Just-In-Time Biotech


Written 2021-08-24

Recently, I've had a bit of an issue with our media preparation protocols. We found that media, even after being autoclaved and closed (after cooling), sometimes got contamination. This could be 1 of 2 problems - it could be that our pressure cooker (that we use as an autoclave) isn't getting hot enough, or it could be that the room that we cool the media bottles in isn't sterile enough (and air should enter the bottle while it cools). Though I suspect the latter, there aren't a lot of good ways to test this, since it doesn't always happen.

What really got me thinking was what we were growing. The contaminated media was LB3 media, which we use for growing Vibrio natriegens (Vnat). Vnat is the *fastest growing* bacteria humanity has discovered. There is no way that any environmental bacteria strain will be able to compete in Vnat's optimal conditions with Vnat. We use antibiotics and a tiny bit of contamination isn't even meaningful for my lab, since we ship plasmids and do QA/QC on outgoing samples, so we'll catch anything significant at that step. So to beg the question, why even sterilize our media?

The paper that got me into Vnat, "Vibrio natriegens, a new genomic powerhouse"

The reason we currently sterilize our media is that we store 500ml bottles and aliquots from those bottles. During storage at room temperature, contamination has a bunch of time to grow. What if, instead of storing, we always used media the day of? In essence, bring JIT to a biotechnology process.

Just-In-Time compilation, or JIT compilation, is a method in computer science where code is compiled during run-time, just in time for it to be used. In manufacturing, this generally means that resources are used as they come in to reduce buffers and increase utilization.

Just-In-Time compilation wikipedia article

Just-In-Time manufacturing wikipedia article

My current plan is to bring JIT manufacturing to my foundry by only producing media that will be used the day of. This should nearly eliminate contamination, while giving us useful statistics on media usage.

Keoni Gandall