Author: Johan

Welcome Vi and Marcus

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!

Einhorn SIGHT Award

It’s been a busy couple of days at the DDLS Annual Meeting, so I did not have the time to post about this exciting news yesterday, but it is very exciting nonetheless.

I have been selected by the board of the Royal Swedish Academy of Sciences as the 2022 recipient of the Einhorn SIGHT award. The award recognizes outstanding global health research work by young researchers in the context of low- and middle-income countries, and specifically I have been selected thanks to my “outstanding research and development of tools to limit the global challenge of infectious diseases and antibiotic resistance.”

In a global health context, what is particularly important in the coming years is improved access to clean water and sewage systems. In addition, we also need to develop data-driven systems that can be used to implement easy-to-handle, inexpensive early warning systems and risk models for antibiotic-resistant bacteria, which we hope will be the outcome of the EMBARK program.

Clearly, a large part of this is the result of the work the entire EMBARK team has put together in the past couple of years. Another big part has been the work I have done together with Joakim Larsson in the area of antibiotic resistance in the environment. I am deeply grateful both to Joakim and my EMBARK collaborators for their contributions towards this award. Science is a teamwork, and it is a bit of a pity that we celebrate individuals to the extent we do (even though the recognition of my contribution of course is nice for me personally). Thanks to everyone who have been involved over the years!

There will be an award ceremony at the Royal Academy of Sciences on November 22, as part of a very nice event on Global Health, with the theme ‘Food Safety in conflict’. You can read a short interview I did in relation to the award here.

In other notes, I was also selected as one of Clarivate as one of this year’s Highly Cited Researchers (for the third year in a row!) This is of course also exciting news, although the most important aspect of that is that it shows that the research we do is useful to others!

DDLS Talks

I will be giving talks on data driven life science – specifically on antibiotic resistance and pathogenicity – on two different events organised within the Data Driven Life Science program (DDLS) in the next month. First up is on the DDLS Annual Conference, coming up already next week (15-16 November). Here, I will give a talk on the evolution of pathogenicity, outlining some of our ongoing work towards finding novel virulence factors. There will also be talk from the other DDLS fellows, as well as Samuli Ripatti and Cecilia Clementi.

On-site registration closes on November 9 so make sure to grab one of the last spots at this exciting event! Register here – online attendance is also possible for those who don’t want to travel to Stockholm.

Then in December, I will be talking at the Data-driven Epidemiology and biology of infections Research Area Symposium in Gothenburg on how to predict the disease threats of the future. This symposium takes place in Gothenburg on December 7 to 8, but again online participation is also possible. Aside from me, Nicholas Croucher will talk about genomic surveillance data and bacterial epidemiology, Bill Hanage will talk about decisions in an imperfect world and Tove Fall will talk about dynamic disease surveillance. There will also be talks about the new DDLS fellows in epidemiology and infection biology, which is what I am perhaps most excited about: Thomas van Boeckel, Luisa Hugerth and Laura Carroll! It seems like registration has not yet opened for this event, but keep monitoring this site.

I look forward to see you at these events!

There is some hope for diversity in science

I became quite happy this morning while scanning though the new Chalmers recruitments for new assistant professors in the Area of Advance calls this year (unfortunately this news item went out only on the intranet for some reason, but I will recap with names for easy googling).

Out of 15 recruitments, 10 are women – that’s almost 70%, which must be regarded very positive in terms of gender balance at a university with a male-dominated faculty. Of the five men, only two seem to be of European background, with the other three being non-white from different cultural spheres. In the end, only two out of fifteen (<15%) are the “traditional” Swedish university type (white men) who dominate the Chalmers faculty today.

Well done with the recruitments, especially if these are also the best persons for the positions (which I assume they are given how hard these positions are to get!) Also, good luck to the new PIs, I have already spoken to two of them who will land at the same department as I am in, and I can’t wait to start working with these brilliant minds!

Here’s the complete list of recruitments:

  • Mathilde Luneau, Area of Advance Energy – Department of Chemistry and Chemical Engineering
  • Alexander Giovannitti, Area of Advance Material – Department of Chemistry and Chemical Engineering
  • Varun Chaudhary, Production Area of Advance – Department of Industrial and Materials Science
  • Maud Lanau, Sustainable Cities – Department of Architecture and Civil Engineering
  • Margaret Holme, Basic science – Department of Biology and Biological Engineering
  • Annikka Polster, Health Engineering Area of Advance – Department of Biology and Biological Engineering
  • Eszter Lakatos, Health Engineering Area of Advance – Department of Mathematical Sciences
  • Elena Pagnin, Information and Communication Technology Area of Advance – Department of Computer Science and Engineering
  • Ilaria Torre, Technology in Society – Department of Computer and science engineering
  • Kun Gao, Transport Area of Advance – Department of Architecture and Civil Engineering
  • Angela Grommet, Excellence Initiative Nano – Department of Chemistry and Chemical Engineering
  • Georgia Panopoulou, Basic Science – Department of Space, Earth and Environment
  • Hans Chen, Basic Science – Department of Space, Earth and Environment
  • Saara Matala, Technology in Society – Department of Technology Management and Economics
  • Nils Johan Engelsen, Excellence Initiative Nano – Department of Microtechnology and Nanoscience

September 2022 Pod: Environmental Antibiotic Resistance

Finally the lab podcast is back! In this episode Microbiology Lab Pod, the team (Johan Bengtsson-Palme, Emil Burman, Anna Abramova, Marcus Wenne, Mirjam Dannborg and Agata Marchi) discusses the environmental antibiotic resistance in anticipation of the EDAR conference coming up later this week!

The specific papers discussed in the pod are as follows:

  • Marcoleta, Andrés E., Patricio Arros, Macarena A. Varas, José Costa, Johanna Rojas-Salgado, Camilo Berríos-Pastén, Sofía Tapia-Fuentes, et al. “The Highly Diverse Antarctic Peninsula Soil Microbiota as a Source of Novel Resistance Genes.” Science of The Total Environment 810 (March 2022): 152003.
  • Yi, Xinzhu, Jie-Liang Liang, Jian-Qiang Su, Pu Jia, Jing-li Lu, Jin Zheng, Zhang Wang, et al. “Globally Distributed Mining-Impacted Environments Are Underexplored Hotspots of Multidrug Resistance Genes.” The ISME Journal 16, no. 9 (September 2022): 2099–2113.
  • Johnning, Anna, Erik Kristiansson, Jerker Fick, Birgitta Weijdegård, and DG Joakim Larsson. “Resistance Mutations in GyrA and ParC Are Common in Escherichia Communities of Both Fluoroquinolone-Polluted and Uncontaminated Aquatic Environments.” Frontiers in Microbiology 6 (2015): 1355.
  • Flach, Carl-Fredrik, Chandan Pal, Carl Johan Svensson, Erik Kristiansson, Marcus Östman, Johan Bengtsson-Palme, Mats Tysklind, and D. G. Joakim Larsson. “Does Antifouling Paint Select for Antibiotic Resistance?” The Science of the Total Environment 590–591 (July 15, 2017): 461–68.

The podcast was recorded on September 12, 2022. 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.

Published paper: The vaginal transcriptome

Last week, we published a paper which has been cooking for a long time. It is the result of years of hard work from particularly the first author – Tove Wikström – but also Sanna who did the bulk of the bioinformatic analysis with some help from me (well, I mostly contributed as a sounding board for ideas, but hopefully that was useful). The paper describes the gene expression of both the human host and the microbial community in the vagina during pregnancy and how the expressed genes (and the composition of bacteria) are linked to early births (1) and was published in Clinical and Translational Medicine.

We found 17 human genes potentially influencing preterm births. Most prominently the kallikrein genes (KLK2 and KLK3) and four different forms of of metallothioneins (MT1s) were higher in the preterm group than among fullterm women. These genes may be involved in inflammatory pathways associated with preterm birth.

We also found 11 bacterial species associated with preterm birth, but most of them had low occurrence and abundance. In contrary to some earlier studies, we saw no differences in bacterial diversity or richness between women who delivered preterm and women who delivered at term. Nor did Lactobacillus crispatus – often proposed to be protective against preterm birth (2,3) – seem to be a protective factor against preterm birth. However, most other studies have used DNA-based approaches to determine the bacterial community composition, while we used a metatranscriptomic approach looking at only expressed genes. In this context it is interesting that other metatranscriptomic results (4) agree with ours in that it was mainly microbes of low occurrence that differed between the preterm and term group.

Overall, the lack of clear differences in the transcriptionally active vaginal microbiome between women with term and preterm pregnancies, suggests that the metatranscriptome has a limited ability to serve as a diagnostic tool for identification of those at high risk for preterm delivery.

Great job Tove and the rest of the team! It was a pleasure working with all of you! The entire paper can be read here.


  1. Wikström T, Abrahamsson S, Bengtsson-Palme J, Ek CJ, Kuusela P, Rekabdar E, Lindgren P, Wennerholm UB, Jacobsson B, Valentin L, Hagberg H: Microbial and human transcriptome in vaginal fluid at midgestation: association with spontaneous preterm delivery. Clinical and Translational Medicine, 12, 9, e1023 (2022). doi: 10.1002/ctm2.1023 [Paper link]
  2. Kindinger LM, Bennett PR, Lee YS, et al.: The interaction between vaginal microbiota, cervical length, and vaginal progesterone treatment for preterm birth risk. Microbiome, 5, 1, 1-14 (2017).
  3. Tabatabaei N, Eren AM, Barreiro LB, et al.: Vaginal microbiome in early pregnancy and subsequent risk of spontaneous preterm birth: a case-control studyBJOG, 126, 3, 349-358 (2019).
  4. Fettweis JM, Serrano MG, Brooks JP, et al.: The vaginal microbiome and preterm birth. Nature Medicine, 25, 6, 1012-1021 (2019).

Opinion article in Swedish

Together with 1943 other Swedish scientists, I co-signed an opinion article in the Swedish newspaper Aftonbladet with the translated title “Enough, politicians – take climate change seriously“. In short, we argue that the facts have been on the table of many years, but little action has been undertaken. Compare the action taken against covid-19 to the dull inaction taken to address the climate crisis, and you may see where the frustration comes from. Action is still possible, but not if we refuse to acknowledge climate change as a problem. The piece ends with (my translation):

The situation is dire – the emissions continue to rise when they would need to be dramatically reduced. We now plead with all politicians in Sweden: put the climate crisis on the top of the agenda! Use the available scientific expertise; start by enacting the recommendations you have already got from the Climate council.

Treat the climate crisis as the acute and life changing crisis it is, and show political leadership!

The opinion piece can be read here (in Swedish)

Future Research Leaders

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.

Thanks for the applications

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!

We’re hiring 2 PhD students and a postdoc

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.