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

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]

Erik Kristiansson, who was co-supervisor for my PhD thesis, has an opening for a PhD student funded by the DDLS program. The project is combining bioinformatics and artificial intelligence with a focus on large-scale data analysis to better understand antibiotic resistance and the emergence of novel resistance genes. The research will be centered on DNA sequence analysis, inference in biological networks, and modelling of evolution. The primary applications will be related to antibiotic resistance and bacterial genomics.

I am particularly excited about this position because I will have the benefit of co-supervising the student. The student will also be part of the DDLS research school which is now being launched, which is also super-exciting for Swedish data driven life science.

The candidate is expected to have a degree in bioinformatics, mathematical statistics, mathematics, computer science, physics, molecular biology, or any equivalent topic. Previous experience in analysis of large-scale biological data is desirable. It is important to have good computing and programming skills (e.g. in Python and R), experience with the Linux/UNIX computer environment, and, to the extent possible, previous experience in working with machine learning and/or artificial intelligence.

I had such a good time with Erik as my co-supervisor, and he has put together a truly amazing supervision team with Joakim Larsson, Anna Johnning and myself. I could not imagine a better place to apply bioinformatics and ML/AI on antibiotic resistance! Deadline is June 7! Application link here: https://www.chalmers.se/om-chalmers/arbeta-hos-oss/lediga-tjanster/?rmpage=job&rmjob=12840&rmlang=SE

I have had the fortune to be involved in a study on the quality of reference material for mosquito barcoding for biodiversity studies. The study, which was led by Maurício Moraes Zenker at the Universidade Federal de São Carlos in Brazil, looked at the availability of public data for mosquitoes in online databases for two widely used DNA barcoding markers in Culicidae: the COI and ITS2 regions (1). Last week, this study was published in Scientific Reports.

The paper shows that around 30% of known species were covered for the COI gene in BOLD  and  GenBank, and 12% of species for ITS2 in GenBank. The Afrotropical, Australian and Oriental biogeographic regions had the lowest coverages, while the Nearctic, Palearctic and Oceanian regions had the highest. Countries with a higher diversity of mosquitoes tended to have lower coverage, which was surprisingly also the case for countries with higher numbers of medically important species. At the same time, countries with a higher number of endemic species tended to have a higher species coverage in the databases.

With this study, we would like to advocate for better curatorship of voucher specimens representing sequences in the databases. Also, an integrative taxonomic approach that combines various genetic markers with morphological analyses is important to allow a better use of DNA barcoding and metabarcoding in a diverse array of applications, including vector species detection and biodiversity monitoring.

Importantly, this work underscores how reliant DNA barcoding is on proper taxonomic foundations, including morphological characterisations. Molecular identification of species cannot happen in a vacuum! I would like to extend a big thanks for Maurício who invited me to take part in this study and who have done an excellent job putting it all together!

Reference

• Moraes Zenker M, Pineda Portella T, Costa Pessoa FA, Bengtsson-Palme J, Galetti PM: Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity. Scientific Reports, 14, 7432 (2024). doi: 10.1038/s41598-024-58071-1 [Paper link]

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!

My PhD supervisor Joakim Larsson has an opening for a PhD student at University of Gothenburg. The project is on the role of different wastewaters in the evolution of antibiotic resistance, and will be centered on bioinformatic analyses of large-scale data. The project will encompass analysis of bacterial growth curve data through machine learning to antibiotics with selective effects in different wastewaters. Comparative genomics and different AI-based approaches will be applied to large-scale public genome and metagenome data to better understand how resistance genes are mobilized and transferred to pathogens.

Joakim is a great scientist with a vibrant group, so if your interests is in line with the position, I strongly suggest you take a look at it! Deadline is October 30! Application link here: https://web103.reachmee.com/ext/I005/1035/job?site=7&lang=UK&validator=9b89bead79bb7258ad55c8d75228e5b7&job_id=30401

My colleague and friend Clemens Wittenbecher has an open doctoral student position at Chalmers in Data-Driven Precision Health Research. Clemens works with developing novel biomarker panels to quantify individual disease risk. The project itself will focus on innovative machine learning and artificial intelligence approaches to integrate multi-layer -omics data with bioimages of cardiovascular and metabolic tissues (computer tomography, ultrasound and magnetic resonance imaging).

Clemens is a fantastic person and a great supervisor so if your interests is in line with the position, I strongly suggest you take a look at it! Application link here:

https://www.chalmers.se/en/about-chalmers/work-with-us/vacancies/?rmpage=job&rmjob=11810&rmlang=UK

Time to do a rundown of conferences and meetings I will attend this fall. Double-check with your calendars and please reach out if you’re also going, so we can meet up!

September 21-24: Nordic Society of Clinical Microbiology and Infectious Diseases (NSCMID), in Örebro, Sweden. I will give a talk about the EMBARK work in the Saturday session on Metagenomics in infection, inflammatory disease and the environment

October 5-6: Conference on ‘Optimal practices to protect human health care from antimicrobial resistance selected in the veterinary domain’ organised by The Netherlands Food and Consumer Product Safety Authority (NVWA) in Amsterdam, the Netherlands. I will chair a session on October 6 on Next generation sequencing for bioinformatic based surveillance.

October 18-22: 32º Congresso Brasileiro de Microbiologia, in Foz do Iguaçu, Brazil. I will give a talk in the Saturday session (the 21st) on the use of model systems all the way to global surveillance systems to prevent future pandemics.

November 15-16: DDLS Annual Meeting, in Stockholm Sweden. I am in the organising committee for this event with the theme “The emerging role of AI in data-driven life science”.

November 17: DDLS Cell and Molecular Biology Minisymposium.

November 29: GOTBIN Annual Workshop, in Gothenburg Sweden.

This will be a fun (but intense!) fall!

I just want to point potential doctoral students’ attention to this fantastic opportunity to work with my EMBARK colleague Luis Pedro Coelho as he sets up his new lab in Brisbane in Australia at the relatively new Centre for Microbiome Research. Luis is looking for two PhD students, one who will focus on identifying and characterising the small proteins of the global microbiome and one more related to developing novel bioinformatic methods for studying microbial communities.

I can highly recommend this opportunity given that you are willing to move to Australia, as Luis is one of the most brilliant scientists I have worked with, is incredibly easy-going and fosters a lab culture I strong support. More information and application here.

On the 5th and 6th of October this year, I will be taking part in a relatively small, but very interesting conference on veterinary and environmental AMR, held in Amsterdam. The theme of the event will be “Optimal practices to protect human health care from antimicrobial resistance selected in the veterinary domain”.

The aim of the conference is to discuss innovative additional measures to prevent development of resistance in animals. In addition, the participants will explore possibilities to prevent transfer to human health care after selection has taken place. The conference program will consist of both lectures and break-out sessions and is intended for researchers as well as for policy makers involved in the battle against antimicrobial resistance. The results of the break-out sessions are to be published in an open access journal, and I will be charing one of these break-out sessions. Please see the conference web site for the entire program: https://www.nvwa.nl/amrconference

There is an upper cap of 120 participants for the event, so if you’re interested make sure to register soon! The conference will be held on October 5 and 6 2023 in the Park Inn by Radisson in Amsterdam, The Netherlands. The hotel is easy to reach by a 12 minutes train ride from Schiphol airport and a 5 minutes train ride from the city center. 

I look forward to seeing you in Amsterdam!

I am happy to share with you that since a couple of months back there is an up-to-date version of ITSx available through Galaxy! The tool can be found here: https://usegalaxy.eu/root?tool_id=itsx

The person behind this is really Björn Grüning at the University of Freiburg. I am immensely thankful for the work he has put into this. Our intention to make sure that both the Galaxy version and the bioconda version are maintained in parallel to the one on this website, and continuously up to date!

Happy barcoding!