Novel microbial strain discovery to enhance industrial production efficiency

Production platform

Fermentation

Technology sector

Host strain development

Resources

Current challenges

Microbial strains offer immense biological diversity, which can be leveraged to identify or create strains with enhanced growth potential, nutritional characteristics, flavour profiles, or feedstock preferences. However, the vast majority of biomass and precision fermentation processes use a very limited number of strains. Most biomass fermentation companies making mycoprotein (e.g., Quorn, Better Meat, ENOUGH) primarily rely on a very limited number of fungal species, primarily Fusarium venenatum (genus Ascomycota). Similarly, precision fermentation efforts at industrial scales generally rely on a handful of well-characterized species of yeast (e.g., Pichia pastoris, S. cerevisiae, Y. lipolytica) or bacteria (e.g., E. coli, B. subtilis, and lactic acid bacteria). To broaden the spectrum of available microorganisms, systematic screening and investigation into the physiology of novel microbial strains is needed to identify strains suitable for fermentation.

Strain improvement also plays a pivotal role in boosting the efficiency of the fermentation process and determining the overall economics. For instance, an improved strain that is capable of synthesising a higher proportion of end-product while utilising the same quantity of raw materials or low-cost materials has the potential to substantially decrease both material and manufacturing expenses.

Proposed solutions

Research into strains other than Fusarium spp. may offer distinct benefits in terms of growth characteristics or nutritional enrichment for biomass fermentation. For example, fungal strains in many genera (Aspergillus, Malbranchea, Talaromyces, Trichoderma, Chaetomium, Rhizopus) have outperformed Fusarium species with respect to enzyme production and cellulolytic activity on diverse substrates. Other research has demonstrated robust growth of non-Fusarium species (e.g., Pleurotus, Agaricus, and Auricularia) in solid-state fermentation, using industry co-products such as brewer-spent grain, grape bagasse, or other agricultural wastes, and using low-grade inputs such as seaweed.
Comprehensive screening of new species as production platforms for precision fermentation may offer advantages such as high expression levels of recombinant proteins, greater stress tolerance, the unique ability to synthesise novel natural products, and even remarkable metabolic versatility signalling potential to use with non-standard medium inputs.
Strain improvement strategies can be employed to increase the titer and yield of target molecules and protein biomass.
- To compete with animal-based proteins, researchers and companies must increase the titer (amount of an expressed target molecule relative to the volume of total upstream-produced liquid containing the agent; primary benchmark of upstream efficiency) and yield (the ratio of mass of final purified protein relative to its mass at the start of purification; primary benchmark of downstream efficiency) of target molecules and protein biomass in industrial fermentation processes.
Metabolic engineering techniques may also unlock the potential to use cheaper fermentation feedstocks.
- There is immense potential to use diverse and malleable feedstocks in fermentation, such as leveraging existing agricultural side streams for economic and sustainability advantages. Advancements in biofuel production have involved utilising an array of biomass feedstocks – ranging from starch-based to lignocellulosic sources – achieved through the modification of metabolic pathways in a range of microbial hosts. Similarly, using strain engineering, we can generate deeper insights about microbial biology, such as which genetic signatures indicate suitability for various feedstocks or growth conditions for GRAS strains in food fermentation.