Identification of Microbial Mixtures

From: Innovation, Science and Economic Development Canada

Health Canada (HC) is seeking a method to accurately identify and characterize micro-organisms found in microbial mixtures, and predict their interactions that could mask or enhance adverse effects with a view to determining risks to the environment and human health.

Sponsoring department: Health Canada

Funding mechanism: Contract

Opening date: August 26, 2019
Closing date: October 18, 2019 14:00 Eastern Daylight Time

Please refer to the tender notice for this challenge on Buy and Sell.

Challenge

Problem statement

Micro-organisms and microbial mixtures have the capacity to perform novel and complex tasks in a diverse array of biotechnology applications, many of which support the goals of sustainability. The testing required under the regulations for assessment can be expensive. When multiple micro-organisms are used together in a mixture, the cost of testing becomes prohibitive to the small-medium enterprises that represent the majority of notifiers. Companies have requested the option to conduct testing on the microbial mixture, but it is unknown how interactions between micro-organisms in the mixture during testing could affect prediction of an adverse effect subsequent to environmental release. Lack of suitable test methodologies and novel approaches to determine the adverse effects of microbial mixtures also puts pressure on the program to provide timely guidance to notifiers to meet the regulatory requirements or to assess the notifications within regulated timelines, which prevents Canadian companies from bringing products to the market. The solution will equip HC with complete information needed to conduct the risk assessment of biotechnology-derived products containing microbial mixtures, and meet its operational and regulatory responsibility. It would enable HC to provide informed guidance to notifiers on cost-effective, reliable test methods required to fulfill the regulatory requirements prior to the manufacture or import of microbial mixtures into Canada.

Desired outcomes and Considerations

Essential outcomes

The solution must be a cost-effective*, robust and reliable** method to: (i) identify members of microbial mixtures; (ii) characterize their stability and population dynamics; and (iii) predict possible interactions among the micro-organisms in the mixture (e.g. using omic approaches such as genomics, transcriptomics, proteomics, etc.), that may mask or enhance adverse effects (e.g. pathogenicity, toxicity) in humans.

*Cost-effective: Current cost estimate is about $150K per micro-organism for accurate identification and characterization of micro-organisms in microbial mixtures, and conducting pathogenicity/toxicity testing for one micro-organism with Good Laboratory Practices (GLP). The solution must aim to reduce these testing costs significantly and make it affordable for SMEs.

**Robust and reliable: The solution must provide a well-constructed method with demonstrated sensitivity (capable of identifying wide range of target micro-organisms in the mixture with threshold of detection limits defined), specificity (capable of distinguishing different micro-organisms in the mixture at least to species level) and reproducibility (reliable for any microbial mixtures containing different micro-organisms.

Background and Context

There is an increasing demand to enrich natural microbial consortia and formulated microbial mixtures. These complex microbial products often display an enhanced adaptability to complex nutrient substrates and tolerance to environmental stressors. The capacity of microbial mixtures to perform novel and complex tasks has diverse biotechnology applications, many of which support the goals of sustainability (e.g. contaminated site remediation, production of hydrogen fuels, biofuels, biogas or bioplastics, or replacement of harmful substances in products such as cleaners, complete waste recycling for space missions). In order to comply with the New Substances Notifications Regulations (Organisms) [NSNR (Organisms)], notifiers intending to manufacture or import micro-organisms contained in such products are required to submit data from tests supporting the taxonomic identity and characterization of micro-organisms in these mixtures as well as to determine their potential to cause adverse effects (pathogenicity, toxicity, etc.) to humans and the environment. The testing required under the regulations for assessment can be expensive for companies. When multiple micro-organisms are employed together in a mixture, the cost of testing quickly becomes prohibitive to the small-medium enterprises (SMEs) that represent the majority of our notifiers. In addition, there currently exist no tests or models to predict the fate or complex interactions between multiple micro-organisms in various environments, including conditions found in human body. Lack of suitable test methodologies and novel approaches to determine the adverse effects of complex microbial mixtures also place an increasing demand on the Department's capability to provide timely guidance to notifiers to meet the NSNR (Organisms) requirements or to assess the notifications within regulated timelines. The goal of this research is to develop a cost-effective, robust and reliable automated method to identify members of microbial mixtures and consortium, characterize their stability and population dynamics, and predict possible interactions between individual micro-organisms of the mixture (e.g. using OMIC approaches such as genomics, transcriptomics, proteomics, etc.) that may mask or enhance adverse effects (pathogenicity, toxicity, allergenicity, hypersensitivity, etc.) in humans. The outcomes from the challenge will empower the program with cutting-edge science-based methods and tools to assess complex microbial mixtures and consortia, as well, provide informed guidance to biotechnology industry stakeholders on cost-effective, reliable test methods and help them to meet the regulatory requirements of the NSNR (Organisms). This challenge will particularly benefit the small-medium enterprises, as they will have the option of using alternative methods to test microbial mixtures that are less expensive than testing individual microbial constituents present in the mixtures.

Maximum value and travel

Maximum funding available in Phase 1: $150,000

Maximum funding available in Phase 2: $1,000,000

Travel

For Phase 1, it is anticipated that up to five meetings will require the successful bidder(s) to travel to the locations identified below:

Kick-off meeting Ottawa, Ontario
Progress Review Meetings: one to three design/progress review meetings by teleconference/videoconference
Final Review Meeting Ottawa, Ontario

Eligibility

Solution proposals can only be submitted by a small business that meets all of the following criteria:

for profit
incorporated in Canada (federally or provincially)
499 or fewer full-time equivalent (FTE) employees^{Footnote *}
research and development activities that take place in Canada
50% or more of its annual wages, salaries and fees are currently paid to employees and contractors who spend the majority of their time working in Canada^{Footnote *}
50% or more of its FTE employees have Canada as their ordinary place of work^{Footnote *}
50% or more of its senior executives (Vice President and above) have Canada as their principal residence^{Footnote *}

Application guide

Evaluation Criteria

The official source of the Evaluation Criteria for this challenge is the Government Electronic Tendering System (Buy and Sell) (https://buyandsell.gc.ca/procurement-data/tender-notice/PW-18-00846769)

In the event of a discrepancy between the information below and the information published on Buy and Sell, Buy and Sell will take precedence.

Part 1: Mandatory and Minimum Pass Mark Criteria

Proposals must meet all mandatory criteria (Questions 1a and 2) and achieve the minimum pass mark for Question 3 in order to be deemed responsive and proceed to Part 2.

Mandatory and Minimum Pass Mark Criteria (Applicant/Bidder's proposal must address)
Question	Evaluation Schema
1 a. Scope Describe your proposed solution and how it responds to the challenge. Include in your description the scientific and technological basis upon which your solution is proposed and clearly identify how your solution meets all of the Essential Outcomes (if identified) in the Desired Outcomes and Considerations section in the Challenge Notice.	Mandatory — Pass/Fail Pass The Applicant/Bidder's proposed solution is clearly articulated, within the scope for the challenge and addresses all Essential Outcomes (if identified) in the Challenge Notice. Fail There is little or no evidence that the proposed solution is likely to meet the challenge. OR The proposed solution is articulated as out of scope for the challenge. OR The proposed solution does not address all Essential Outcomes listed in the challenge. OR The proposed solution is poorly described and does not permit concrete analysis.
2. Current Technology Readiness Level (TRL) Indicate the current TRL of your proposed solution. (Drop Down Menu of the Application/Bid Submission Form) Describe the research and development activities that have taken place to bring the proposed solution to the stated TRL.	Mandatory — Pass/Fail Pass: The Applicant/Bidder has demonstrated that the proposed solution is currently between TRLs 1 and 4 (inclusive), and provided justification by explaining the research and development (R&D) that has taken place to bring the solution to the stated TRL. Fail: The Applicant/Bidder has not provided sufficient evidence to demonstrate that the current TRL is between 1 to 4 (inclusive) including: There is insufficient/no evidence provided for TRL judgment. The solution involves the development of basic or fundamental research. The solution is at TRL 5 or higher. Insufficient/unclear/no justification explaining the R&D that took place to bring the solution to the stated TRL. The explanation simply paraphrases the description of a given TRL level.
3. Innovation Describe the novelty of your solution and how it advances the state-of-the-art over existing technologies, including competing solutions.	Point Rated with Minimum Pass Mark The minimum pass mark for this criteria is 4 points. 0 points/Fail: The Applicant/Bidder has not demonstrated that the proposed solution advances the state-of-the-art over existing technologies, including available competing solutions; OR The stated advancements are described in general terms but are not substantiated with specific, measurable evidence. 4 points: The Applicant/Bidder has demonstrated that the proposed solution offers one or two minor improvements to existing technologies, including available competing solutions, that have potential to create competitive advantages in existing market niches. 6 points: The Applicant/Bidder has demonstrated that the proposed solution offers three or more minor improvements to existing technologies, including available competing solutions, that together are likely to create competitive advantages in existing market niches; OR The Applicant/Bidder has demonstrated that the proposed solution offers one significant improvement to existing technologies that is likely to create competitive advantages in existing market niches 8 points: The Applicant/Bidder has demonstrated that the proposed solution offers two or more significant improvements to existing technologies, including available competing solutions that are likely to create competitive advantages in existing market niches and could define new market spaces; OR The Applicant/Bidder has demonstrated that the proposed solution can be considered a new benchmark of state of the art that is clearly ahead of competitors and that is likely to define new market spaces

Part 2: Point-Rated Criteria

Proposals that do not achieve the overall minimum score of at least 55 points out of a possible 110 points (50%) will be declared non-responsive and given no further consideration.

The overall minimum score is determined by adding the Applicant/Bidder's scores from the following questions together (1b, 3, 4-13).

Point-Rated Criteria (Applicant/Bidder's proposal to address)
Question	Evaluation Schema
1b. Scope Describe how your proposed solution addresses the Additional Outcomes (if identified) in the Desired Outcomes and Considerations section in the Challenge Notice. If no Additional Outcomes are identified in the Challenge Notice, text entered in this section will not be considered. If no Additional Outcomes are identified in the Challenge Notice, Bidders/Applicants will receive 10 points	Insufficient or no information provided to demonstrate that the solution will address any of the Additional Outcomes. 0 points Information provided clearly demonstrates that the solution will address some (<50%) of the Additional Outcomes. 5 points Information provided clearly demonstrates that the solution will address most (50% or more) of the Additional Outcomes. 8 points Information provided clearly demonstrates that the solution will address all (100%) of the Additional Outcomes. 10 points
4. Phase 1 Science and Technology Risks Identify potential scientific and/or technological risks to the successful development of the proof of concept and how they will be mitigated in Phase 1?	Insufficient or no information provided to demonstrate that the Applicant/Bidder has considered potential risks and mitigation strategies and/or information provided contains significant gaps. 0 points Information provided demonstrates that the Applicant/Bidder has considered some potential risks and associated mitigation strategies but there are minor gaps in risks and/or associated mitigation strategies. 5 points Information provided clearly demonstrates that the Applicant/Bidder has sufficiently considered the risks and defined associated mitigation strategies. 10 points
5. Benefits to Canada Describe the benefits that could result from the successful development of your solution. Applicants/Bidders should consider the potential benefits using the following three categories: Innovation Benefits: Expected contribution towards the enhancement or development of new industrial or technological innovation within your firm. Assessment factors could include: potential spillover benefits, creation of intellectual property, impact on productivity of the new technology, etc. Economic Benefits: Forecasted impact on the growth of Canadian firms, clusters and supply chains, as well as its expected benefits for Canada's workforce. Assessment factors could include: number of jobs created, number of high-paying jobs, project-related revenue growth, etc. Public Benefits: Expected contribution to the broader public, including inclusive business and hiring practices (e.g., gender balance), investment in skills and training and environmental best practices. Assessment would consider the degree to which the Applicant/Bidder demonstrates that the solution is expected to generate social, environmental, health, security or other benefits to Canada. Assessment factors could include: solution-related environmental benefits, investment in local communities and solution-related impact on Indigenous communities.	Innovation Benefits Benefit not identified or insufficient claim of benefit. 0 points Benefit has marginal increment or limited justification. 1.5 points Benefit is significant and well justified. 3 points Economic Benefits Benefit not identified or insufficient claim of benefit. 0 points Benefit has marginal increment or limited justification. 1.5 points Benefit is significant and well justified. 3 points Public Benefits. Benefit not identified or insufficient claim of benefit. 0 points Benefit has marginal increment or limited justification. 1.5 points Benefit is significant and well justified. 3 points
6. Phase 1 Project Plan Demonstrate a feasible Phase 1 project plan by completing the table. Include: Project milestones; project activities under each milestone; time required to complete each milestone (e.g., days, weeks and/or months); (Indicate if any milestones and activities will be completed concurrently) total time required to complete the project; and key success criteria. Note: Phase 1 cannot exceed 6 months and TRL 4.	Insufficient or no information provided to demonstrate a feasible project plan for Phase 1 and/or the project plan exceeds the maximum duration indicated in the Challenge Notice. 0 points Project plan for Phase 1 is conceivably feasible but not clearly demonstrated and/or includes gaps. 5 points Information provided clearly demonstrates a feasible project plan for Phase 1. 10 points
7. Phase 1 Project Risks Identify potential project risks (eg. Human resources, financial, project management, etc) to the successful development of the proof of concept and how they will be mitigated?	Insufficient or no information provided to demonstrate that the Applicant/Bidder has considered potential risks and mitigation strategies and/or information provided contains significant gaps. 0 points Information provided demonstrates that the Applicant/Bidder has considered some potential risks and associated mitigation strategies but there are minor gaps in risks and/or associated mitigation strategies. 5 points Information provided clearly demonstrates that the Applicant/Bidder has sufficiently considered the risks and defined associated mitigation strategies. 10 points
8. Phase 1 Implementation Team Demonstrate how your project implementation team has the required management and technological skill sets and experience to deliver the project plan for Phase 1 by completing the table. A member of the implementation team can have more than one role. Include the labour rates and level of effort for each member. A day is defined as 7.5 hours of work, exclusive of meal breaks. The labour rates and level of effort will be reviewed as part of the evaluation for Question 10.	Insufficient or no information provided to demonstrate that the project team has the required management and technological skill sets and experience to deliver the Phase 1 project plan. 0 points Information is provided but there are minor gaps in required management and/or technological skill sets and/or experience to deliver the Phase 1 project plan. 5 points Information provided clearly demonstrates that the project team has the required management and technological skill sets and experience to deliver the Phase 1 project plan. 10 points
9. Inclusivity If your business were to receive funding from Innovative Solutions Canada, describe what actions (e.g., recruitment strategy, internships, co-op placements, etc.) might be taken in Phase 1 to support the participation of under-represented groups (e.g., women, youth, persons with disabilities, Indigenous people, visible minorities) in the research and development of the proposed solution. Each bidder/applicant in their response to this question must focus only on describing relevant programs, policies, or initiatives that it currently has in place or would put in place to support the R&D effort in Phase 1. Do not provide any personal information of individuals employed by your company or that of your subcontractors in the response below.	No description and/or concrete examples of actions provided that would be taken to encourage greater participation of under-represented groups. 0 points A description and concrete examples of actions to encourage greater participation of under-represented groups provided. 3 points
10. Phase 1 Financial Proposal Demonstrate a realistic financial proposal for the Phase 1 project plan by completing the table.	Insufficient information provided and/or information provided significantly lack credibility. Does not demonstrate a realistic financial proposal for the Phase 1 project plan. 0 points Information is provided but some costs appear to be either over or under estimated for the Phase 1 project plan. 5 points Information provided contains credible elements to clearly demonstrate a realistic financial proposal for the Phase 1 project plan. 10 points
11. Phase 1 Financial Controls, Tracking and Oversight Describe the financial controls, tracking and oversight that will be used to manage the public funds throughout Phase 1.	Insufficient or no information provided to demonstrate the Applicant/Bidder's ability to manage public funds in Phase 1. 0 points Information provided is vague and/or contains gaps. The Applicant/Bidder has some controls, tracking and/or oversight in place to manage the public funds in Phase 1. 5 points Information provided clearly demonstrates that the Applicant/Bidder has strong financial controls, tracking and oversight to manage public funds in Phase 1. 10 points
12. Phase 2 Strategy Describe a realistic strategy for the prototype development if selected to participate in Phase 2. Responses should include: anticipated barriers key tasks estimated cost	Insufficient or no information provided to demonstrate that the Applicant/Bidder has contemplated a realistic strategy for the Phase 2 prototype development. 0 points Information provided demonstrates a conceivably realistic strategy for Phase 2 prototype development, however there are gaps and/or the strategy is vague. 5 points Information provided demonstrates that the Applicant/Bidder has a clear and realistic strategy. 10 points
13. Commercialization Approach Describe your overall commercialization approach for the proposed solution. Responses should include: Target markets (excluding Government of Canada) Non-ISC funding sources Transition to a commercially-ready product or service Any other indicators of commercial potential and commercial feasibility	Insufficient or no information provided to demonstrate that the proposed solution has commercial potential. 0 points Some information provided to demonstrate that the proposed solution has commercial potential, however there are gaps in the commercialization approach. 5 points A realistic commercialization approach is provided that demonstrates that the proposed solution has commercial potential. 10 points

Questions and answers