Tag: Lab news

Two fun things

Fun things on a Friday! First of all, we have updated our lab member page with some beautiful photos! Thanks Marcus for brining your camera today!

Second, our review of factors important for antibiotic resistance development in the environment has been recognised by FEMS Microbiology Reviews as one of the papers which have made the most impact across their portfolio. It has been added to a new (well, this is old news, so semi-new) collection of papers – ‘Articles with Impact’ – many of which are very well worth a read!

Have a nice weekend!

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!

The Microbiology Lab Pod

As the regularly returning reader might already have seen, the lab has started podcasting! Two weeks ago, we started recording our journal clubs (on Zoom) along with some other science-related chatter. This is mostly an experiment this far, so we will see where it goes, but it was a fun an interesting experience, and I look forward to recording the next episode in May!

The experiment is called the “Microbiology Lab Pod” and can be heard on this website, on Apple podcasts, Google podcasts, Stitcher etc.

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.

Open postdoc position

We are hiring a postdoc to work with environmental monitoring of antimicrobial resistance. The project is part of the EMBARK program and will consider different aspects of establishing a baseline for background antibiotic resistance in the environment, standardization of monitoring protocols and development of methods to detect emerging resistance threats. The project will involve work with environmental sampling, DNA extractions, bacterial culturing and generation of large-scale DNA sequence data. In terms of bioinformatic analyses, the project will encompass analysis of next-generation sequence data, genome-resolved metagenomics, short-read assembly and network analysis.

We look for a skilled bioinformatician, preferably with experience of experimental laboratory work. If you feel that you are the right person for this position, you can apply here. More information is also available here. We look forward to your application! The deadline for applications is January 3.

Open PhD position

We are hiring a PhD student to work with effects of antibiotics on microbial communities! The project will use large-scale techniques to investigate how sub-inhibitory concentrations of antibiotics affect microbial communities. Specifically, the project will examine how the ability for bacteria to colonize and invade established microbial communities is impacted by antibiotics. The project will also explore how antibiotics influence the interactions between different species in bacterial communities and if this may change their ability to withstand invasions. The goal is to identify the genes and mechanisms that contribute to change and stability in microbial communities.

A cool thing about this position is that it is fairly adaptable to the eventual candidate, and the project can be somewhat tailored to suit the profile of the PhD student. This means that we’re looking for someone who is either a bioinformatician or an experimentalist (or both). Previous experience with microbial communities is a plus, but not a must.

If you feel that you are the right person for this position, you can apply here. More information is also available here. We look forward to your application! The deadline for applications is December 9.

Goodbye Adriana and Welcome Emil

The shift to October marked the last days that our visiting doctoral student Adriana Osińska spent in the lab. Adriana was working on the sequencing data generated from the invasion experiments I performed in Jo Handelsman’s lab. She managed to dig out a great number of genes that seems to have an influence on bacterial community invasion success. Those genes are now candidate genes that will be tested in follow-up studies, which brings us to….

That I forgot to introduce our newest lab member – Emil Burman! Emil is a master student performing his thesis project in the lab and will stay with us until May 2020. Emil will work on experimentally characterizing the candidate genes that Adriana has identified. We are excited to have Emil in the lab and think that he has been off to a great start already. Welcome Emil!

Adriana will no go back to Poland to complete here PhD thesis early next year. We have loved to have her in the lab and she has contributed with data and analyses of tremendous value. We wish her all the best of luck with defending her thesis!

Reshaping this site

This spring I am on part time parental leave with my son, and I have taken the opportunity to reshape this web site a bit – after all its design has not been updated since I launched the site in 2010. With the new site, I want to extend the scope of the web page a bit, focusing more on the lab I am setting up at the University of Gothenburg and less on myself alone. This will be a bit by bit process, and as you will notice most of the content does not yet reflect this change (yet).

The fact that I am on part-time parental leave (actually more like “most-time”) means that I will be slower than usual at responding to e-mails until (at least) the beginning of June. It also (sadly) means that I will have to decline a lot of nice invitations and proposals, or at least move them into the future when possible.

Finally, here’s a few things that will happen this year regardless. In April (16th to 18th), I will be at ICOHAR in Utrecht, where I will give a talk in a session on the role of the environment in the spread of antimicrobial resistance. Then in June, I will attend ASM Microbe in San Fransisco (June 20-24), where I will co-chair a session on Environmental Resistomes together with Ashley Shade. In this session I will also give a talk on the effect of antibiotics on interactions in microbial communities. However, I will not attend EDAR-5 in Hong Kong this year – there simply wasn’t time to fit that into the agenda as well. (Also, I am trying to cut down on air travel which contributed to the decision not to go this year.)