Media change best practice with long tubing?


Question about best practice for a media change to a container with long tubing:

I’m planning to connect my ongoing experiment with a larger media container (40L carboy). The tubing is several feet, since the carboy rests on the floor. When I change the media, all that tubing will be full of air. After that I could:

  1. Just connect the vial, and let the pumps try to dilute until media has been brought all the way through the tubing. Pro: automatic. Con: seems like this could mess with the growth rate by being logged as separate pump events due to the intake time of >20s.
  2. Connect the vial and then run the fluid_test script to pull media up till it is near the vial. Pro: won’t be logged as separate pump events within the script. Con: risks overflowing the vials if I estimate the pump time wrong.

Has anyone tried changing media to containers with long tubing before? And/or Brandon do you have advice?


For my experiments, I usually just change out the media and let the pumps do their thing automatically. Assuming you’re running a turbidostat, the pump_log file will have multiple events listed as you said, but since the OD of the culture hasn’t gotten close enough to the lower threshold, it won’t affect the ODset log file. This is why I use ODset to segment my OD data into growth windows for calculation rather than pump_log.

Sometimes I have run pumps in order to remove dead-space in the tubing, either by disconnecting temporarily and pumping into a bucket (PRO: also removes leftover media, CON: potential for contamination) or by running both influx and efflux simultaneously to avoid overflows (PRO: easy, CON: will dilute vial with any leftover media in the line).


Thanks for the advice! Really appreciate it.