Tag: Lab news

Time is passing quickly, and I have not appropriately acknowledged the many newcomers we’ve had to the lab in the past couple of months. With this post I would like to say welcome to the lab to Máté Vass and Dani Jáen Luchoro (both postdocs), Jorge Agramont and Josue Mamani Jarro (doctoral students), as well as Nathália Abichabki (visiting doctoral student from Brazil)! Some of you have already spent a couple of months in the group and we very much enjoy having you here!

A week or so ago, we took this new lab picture with everyone (except for Lisa, who is in Amsterdam). I am very proud to be working with group of extremely talented, smart, funny and goodhearted people!

Very briefly, Dani will be working on updating the BacMet database as part of the BIOCIDE project, and shares his time between my group, Joakim Larsson‘s group and the Sahlgrenska hospital. Máté was recruited within the DDLS program and will work on inferring the metacommunity ecology of antibiotic resistance based on analysis of large-scale datasets. Jorge and Josue are part of the same SIDA-funded doctoral student exchange program with Bolivia and will work on different aspects of environmental antibiotic resistance and the spread of diarrheal pathogens through the environmental matrix. Nathália, finally, is working on understanding the tolerance mechanisms to antibiotics in Klebsiella pneumoniae.

All of you are very welcome to the group!

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!

Thanks a lot to all of those who applied to the PhD position opening that closed a week ago. In total we received 59 applications, of which the vast majority were of high quality – I am sure that at least half the candidates would have made a great job in the position. However, we have to make a selection among these 59 candidates, so after reading and evaluating all 59 applications, we have now nailed down ten top candidates that we will initially move forward with. Those ten candidates should have received an e-mail today about how the process will move forward.

If you have not received an e-mail from us, the most likely explanation is that you were not among these top ten candidates (but remember to also check your spam!) In that case, you will get a follow-up once the position is filled.

Again, thanks a lot for your interest. I have been overwhelmed by the high quality and relevance of the applications.

We are hiring a PhD student to work with interactions between the bacteria in human and environmental microbiomes that are important for community stability and resilience to being colonized by unwanted bacteria (including pathogens). The project seeks to unearth which environmental and genetic factors that are important determinants of bacterial invasiveness and community stability. You can read more at our Open Positions page.

We are looking for a candidate with experience with both bioinformatics and experimental microbiology. Previous experience with microbial communities is a plus, but not a must, as is work with human cell lines.

The project is fully funded by a grant from the Swedish Research Council and the position is planned for 4.5 years, with 4 years of research and course work and half a year of teaching.

If you feel that you are the right person for this position, you can apply here. We look forward to your application! The deadline for applications is October 21.

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!

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!

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.

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.

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.

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.