Chemistry to microbiology- an odyssey of odours

Jacob Hamilton graduated with a first and following a year in industry is pursuing a career as a researcher, focusing on antibiotics and antimicrobial resistance. Here he shares the challenges and delights of swapping chemistry for microbiology

As a chemist, I thought I had smelt the worst science could offer… then I walked into a microbiology lab.

My undergraduate in Pharmaceutical Science prepared me for chemistry labs filled with the smells of a wide variety of organic compounds with potent, unique odors from benzene (sweet, similar to petrol) to butanal (a rotting banana) and butanoic acid (rancid butter), but walking into a microbiology lab for the first time when I started my masters by research was a shock.

Gone were these smells, replaced by the constant whiff of agar and a delightful stench as you open an incubator full of Salmonella (semen and rotten chicken) and Pseudomonas. Before starting my research project, I had only been in a microbiology lab once in my first year of undergraduate. Now, I’m in there full time.

The chemical structure of butanal – images like these strike fear into the hearts of my lab mates. Structure generated using ACDLabs/Chemsketch
Butanol chemical structure.jpg

Going far with AMR

The decision to transfer from chemistry to microbiology wasn’t easy. I still love organic chemistry, but as I progressed through my degree it became clear I wanted to apply myself to truly helping people and tackling the real problems of my generation.

As part of my undergraduate, I studied antibiotics from a chemist’s perspective – structure activity relationships and bioavailability, as well as differences in admission routes. This was when I first started to appreciate the serious nature of the antimicrobial resistance problem.

About halfway through my final year, I made one of the scariest decisions I’ve ever made; I turned down my graduate job offer from GSK, where I had completed an industrial placement, and started applying for PhDs.


Meeting a mentor

Even PhDs advertised as biochemistry still featured a heavy microbiology element. Although I got a few interviews, my desire to work closely with bacteria meant it was hard to get anything but rejection emails – as I learnt later it takes a lot of trust to throw a chemist into a micro lab!

My housemate at the time was already really into microbiology. He told me about a professor at the university who might be kind (or brave) enough to take me.

Shortly after this, my university held a mini internal research conference, which is where I first met Mark Fielder and introduced myself. After a few meetings between us and Simon Gould, I was offered a Masters by Research in their lab, if I couldn’t find a PhD supervisor brave enough to take me.

milky bottles in the lab

Masters and the universe

Since starting my Masters, I’ve been offered a PhD position elsewhere, but in the meantime, I have really enjoyed my move into the micro lab and I’ve noticed a lot of differences, other than the smell.

In an organic chemistry lab, it isn’t unusual to have reactions that you leave alone over the weekend or even for multiple weeks, boiling away in fume hoods with all sorts of warning labels on them and a hope that no-one decides their experiment is more important.

In a micro lab, you must ensure your bacteria are ‘fresh’ and hasn’t sucked all the nutrients out of whatever agar you’ve grown it on, meaning most experiments happen over the course of a day or two (excluding any prep time).

Sampling is also a much bigger issue for biologists, as part of my project I’ve been swabbing fresh bird poo – much harder than just ordering a chemical online.

statue-bird poo

Swab life

Keeping these samples useable is also something I’ve struggled with, with some bacteria dying on the swab before we get back to the lab. Transporting those samples has its own logistical – and legal – issues I never faced as a chemist pouring a liquid out of a bottle.

There’s also a lot of new stuff to learn – knowing the relative mass of the elements in the top three periods of the periodic table isn’t much use, but knowing what it means when MacConkey agar turns red is a useful diagnostic tool.

There’s still plenty more for me to experience in microbiology, including all the unusual smells, but I’m sure the rest of my Masters, and future PhD, will continue to exploit my experiences in a chemistry and micro lab both.

Jacob Hamilton

Categories: Feature Articles

1 reply

  1. Do you still notice the smell, or have you gotten used to it?

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