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



Blogging: good or bad procrastination?

Okay, so I know I’m relatively new to the blogging world, but already I find myself loving it and continuously want to post and post and post…

Although I think it is a great way communicate ideas, opinions and funny facts, or just simply have a nosey at what everyone else is up to, I have been left thinking… is it a good or a bad distraction? For instance, I am currently meant to be starting a literature review for my PhD, however all I want to do is blog and write summary articles relating to current science news. At least the latter may actually help! 🙂

Let me backtrack a little so you’re up to date – I recently started writing articles for my old University newspaper, where I actually got a few articles published (shocked?! Me too!). They were only small articles, for example I did one on the development of breathalysers to detect Parkinson’s disease, but having them published is such a sense of achievement. This is a similar feeling I get when I post a new blog. It’s so great to see the views tallying up and having people I’ve never met before like my blog, or better yet, re-blog it! Knowing that people are reading my work and may like it or want to read more makes me feel proud and helps to boost my confidence – which is never a bad thing, despite what most people think!

So back to the requirements of my PhD… I have a deadline for Janurary, which may seem quite far away for now, but I am doing a PhD and that means I always have a lot going on. Nevertheless, it needs to be done and it is still important. But all I want to do right now is write about new science-related topics and make sure everyone knows about them. Being a newbie ‘SciCommer’ I am very much getting involved in wanting all audiences to understand about the science world and what kind of research is going on out there that could potentially help them one day. Or just attract their interest.

Even though blogging and writing articles is distracting me from my university work, is it really a bad thing?! I think not. Okay yes, I’m probably not spending as much time as I should be on my written projects, but I am fitting my writing around my lab work. This shows organisational and multi-tasking skillsgreat aspects to include on my CV. It also helps me to engage more with the news, keeping up to date with what is going on across the globe, a job I used to find quite difficult. What’s even better is that I am learning about all types of science, not just my own area of interest. I think this is imperative, as most jobs require a broad knowledge base and not just a specific understanding of a subject. Additionally, this allows me to develop and grow my intellect, adding to my scientific expertise. And last but not least, I am beginning to network and interact with fellow scientists, scientific communicators, students and lecturers, growing discussions and sharing ideas and opinions. I now find myself being more acquainted with different subjects in greater detail, enabling me to discuss these topics with co-workers, colleagues and lecturers, when previously I was nervous to do so as I felt inexperienced and that I lacked specific familiarity. I am also writing for my own selfish desires: because I enjoy it! And that can’t be a bad thing, surely?!

Credit: funny-joke.com

Credit: funny-joke-pictures.com

So taking all this into account, I think writing in an informal and ‘chatty’ manner, in contrast to the strict and awkward way in which we have to write to gain attention within University and the science world, is surprisingly helping my career in many ways. And even if it is classed as ‘procrastination’ in some people’s eyes, I believe it is good procrastination – disagree with me if you must!




Devon Smith

The University of Sheffield