Multi-Reactor Anaerobic Fermentation System with Dialysis Capability

This Request for Proposals (the “RFP”) is an invitation by the University of Ottawa (the “University”) to prospective proponents to submit proposals for a Multi-Reactors Automated Fermentation System with Absorption Module for Region-Specific Gut Microbiome Simulations, funded by the Canada Foundation for Innovation and the Ontario Research Fund, as further described in Appendix D (RFP Particulars) Section A (the “Deliverables”).

The University seeks proposals from qualified vendors for the supply, delivery, installation, commissioning, and training of a Multi-Reactor Anaerobic Fermentation System with Dialysis Capability (absorption) designed to simulate the human gastrointestinal and colonic environments and support controlled cultivation of complex gut microbial communities. The system will serve as a preclinical research platform to investigate microbiome-driven health disorders.

THE DELIVERABLES
Scope of the Project:
The University is soliciting prospective proponents to submit proposals for the supply, installation, commissioning, and training assocaited with a a multi-reactor anaerobic fermentation system with dialysis capability (absorption) designed to simulate the human gastrointestinal and colonic environments and support controlled cultivation of complex gut microbial communities. The system will serve as a preclinical research platform to investigate microbiome-driven health disorders, with a particular focus on women’s health, which is central to the research program.

Research conducted using this platform involves inoculation of fresh human fecal samples and long-term fermentation runs that reproduce ecological conditions of different gut regions. Experiments may extend from several weeks to months depending on the research objectives.

Samples processed and generated in the system include fecal inocula and multiple reactor-derived fractions, including luminal samples (liquid phase), mucosal-associated communities recovered from mucin-coated carriers, and dialysate fractions obtained through the dialysis module. These samples will subsequently be analyzed using downstream multi-omic approaches, including microbiome sequencing (16S rRNA gene or shotgun metagenomics) and metabolomics.

General Description:
The system must consist of interconnected bioreactors capable of reproducing different regions of the human gastrointestinal tract while maintaining precise control of temperature, pH, anaerobic atmosphere, and nutrient delivery. The system must support continuous or semi-continuous operation and enable repeated aseptic sampling throughout long-term fermentation experiments.

Individual reactors must support working volumes in the range of approximately 150–1000 mL, allowing cultivation of complex microbial communities and repeated sampling. Reactors must be equipped with magnetic stirring systems and compatible magnetic stirring plates to ensure homogeneous mixing during fermentation. Temperature regulation must be achieved through an integrated circulating water bath connected to double-jacketed reactors, or an equivalent temperature control system. Reactors must be autoclavable.

The system must allow programmable sequential delivery of nutrient media, digestive secretions, and removal of effluents through automated pumping systems. Flow rates and cycle programming must be independently adjustable for each reactor. Fluid transfer between reactors must be programmable and controlled through automated pumping systems. The system must allow simultaneous cultivation of luminal and mucosal-associated microbial communities within the reactors. The platform must support dedicated carriers or microenvironments enabling attachment and growth of mucosal-associated microbiota.

The fermentation platform must include an integrated dialysis module allowing exchange of small metabolites between the reactor environment and an external compartment. The dialysis system must support controlled diffusion of low-molecular-weight compounds, enabling simulation of absorption and metabolite removal processes.
The system must be computer-controlled, allowing real-time monitoring of operational parameters (ethernet connection). The system must include automated diagnostics and alert functions capable of detecting deviations or equipment malfunction within individual reactors. Operational parameters must be continuously recorded and visualized as time-series data.

The equipment must comply with applicable electrical and laboratory safety standards.

The system should allow future expansion, enabling additional reactor units to be integrated if required.

Description of Software:
The multi-reactor fermentation system must be computer-controlled through dedicated software allowing real-time monitoring and control of key operational parameters, including pH, temperature, sequential delivery of media, secretions and waste removal, and maintenance of anaerobic conditions through gas flushing. The software must allow users to program, monitor, and adjust operational parameters, including pump flow rates, timing cycles, and experimental protocols across multiple reactors. 

The software must allow programmable multi-step experimental protocols and automated scheduling of reactor operations.

The software must allow continuous recording and visualization of system parameters over time, enabling monitoring of physicochemical conditions within each reactor unit. Time-series data integration and visualization for individual reactors must be supported.

The software must include automated system diagnostics and alert functions capable of detecting abnormal operating conditions (e.g., deviations in pH, temperature, or pump operation) within individual reactor units. The system must notify the user through on-screen alerts and/or email notifications to ensure rapid intervention and prevent experimental failure during long-term fermentation runs.

System data must be exportable in standard formats compatible with spreadsheet software (e.g., .xls or .xlsx).

Software must be compatible with Windows 11 operating systems.

Description of Service:
The supplier must provide the following services associated with the purchase, delivery, installation, and operation of the multi-reactor fermentation system.

Installation and start-up: The supplier must deliver, install, and assemble the full fermentation platform at the purchaser’s facility. Installation services must include: (i) Delivery of the complete system and all required components; (ii) Assembly and installation of the equipment on site; (iii) Verification of system functionality and operational readiness; and (iv) Start-up of the system, including the execution of an initial test run to confirm proper operation of all reactor units, pumps, sensors, and control software.
Site acceptance test: Following installation, the supplier must perform a site acceptance test to verify that the equipment meets the required operational specifications. Acceptance testing must include verification of: (i)Proper operation of all reactor units; (ii) Functionality of pumps and fluid transfer systems; (iii) Correct monitoring and control of temperature and pH; (iv) Proper functioning of the control software and data acquisition system. Successful completion of the site acceptance test will constitute formal acceptance of the system.
Preventative maintenance: The supplier must provide recommendations for preventative maintenance, including the expected maintenance schedule and required procedures to ensure proper operation of the equipment. Documentation must include: (i) Recommended maintenance frequency; (ii) Description of maintenance procedures; (iii) Identification of consumable parts requiring periodic replacement.
Warranty period: The supplier must provide a minimum one (1) year warranty covering defects in materials, manufacturing, and normal equipment operation. The warranty must include: (i) Repair or replacement of defective components; (ii) Real-time technical support for troubleshooting, including assistance with system operation, guidance on experimental setup and optimization, and support for troubleshooting and interpretation of system outputs; (iii) Replacement of faulty system components due to construction or operational defects.
Training: Upon reception of the system, the supplier must provide on-site training for personnel (PI, student trainees, and/or research assistant) responsible for operating the equipment. Training must include: (i) Operation of the fermentation system and control software; (ii) System start-up and shutdown procedures; (iii) Basic troubleshooting and maintenance procedures; (iv) Best practices for experimental operation, calibration and quality control checking. Training should accommodate 2–3 personnel and require approximately one to two working day.
Starter kit: The supplier must provide all consumables, reagents, and materials necessary to conduct an initial fermentation experiment of approximately four weeks using five reactor units, ensuring full operational readiness of the system upon installation.

Laboratory Infrastructure:
Space dimensions: The equipment will be installed in a dedicated laboratory room with an approximate surface area of 13 m². The available space is sufficient to accommodate the fermentation system, associated control unit, and gas cylinder while allowing safe access for operation and maintenance, with a biosafety cabinet and sink present in the room.
Surface for the equipment: The equipment will be installed along the long wall of the room, opposite the doorway and the existing biosafety cabinet. The system must fit within approximately 3.5 m in length and must not exceed 150 kg in total weight to ensure compatibility with existing laboratory benches or support structures.
Electrical: The laboratory is equipped with eight electrical outlets, including emergency power outlets, which are accessible from the installation location. These outlets will be used to power the fermentation system and associated control equipment.
Plumbing: No additional plumbing connections should be required for the installation or operation of the system.
Gas connection: The system will require connection to a nitrogen gas cylinder to maintain anaerobic conditions during operation. The cylinder will be installed and secured according to institutional safety procedures.
Chiller: Temperature control will be achieved through the integrated water bath system provided with the equipment. No external chiller infrastructure will be installed.
Data connection: The room is equipped with an Ethernet connection that will be used for the computer control system and potential network connectivity of the equipment.

Mandatory Technical Specifications Requirements:

1.0 - Multi-reactors automated fermentation system
1.1 - Must be computer-controlled with ethernet connection, allowing real-time monitoring of operational parameters including pH, temperature, anaerobic atmosphere, nutrient and digestive secretion deliveries.
1.2 - Must minimally contain 5 complete reactors, each interconnected.
1.3 - Each reactor must support working volumes between 150 mL and 1 L.
1.4 - Each reactor must be double-jacketed to allow circulation of temperature-controlled water (37 °C) to ensure uniform and stable temperature regulation. This design is required to provide homogeneous heating across the reactor, as surface heating methods such as hot plates may result in uneven temperature distribution.
1.5 - A water bath system must be provided to regulate the temperature of the fermentation system
1.6 - 5 pH probes must be provided to ensure the precise control of pH in each reactor
1.7 - The system must maintain strict anaerobic conditions within each reactor, including gas-tight reactor design and controlled nitrogen flushing.
1.8 - The system must support long-term microbial fermentation experiments lasting minimally 4 weeks while maintaining stable physicochemical conditions.
1.9 - Each reactor must be equipped with a magnetic stirring system with compatible magnetic stirring plates to ensure homogeneous mixing during fermentation. Stirring mechanisms integrated into the reactor lid (e.g., rotor or shaft-based agitation systems) are not acceptable, as the reactor must be regularly opened for experimental manipulation, including periodic replacement of mucosal carriers, which could interfere with or become entangled in lid-mounted agitation systems.
1.10 - Each reactor lid must minimally have 8 ports architecture for aseptic sampling (1), liquid in (1), delivery of base (1), delivery of acid (1), liquid out (1), port for pH probe (1), gas evacuation (1), to hold the wire of the mucin bead bag (1).
1.11 - Each reactor must be autoclavable.
1.12 - The system must support dedicated mucosal carrier holders or equivalent containment devices that allow attachment, stable suspension, and routine replacement of mucosal carriers during fermentation, while preserving mixing efficiency and anaerobic integrity.
1.13 - The system must support continuous or semi-continuous operation with programmable sequential delivery of nutrient media, digestive secretions and removal of effluents through automated pumping systems. The pumps must be able to be independently calibrated and programmed.
1.14 - Flow rates and cycle programming must be independently adjustable for each reactor.
1.15 - The system must include a minimum of 18 programmable peristaltic pumps with a maximum speed of approximately 30 rpm.
1.16 - Must include 1 Nitrogen gas flushing unit for up to 3 gas circuits.
1.17 - Must provide an integrated dialysis module for each reactor, allowing exchange of small metabolites, enabling simulation of absorption and metabolites removal processes.
1.18 - Must provide all consumables, reagents, and materials necessary to conduct an initial fermentation experiment of approximately four weeks using five reactor units, ensuring full operational readiness of the system upon installation.
1.19 - Each reactor must allow independent control and monitoring of pH, feeding cycles, pumping rates, and gas flushing, enabling different experimental conditions to be applied across reactors simultaneously.
1.20 - Reactor design must allow regular manual access for experimental manipulation (e.g., replacement of mucosal carriers) without requiring disassembly of agitation systems.
1.21 - The system must allow calibration of pH probes and sensors without disassembling the system.
1.22 - The system must provide automated alerts in case of deviations from programmed parameters (e.g., pH drift, pump malfunction, temperature deviation).
1.23 - The system must allow real-time replacement of tubing and fluid lines associated with pumping systems without requiring disassembly of the full platform.

2.0 - Computer and Software
2.1 - Must include an embedded computer with a UPS
2.2 - Must include a monitor with HDMI connector, keyboard and mouse
2.3 - Must include a perpetual software licence for operation of the system
2.4 - The control software must allow programming of multi-step experimental protocols including feeding cycles, secretion delivery, and waste removal.
2.5 - Operational parameters must be continuously recorded through the software.

3.0 - Other Requirements
3.1 - Installation and training on-site must be included for a minimum of 3 persons.
3.2 - The system must allow modular expansion with the addition of up to 5 additional reactor units within the same platform design, for a total of 10, including 18 additional pumps.
3.3 - Must fit on the lab bench of 90 cm depth and maximum 3.5 m length.
3.4 - The supplier must ensure availability of replacement parts and consumables for a minimum of 5 years.






 

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