Pakinee Thianheng

Exploring the native pulp and paper sludge microbiome to inspire new biotechnologies for waste minimization. Thianheng P, Schroeter KL, Larsbrink J, McKee LS. Microbiology Spectrum (2026)

Being a successful PhD student is not only about being able to conduct hands-on experiments, but communication and sharing new knowledge to others is equally important. One of the most important ways to do this is through publishing scientific articles.

Until now, I was mostly familiar with research articles as a reader, and I had been a co-author on some papers before my PhD. This time, however, I had to write about my own research as the first author, which turns out to be a big task and a big responsibility. When reading other people’s papers, it often seems straightforward. They just described what they did, what they discovered, and how their findings compared with previous studies – easy! However, when it came to write my own manuscript, I realised it was far from easy. I had to spend a great deal of time organising my thoughts and figuring out how to communicate them clearly and effectively.

Here, I am proud to share my first research article, entitled “Exploring the native pulp and paper sludge microbiome to inspire new biotechnologies for waste minimisation”, published in the ASM journal Microbiology Spectrum. In general, research articles are written in an academic style. If you are not familiar with this field, you may find some sections difficult to follow, particularly those involving specialised concepts in biochemistry. Don’t worry! I would like to take this opportunity to explain my work once again in a more accessible language. I would like to highlight what my team and I did and the significance of the discoveries we made.

My PhD project focuses on waste minimisation for the pulp and paper industry. Every year, the pulp and paper industry in Sweden produces many thousands of tonnes of sludge waste. Most of this waste is sent to landfill. On the surface, this seems like a simple solution, just bury the waste underground and move on. In reality, however, sending sludge waste to landfill is not the best solution anymore.

This sludge contains leftover chemicals from paper and cardboard manufacturing, especially heavy metals such as iron and aluminium. When the waste is buried underground or left to stand out on the soil in big piles, these chemicals can slowly leak into groundwater and cause environmental damage. Moreover, sludge is persistent in nature. It breaks down very slowly in landfills. Consequently, the company needs to pay for monitoring metal leakage until the sludge will be completely decomposed. Furthermore, there is a tax on waste sent to landfills in Sweden. This means that the company needs to pay tax for sludge they sent to landfill. With many thousands of tonnes of this waste, the tax is not cheap. Overall, landfill is very expensive. Instead of spending money on landfill to store the waste underground, why don’t we find a better solution that actively reduces this waste, and invest in developing treatment technologies? As a PhD student with a microbiology and biochemistry background, I proposed using microbial treatment to break down sludge waste, which is a better solution than landfills. I hope that we can use microbes to reduce the volume of the waste, so that less needs to be stored

In nature, microorganisms exist as complex communities that interact with one another. This is well-studied in a lot of natural ecosystems, but man-made or human-influenced environments like industrial waste are not as well studied. In the samples we collected, using DNA sequencing, I discovered diverse bacterial and fungal communities were present in the sludge. However, those bacteria and fungi in sludge are obviously not highly active in degrading sludge under the storage conditions used by industry. To enhance their activity, I developed some simple enrichment strategies that stimulated their growth and metabolic functions. Once activated, these microorganisms began producing fibre-degrading enzymes. Enzymes are natural biological catalysts that break down complex materials into simpler compounds. In this case, the enzymes helped to degrade fibre components within the sludge. After fibre clean-up, the overall volume of sludge was reduced, quite significantly in some cases. If you imagine applying this idea at scale, this can result in the minimisation of sludge sent to landfills. In my article, you can find out what those bacteria and fungi were, how I was able to enhance them to grow in the metal-rich sludge, and how successfully I could remove the low-quality fibres.

Although many bacteria and fungi were enriched to be active, it is still a mystery what fibre-degrading enzymes they used. As we tested in the article, existing enzyme cocktails that are good at breaking down other kinds of biomass are not good at breaking down this particular sludge, so I believe that the enzymes in my sludge community might be quite special. In ongoing research, I am using metagenomics and metatranscriptomics to reveal what enzymes the microbes produced and secreted to break down the fibres. This discovery will be published in future articles during the next stage of my PhD. You can follow my future publications on my ResearchGate profile. I have been joined by some master’s students in the enzyme characterisation work, so this project has also given me a lot of supervision experience.

Finally, this writing experience has taught me that publishing a scientific article is not easy, especially for a first-time lead author. However, it is not impossible. It just requires time, effort, perseverance, and attention to details. After seeing my first article get accepted and published, it fills me with both happiness and pride to reflect on what I have accomplished. Moreover, it gives me confidence in my abilities as a researcher and inspired me to begin writing my next research paper, with the hope of contributing even more to the field in the future. Stay tuned!

When I just started my PhD in 2023, I was very excited to be surrounded by a new environment, new systems, new people, and, most importantly, to enter my new role as a PhD student. I had a lot of fun in the first months with several trips, social activities, and also learning new things. However, there has always been one thing that I have never felt comfortable with, even before my PhD started. I never enjoyed any task that involved giving a presentation in front of a group of people. I am kind of a nervous person when I have to give an oral presentation and feel many eyes staring at me.

One of the presentations I was most nervous for was the half-time evaluation seminar that all PhD students at KTH CBH School must do after completing half of their PhD work. The goal of having a half-time seminar is to reflect on what I have done over the past two years such as how many course credits I have completed so far, how much I have progressed on my research, and importantly to see if I will be able to successfully exit the PhD programme on-time as a graduated student (of course, I don’t plan to quit the PhD).

Pakinee at a WWSC conference event in 2025.

As we have a 4-year PhD programme at KTH, most of us present their half-time seminar after about two years. It is undeniable that time flies so fast… Suddenly, somehow, two years have already passed since I arrived in Stockholm, and the time for my half-time evaluation was knocking at the door. While preparing for my evaluation, I had the chance to pause and reflect on myself. I found that two years in the PhD role was changing me. No, no, don’t worry! I don’t mean that it made me bipolar or gave me depression… In contrast, this role shaped my strength and made me more mature in my character. For example, I feel more comfortable to communicate openly, especially in sharing my opinion and seeking for help when I have a problem. Moreover, I feel more confident in giving presentations such as at Glycoclub, which is our every-Friday group meeting, because I have received warm support from friends, colleagues, and my supervisor.

In addition to changing in my character, two years of working as a PhD student have changed my way of thinking as well. For example, I no longer see scientific publications as just a cool thing I can achieve. Instead, I recognise that the outcomes of my work can provoke promising new applications that have a meaningful impact on the environment and society. Moreover, I also stopped viewing myself as just a pair of hands in the lab producing data day after day; I began to see that I could teach and transfer my knowledge during teaching and supervision of other students, and I could inspire younger generations interested in science. Because I work alongside other PhD students and have attended a few conferences, I can also see myself as a member of scientific community, which starts to feel really good.

After this reflection on myself, I also took time to properly reflect on my research. When you are busy doing experiments and trying to keep up with many deadlines, it is easy to be so focussed on the details that you forget the big picture. I realised that I have produced good results in my research, and it was definitely enough for the half-time presentation. So, my results were ready to be evaluated…but I myself was not. I didn’t want to believe that I had already finished my second year, and I was going to become a third-year PhD student. There are many things I still want to do and things I want to learn, and just two years left seems not enough. I realised that I had planned to take too many course credits, and I will have to cut some of them out to make sure I have time for my research. But this contrasts with my feeling that I still want to take more courses and gain more new knowledge!

While preparing the 10-page report and 30-min presentation for the half-time evaluation, honestly, I felt tired and a bit stressed about having to do it, and I knew I didn’t want to embarrass myself. It was going to be a big day for me and my supervisor. I needed to prepare well and push myself to get through it. I thought to myself, how can I reach my defence and achieve an academic position in the future if I already feel so frustrated with this half-time seminar! With that feeling, I jumped out of bed, turned on my laptop, and started writing.

On the day of the seminar, I was happy to see many familiar faces from the Glycoscience and Industrial Biotechnology groups. I felt a lot of support from the audience and I felt happy that many people were interested to listen to my talk. Well, I started my presentation with less nervousness than usual. I was surprised that I actually presented better than when I had practiced at home. Although I had less nerves than I expected, the 30-min speaking time still felt like an eternity. I now truly understand how tiring it must be for teachers who give a two-hour lecture… After finishing the presentation, the evaluators were kind and asked reasonable questions. They were both professors from other departments at KTH, with expertise in sequencing technologies and polymer recycling. Most of their questions focused on the challenge of designing industrial applications and how my work is relevant to address current issues of waste disposal in the Swedish pulp and paper industry. Their questions emphasised that what I was doing is something valuable and meaningful. Furthermore, some questions were very useful to help me identify gaps I missed or I hadn’t noticed before.

After the presentation and Q&A session, it was a time for evaluation, so the audience was asked to leave the room. There was only me, my co-supervisors, the two opponents, a director of third-cycle studies, and of course, my awesome supervisor. Alone in the room with them, I felt like there was a group of grey clouds flying around me and above my head. I totally had no clue what would come next… But then the clouds start fading away when one of the opponents said my Individual Study Plan (ISP) was the best that she has ever seen. It felt like the sun came out and I could relax again. Next, the director of third-cycle studies said the overview of my PhD project was great and made her understand easily what I was doing. These words felt like a huge compliment that killed the anxiety I felt before. During the evaluation, there were no more questions about my academic knowledge or my research. We mostly talked and discussed about my study plan, the structure of supervision I receive from Lauren, and my ability to handle the work still to come and to achieve the PhD. In the end, I got evaluated to pass the half-time. What a relief!

After my half-time evaluation, I felt proud of myself. I go through something that I wasn’t looking forward to, and I did it better than I expected. From this, I learn that I should not underestimate myself and I should be more confident in my ability to perform. Undeniably, I now accept I am a third year PhD student. Time is running out. I must do what I still need to do to create myself as a potential researcher that others would want to hire and work with in the future. There is still so much I want to learn but now I can see more clearly what the next two years will look like, and I can see the progress I have made already. My next milestones for this year are finishing some more courses, supervising a project student, and submitting my first research paper to a journal. I’m feeling hopeful for the next two years but I am really glad that the half-time evaluation is over now!!