Commercial continuous fermentation has its best prospects with rugged strains that are producing either cell mass or a simple enzyme or metabolite. Processes with finely tuned mutants for special products are carried out in batches to minimize reversion to less productive strains. Another barrier to progress for continuous fermentation is the cost of each research station. Rapid advancement in research and development requires multiple vessels for screening many variables, but there are usually very few continuous fermenters because the cost of pumps, reservoirs, sterilizers, and controls is relatively high. Furthermore, much labor is needed to start a run, to keep the instruments working, and to monitor results.
Continuous industrial microbial processes are much less common than batch processes, but most biological waste treatment steps are operated continuously because the waste stream keeps flowing in.