Tag: Marcus Wenne

I’ve been terribly bad at keeping updates on what we have published in the last year or so – there have just been a bit too much other things to do. So I thought it was time to take a look at what we have published in the last year before some really cool stuff hits the press this summer and fall (hopefully more on that soon!!)

Let’s start with some EMBARK/SEARCHER output. Several lab members (Anna, Marcus and I) have been involved in a paper using functional metagenomics to find novel cefiderocol resistance genes (1). We found four resistance genes, including three ꞵ-lactamases (VEB-3, an OXA-372 homolog, and a YbxI homolog) and a partial penicillin-binding protein homolog, none of which had been previously reported as a cefiderocol resistance gene. The blaVEB-3 gene was associated with a mobile genetic element. We could find three of them using shotgun metagenomics, showing that the blaVEB-3 gene was widespread across France, Sweden, Germany and Pakistan, hinting at efficient dissemination of this gene.

I have also been involved in a collaboration paper with Thomas Berendonk and Uli Klümper‘s labs, where we investigate if fish can be sentinels of environmental antibiotic resistance, and it turns out that they are… not great for that (2).

On the topic of antibiotic resistance gene (ARG) dissemination, Máté Vass (now at SLU) lead a study published in Communications Biology investigating how water stratification affects horizontal gene transfer, with a focus on ARGs (3). The main finding of this paper is that water stratification is a constraint on horizontal gene transfer, which may have implications on how we think about ARG spread through water environments.

While we are at the topic of large-scale quantifications of ARGs in big data sets, I was super-happy to be part of a collaboration with Katariina Pärnänen on how gender (and other factors) impact ARGs in the human microbiome (4). I kept telling Katariina that this would probably yield nothing – the microbiome data was too noisy, and the signal will get lost. Yet, she persisted, and indeed it turned out we are at the point where there is enough human microbiome data to get a signal even if there is a lot of noise. So hats off to Katariina, this was your “what did I say” moment with me!

Then we have a set of mechanistic AMR studies on ARG evolution. First, Lisa Teichmann published parts of her PhD thesis, first on the gradual evolution of fluoroquinolone resistance in E. coli (5) and how this is related to the SOS response in bacteria. She then followed up with a somewhat similar paper on amoxicillin evolution in E. coli (6). The general picture of these two papers on how E. coli adapts genetically to antibiotic stress is that resistance evolution is highly antibiotic-specific and that canonical stress-response or mutagenic pathways do not uniformly explain adaptive trajectories.

Somewhat connected, Nathália Abichabki recently published a paper where we propose screening cut-off values and tolerance disk tests (TDtests) for detection of tolerance/persistence to ceftazidime-avibactam in Klebsiella pneumoniae (7). This is also related to a bunch of papers on tolerance and low-level resistance to antibiotics that will be coming out of Nathália’s thesis, so there is more coming on this front soon!

Finally – on the AMR front – Anna Abramova led an effort together with Veronika Pettersen to investigate possibility for integration of AMR surveillance systems in the Nordic countries that recently got published in Public Health (8). Anna and Veronika did a huge amount of work on this paper, but this was largely the outcome of several meetings on the NoMoReAMR consortium, where we pinpointed missed opportunities for surveillance in the otherwise relatively homogenous Nordic countries. I hope to get to work more with this consortium in the future, as I think that we have had very fruitful discussions on both AMR research and monitoring and when and where it is useful.

And so two papers not related to AMR: We had a very nice collaboration with Daniel Bojar‘s group coming out late last year in Nature Communications, looking – from many different angles – at seal milk oligosaccharides and their potential uses. While the cool finding in this paper is that seal milk seems even more complex than human breast milk in terms of milk oligosaccharides (9), we did not contribute too much in that part. Instead, Mirjam Dannborg was studying the effects of these oligosaccharides on pathogen biofilms, work that will also be part of her PhD thesis when she defends this fall!

Finally, in a collaboration with colleagues in Brazil, we published a review article on the outlook for combining 3D organoid cultures and high-throughput analysis techniques to better understand host-pathogen interactions (10). This was the result of a cross-visit collaboration between Brazil and Sweden, where me and Mirjam visited the lab of Elaine de Martinis, and Elaine, Leonardo Andrade and Nathália Abichabki visited our lab back in 2023. It’s nice to see our discussions take paper form and I hope to be working more with this wonderful team in Brazil!

Papers mentioned:

1. Gschwind R, Bonnet M, Abramova A, Jarquín-Díaz VH, Wenne M, Löber U, Godron N, Kampouris ID, Tskhay F, Nahid F, Debroucker C, Bui-Hai M, El Aiba I, Klümper U, Berendonk TU, Forslund-Startceva SK, Zahra R, Bengtsson-Palme J, Ruppé E: Cefiderocol resistance genes identified in environmental samples using functional metagenomics. ISME Journal, 20, 1, wrag010 (2026). doi: 10.1093/ismejo/wrag010 [Paper link]
2. Tskhay F, Köbsch C, Elena AX, Bengtsson-Palme J, Berendonk TU, Klümper U: Fish are poor sentinels for surveillance of riverine antimicrobial resistance. One Health, 20, 101026 (2025). doi: 10.1016/j.onehlt.2025.101026 [Paper link]
3. Vass M, Abramova A, Bengtsson-Palme J: Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters. Communications Biology, 9, 435 (2026). doi: 10.1038/s42003-026-09857-8 [Paper link]
4. Salehi M, Laitinen V, Bhanushali S, Bengtsson-Palme J, Collignon P, Beggs JJ, Pärnänen K, Lahti L: Gender differences in global antimicrobial resistance. npj Biofilms and Microbiomes, 11, 79 (2025). doi: 10.1038/s41522-025-00715-9 [Paper link]
5. Teichmann L, Luitwieler SH, Bengtsson-Palme J, ter Kuile BH: Fluoroquinolone-specific resistance trajectories in E. coli and their dependence on the SOS-response. BMC Microbiology, 27, 37 (2025). doi: 10.1186/s12866-025-03771-5 [Paper link]
6. Teichmann L, Wenne M, Luitweiler S, Dugar G, Bengtsson-Palme J, ter Kuile B: Genetic Adaptation to Amoxicillin in Escherichia coli: The Limited Role of dinB and katE. PLoS ONE, 20, 2, e0312223 (2025). doi: 10.1371/journal.pone.0312223 [Paper link]
7. Abichabki N, Bellissimo-Rodrigues F, Gaspar GG, Pocente RHC, Lima DAFS, Bollela VR, Braga GUL, De Martinis ECP, Ferreira JC, Darini ALC, Bengtsson-Palme J, Andrade LN: Proposal for screening cut-off values and use of Tolerance Disk Test (TDtest) for detection of tolerance/persistence to ceftazidime-avibactam in Klebsiella pneumoniae. Diagnostic Microbiology and Infectious Disease, 116, 3, 117515 (2026). doi: 10.1016/j.diagmicrobio.2026.117515 [Paper link]
8. Abramova A, Baral A, Osińska AD, Metsä-Simola N, Räisänen K, Ribeiro Duarte AS, Helgason KO, Halldórsdóttir AM, Pärnänen K, Skov Simonsen G, Sariola S, Lahti L, Bengtsson-Palme J, Wasteson Y, Munk P, Pettersen VK: Roadmap for integrated One Health AMR surveillance in Nordic countries. Public Health, 255, 106285 (2026). doi: 10.1016/j.puhe.2026.106285 [Paper link]
9. Jin C, Lundstrøm J, Cori CR, Guu S-Y, Bennett AR, Dannborg M, Bengtsson-Palme J, Hevey R, Khoo K-H, Bojar D: Seal milk oligosaccharides rival human milk complexity and exhibit functional dynamics during lactation. Nature Communications, 16, 10067 (2025). doi: 10.1038/s41467-025-66075-2 [Paper link]
10. de Martinis ECP, Alves VF, Pereira MG, Andrade LN, Abichabki N, Abramova A, Dannborg M, Bengtsson-Palme J: Applying 3D cultures and high-throughput technologies to study host-pathogen interactions. Frontiers in Immunology, 16 (2025). doi: 10.3389/fimmu.2025.1488699[Paper link]

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!

In this episode Microbiology Lab Pod, the team (Johan Bengtsson-Palme, Emil Burman, Anna Abramova, Marcus Wenne, Sebastian Wettersten and Mahbuba Lubna Akter, Shumaila Malik, Emilio Rudbeck and Camille Wuyts) discusses the evolution of antibiotic resistance from different perspectives. We also interview Rémi Gschwind about his work on novel antibiotic resistance genes in the EMBARK program.

The specific papers discussed in the pod (with approximate timings) are as follows:

• 7:45 – EMBARK website: http://antimicrobialresistance.eu
• 26:15 – Seemann, T., 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069. https://doi.org/10.1093/bioinformatics/btu153
• 29:00 – Bengtsson-Palme, J., Larsson, D.G.J., 2015. Antibiotic resistance genes in the environment: prioritizing risks. Nature reviews Microbiology 13, 396. https://doi.org/10.1038/nrmicro3399-c1
• 29:30 – Ebmeyer, S., Kristiansson, E., Larsson, D.G.J., 2021. A framework for identifying the recent origins of mobile antibiotic resistance genes. Communications Biology 4. https://doi.org/10.1038/s42003-020-01545-5
• 54:15 – Gillings, M.R., Stokes, H.W., 2012. Are humans increasing bacterial evolvability? Trends in Ecology & Evolution 27, 346–352. https://doi.org/10.1016/j.tree.2012.02.006
• 55:15 – Woods, L.C., et al., 2020. Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation. Proc Natl Acad Sci USA 117, 26868–26875. https://doi.org/10.1073/pnas.2005331117
• 76:15 – Card, K.J., Thomas, M.D., Graves, J.L., Barrick, J.E., Lenski, R.E., 2021. Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli. Proc Natl Acad Sci USA 118, e2016886118. https://doi.org/10.1073/pnas.2016886118

The podcast was recorded on March 18, 2021. If you want to reach out to us with comments, suggestions, or other feedback, please send an e-mail to podcast at microbiology dot se or contact @bengtssonpalme via Twitter. The music that can be heard on the pod is composed by Johan Bengtsson-Palme and is taken from the album Cafe Phonocratique.

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The Microbiology Lab Pod is back with season two. This first episode was recorded on February 4 and has the theme of global change and effects on microbes. The crew (Johan Bengtsson-Palme, Emil Burman, Anna Abramova, Marcus Wenne, Sebastian Wettersten and Mahbuba Lubna Akter) is joined by two guests – Shumaila Malik and Emilio Rudbeck – and talks about the lab’s most recent publication, the one-year covid anniversary, the effects of global warming and other global change factors on soil microbial communities, and thawing permafrost.

The specific papers discussed in the pod (with approximate timings) are as follows:

• 5:45 – Abramova, A., Osińska, A., Kunche, H., Burman, E., Bengtsson-Palme, J., 2021. CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data. Bioinformatics. https://doi.org/10.1093/bioinformatics/btaa1086
• 8:00 – Bengtsson, J., et al., 2011. Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie van Leeuwenhoek 100, 471–475. https://doi.org/10.1007/s10482-011-9598-6
• 29:30 – Donhauser, J., Niklaus, P.A., Rousk, J., Larose, C., Frey, B., 2020. Temperatures beyond the community optimum promote the dominance of heat-adapted, fast growing and stress resistant bacteria in alpine soils. Soil Biology and Biochemistry 148, 107873. https://doi.org/10.1016/j.soilbio.2020.107873
• 54:30 – Zhou, Z., Wang, C., Luo, Y., 2020. Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nat Commun 11, 3072. https://doi.org/10.1038/s41467-020-16881-7
• 60:45 – Bahram, M., et al., 2018. Structure and function of the global topsoil microbiome. Nature 320, 1039. https://doi.org/10.1038/s41586-018-0386-6
• 68:15 – Lozano, G.L., et al., 2019. Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. mBio 10. https://doi.org/10.1128/mBio.02846-18
• 70:15 – Bengtsson-Palme, J., 2020. Microbial model communities: To understand complexity, harness the power of simplicity. Computational and Structural Biotechnology Journal 18, 3987–4001. https://doi.org/10.1016/j.csbj.2020.11.043
• 72:00 – Sajjad, W., et al., 2020. Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? Science of The Total Environment 735, 139275. https://doi.org/10.1016/j.scitotenv.2020.139275
• 74:00 – Yashina, S., et al., 2012. Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost. Proceedings of the National Academy of Sciences 109, 4008–4013. https://doi.org/10.1073/pnas.1118386109
• 74:30 – Pikuta, E.V., et al., 2005. Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska. International Journal of Systematic and Evolutionary Microbiology 55, 473–478. https://doi.org/10.1099/ijs.0.63384-0
• 75:00 – Bidle, K.D., Lee, S., Marchant, D.R., Falkowski, P.G., 2007. Fossil genes and microbes in the oldest ice on Earth. Proceedings of the National Academy of Sciences 104, 13455–13460. https://doi.org/10.1073/pnas.0702196104
• 75:15 – Timofeev, V., et al., 2019. Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS ONE 14, e0209140. https://doi.org/10.1371/journal.pone.0209140
• 83:15 – Bengtsson-Palme, J., Boulund, F., Fick, J., Kristiansson, E., Larsson, D.G.J., 2014. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in microbiology 5, 648. https://doi.org/10.3389/fmicb.2014.00648
• 84:00 – Bengtsson-Palme, J., Larsson, D.G.J., 2015. Antibiotic resistance genes in the environment: prioritizing risks. Nature reviews Microbiology 13, 396. https://doi.org/10.1038/nrmicro3399-c1

The podcast was recorded on February 4, 2021. If you want to reach out to us with comments, suggestions, or other feedback, please send an e-mail to podcast at microbiology dot se or contact @bengtssonpalme via Twitter. The music that can be heard on the pod is composed by Johan Bengtsson-Palme and is taken from the album Cafe Phonocratique.

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The fall is here and with it comes the arrival of three new group members. This fall, we are joined by Mahbuba Lubna, Sebastian Wettersten and Marcus Wenne. All three are master students from the University of Gothenburg and they will work on very different things.

Mahbuba will work together with Emil Burman on genes responsible for invasion in microbial communities (primarily THOR), expanding on Emil’s work and testing new and existing candidate genes in a wider diversity of conditions.

Sebastian will work on improving Metaxa2, making its classifications better and also enabling even better automation of database creation. Hopefully this will increase the pace of the Metaxa2 development, which has been stagnating a bit over the last two years.

Marcus, finally, will work together with Anna Abramova on analysing antibiotic resistance in a huge metagenomic dataset previously generated in the lab.

This means that we are now seven people in the lab (so if it weren’t for the covid-associated work from home recommendations, it would start to get crowded…) We welcome our three new members and look forward to an exciting fall!