Category: Thoughts

Welcome Mahbuba, Sebastian and Marcus

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!

Emil Burman defends today

Emil Burman, master student in the lab, defends his master’s thesis today, titled “Biofilms, how cool are they? Effects of temperature and invasion on model microbial communities“. We wish him the best of luck today presenting this excellent work!

More podcasting: The AMR Studio

Not only did we release the most recent episode of the lab’s podcast this weekend. Today, the episode of The AMR Studio where I’m interviewed by Eva Garmendia of the Uppsala Antibiotic Center was put online. We talk mostly about antibiotic resistance in the environment and the role that the EMBARK program can play in mitigating environmental resistance. I think it’s a nice listen (recorded in the beautiful world pre-covid-19). Find it where you find podcasts (e.g. Apple or Spotify).

And like that, the world had changed

I guess it hasn’t passed anyone by that we are under a global lockdown (although to very different degrees – Sweden, where we’re based, has a pretty relaxed attitude to quarantining people (1), so it could be worse for us, I guess). In any case, the novel coronavirus has forced the lab to largely work from home and has upended essentially all my plans for this spring, expect for writing grant applications (which I have done a lot).

First of all, I want to thank my fellow lab members for holding out strongly in these trying times. They have consistently shown that they are the best co-workers I could ask for, and have kept calm even when anxiety hits. Thanks a lot for that. I also would like to thank the university for providing rather clear guidance on how to handle different issues that come up in these time of crisis.

With that said, I am also sad to say that there will not be a Microbiome & Probiotics Collaboration Forum in Rotterdam on May 18-20. Instead that meeting has been postponed to early December. Similarly, I will not be in Helsinki next week to talk about EMBARK. That workshop will instead, hopefully, take place on August 28. And the same story goes for the NordicMappingAMR organised by the Swedish Medical Products Agency, which will take place at a later date (I am not sure exactly when this is planned yet).

These are trying times for all of us. I hope that you stay healthy and take care of your loved ones – particularly the elderly, but not unnecessarily visiting them. My grandparents (aged 93 and 95) have started FaceTiming us, so I guess some good things come out of this mess as well. We will come out of this crisis stronger, eventually.

Footnotes

  1. There are many things I could say about the Swedish strategy regarding covid-19, but this is not really the forum. In very brief, though, I have quite some faith in that the Swedish Public Health Agency is doing a decent job. Mistakes have been made (particularly early in the pandemic) and I am slightly anxious whether the Swedish strategy will play out as well as in other countries in Northern Europe, but right now data suggest that we are doing reasonable fine. I might return to this issue in another post if time permits.

How to understand complexity?

As I have been indicating before, I will be presenting at the Microbiome & Probiotics Collaboration Forum in Rotterdam on May 18-20. In relation to this, I was asked to write a shorter blog post on (or, if you will, some type of extended abstract) what I will talk about, which is how simple model systems for microbial communities can be used to understand complex systems with loads of interactions, similar to how E. coli and yeast have enabled a much more wide-reaching understanding of molecular biology than just about those two single-celled organisms themselves. The entire post can be read here, and I hope that I will see you in Rotterdam in May!

Grant successes!

I am a bit late on the ball here, but January was a great month for the lab in terms of funding. First, we got awarded an Sahlgrenska Academy International Starting Grant – a faculty grant for young researchers comprising of 1 million SEK, intended to support the overall research plan for the lab.

The second grant was awarded by the Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg and is a project grant focusing on opportunistic pathogens and their role in the emergence and transmission of antibiotic resistance. For this project, we got almost 600,000 SEK over two years to investigate how genes enhancing invasion ability and virulence interact with selection for antibiotic resistance in opportunistic pathogens. The project is somewhat related to the work I did in Prof. Jo Handelsman‘s lab, but extends it to more mechanistic details about how these phenomena are interconnected.

Conferences and a PhD position

Here’s some updates on my Spring schedule.

On March 19, I will be presenting the EMBARK program and what we aim to achieve at a conference organised by the Swedish Medical Products Agency called NordicMappingAMR. The event will feature an overview of existing monitoring of antibiotics and antibiotic resistant bacteria in the environment. The conference aims to present the results from this survey, to listen to experts in the field and to discuss possible progress. It takes place in Uppsala. For any further questions, contact Kia Salin at NordicMappingAMR@lakemedelsverket.se

Then on May 18 to 20 I will participate in the 7th Microbiome & Probiotics R&D and Business Collaboration Forum in Rotterdam. This industry/academia cross-over event focuses on cutting-edge microbiome and probiotics research, and challenges and opportunities in moving research towards commercialisation. I will talk on the work we do on deciphering genetic mechanisms behind microbial interactions in microbiomes on May 20.

And finally, I also want to bring the attention to that my collaborator Erik Kristiansson has an open PhD position in his lab. The position is funded by the Environmental Dimensions of Antibiotic Resistance (EDAR) research project, aiming to describe the environmental role in the development and promotion of antibiotic resistance. The focus of the PhD position will be on analysis of large-scale data, with special emphasis on the identification of new forms of resistance genes. The project also includes phylogenetic analysis and development of methods for assessment of gene evolution. More info can be found here.

FEMS Microbiology Reviews Award

We have been awarded with the first best article award from FEMS Microbiology Reviews for our 2018 review Environmental factors influencing the development and spread of antibiotic resistance. I and my co-authors Joakim Larsson and Erik Kristiansson are honoured and – of course – very happy with this recognition of our work. I was interviewed in relation to the prize, an interview that can be read here. But, also, the paper is open access, so you can go and check it all out in its full glory right now!

Quick update on the PhD position

I just wanted to very quickly brief applicants to the recently announced PhD position in the lab. We got 71 applications in total, most of which I consider relevant for the position. The bottom line is that this will take a few days to go through, but we are working on it, and will get in touch with the top candidates when we are done. I would, however, already like to thank everyone who applied – it’s amazing that you want to spend your time doing research that I find exiting!

EMBARK funded by JPIAMR

I am very happy to announce today (on the European Antibiotic Awareness Day), that the EMBARK project that I am coordinator for got funded by JPIAMR with almost 1.4 million Euros over three years!

The primary goal of EMBARK is to establish a baseline for how common resistance is in the environment and what resistance types that can be expected where. That background data will then underpin efforts to standardize different methods for resistance surveillance and identify high-priority targets that should be used for efficient monitoring. In addition, EMBARK will develop and evaluate methods to detect new resistance factors and thereby provide an early-warning system for emerging resistance threats.

EMBARK is an international collaboration funded by JPIAMR. The consortium consists of myself, Thomas Berendonk (TU-Dresden, Germany), Luis Pedro Coelho (Fudan University, China), Sofia Forslund (ECRC Max-Delbrück-Centrum für Molekulare Medizin, Germany), Etienne Ruppé (INSERM, France) and Rabaab Zahra (Quaid-i-Azam University, Pakistan).

EMBARK has a website where the protocols and data generated during the project will be released. Follow our progress towards better monitoring of antimicrobial resistance in the environment here and on the EMBARK Twitter account: @EMBARK_JPIAMR!