It’s 8:09 and I just made it into the lab, the sun is rising. It looks absolutely stunning, especially the reflection of the golden light on the glassware. However, don’t be mistaken by the peaceful image. The machines in the room are making so much noise it is as if you are standing directly next to a busy highway.
Usually, people never understand when I say ‘I am in the lab’, except for other scientists that work in the same field. Most people simply don’t have a clue what’s going on. It is a whole different world out there. So…
What does it mean ‘to be in the lab’?
I will tell you! But, before I dive into my lab day from the 11th of February, let me shortly introduce you to my research. It might provide some helpful context.
Basically, I Am Growing Poo.
Simply put, with my research, I am looking at the impact of antibiotics on a microbial ecosystem. To get a better understanding of the implications of antibiotic treatment in humans. Besides, it might give more insight into how antibiotic resistance is developed.
I run a small bioreactor that is continuously being fed with fresh medium (aka ‘food’) and at the same rate fluid from the reactor is being pumped out. At the beginning of my experiment, I added a tiny bit of human poo to my reactor as a start community.
Besides food remains our poo contains bacteria and other microbes that normally inhabit our gut, also known as our gut microbiome. The cells (bacteria & co) added to my reactor will grow and adapt to their new habitat and diet. Some will probably not like it and die, others will thrive.
Eventually, a new bacterial ecosystem will be established. Theoretically, I guess you could say that I am growing poo or at least growing some of the bacteria that live in poo. After giving the cells time to adjust to my reactor the next step is performing an antibiotic treatment.
For a couple of days, the reactor will be spiked with antibiotics. Samples before, during and after this period will be taken to determine how the bacterial community changed over time and how their abilities were impacted.
Thursday the 11th of February 2021
(the second day of antibiotic treatment)
8:10—I start the day by checking my whole set-up, write down the numbers from the scales and my visual observations of the reactor. E.g. how does the culture look? Today the set-up looks fine however, my culture looks rather sad.
Looking at the density of the fluid in my reactor it seems that I didn’t have that much growth overnight. This was expected as yesterday I started with the antibiotic treatment, which is designed to kill bacteria.
8:20 — Next, I prepare everything to be able to sample. Taking stuff out of the fridge, getting pipets, cleaning my bench with 96% ethanol. The usual.
8:30 — Getting some fire and ready to sample. As I don’t want to contaminate my culture with bacteria from outside my reactor I work ‘under’ a flame every time I take out fluid. The flame will ‘clean’ the surrounding air from microbes, preventing them from entering my reactor.
The next thirty minutes or so I walk around with a bucket of ice with my samples. From one room to another, using different machines. However, while my samples are in the centrifuge I notice that the pressure in one of my reactor tubes seemed to have dropped. PANIC.
My medium is pumped into the reactor with a hydraulic pump, and the pressure was gone. The tube was empty and no medium was being pumped in. Problematic on different levels, I will spare you the details.
No biggie though, I have fixed the problem within 10 minutes without realising what was the problem or how I fixed it. Quite annoying.
9:05 — I have to hurry. Due to the pressure problem, I couldn’t prepare the antibiotic treatment yet and I still have to handle my samples. They are finished in the centrifuge and need to be stored at -20C /-80C as fast as possible.
9:15—After some rushing and a heart rate going through the roof I managed to store my samples and to prepare everything in time to spike the reactor with antibiotics, which had to be done at a certain time. Somehow I don’t like spiking my reactor with antibiotics.
It took 10 days to reach a stable community and now I am destroying it. I am afraid I am killing all the bacteria, which is not the idea behind my experiment. If it would happen I would have to start over and change my experimental set-up. I don’t want to do that.
9:20 — Can’t sit down just yet and have to finish with the sampling. When I sample, I take samples for different measurements. Some need to be frozen as soon as possible for others I can take a little longer.
I do some more walking around, weighing, measuring and try not to burn myself when using the 105°C or 550 °C oven. When ready with the samples from today, I weigh and measure the samples from the day before that are now ready to continue with the next step.
10:00 — First time I sit down since I left my home this morning at 7:45. In the office, I start entering data from this morning in my excel sheets only to realise that during the night my reactor received less medium than it was supposed to — trouble with the tubing seemed to have been going on for longer than just this morning.
Nothing I can do about it anymore, data is never perfect and as long as I write down everything that I observe I can at least explain what happened if I get any weird data back. As a perfectionist, this really stresses me out.
I want to have clean data without any interruptions coming from outside my experiment. However, when you work with machines and people (incl. yourself), mechanical and human errors are simply guaranteed.
The antibiotic treatment has a clear effect on my bacterial population looking at my visual observations as well as the real-time off-gas data. (The gas (carbon dioxide, hydrogen & oxygen) leaving my reactor is directly analysed.) I spend some time thinking about what could be going on and scan through some research papers.
11:00 — I went back to the lab to check on the tubing. I got a bit paranoid that it was going wrong again. Everything seemed to be working fine though.
11: 15— I run into one of the technicians in the lab and we discuss the tubing problem. If the pressure in the tube was gone there had to be a ‘leak’ resulting in air being sucked in instead of my medium.
Turns out that one of my connectors in my tubing was not airtight when moved in a specific way. Some tape with the notification “DO NOT TOUCH/MOVE !!!” should solve the problem… (it did).
12:00— Lunch. Just in time. I was starting to get hungry. You’re not allowed to eat nor drink in the lab and somehow I forget to snack when I am in the office. Staying hydrated is something I have under control these days. I end up staring at my colleagues, I am tired.
13:00 — Back to the lab as I booked the ‘kitchen’ to prepare medium. This involves weighing a bunch of different chemicals and filling bottles of 10/20L. Which unfortunately I also have to lift on and off a cart. Arm workout of the day: check!
14:15 — In the office, I troubleshoot with one of my colleagues about something I did the day before that didn’t yield the results I wanted. Obviously without knowing what went wrong.
14:20—I decide to do it slightly differently, to see if that works. So back to the lab for a redo. Let me tell you, everything you do in the lab never works for the first time. Never.
15:15 — Another round of sampling just as this morning. In total it takes more or less an hour to finish all the different samples. Afterwards, I prepare the tubes and labels for the next day. Everything has to be labelled properly. I always forget how much time it takes.
16:00 — I am tired, my back aches and I am losing concentration. Dangerzone. I still have to finish something in the lab so I can’t leave just yet.
16:30 — Forced tea break to ensure I stay hydrated and rest a little bit. I end up looking at my data. So I guess it is not really a break. Technically I am still working, it’s just a break from the lab.
17:00 — Lab again, quick preparation and at 17:15 I do the second spike of antibiotics. I do a final check to see if everything works accordingly, clean everything with a squirt of 96% ethanol and say goodnight to my cells.
When I leave the building at 17:30 the fresh air filling my lungs makes me smile. It is quite smelly in the room I have my bioreactor. And it feels good to go home after a day of hards work.
Often I am too tired to write my afternoon logs in my excel sheets so I will do that when I arrive home and had a snack. Additionally more or less every second hour I will check my online data coming from my reactor, to see how the gas profiles look and to make sure nothing is exploding. Not that I would see that on the profiles though… Or be able to do something about it.
Tomorrow my day will be the same, it will however have its own set of ‘problems’. As cells don’t take the weekend off I will have to go back in the weekend to do some sampling — just for an hour so; not too bad. Lab work with living cells requires some serious dedication.
Never The Same, Constantly Troubleshooting
In my experience lab work is physically exhausting, you walk so so much. If I have an extensive lab day I easily reach more than 10 000 steps before I go home. And, then there is the mental part to it.
No lab day is ever the same which is exciting. Nevertheless, it requires constant thinking and adjusting. Everything takes at least three times as long as you initially planned. My supervisor hands it to Murph’s law; “Anything that can go wrong will go wrong”.
Yet, at the end of the day research is intriguing and awesome. The feeling when you achieve what you were going for or when you find something unexpected is thrilling. Like you found the last piece of the puzzle.
This is what it means to be ‘in the lab’, at least for me. Running around solving problems, doing mundane tasks like labelling tubes, stressing about things you can’t control (if you are like me), pure excitement when things do go right, the thrill of finding out new stuff, the enthusiasm when you (start to) understand something.
It’s like being a curious kid in an awe-inspiring playground. With the addition of a lot of compounds and, or machines that are dangerous and might explode. I simply don’t know when I will be home.
I am honestly impressed if you made it this far! Let me know if you thought this was interesting and whether you would like to know more about my research. I would be happy to explain all the details!