New Approaches for Manufacturing Gut Microbial Biotherapeutics (Round 22)

The Opportunity

Recent research has demonstrated that the clinical outcomes of undernutrition in infants are associated with gut dysfunction as well as altered gut microbiota with reduced diversity.^[1] Furthermore, existing nutritional rehabilitation therapies do not completely and sustainably restore healthy growth or reverse the gut dysfunction and gut microbiota alterations associated with growth faltering.^[2] These observations suggest that new therapeutic strategies may need to include administering or promoting health-associated, living gut microbes - live biotherapeutic products^[3] - that perform vital metabolic functions and confer growth and resilience in the gastrointestinal tract and throughout the body.

Fermenting individual commercial probiotic strains such as Lactobacillus spp. or Bifidobacterium spp. is commonly done at scale and at relatively low cost. However, to restore the microbial diversity characteristic of a robust gut microbiome, it is likely that a consortium composed of a substantially larger number of difficult to grow commensal strains must be administered. Currently these gut microbes are manufactured individually and then mixed together to form a live biotherapeutic product, a process which is complex, costly and not scalable. Many of these organisms are strict anaerobes with complex, and at times, unknown nutrient requirements and poor or variable growth. Often, they require expensive media components, which accounts for a substantial fraction of the cost of manufacturing, and the inclusion of animal products in media may pose challenges in terms of regulatory approval and cultural acceptability. In addition, manufacturing must be done within good manufacturing practice (GMP) facilities, substantially increasing the cost of utilizing large batch fermenting vessels and anaerobic chambers for manipulation. To reach the cost of goods required for global health applications significant cost reductions in manufacturing, likely several orders of magnitude, are required.

The Challenge

New approaches could substantially reduce the cost of manufacturing microbial biotherapeutics. Biology offers hope that a lower cost solution is possible: the gastrointestinal tract of humans and animals can be considered a living "bioreactor" that is capable of taking in food and producing highly complex microbiota. In other fields, such as vaccine and biologics manufacturing, new integrated and portable systems have substantially reduced the cost of goods. In the food industry, microbial consortia are commonly manufactured at scale within fermented products such as yogurt and kombucha. In wastewater treatment, sludge reactors can stably host a high degree of microbial diversity. Wholly new manufacturing strategies that take into account the underlying biology and ecology of gut microbial communities could yield substantial advances in the arena.

What we are looking for:

This call for proposals seeks fundamentally new strategies for manufacturing gut microbial biotherapeutics to achieve manufacturing efficiency and cost reductions necessary for global health applications. We are particularly open to high risk, unproven concepts that could yield novel systems. We also encourage approaches that may be carried out in low- and middle- income countries (LMIC) and proposers currently working in these settings.

Strategies could include (but are certainly not limited to or constrained by) the following ideas:

Different reactor designs including continuous stirred-tank, multistage and/or multiphasic bioreactors with small footprints
Disposable or low capital cost bioreactor designs
Spatial structuring or immobilization at varying length scales, spatial gradients, media viscosity (i.e. liquid or solid state)
Dynamically changing growth conditions and inoculation strategies reducing batch-to-batch variability
Various growth conditions including temperature, gas composition, mixing and dilution rate
Novel, low-cost media components

Proposals should specifically detail how they will demonstrate a prototype process operating at lab-scale or greater enabling the manufacture of a diverse health-associated gut microbiota as may be expected in a live biotherapeutic product, specifically 1) production of at least 10 distinct strains derived from the healthy human gut 2) including at least two strains from the Firmicutes phylum of which at least one strain is highly oxygen-sensitive, at least two strains from the Bacteroidetes phylum and at least two strains from the Actinobacteria phylum. These strains could be obtained from commercial culture collections (i.e. ATCC or DSMZ) or may be novel isolates. It is likely that growth of multiple strains together simultaneously may be required for efficiency although other strategies can be pursued.

In addition, proposals should include how they will address all the following three key criteria:

Low cost: How does the strategy enable a significant cost reduction over current batch fermentation and mixing practices towards an eventual target cost of ~$0.10 USD per dose, where each dose consists of ~10⁹ bacteria?
Scalability: Could the strategy be easily scaled up in the future, for example to a pilot scale of tens of thousands of doses per week of clinical grade material? Can potential risks in scale-up be addressed up front? How is the batch-to-batch production variability and risk of contamination minimized to meet purity, potency and consistency standards acceptable by the US Food and Drug Administration (FDA)^[4] and other regulatory agencies for live biotherapeutic products?
Universality: How can the strategy be easily adapted for the production of live biotherapeutic products representing diverse health-associated gut microbes and composed of larger or smaller numbers of strains than specified here?

What we will not consider funding:

Basic research in microbial growth or reactor design that does not address the criteria as outlined above
Proposals only focusing only on novel media formulations without demonstrating a prototype manufacturing process
Purely computational or simulation-based research with no experimental component
Proposals not specifically addressing the growth of human gut bacterial organisms
Proposals solely addressing the growth of common probiotic bacteria (i.e. Lactobacillus spp., Bifidobacterium spp.), a single bacterial strain, or not meeting the specific requirements detailed above
Proposals focused on formulation and preservation of microbes, which is outside the scope of this call for proposals
Proposals focused on simply optimizing standard known approaches and techniques, without adding innovative improvements
Proposals where there is no clear path forward to scale to meet the stated foundation needs

Useful references:

^[1] https://www.nature.com/articles/nature13421

^[2] http://science.sciencemag.org/content/352/6293/1533.long

^[3] https://www.nature.com/articles/nmicrobiol201757

^[4] https://www.fda.gov/downloads/Biologi%E2%80%A6/UCM292704.pdf

^*Applicants are encouraged to review the US FDA guidance document (ref. 4 above) around Chemistry, Manufacturing and Controls for live biotherapeutic products to better understand regulatory considerations in the area.