Product toxicity is a major problem for many IBBE processes involving production of small molecules by living cells. Industrial chemical targets are generally lipophilic and some (e.g. alkenes, aldehydes, epoxides) are also reactive, and known to damage certain cell components. Likewise, small molecules in lignocellulosic feedstocks inhibit bacterial fermentations & ultimately depress product yields.

Various solutions to toxicity have been proposed and tested. Engineering approaches based on in situ liquid-liquid extraction often prove successful, but only when a non-toxic extraction solvent can be identified.  Therefore, complementary biological solutions are also needed.

Some improvements in product resistance have been obtained for specific chemicals, using directed evolution of product-resistant hosts through sequential batch or continuous cultures.  Reverse engineering the host cells has also delivered small improvements, by using ‘omic analyses to identify and exploit native resistance/adaptation systems.  However, the experimental systems have mostly been based on simple batch cultures, where the cells are exposed to the toxic chemical added outside the cells.  By contrast, the most process-relevant situation is where the product is actually being produced inside the cell.  The “enemy within” is, of course, much more damaging than an extracellular chemical, which is excluded from the cell interior by the cell surface layers.

Furthermore, all studies have focused on single types of chemicals, so any improvements are chemical-specific rather than generic. As a result, these approaches have yielded only incremental improvements. In addition, new problems have emerged arising from the use of sustainable feedstocks derived from pre-treatment of lignocellulose, that contain toxic chemicals like furfural and phenolics like ferulate that can inhibit downstream fermentation.