Category: Thoughts

Update on the PhD candidate evaluation

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.

Open PhD position

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 hereWe look forward to your application! The deadline for applications is October 21.

Some media coverage

Here’s a nice popular summary of the paper that I published with Emil Burman last month on how temperature affects the microbial model community THOR. I think Miles Martin at The Academic Times did a great distilling my ramblings into a coherent story. Good job Miles!

I did not know about The Academic Times before this but will keep an eye on this relatively new publication aiming to popularize and distill scientific content for other scientists.

In other popularization-of-science-news, I got interviewed last week by New Scientist about a very exciting paper that came out this week on travelers picking up antibiotic resistance genes in Africa and Asia. The study was quite similar to what we did back in 2015, but used a much larger data set and uncovered that there are many, many more resistance genes that are enriched after travel than what we found using our more limited dataset. Very cool study, and you can read the New Scientist summary here.

Metaxa2 Genome mode fixes

Yes, Saturdays are somewhat weird days for software updates, but if you’re doing weekend work anyway, why wait to push bug fixes to the community? A very minor bug-fix update to Metaxa2 was released today, bringing the software to version 2.2.3.

Two things have changed in this version, both related to the genome mode. 1) We fixed a file reading bug in the ‘genome’ mode of the software. This bug caused the last sequence in an input FASTA file not to be read unless there was a newline after it. Since the ‘genome’ mode is rarely used by most users, we suspect not a lot of users have been affected by this bug.
2) While we were at it, we changed the behavior of the ‘genome’ mode to mirror that of the ‘auto’ mode, as the strict genome mode dropped sequences shorter than 2500 bp. We considered this behavior counter-intuitive to what most users would want, and has now changed the ‘genome’ mode to behave the same as the ‘auto’ mode and not drop short sequences.

No other changes have been made in this version. The update can be found at the Metaxa2 software page.

Published paper: CAFE

We start the new year with a bang, or at least a new paper published. Bioinformatics put our paper (1) describing the software package CAFE online today (although it was accepted late last year). The CAFE package is a combination of Perl and R tools that can analyze data from paired transposon mutant sequencing experiments (2-4), generate fitness coefficients for each gene and condition, and perform appropriate statistical testing on these fitness coefficients. The paper is short, but shows that CAFE performs as good as the best competing tools (5-7) while being superior at controlling for false positives (you’ll have to dig into the supplement to find the data for that though).

Importantly, this is a collaborative effort by basically the entire research group from last spring: me, Haveela, Emil, Anna and our visiting student Adriana. A big thanks to all of you for working on this short but important paper! You can read the full paper here.

References

  1. Abramova A, Osińska A, Kunche H, Burman E, Bengtsson-Palme J (2021) CAFE: A software suite for analysis of paired-sample transposon insertion sequencing data. Bioinformatics, advance article doi: 10.1093/bioinformatics/btaa1086
  2. Chao,M.C. et al. (2016) The design and analysis of transposon insertion sequencing experiments. Nature reviews Microbiology, 14, 119–128.
  3. van Opijnen,T. and Camilli,A. (2013) Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms. Nature reviews Microbiology, 11, 435–442.
  4. Goodman,A.L. et al. (2011) Identifying microbial fitness determinants by insertion sequencing using genome-wide transposon mutant libraries. Nature Protocols, 6, 1969–1980.
  5. McCoy,K.M. et al. (2017) MAGenTA: a Galaxy implemented tool for complete Tn- Seq analysis and data visualization. Bioinformatics, 33, 2781– 2783.
  6. Zhao,L. et al. (2017) TnseqDiff: identification of conditionally essential genes in transposon sequencing studies. BMC Bioinformatics, 18.
  7. Zomer,A. et al. (2012) ESSENTIALS: Software for Rapid Analysis of High Throughput Transposon Insertion Sequencing Data. PLoS ONE, 7, e43012.

Published paper: Microbial model communities

This week, in a stroke of luck coinciding with my conference presentation on the same topic, my review paper on microbial model communities came out in Computational and Structural Biotechnology Journal. The paper (1) provides an overview of the existing microbial model communities that have been developed for different purposes and makes some recommendations on when to use what kind of community. I also make a deep-dive into community intrinsic-properties and how to capture and understand how microbes growing together interact in a way that is not predictable from how they grow in isolation.

The main take-home messages of the paper are that 1) there already exists a quite diverse range of microbial model communities – we probably don’t need a wealth of additional model systems, 2) there need to be better standardization and description of the exact protocols used – this is more important in multi-species communities than when species are grown in isolation, and 3) the researchers working with microbial model communities need to settle on a ‘gold standard’ set of model communities, as well as common definitions, terms and frameworks, or the complexity of the universe of model systems itself may throw a wrench into the research made using these model systems.

The paper was inspired by the work I did in Jo Handelsman‘s lab on the THOR model community (2), which I then have brought with me to the University of Gothenburg. In the lab, we are also setting up other model systems for microbial interactions, and in this process I thought it would be useful to make an overview of what is already out there. And that overview then became this review paper.

The paper is fully open-access, so there is really not much need to go into the details here. Go and read the entire thing instead (or just get baffled by Table 1, listing the communities that are already out there!)

References

  1. Bengtsson-Palme J: Microbial model communities: To understand complexity, harness the power of simplicity. Computational and Structural Biotechnology Journal, in press (2020). doi: 10.1016/j.csbj.2020.11.043
  2. Lozano GL, Bravo JI, Garavito Diago MF, Park HB, Hurley A, Peterson SB, Stabb EV, Crawford JM, Broderick NA, Handelsman J: Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. mBio, 10, 2, e02846-18 (2019). doi: 10.1128/mBio.02846-18

Funding from the research council!

I am very happy to share the news that our starting grant application to the Swedish Research Council has been granted 3.3 million SEK of funding for four years! This is fantastic news, as it allows us to further explore the interactions between bacteria in the human microbiome that are important for community stability and resilience to being colonized by pathogens. In the granted project, we will investigate environmental and genetic factors that are important for bacterial invasiveness and community stability in the human gastrointestinal tract.

Within the scope of the project, we will establish model bacterial communities and experimental systems for the human stomach and intestine. We will then investigate how disturbances, such as antibiotic exposure, change the interactions in these microbial communities and their long-term stability. Finally, we aim to identify genes that contribute to successful bacterial colonization or resilience to invasion of established communities in the human microbiome.

Aside from myself, Prof. Sara Lindén and Dr. Kaisa Thorell from the University of Gothenburg as well as Prof. Ed Moore at the university’s Culture Collection will be involved in this project in different ways. We will also collaborate with my former postdoc supervisor Prof. Jo Handelsman as well as Dr. Ophelia Venturelli at the University of Wisconsin-Madison. Finally, we will also collaborate with Dr. Åsa Sjöling at the Karolinska Institute. I look forward to work with you all over the coming four years! A big thanks to the Swedish Research Council for believing in this research and investing in making it happen!

The Gothenburg Society of Medicine’s research prize

I am very happy to share the news that I have been awarded with the Gothenburg Society of Medicine and the Sahlgrenska Academy’s prize to young researchers for our research on the effects of antibiotics on bacteria, including, of course, antibiotic resistance.

I am incredibly honoured by being selected for this award. I am also thrilled with that the Gothenburg Society of Medicine, which is a society mostly for medical doctors, sees the value in our broad, one-health, take on antibiotic resistance as well as other effect that antibiotics may have on microbes, both in the human body and in the environment. The recognition of antibiotic resistance as a one-health problem with solutions both within and outside of the typical medical setting is instrumental for our ability to curb future resistance development.

The award ceremony will take place in connection with the Gothenburg Society of Medicine’s closing meeting on 2 December, where I will present our research together with the senior awardee Professor Claes Ohlsson, who is awarded for his groundbreaking research on osteoporosis.

EFSA Public Consultation

For a bit more than a year, I have been part of an EFSA panel on biological hazards on cross contamination with antibiotic substances in animal feed. This week the panel has launched an open consultation on sections of the draft scientific opinion, including the proposed methodology and the data gaps identified. Anyone who are interested can submit written comments before 18 November 2020, and the full information can be found at the EFSA website.

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!