Welcome

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. 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. We work closely with the groups of Joakim Larsson, Jo Handelsman, Erik Kristiansson and Henrik Nilsson. To contact me, feel free to send an e-mail to my firstname.lastname@microbiology.se

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. https://doi.org/10.1016/j.scitotenv.2021.152003
  • 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. https://doi.org/10.1038/s41396-022-01258-z
  • 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. https://doi.org/10.3389/fmicb.2015.01355
  • 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. https://doi.org/10.1016/j.scitotenv.2017.01.213

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.

References

  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.

My first day at Chalmers

Today was a big day, as it was my first ‘real’ working day at SysBio at Chalmers University of Technology. (Quotation marks as I have had access to an office at SysBio for a few weeks, and also because I spend the afternoon on meetings at Sahlgrenska.) Regardless, this marks the start of a transition period where the lab will be moving more and more of our routines to Chalmers, which will culminate when the lab-dependent persons will move into our new labs after the summer.

We also welcomed our Erasmus intern Manuela Seehauser to the lab today, as well as Marius Surleac who is visiting us for a few weeks from Romania.

Finally, we have announced new positions related to my new Chalmers-funding. More on those soon. Speaking of jobs, if you’re interested in doing a bioinformatics postdoc with me and Joakim Larsson you have two more days to apply for that position!

Open postdoc position

Together with Joakim Larsson‘s lab, we now have an open two-year postdoc position in bioinformatics on antibiotic resistance and biocide resistance. The development of antibiotic resistance has been driven by use of antibiotics, but antibacterial biocides also have the potential to select for antibiotic resistance. However, knowledge of which genes that contribute to biocide resistance and could be associated with antibiotic resistance is sparse. To some extent, such genes are documented in the BacMet database which we have developed, but this collection of resistance genes is only scratching the surface of all biocide resistance that exists among bacteria in the environment.

We are now looking for a postdoctoral fellow to continue the important work on bioinformatic analysis of biocide and antibiotic resistance to answer the question whether increasing biocide resistance would be a threat to human health. The postdoc will be working with the development of the BacMet database to make it more targeted towards biocidal substances and products in addition to resistance genes. The tasks include bioinformatic sequence analysis, literature studies and database and web programming. The work will also include investigations of the prevalence of the identified resistance genes in genomes and metagenomes.

The recruited person will work closely with both my group and the group of Prof. Joakim Larsson, and will participate in the JPIAMR-funded BIOCIDE project. You can apply to the postdoc position at the University of Gothenburg application portal: https://web103.reachmee.com/ext/I005/1035/job?site=7&lang=UK&validator=9b89bead79bb7258ad55c8d75228e5b7&job_id=25122

The deadline is May 4, 2022. Come work with us on this exciting topic in the intersect between two great research environments (if I may say it myself!) We look forward to your application!

BIG NEWS: We’re moving to Chalmers

I have very big and exciting news to share with you. After more than 10 years at the Sahlgrenska Academy, me and my lab will be moving from the University of Gothenburg to Chalmers University of Technology (which is physically a move of less than a kilometer, so still within Gothenburg). I have been offered a position at the Division of Systems Biology, funded by the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS). The total funding to my lab will be 17 million SEK, with some co-funding from Chalmers added in on top of that.

I am of course very excited about this opportunity, which will bring some infrastructure that we need in-house that we don’t have easy access to today. At the same time, I am sad to leave my academic ‘home’, and the fantastic people we have been working with there for the years. I am also endlessly thankful for the support and trust that the Sahlgrenska Academy, the Institute of Biomedicine and the Department of Infectious Diseases have put into me and my research over the past years.

The transition to Chalmers will start already in May, but will be gradual and continue for a long time. We have close ties to the Sahlgrenska Academy and we will keep closely collaborating with researchers there. I will also retain an affiliation to the University of Gothenburg, at least for the near future.

All in all, this year will bring very interesting development, and this additional funding from the DDLS program will allow us to venture into new areas of bioinformatics and try out ideas that have previously been out of reach. I look forward to work with our new colleagues at Chalmers and within the DDLS program in the coming years!

Portrait on my research

As part of a series highlighting the research at the Institute of Biomedicine, I was a few weeks a go interviewed about the research in the lab and my history. This interview has now been published on the department website, both in Swedish and English. I think it is a pretty nice read and a good introduction to our work and why we do what we do. Could make for a good weekend read!