Hey, so it’s been a while since I checked in with myself or paused to externalise my thoughts. It is the 3rd of September 2026, and I am 2 months into starting a postdoc on the oral microbiome. I have been busy! In this time period, I have learned how to do DNA extractions, successfully extracting and quantifying DNA from 50+ oral swabs; learned how to use and program Nextflow (game changer); moved back up to Dublin from Cavan; started an orchard (5 trees so far - 3 apple, 2 pear); and I even bought a dilapidated cottage over the road. This has been a lot to process and just to keep on top of - making sure I’ve added the correct enzymes in the correct protocol steps, keeping HR and solicitors happy with millions of emails and back and forth. Overall, it’s good. I’m happy to be busy and getting my ducks in a row. It’s certainly a change of pace from earlier this year, when I was broke and bedrotting in my parents’ house, looking for a job while finishing up the PhD.

I would be lying if I said it was all straightforward and carefree. There was a lot of stress and uncertainty baked into this transition. I tried to push back the resurfacing thoughts that the previous 5 years of my life dedicated to a PhD had been a waste of my life. Maybe I will make a Gantt chart of the number of jobs I applied to (it would be a lot of rejections), but thankfully it all seemed to come together around April, when I submitted my thesis and also got offered this job in the Dublin Dental University Hospital. The day after my PhD defence on the 10th June, a tiny dilapidated cottage near my parents’ farm went for auction online, and we got the winning bid. It seemed like, for the first time in 5 years, things were starting to work out for me.

Prior to getting this offer, I had probably entertained around 5 interviews - all microbiome or bioinformatics related - and had faced some tough rejections; with others, I knew in my gut it was a bad fit for me. I had almost given up on the thought of staying in microbiome science and was weeks away from booking a one-way flight to work in a cafe in some remote mountain town. A number of roles I was lukewarm about: for example, a bioinformatician role in a microbiology startup in London - it was just developing pipelines and moving data around - a role I was qualified for before ever completing a PhD. She asked me what I would be most excited to learn in the role. I said that I was interested in ML and LLMs in particular. Her face dropped, and she said that their data science team deals with all that. Oh, ok. I knew I would rather be doing the analysis and, you know, discovering new stuff rather than doing the bioinformatic plumbing. It was still a bummer, as the team was filled with young, dynamic and ambitious microbiologists, definitely an environment I’d enjoy being in. Another role was a postdoc in the University of Hawaii, coming up with new statistical methods to quantify fungi and other microbiome components. The project didn’t align 100% with me - I wasn’t exactly thrilled at the prospect of learning algebraic statistics and then having to further build on these theorems. I’m more into the trees than the wood. Hawaii, on the other hand, was of course novel and appealing. I churned myself up ruminating on “what if” and maybe I should have presented myself as more enthusiastic in the interview.

Anyway, life has a weird way of putting you exactly where you need to be. While I know I would thoroughly enjoy hiking some volcano at the weekend and the beach bum lifestyle, the truth is I am not built for heat or being isolated on an island 7,000 miles from my cat and dog, doing unique maths problems. I have access to a farm here and have a duty to the land and wildlife on my doorstep to try my best to sustain and evolve it. This summer has been my first real effort to extend my garden outside the polytunnel and plant permaculture roots. There’s so much to be done, but this small connection to nature - a tiny wild plot in a field in Cavan - brings me more joy and satisfaction than anything else. Maybe I should make a separate post about all the wildlife I’ve noticed here over the summer. Lots and lots of frogs!

This brings me to where I am now, working on oral samples. I feel blessed that I am specialised in metagenomics and can apply the techniques I’ve learned during the PhD to a new environment. We are looking for changes in microbiome composition on dysplasia lesions, which can sometimes progress to oral squamous cell carcinoma, compared to healthy controls or even the contralateral side of the mouth. The lab had previously done 16S and found that F. nucleatum is associated with these lesions, so I am excited to embark on a comprehensive shotgun discovery of the oral microbiome. I am curious what kind of bacteriophages are present in the mouth. Can I classify fungi there too? This project will certainly keep me busy. I almost have all the samples - over 100 - DNA extracted and organised to send away for sequencing, after which I will deploy Nextflow to extract MAGs and everything else. I am remaining positive and optimistic that there will be a markedly different microbial signature between the different grades of dysplastic samples and healthy controls. I’m sure Random Forest will be pivotal in this analysis. In the meantime, I’ve also signed up to do some talks on the Caudoviricetes work, I’m trying to squeeze as much analysis out of the Irish soil data to get another jumbo paper and feather in my cap, and I have to oversee “problem-based learning” sessions on organic chemistry and thermodynamics for first year dental students, so I have been revising bonding, hybridization and org chem nomenclature in the form of YouTube videos in my spare time. So this is my lot for now, got to hunker down and stay focused - publish some papers, save some money and expand my orchard.