Category: Lab

I am happy to share the news that my first doctoral student – Emil Burman – successfully defended his thesis yesterday, and can now introduce himself as Dr. Burman.

And in what a way he defended! During the three hour defense, he was asked all the hard questions from his opponent – Akos Kovács – who did an amazing job bringing out Emil’s vast and diverse knowledge of the field. In fact, the committee noted afterwards that it took more than one and a half hours of questioning before Emil had to admit “I don’t know the answer to that”.

Emil’s thesis, titled “Genetic Contributions to Invasion and Biofilm Disruption in a Microbial Model Community“, used the microbial model community THOR (1) to investigate community responses to environmental stress and microbial invasion. The thesis (2) consists of five papers, the first dealing with how temperature affects THOR (3), the second with how pathogenicity is related to competition ability in a community setting, the third about the genetic determinants of antibiotic susceptibility in Pseudomonas aeruginosa, the fourth about invasion with P. aeruginosa into THOR, and the last one is a proteomics study about one of the strongest hits in paper IV.

Emil has used a range of techniques, including traditional microbiological assays, transposon mutagenesis (INSeq), and proteomics, to identify genetic determinants of community stability and disruption. This has allowed him to explore how cooperative traits emerge and how pathogens like Pseudomonas aeruginosa interfere with community dynamics. His thesis can be found in an online version here.

References

1. Lozano GL, Bravo JI, Garavito Diago MF, Park HB, Hurley A, Peterson SB, Stabb EV, Crawford JM, Broderick NA, Handelsman J: Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. mBio, 10, 2, e02846-18 (2019). doi: 10.1128/mBio.02846-18
2. Burman E: Genetic Contributions to Invasion and Biofilm Disruption in a Microbial Model Community. PhD Thesis, University of Gothenburg (2025). https://gupea.ub.gu.se/handle/2077/87262
3. Burman E, Bengtsson-Palme J: Microbial community interactions are sensitive to small differences in temperature. Frontiers in Microbiology, 12, 672910 (2021). doi: 10.3389/fmicb.2021.672910

Over the last week, I have been featured in media in different ways, so here’s a quick summary.

I was asked to provide a comment on a recent paper on how microplastics affect antibiotic resistance development (1) for an article in Scientific American (2). I am not sure I had that much intelligent to say, other than to caution about jumping to conclusions, as we still know quite little about the risks associated with microplastics and AMR: “How much of a threat plastic-derived drug-resistant pathogens pose to humans is a question that remains to be fully understood” is one of my two quotes from the article.

I also was interviewed last week for Swedish Radio’s Vetenskapsradion (in Swedish) about another study showing that, e.g., ibuprofen could drive bacteria to higher mutation rates, indirectly triggering antibiotic resistance development (3). Such interaction effects have also been seen elsewhere (4), but the fact that they see this effect for such a commonly used drug as ibuprofen – one of our most standard painkillers – is a little bit concerning. Still I stress in the interview that we need to know much more about these interaction effects before jumping to clinical guidance.

Finally, the Foundation for Strategic Research has released the video they recorded about our research last fall. It is in Swedish, but with English subtitles, so this could be worth a watch!

References

1. Gross N, Muhvich J, Ching C, Gomez B, Horvath E,Nahum Y, Zaman MH: Effects of microplastic concentration, composition, and size on Escherichia coli biofilm-associated antimicrobial resistance. Appl Environ Microbiol, 91, e02282-24, (2025). https://doi.org/10.1128/aem.02282-24
2. Zaraska M: Microplastics Could Be Turning Bacteria into Drug-Resistant Superbugs. Scientific American, 2025-08-26. https://www.scientificamerican.com/article/microplastics-could-be-creating-dangerous-antibiotic-resistant-bacteria/
3. Chen H, Sapula SA, Turnidge J, et al.: The effect of commonly used non-antibiotic medications on antimicrobial resistance development in Escherichia coli. npj Antimicrob Resist 3, 73 (2025). https://doi.org/10.1038/s44259-025-00144-w
4. Maier L, Pruteanu M, Kuhn M, et al.: Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555, 623–628 (2018). https://doi.org/10.1038/nature25979

This spring and summer have seen some changes to the composition of the research group, with people both coming and going. First of all, we have said goodbye to two postdocs who have worked in the lab for quite some time – Máté Vass and Daniel Jaén Luchoro. Máté is moving on to a position in Uppsala, at the Swedish University of Agriculture where he will start building up his own research group. Daniel is returning to a full time position at the Sahlgrenska Hospital, where he will keep doing part-time research. We look forward to keeping on working with both of them in their new roles!

Furthermore, we also say goodbye and thank for their wonderful contributions to the lab our two master students: Emilia Valfridsson and Felix Blomfelt. Both will be greatly missed, and they have made very valuable contributions to the group’s work, which (hopefully…) will result in publications relatively soon!

Finally, we would like to extend a somewhat belated welcome to our new postdoc Yuselys Garcia-Martinez who joined us in January. Yuselys will be working in the SEARCHER project on discovering novel antibiotic resistance genes in environmental and animal microbiomes.

On a personal note, this is the first time some of my long-term lab members leave the lab, so this feels especially sad to me. At the same time, they are moving on to new exciting roles, and maintaining and developing these relationships will be an interesting continuation of my journey as a group leader.

I am very happy to welcome Agata Marchi back to the group as a PhD student! Agata was a master student in the group last year, doing a thesis focused on implementing a bioinformatic approach to identify differences between the genomes of host-associated and non host-associated strains of Pseudomonas aeruginosa. While one of her first tasks will be to complete this work and prepare it for publication, her doctoral studies will primarily be on the interactions between bacteria and between bacteria and host in the human microbiome and how these relate to complex diseases. She will focus on developing and applying machine learning methods to better understand this interplay.

I am – as the rest of the group – very happy to welcome Agata back to the lab!

Time is passing quickly, and I have not appropriately acknowledged the many newcomers we’ve had to the lab in the past couple of months. With this post I would like to say welcome to the lab to Máté Vass and Dani Jáen Luchoro (both postdocs), Jorge Agramont and Josue Mamani Jarro (doctoral students), as well as Nathália Abichabki (visiting doctoral student from Brazil)! Some of you have already spent a couple of months in the group and we very much enjoy having you here!

A week or so ago, we took this new lab picture with everyone (except for Lisa, who is in Amsterdam). I am very proud to be working with group of extremely talented, smart, funny and goodhearted people!

Very briefly, Dani will be working on updating the BacMet database as part of the BIOCIDE project, and shares his time between my group, Joakim Larsson‘s group and the Sahlgrenska hospital. Máté was recruited within the DDLS program and will work on inferring the metacommunity ecology of antibiotic resistance based on analysis of large-scale datasets. Jorge and Josue are part of the same SIDA-funded doctoral student exchange program with Bolivia and will work on different aspects of environmental antibiotic resistance and the spread of diarrheal pathogens through the environmental matrix. Nathália, finally, is working on understanding the tolerance mechanisms to antibiotics in Klebsiella pneumoniae.

All of you are very welcome to the group!

Some good news from the lab! Emil Burman today passed his halftime control, which means that we now can look forward to around more years of fun science together! We all congratulate Emil on this great achievement which marks an important milestone in the group, as Emil is the first of the PhD students who have reached it to this point!

I am very happy to share with you that our two doctoral students funded by the Wallenberg DDLS initiative have now started. One of them – Marcus Wenne – is already a well-known figure in the lab, as he has been with us as a master student and then as a bioinformatician for more than a year. The other student – Vi Varga – is a completely new face in the lab and just started yesterday.

Marcus will work in a project on global environmental AMR. He will also continue on his work on large-scale metagenomics to understand community dynamics and antibiotic resistance selection in microbial communities subjected to antibiotics selection. Marcus will work very closely to EMBARK and continue the important work we have done in that project over the next four years.

Vi will study responses of microbial communities to change, with a particular focus on comparative genomics and transcriptional approaches. We will link this to both community stability, pathogenesis and resistance to antibiotics, so this project involves a little bit of everything in terms of the lab’s research interests. Vi’s background is in comparative genomics and pathogenesis, so this seems to be the perfect mix to be able to carry out this project successfully!

Very welcome to the lab Marcus and Vi! We look forward to work with you for the next four years or so!

I am extremely happy to share the news that the Swedish Foundation for Strategic Research has selected me as one of 16 young research leaders to receive their 15 million SEK grant awarded to give newly established researchers with high scientific and pedagogical competence the opportunity to develop as research leaders.

This grant is one of the more prestigious grants for young researchers in Sweden that I know of and I am very honored and thankful, both towards the foundation and my research group who have made this possible, to receive this grant. In combination with the DDLS funding from the Wallenberg Foundation, this will provide the lab with some very nice opportunities to explore more far-reaching endeavors in the next couple of years, which sets the stage for a very exciting half-decade to come!

Finally, I am also happy to see (after my ten-years old criticism of the gender distributions of these grants) that the distribution of grants this year was approximately gender-equal (seven out of 16 recipient were women). This is a good sign for both future Swedish research and the trustworthiness of these grants themselves.

Our open doctoral student and postdoc positions closed over the weekend, and in total we had 110 applications, although some persons applied to more than one of the positions, bringing the total number of applicants down a bit. Still, this will be a lot of work for me. I will prioritize the postdoc position, as this had the fewest applications. So if you applied to one of the two PhD student positions, please give it some time.

A quick skimming of the applications shows that we have had extraordinary high quality of applications overall, although some of the applicants will be a bit too wet-lab oriented for these specific positions.

Thanks a lot for your interest in the lab’s work! I appreciate all of your efforts!

As I wrote a few days ago, I have now started my new position at Chalmers SysBio. This position is funded by the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS), which also funds PhD and postdoc positions. We are now announcing two doctoral student projects and one postdoc project within the DDLS program in my lab.

Common to all projects is that they will the use of large-scale data-driven approaches (including machine learning and (meta)genomic sequence analysis), high-throughput molecular methods and established theories developed for macro-organism ecology to understand biological phenomena. We are for all three positions looking for people with a background in bioinformatics, computational biology or programming. In all three cases, there will be at least some degree of analysis and interpretation of large-scale data from ongoing and future experiments and studies performed by the group and our collaborators. The positions are all part of the SciLifeLab national research school on data-driven life science, which the students and postdoc will be expected to actively participate in.

The postdoc and one of the doctoral students are expected to be involved in a project aiming to uncover interactions between the bacteria in microbiomes that are important for community stability and resilience to being colonized by pathogens. This project also seeks to unearth which environmental and genetic factors that are important determinants of bacterial invasiveness and community stability. The project tasks may include things like predicting genes involved in pathogenicity and other interactions from sequencing data, and performing large-scale screening for such genes in microbiomes.

The second doctoral student is expected to work in a project dealing with understanding and limiting the spread of antibiotic resistance through the environment, identifying genes involved in antibiotic resistance, defining the conditions that select for antibiotic resistance in different settings, and developing approaches for monitoring for antibiotic resistance in the environment. Specifically, the tasks involved in this project may be things like identifying risk environments for AMR, define potential novel antibiotic resistance genes, and building a platform for AMR monitoring data.

For all these three positions, there is some room for adapting the specific tasks of the projects to the background and requests of the recruited persons!

We are very excited to see your applications and to jointly build the next generation of data driven life scientist! Read more about the positions here.