Fermentation problems and how to solve them

  1. 14th Aug, 2020

Fermentation is essential for scaling up bioprocesses in the sustainable manufacture of chemicals, biologics, pharmaceuticals and biofuels and, here at Ingenza, our richly diverse, multidisciplinary team has built up a wealth of experience to help you do just that. We can help you solve your fermentation problems, whether they’re related to host systems, technologies, efficiency or yield. Here’s just a taster of the challenges you might encounter and our top tips for the key questions you need to ask. 

Which host organism should I use?

The first step that is crucial in dictating the success or failure of an efficient fermentation process is to choose the right host organism. There are several different options that you could use, each with unique features and different growth conditions; while E. coli is versatile and a popular choice – simply because it’s the most widely known and understood – it’s not always the best option. Often, researchers are either hesitant or inexperienced in trying different hosts, there are so many determining factors:

  • if the gene you want is derived from a eukaryote, such as yeast, it won’t necessarily express very well in a prokaryote host, leading to slow growth and/or low yield; 
  • the product you’re making might simply be toxic to some hosts;  
  • lack of facilities might limit you to class 1 microorganisms, for example, when in fact you should be using class 2; 
  • if you’re trying to develop a process for manufacturing based on GMP, do you need a stable cell line, or one made to the principles of GMP before you even start the fermentation development? 

There are answers to all these challenges and often a simple switch to a different microbe can make the whole expression process so much faster, which in turn makes it more cost-effective. However, it takes time and experience to know just what host to use in each situation and, at Ingenza, our experience of working with many different organisms over many years means we have already almost certainly encountered and solved the challenges that each system brings. Not least, the growing conditions each one prefers.

Picking the right conditions

Temperature, media composition and timing all need to be optimised to ensure the best results from whatever host system you choose. Luckily, we at Ingenza have an idea of exactly where to start with the optimisation process, speeding up the whole workflow.

  • Temperature 

The question of temperature is not as simple as it may seem; generally, if you grow things at a higher temperature they grow faster but, for some organisms, they might not express your protein of interest as well as they would under lower temperatures. It’s all a matter of balance.

  • Media

We can offer many options of bespoke media, as well as mixtures that are optimised for different host systems to efficiently yield your proteins of interest. For each organism, we have a good idea of where to start – with maybe three or four media recipes for each one – and also have the advantage of several small-scale automated systems that help us optimise for each project.

  • Timing

If you’re expressing a protein, it’s often a good idea to look at the effect of varying incubation times;

some microorganisms grow more slowly than others, but it depends on what you’re making as to whether that is a good or a bad thing. 

Choosing right mode of operation

Yield is another question of balance. Batch fermentation – where you put everything in at the beginning and just leave it – is common for proof of concept, and is often a short process turned around quite quickly, but yields are typically not high. Fed-batch processes rely on trying to prolong the log phase to boost the biomass and improve protein expression. Another option is continuous culture, where the process itself takes longer but continually generates product, with no set up or and clean down stages between the runs. Although productivity in terms of grams per litre per hour might be lower than other methods, the volumetric productivity might be higher because it’s a constant process, and the equipment requires a smaller footprint, reducing capital costs. 

Ultimately, there is no right or wrong with regard to getting the ‘best’ yield. Many factors contribute to the final choice, and that’s true of many aspects of fermentation. It’s a minefield of decisions, but one that we at Ingenza can help you with. We are well-equipped and well-experienced to help you overcome your challenges, so contact us to find out how we can help.