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Acetate and glycerol, as well as organic acids (citric acid, α-ketoglutaric acid, gluconic acid, 2-ketogluconic acid, pyruvic acid, succinic acid, lactic acid, formic acid, and fumaric acid), were quantified in filtered culture supernatants (Costar Spin-X; 0.22-μm-pore-size filters) using isocratic high-performance liquid chromatography (Agilent 1260 Infinity series; Aminex HPX-87H column) (65°C; flow rate of 0.5 ml min⁻¹) equipped with refractive index (RI) and UV detectors (210 nm) with 50 mM H₂SO₄ as the eluent (94 (link)). Concentrations were determined from commercial standards which were analyzed on the same run. These data were then used to calculate specific uptake and formation rates and yields for acetate, glycerol, and secreted by-products (see Data Set S2 in the supplemental material).

Mice were infected intravenously with 0.2ml Salmonella Typhimurium M525 (phoN::tetC) containing 5x10⁵ CFU of bacteria in sterile phosphate buffered saline (Sigma-Aldrich). At various time points as indicated in the text, mice were sacrificed and the spleen and liver were harvested and blood collected via cardiac puncture under Isoflurane anaesthesia and placed into heparin tubes for the isolation of plasma. Prior to analysis (as above) plasma was filtered through 0.22 μm spin filters (Costar Spin-X) to eliminate any circulating bacteria. Organs were homogenised in sterile water and bacteria enumerated by serial dilution and plating onto agar plates (Oxoid). Mice were weighed daily throughout the infection and were humanely sacrificed if they lost more than 20% of their starting weight or were demonstrating clinical symptoms in accordance with UK Home Office regulations (United Kingdom Animals Scientific Procedures Act 1986).

The dorsolateral striatum from both the left and right sides (n = 10, per group) was dissected and frozen at −80°C. Brain tissue samples were weighed and then homogenized in 700 μL of ice-cold lysis buffer [19 (link)], containing o-phthalaldehyde 27 mg, anhydrous ethanol 1 mL, tetraborate buffer 9 mL, andβ-mercaptoethanol 5 μL.
The homogenate was centrifuged at 14000 rpm for 15 min at 4°C and filtered through a 0.22 μm filter (Costar, Spin-X) and then centrifuged at 7000 rpm. Standard solution or the filtrate obtained from brain homogenate (20 μL) was injected into the HPLC. Chromatographic conditions were as follows. The precolumn was Shiseido (Guard Cartridge, Capcell C18 MG S-5, 4.0 × 10 mm). The chromatographic column was Waters XTerra MS (3.0 × 50 mm, 2.5 um, Part no. 186000598). The mobile phase was composed of 100 mM disodium hydrogen phosphate, 25% methanol, and 10% acetonitrile (pH 6.70). The flow rate was 0.6 mL/min. The column oven was held constant at 40°C. Working solutions of GABA (40, 20, 8, 4, 2, 1, and 0.5 μg/mL) were used. The calibration curve of each compound was determined by plotting the ratio of peak area to internal standard versus concentration of the spiked standard solution. A linear regression equation (y = ax + b) was evaluated, where x is the concentration of the analytes and y is the peak area ratio. The correlation coefficient (R²) was calculated.

Liquid chromatography–tandem mass spectrometry (LC–MS/MS) was used to analyse faecal BA. These included CA, CDCA, DCA, LCA, UDCA, and glycine- and taurine conjugated forms of these BA. A detailed overview of the BA are found in Additional file 2. The method for extraction of BA was based on Hagio et al. [35 (link)] with the following modifications: A total of 100 µL of 0.1 µg/mL internal standard was added to each freeze-dried faecal sample of 100 mg. Centrifugation of samples were performed at 4 °C. The evaporation steps were performed at room temperature. The methanol extracts were purified with solid phase extraction using an Oasis HLB cartridge (Waters, Milford, MA, USA), following the generic Oasis HLB protocol. The eluates were evaporated to dryness at room temperature under a stream of air and the dry residues were reconstituted in 1 mL methanol/10 mM ammonium acetate (1 + 1). The extracts were filtered through 0.22 µm nylon spin filters (Spin-X, Costar, Corning Inc., Corning, NY, USA) for 3 min at 11,000×g. The filtered extracts were transferred to HPLC-vials and subsequently stored at − 20 °C until LC–MS/MS analysis.

Nasosorption was performed by placing strips of a hydrophilic polyester absorptive matrix (Mucosal Diagnostics, Hunt Developments (UK) Ltd., Midhurst, UK: available as a CE-marked device) measuring 7 × 35 mm into each nostril for 2 min (Jackson et al., 2014 (link)). Having removed the SAM strip, it was washed in PBS buffer pH 7.4 (100 μl) containing BSA (1%) and Triton X 100 (1%) within the cup of a spin filter insert (Costar® Spin-X®). Mucosal lining fluid was then eluted from the SAM by spin filter centrifugation (5 min at 16,000G at 4 °C), and aliquots frozen at − 80 °C.