My name is Johan Bengtsson-Palme. I am an assistant professor at the Division of Systems Biology at Chalmers University of Technology in Gothenburg and the Sahlgrenska Academy at University of Gothenburg, funded by the Wallenberg DDLS initiative. My research group works with data driven microbiology and microbial ecology, primarily focusing on investigating antibiotic resistance, pathogenesis and interactions in bacterial communities through large-scale experimental work, metagenomics and bioinformatics. I also have an interest in molecular taxonomy and improving the quality of reference databases. You can read more about our research interests here. To contact me, feel free to send an e-mail to my firstname.lastname@microbiology.se

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 have written an editorial piece for the Swedish Pathogens Portal in which I reflect a bit on the upcoming EU legislation requiring monitoring of AMR in major wastewater treatment plants (1). I also veer a bit into where environmental monitoring outside of sewage may play a role, using our review paper resulting from EMBARK as the starting point (2).

This is timed to coincide with the registration deadlines for two upcoming workshops on AMR surveillance in the environment; the first being the DDLS Symposium on Data-Driven Environmental Monitoring of Infectious Disease on 7th-8th October in Uppsala, which I have been part of organising. The second is a workshop organised by CARe in Gothenburg on 28th October on the theme of sewage surveillance of antibiotic resistance, focusing on the new EU requirements.

My hope is that you will be a bit provoked by this and come to one of these workshops to discuss AMR surveillance and where to go next!

1. Bengtsson-Palme J: Surveillance of antimicrobial resistance – flying blind or flying behind? The Swedish Pathogens Portal, Editorial (2024). doi: 10.17044/scilifelab.27045433 [Link]
2. Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquin-Diaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R: Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? Environment International, 178, 108089 (2023). doi: 10.1016/j.envint.2023.108089 [Paper link]

Together with Anna Székely, I have been working on the organization of a DDLS Symposium on Data-Driven Environmental Monitoring of Infectious Diseases on October 7 – 8, in Uppsala.

The symposium will focus on promoting and enhancing data-driven environmental assessment for infectious diseases (including antibiotic-resistant bacteria) across various settings using diverse approaches. We now invite submission of abstracts for short talks.

Deadline for abstract submission: 18 September 
Deadline to register to attend: 25 September –> REGISTER HERE! <– This includes abstract submission.

Link to more information and the PROGRAM

I hope to see all of you working with AMR in the environment in Uppsala in October!

Ákos Kovács had the brilliant idea of putting up a temporary resource for things you bring up in a talk that you can point people to. I did not do this before my talk at ISME today, but I thought the idea was so good, so here’s a summary and collection of my ISME short-talk on the EMBARK outcomes today:

• More information on EMBARK and its successor SEARCHER can be found on the project website, here: http://antimicrobialresistance.eu Importantly, this is a team effort over four years and I only touched on a few selected things
• Within the project we have looked at typical background levels of antibiotic resistance in the environment. We have already published some of these results (for qPCR abundances) in Abramova et al. 2023
• The average resistance gene in the average environment is present in ~1 in 1000 bacteria, but the variation between different genes is huge
• Depending on monitoring goal, different target genes are relevant to use. See this table adapted from Abramova et al. 2023:

• We have also tried to make different monitoring methods for environmental AMR comparable. Those mentioned in the talk were selective culturing for resistant bacteria, qPCR and shotgun metagenomics
• This data is not yet published, but overall we see relatively good correlation between qPCR and metagenomics. This is not true for all genes, though, and unfortunately neither qPCR nor metagenomics is always better than the other
• Culturing data is not very good at predicting specific antibiotic resistance gene abundances as the class level
• Finally, we have developed methods for discovering new types of ARGs, as seen in the ResFinderFG database: Gschwind et al. 2023
• We have also used these new methods to look at differences between established ARGs and latent ARGs in a variety of environments: Inda-Díaz et al. 2023
• Our ultimate goal in EMBARK would be to develop a modular framework for environmental monitoring of antibiotic resistance. You can read more about our thinking and goals in the review paper we published last year: Bengtsson-Palme et al. 2023

Last week, FEMS Microbes published our most recent work on the genomes of Escherichia coli in coastal marine sediments from the Helsingborg area in Sweden (1). Part of our sampled area was next to the discharge point of the city’s wastewater treatment plant (WWTP) effluent. We discovered that the E. coli population in these sediment is diverse, containing serotypes typically associated with both humans, livestock and other animals. We also found that virulence genes were more common among the isolates collected closer to the WWTP discharge site. Only one isolate was phenotypically antibiotic resistant, and carried corresponding tetracycline resistance genes on a plasmid. All isolates were halotolerant, growing at 3.5% NaCl. Since most isolates were also good at forming biofilm, this suggests that marine sediments can select for E. coli with increased survival properties and could be a potential reservoir for E. coli that could be spread to humans when the sediments are disturbed. Furthermore, the naturalisation of these E. coli questions it as an indicator for faecal contamination of marine sediments.

The paper is primarily the work of Isabel Erb, Carolina Suarez, and Catherine Paul at Lund University, and they have made a terrific job on this while I have mostly provided some input on the bioinformatics and genomics analyses. The study is a nice example of how genomics analysis could nuance monitoring for pathogens and antibiotic resistance in environments close to human activities. Since these sediments are also closely connected to humans in terms of exposure – the Helsingborg beach is in the neighbouring area – this highlight potential exposure routes for pathogens and antibiotic resistance (2).

The finding of a single antibiotic resistant isolate highlights the issue of comparing between different monitoring methods (2). While a single isolates might be consider a small number, it is really hard to compare if this is outside of the normal range of resistance (3) as measured by, e.g., qPCR. This further points to the importance of standardisation of antibiotic resistance monitoring in the environment, in a way that is both reliable, feasible and economic. That said, it also shows the potential in monitoring, for example, public beaches for pathogens and resistance, and how this could be used to better design and implement mitigation strategies, including the temporary closing of public beaches in contaminated areas. For this to work, however, a better knowledge of the background levels of resistance is required, as we have been working on in the EMBARK program.

References

1. Erb IK, Suarez C, Frank EM, Bengtsson-Palme J, Lindberg E, Paul CJ: Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance and antibiotic resistance to infer contamination or naturalisation. FEMS Microbes (advance article) xtae024 (2024). doi: 10.1093/femsmc/xtae024
2. Bengtsson-Palme J, Abramova A, Berendonk TU, Coelho LP, Forslund SK, Gschwind R, Heikinheimo A, Jarquin-Diaz VH, Khan AA, Klümper U, Löber U, Nekoro M, Osińska AD, Ugarcina Perovic S, Pitkänen T, Rødland EK, Ruppé E, Wasteson Y, Wester AL, Zahra R: Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs? Environment International, 178, 108089 (2023). doi: 10.1016/j.envint.2023.108089
3. Abramova A, Berendonk TU, Bengtsson-Palme J: A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments. Environment International, 178, 108084 (2023). doi: 10.1016/j.envint.2023.108084

First of all, I just want to do a last reminder of PhD student position in bioinformatics and artificial intelligence applied to antibiotic resistance with Erik Kristiansson as main supervisor that closes tomorrow. More info here!

Second, two of my best and dearest colleagues at University of Gothenburg – Kaisa Thorell and Åsa Sjöling – have open postdoc positions in molecular microbiology (with Åsa) and bacterial proteomics (with Kaisa). Both of these are great opportunities to work with fantastic people on exciting subjects, so you should check these out if you are looking for postdoc positions in microbiology, molecular biology or bioinformatics! There are only a few days left to apply for these positions, so go ahead and do it now!

Finally, I am again tooting our own horn with the postdoc in innovative approaches to antibiotic resistance monitoring (within the SEARCHER program) in my own group. More info here, deadline is on July 31 with interviews to take place in August.

As part of the SEARCHER program, we are now hiring a two-year postdoc to work with innovative approaches to antibiotic resistance monitoring. You can read more about the position here and at Chalmers’ job portal, but in short we are after a wet-lab postdoc who are willing to do field work and laboratory studies to identify novel antibiotic resistance genes.

Please do not send me your CV and application letter via e-mail, but apply through the Chalmers application portal. Sending your CV to me will not increase your changes. Only contact me about this position if you have actual, relevant questions about the position (as I will otherwise get lots of unwanted e-mails…) Those questions, I am happy to answer!

This paper came out just about the same time as the PhD position with Erik Kristiansson where I will be co-supervisor was announced, and I did not want to steal that thunder with another news item, but it is now time to highlight the fantastic work of Víctor Hugo Jarquín-Díaz on antibiotic resistance genes in the gut microbiomes of mice across a gradient of pure and hybrid genotypes in the European house mouse hybrid zone. This came out in mid-April in ISME Communications and presents the interesting hypothesis that hybridisation not only shapes bacterial communities, but also antibiotic resistance gene occurrences (1).

This study is based on 16S rRNA amplicon sequencing of gut bacteria in natural populations of house mice. From this we have predicted the antibiotic resistance gene composition in the microbiomes, and found a significant increase in the predicted antibiotic resistance gene richness in hybrid mice. In other words, more and different antibiotic resistance genes were found in the hybrid mice than in the non-hybridised individuals. We believe that this could be due to a disruption of the microbiome composition in hybrid mice. The aberrant microbiomes in hybrids represent less complex communities, potentially promoting selection for resistance.

It deserves to be mentioned that this is more of a pilot study, which we hope to follow up with a more proper study targeting the resistance genes in the mice microbiomes. That said, our work suggests that host genetic variation impacts the gut microbiome and antibiotic resistance gene, at least in mice. This raises further questions on how the mammalian host genetics impact antibiotic resistance carriage in bacteria via microbiome dynamics or interaction with the environment.

I am very happy to have been part of this EMBARK collaboration with the Sofia Forslund-Startceva and Emanuel Heitlinger labs! And I am especially thankful to Víctor who pulled off this very thought-inducing study!

Reference

1. Jarquín-Díaz VH, Ferreira SCM, Balard A, Ďureje Ľ, Macholán M, Piálek J, Bengtsson-Palme J, Kramer-Schadt S, Forslund-Startceva SK, Heitlinger E: Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice. ISME Communications, ycae053 (2024). doi: 10.1093/ismeco/ycae053 [Paper link]