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

@lisafstinson

https://microbiomemusings.wordpress.com/

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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.

Laura

The University of Nottingham

@laurajaynetenna

 

PhD Life Trips: My Brazilian Experience

In September, I was lucky enough to be invited to join a group of fellow Environmental Scientists on a trip to the beautiful Brazil! The group consisted of three academics and three very over-excited PhD students. The aim of the trip was to set up collaborative work with a University in the North Federal Rural University of the Amazon (URFA) based in Belem. Additional academics, who had previous links with the University of Nottingham, also attended the meetings in Belem facilitating a great collaboration between three Universities in inter-disciplinary areas.

Acai seeds are a waste product in Brazil. While in Brazil, we discussed producing charcoal from Acai and exploring the potential positive benefits on soil.

Acai seeds are a waste product in Brazil. While in Brazil, we discussed producing charcoal from Acai and exploring the potential positive benefits on soil.

Whilst in Brazil, the first thing that struck me was the different approach to research. Many of the Brazilian academics and post-docs couldn’t understand why we wanted to work in collaboration with them, other than the obvious: getting to visit Brazil!! The trip to Brazil was especially exciting for me as the concept on which I base my PhD project, biochar, originated from ancient Amazonian farming practises where charcoal is added to soils to improve fertility. So working with Brazilians on the topic really brought out the geek in me! The local academics loved the enthusiasm, but couldn’t completely relate. I learnt that the agricultural sector faces a lot of social issues. There are the huge companies, such as Monsanto, which dominate the market in the South and are trying to penetrate the North, where farming is seen more on a sustenance level. The North struggle with a reduced capacity for farming due to protection of the rainforest therefore reduced land. The reduced capacity, sustenance levels and pressure from corporations means farmers in the North are reluctant to make any changes to their tried and tested farming practices. Any additions or changes to the farming traditions in the North need to be 100% beneficial due to the heavy reliance on local farms for food. While in Brazil, my understanding of the extent to which locals depend on farming massively increased, putting into context the impact of my own PhD work.

While in Belem I was asked to present my work on soil remediation through biochar amendment to soils, and after seeing the enthusiasm for biochar in the area, I was excited to present my ideas! The language barrier made the presenting difficult, but thankfully a postdoc was on hand to act as translator. The academics then presented suggestions or potential oversights within our projects which, although slightly daunting, turned out to be extremely beneficial. The presentation was given in a fairly relaxed manner allowing the Brazilian academics and postgrad students to be critical without being intimidating. The feedback as extremely useful to really get me thinking and highlighted the importance of having clear aims in order to develop the impact of my work. After the presentations we enjoyed the sun set over the amazon with a beer: I definitely felt I deserved it due to the interrogation after my presentation!
Overall I found the trip extremely interesting as I got to observe first hand how different education, farming and economic systems work globally! It was also great to see the potential impact my work could be having, a long way down the line… The key drive for sustainability in Brazil was brilliant and is something the UK agricultural industry could learn a thing or two from. The country values the magnificence of the rainforest and understands that any newly developed technologies need to respect and maintain the forest. Brazil. It was an absolute pleasure and I have no doubt I will be back- as long as I can string together a few quid for the air fare!

The amazing Amazonian sunset

The amazing Amazonian sunset

Rosie Brian

The University of Nottingham

@dodgy_biology

The Start of my PhD: Take 2

The week before my return date I was a nervous wreck.

I thought to myself: “I need to get psychologically and physically prepared”, so I made myself a first-week plan as well as a plan for the subsequent 3 months. However, when I revisited this, I realised, as per usual, I was extremely optimistic and my first week could have easily been a months work. Thursday evening of the week before quickly arrived, and I received a phone call from my supervisor setting a meeting for Monday. This call really lifted me and I was very excited.

Unfortunately, this feeling didn’t last very long, and by Sunday I became very nervous again. As always, my Mum knew exactly what to say to calm me down. She told me nothing is in my control tomorrow and the only thing I can do is go in with a positive mind, so I did. This was important, as I really dislike not being in control of my life, but for me finding the courage to let go of the things that I cannot change has been a massive achievement.

Monday16th of November 2015: the day that I have been waiting for, for what seemed like an eternity. I woke up at 6am for a 10.30am meeting, which is the earliest time I have seen in a very long while. The commute was different from usual; road layouts had changed and I feared I did not know the way despite travelling to Kingston for over 4 years. The mind games had truly kicked in. After an hour drive came the task of finding a parking space, at which point I was so fatigued i did not know how I was going to get through the day.

As I entered the University I was feeling extremely overwhelmed. A lot had changed since I was last here in the summer (just 4 months ago). There was a new shop in reception, the canteen had been refurbished and there was a lot of new faces. I walked into my supervisor’s office and it was the first time in a long while that I thought things are going to be ok, especially after a good cup of tea.

I know a lot of PhD students have problems with their supervisor. Some may have reduced contact with their supervisor or at the other end of the scale, have an overbearing supervisor. I have been so lucky to have a supervisor like mine, he has been so understanding and at no point did I feel pressurised to return. I have just felt supported throughout a very hard time.

During this meeting my second supervisor and Lab Manger were present and it was agreed that I should have a phased return to work. It was decided that I would start back with a two-day week and, to my surprise, I would not start any lab work until January. That was my first-week lab plan and my monthly plans down the drain…

So what was the plan? I would produce a review paper to ease me back into to the scientific field with a publication aim date for the end of December. I was devastated to not be able to go in the lab but realised, this was the best option for my recovery and I could focus on something and get myself ready for January.

I would like to thank everyone for their support and cooperation, especially my supervisor and lab manager. I always set myself high expectations but sometimes, the reality is that I am not ready. I suppose I better get writing…

writing-cartoon1

Lucky Cullen

Kingston University

@LuckyCullen

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

@devoncaira

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

@LuckyCullen

 

When do you start saying no?

In my first year I said yes to everything. I began my PhD with the attitude that I would say yes to as many opportunities as I could, even if those opportunities scared me. Without knowing for sure what I want to do at the end of my PhD I felt (and was repeatedly told by the internet) that I had to acquire every skill, for every possible job, before I finished. Ok internet, challenge accepted. I got a position as a post-grad blogger for my University and eventually added my own personal blog to the mix. I maintained (and still do) my status as a Registered Scientist with the Royal Society of Biology, completing a minimum of 50 continuing professional development (CPD) points per year. I’ve attended and presented at conferences. I put myself forward as the PhD representative for my department’s Athena Swan working group. I became (and still am) a PhD tutor with the Brilliant Club. I demonstrate on several different undergraduate units within my department. I agreed to speak to the new intake of PhD students and share my experiences of PhD life so far. I take part in open days, doing outreach work both within the University and by going into schools. I made myself known as someone who’s willing to do these things, and as a result more of these opportunities came my way. I acquired a lot of very useful skills for my CV, the most important of these to me was the development of my writing and public speaking skills. Science communication is something I love and hope to pursue one day.

People started to ask how I managed to fit it all in, I don’t know I just made it work, and I enjoyed (and still enjoy) all the things I do. I’m not one of the magical people you see who seem to juggle everything beautifully, although thinking about it probably looks to other people like I have it all together. You might even think I am one of those people, and that just shows you that no one has it more together than you, you just think they do…

Credit: ErrantScience.com

Credit: ErrantScience.com

Earlier this year everything happened at the same time. My boyfriend and I bought our first house :), he had a knee operation :(, I was demonstrating for undergraduates and teaching two different Brilliant Club courses to two different age groups (they were short of a tutor and I stepped in to teach a maths course). I had to work a lot of Saturdays to keep up my lab work, and also had extra things to do at home as my boyfriend was on crutches. I kept going, and I managed to get it all done, but I decided then that I couldn’t keep saying yes to everything. My PhD and my work/life balance were suffering. Luckily with the summer coming up, everything naturally calmed down and I had a little room to re-group. Towards the end of the summer, as things began to pick back up, it was time to try saying no. I had a busy month in September with a conference, a presentation to give and I was also an invited speaker at an event as the result of my personal blog. The Brilliant Club didn’t have a Leicester (where I attend University) based school for me so I accepted a demonstrating opportunity with the University instead, but then a tutor dropped out. My first no was going to have to be to the Brilliant Club :(. It wasn’t easy, but I was professional and polite. My programme officer was understanding and appreciated the alternative offer I put forward of working with this school next term if no other tutor could be found. Basically I said no and they got it, they understood, and they didn’t chuck me out :).

Over the summer I was also asked by Devon and Stewart if I wanted to be a sub-admin on the BioSci PhD forum, I’d said I was interested earlier in the year but didn’t get round to applying before the deadline. I was flattered to be asked when a position came up and took some time to think it over. The chance to be involved with the forum was something I really wanted, but I also only wanted to do it well. It wasn’t something I wanted to half-arse. After talking it through with my boyfriend, we decided together that if I was going to do this something else would have to go. This was the start of my current “one-in, one-out” policy. Now, if I’m thinking about taking on something new, I assess it in the context of what I’m already doing. I said no to be a sub-admin, and Devon and Stewart couldn’t have been nicer about it. Instead they asked if I’d like to blog for them. This was a commitment I could fit in with what I already do, and here I am blogging away :). Saying no didn’t close a door for me, instead it opened the one next to it, the one that fit best with all my other open doors. Once again my decision to say no was respected and appreciated, and it lead to an opportunity I didn’t even know was out there.

Now I’ve learnt to say no without feeling (as) guilty, I have a better balance. At first I worried I was throwing away a lot of the hard work I’d put in early on, but experience has shown me that the relationships I’ve already built will, and do, continue to provide me with the chance to develop all the skills I hope to. If chances come your way I’d encourage you to take them, don’t say no just because you’re scared but please don’t feel guilty about turning some things down, it might even lead to something better.

 

Megan De Ste Croix

The University of Leicester

@MeganDSC