, containing 0.1% formic acid, B) was used as the mobile phase. The elution gradient was optimized as follows: 0 min, 5% B; 3 min, 20% B; 9-13 min, 95% B; 13.1 min, 5% B; 13.1–16 min, 5% B, with an flow rate of 0.4 mL min−1. The injection volume was 10 µL. The optimized conditions of TOF/MS were: ionspray voltage floating, 3.5 kV (ESI+)/-2.8 kV (ESI-); aus gas flow rate, 10 psi; aus gas heater temp, 400 °C; scan range (m/z), 70–1050 Da. The raw data were processed using Progenesis QI software (Waters, Milford, USA). Each sample was analyzed by UPLC-MS in both positive and negative ionization modes to obtain metabolite profiles. The analysis order of all test samples was randomized. The QC sample was a pooled sample in which aliquots of all the extracted samples were mixed, and then analyzed using the same method as that used for the analytic samples.