2.1 | System design
The basic component of the gut model is a standardized bioreactor module (Figure 1). The growth chamber (clear or brown media bottles with GL45 caps; Corning Incorporated) is placed in a jacketed reaction beaker (Chemglass) that serves as the temperature control vessel and is set on top of a stir plate. The temperature control vessel is attached to a recirculating heater/chiller with Prestone®antifreeze/engine coolant as the heat transfer fluid. The growth chamber is equipped with a stir bar and the caps are drilled to accommodate dedicated ports for a pH sensor (Atlas Scientific, Long Island City, NY), inlet and outlet ports for transfer of culture medium, inlet ports for acid and base, inlet port for nitrogen gas, outlet port for venting excess gas, and a valved outlet port for culture sampling. Brown bottles offer protection of light sensitive metabolites from photodamage. The space between the growth chamber and the temperature control vessel is filled with Prestone® antifreeze/coolant to ensure efficient heat transfer. The nitrogen gas inlet can be adapted to permit either an aerobic (port open to the room atmosphere) or anaerobic (constant flow of nitrogen gas) culture environment as required. Mini-peristaltic pumps (Kamoer KPP-DH-B03W), which convey acid (HCl) or base (NaOH) to the growth chamber, and larger peristaltic pumps (New Era NE-9000), which drive the transfer of culture medium from one growth chamber to the next, are all controlled by a Raspberry Pi computer version B-R2 (Raspberry Pi Foundation) running the system control software (Figure S1) written in Python programming language (Python Software Foundation). All the computers controlling each of the modules are connected via an ethernet router. The pH probe is connected to the Raspberry Pi computer through an EZOTM pH circuit stamp (Atlas Scientific, Long Island City, NY). A time server running on a dedicated Raspberry Pi computer fitted with a real-time clock module synchronizes the clocks across all network devices. The number of bioreactor modules operated at a time is flexible (Figure S2). Batch culture mode (growth medium In/Out ports sealed), continuous mode (single bioreactor with growth medium with In/Out ports operational) and series mode can be selected at the start of the experiment and the system parameters are supplied to each control computer through a configuration file.