A ‘crappy’ PhD: my journey into microbiome research

When people ask me what I do, I usually blurt out a bit of jargon along the lines of “I study the microbiome seeding process in the fetal gut and the immune and metabolic consequences of disruptions to this process”. Most people blink at me and then move on to another topic of conversation. I don’t respond in jargon because I have poor scicomm skills, I do it because, if pressed, I’d have to admit that “I study the microbiome seeding process in the fetal gut” translates to “I spend my days digging through freshly excreted baby poop for bacteria” – which is a fairly unglamorous response.

So why on earth have I chosen such an unglamorous PhD? My background is in obstetric (pregnancy) research, and after my masters I decided to take a year off to travel. Before I left for my year abroad, I was lucky enough to catch a presentation by Kjersti Aagaard (a leading microbiome/pregnancy researcher) on the human microbiome.

A microbiome is a community of micro-organisms (bacteria, archaea, viruses, fungi, protozoa), the space they inhabit, and they conditions surrounding them. Essentially it’s a micro-ecosystem – a teeny tiny universe in itself. When we talk about the human microbiome we are referring to the teeny tiny universe of microbes that exist on and in our bodies. Most of these microbes inhabit our guts, where they play an enormous role in our health. Until recently, the sheer number of microbes and their importance in the functioning of our bodies has been overlooked. But the development of better and more affordable metagenomic technologies (that is, technology for sequencing DNA, which allows us to precisely identify different species of bacteria) has ushered in the “microbiome revolution” throughout the past decade. Increasingly we’re recognising the vital role our gut microbiomes play in our health and the way in which modern lifestyles can disrupt the finely tuned relationship we have built with our resident microbes over the millennia. Importantly, our gut microbiota protect us from invading pathogens, produce key nutrients, control our metabolism, influence our behaviour, and calibrate our immune system.

The “microbiome revolution” has seen a rapid spike in microbiome related research following a leap forward in metagenomic technology

The “microbiome revolution” has seen a rapid spike in microbiome related research following a leap forward in metagenomic technology. Graph produced by Lisa Stinson.


I was enthralled by Kjersti Aagaard’s presentation. Throughout my year of travel, news about the human microbiome kept popping up and grabbing my attention. It seemed that the human microbiome was being pinpointed as a culprit for every imaginable human ailment from obesity to asthma. So when I returned to Perth to begin my PhD, it was obvious to me that I had to study the microbiome. Coming from an obstetric background, my first thought was to study the vaginal microbiome. So I launched myself into writing a literature review and quickly hit a wall. I wanted to include a paragraph about the origins of the vaginal microbiome (when and from where is it acquired?). But no one seemed to be able to answer this question. The prevailing dogma stated that the vaginal microbiome and all other human microbiomes are established at birth when a baby passes through its mother’s vagina. But if this were true, what about Caesarean delivered babies? No one had ever demonstrably proven that babies were sterile until birth and acquired a big dose of microbes as they pass through the birth canal. In fact, there were a handful of studies saying the opposite – that neither the fetus nor the womb was sterile at all. I knew then that I had found my PhD project.

My literature review revealed that not only is the fetus seeded with maternal microbes before birth, but these microbes have a role to play in shaping the fetal immune system and preparing it for life outside the womb. Considering the enormous role our gut microbes play in health and disease, I decided to study the establishment of the fetal gut microbiome. Unfortunately for me, this means a life centred on collecting and analysing baby poo for the next 3 years. The very first poo that a baby does (called ‘meconium’) can act as a proxy for the gut contents of the baby before it was born. Other researchers have already established that meconium is not sterile, so I’ll be adding to this knowledge by comparing the meconium microbiomes of babies from normal healthy pregnancies to those from pregnancies complicated by an infection in the womb (called ‘chorioamnionitis’). I’m hoping to find out if a pathological infection can interrupt the normal microbiome seeding process, and if so, if this would have immune and/or metabolic consequences for the child.

Another day, another nappy

Another day, another nappy…

It’s a daunting task that’s thrown me into the deep end of microbiology and metagenomic technologies (areas which I previously had zero experience in), but I have a supportive and knowledgeable team of supervisors and mentors behind me. And even though I sometimes find myself digging through dirty nappies thinking “why am I doing this to myself?”, deep down I really enjoy it. Ultimately I’m doing this to answer questions that I couldn’t find the answer to anywhere else. My rather unglamorous passion for poop has come from pure scientific curiosity. So my crappy project really isn’t all that crappy after all.

Lisa Stinson

University of Western Australia




Is this PhD my dream Job?

I love cows, dairy cows to be exact, and that’s not meant to sound weird at all, I promise… I am doing my dream job, but the first Monday back after the Christmas break was still the hardest.

I am currently studying a PhD in dairy cow nutrition. I specifically look at faecal matter, poo, crap, excrement, sh*t (insert your own slang where appropriate). I am interested in what a dairy cow really thinks of her diet, and seeing how she can’t tell me, I have to dig a little deeper. Most people assume (rightly) that milk yield from dairy cows determines her opinion on her fodder: more food eaten means more milk. However, I want to know what her endocrine system thinks and what affect does that have on digestion. Faecal samples provide a medium where I can measure things like stress, intake and digestion. It’s complicated, ground breaking stuff! Or at least that’s what I am telling myself ;).

poo laura

Getting out of bed that first Monday morning back, was not easy. I had so much data to analyse, lab work to do, papers to write and goodness knows what else. Christmas break was an actual break, as I figured the last 9 months of my PhD are going to be break free.

I can’t moan, thinking back to my first year of my PhD (I’m a third year now), I had a non-working methodology – therefore no results and a general hated for life. Nothing in my former education could have prepared me for the rollercoaster of the first year of my PhD. This PhD stress is a far cry from the relatively stress free world of my bachelor’s degree in Animal science, my masters degrees, oh and my job (which I did for 2 years).

A PhD throws you from every high to every low and back again.

Image: Jorge Cham, The Stanford Daily

Image: Jorge Cham, The Stanford Daily

My job got me a piece in the newspaper... the perks of my unglamorous job ;)

My job got me a piece in the newspaper… the perks of my unglamorous job 😉

Do I regret anything? Not at all, with every low comes a high, and scientific highs are addictive. Getting methods working, seeing results, writing papers, and attending conferences all around the world. They are just some of the addictive traits of PhD life. All this whilst potentially making a scientific difference – there is no better way of to wind a week away. That’s what got me out of bed that first Monday after Christmas, remembering I am very lucky to be studying a PhD and to be making a difference in the dairy world. Not many can say that…

Of course, it still took a few coffees to get me going, and of course, they were made with only the best of British milk, from the best of the British bovine Ladies :).



I am now into February and not much has changed, bar my stress levels, they seem only to go up. I am making progress though, and I celebrate the little victories often… it keeps you sane, oh and gin… that helps too.


The University of Nottingham



The Dreaded PhD Suspension

The first year of my PhD was not dissimilar in many ways to most postgraduate students. I spent days on end ploughing through literature to gain an understanding of my topic, I produced a literature review and I experienced the multiple failures of research after spending a good seven months modifying my experimental approach. I am a keen sportsperson and played competitive football during my first year, as well as working every Saturday in a sports club for children and young adults with disabilities. On top of this, like most of us, I had a problem with saying no, and amongst other things, I decided to become an Academic Mentor and look after Undergraduate and Masters students in the lab.

As you can imagine it, was virtually impossible to keep this up and as my experiments now required observation 7 days a week…. I sadly decided to pack up my football boots! Towards the end of the first year the atmosphere amongst the postgrads took a nosedive, as we were approaching the dreaded PhD transfer. This entailed endless sleepless nights, as my transfer report was double the word limit and I was reluctant to remove any of it. After the transfer report came the VIVA and, I can say, I have never been so nervous in my life! Having said that, it went extremely well and I was given lots of suggestions, which I was keen to crack on with. At the same time my experiment was finally starting to work, and I felt like a huge weight had been lifted off my shoulders. Success!

Another Monday morning came around and I got to university at 7.30am and I sat in the library for an hour, as I felt unwell. I went to the lab to check my experiments, but I knew something wasn’t right with me, and I was told by my lab manager to go home. After progressively getting worse on Tuesday I was taken to my doctors, and from then on everything was a blur. I was surrounded by doctors, injected in the buttock with Penicillin and rushed to hospital in an ambulance. When I arrived in A&E I was surrounded by so many doctors and nurses, and was told I was being treated for Meningitis. As a microbiologist it was the first time I felt knowing too much was not a good thing, and I thought I was going to die. I was placed in isolation and pumped with antivirals and antibacterial agents whilst my Doctor conducted a lumbar puncture. After laboratory analysis it was confirmed that I had viral meningitis, which was a relief to everyone – especially me. As I was lucky and only had viral meningitis, there was no treatment and I was given fluids, antiemetics (to prevent nausea) and pain relief and was warned of the intense recovery period. I was discharged a few days later.

After two weeks of being out of hospital, I received a call from my supervisor who suggested we suspend my PhD. I was inconsolable. I knew that suspending my PhD was almost inevitable, but I couldn’t help remember the blogs I’ve read stating that a suspension is a polite way of your supervisor telling you to get lost. What upset me the most was the length of time of my suspension, which was 3 months. In my head I had that I would be up and running within a month. But that was not the case at all. In fact, it has been the complete opposite.

Credit: cheaper-than-therapy.tumblr.com

Credit: cheaper-than-therapy.tumblr.com

Two months went by and I had made no significant improvement, so I went back to the back to the doctors who ran further tests. I was then told I was positive for Epstein-Barr virus, glandular fever and (if that wasn’t enough) I also had a urine infection. I was slowly sinking into a depressive state and I felt as though I would never feel well again. The recovery for glandular fever alone is up to a month, with fatigue lasting for up to seven months, so I certainly have a long way to go.

Asides from feeling continually ill for three months, not a day went by where I did not think about my PhD. I felt like my life had been put on hold and the world has gone passing by without me. I would see daily updates and advancements in my field of antibiotic resistance, and targets I had set myself (such as presenting at the SFAM September Conference) had been missed. I felt completely disconnected from the scientific world and my return to life as a researcher seemed further away than ever…

I am now approaching my return to the scientific world that I have felt disconnected from for the past three months. I have to say, I am slightly nervous. But, I have learnt that sometimes you cannot control what life throws at you, but having courage, strength and determination will allow you to overcome any obstacle you are faced with.


Lucky Cullen

Kingston University