Tag: Invasion

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.

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!

In the third episode of Microbiology Lab Pod, recorded in June, a crew consisting of Johan Bengtsson-Palme, Emil Burman, Haveela Kunche and Anna Abramova goes into depth with what we knew about the novel coronavirus at the time. We also talk about Emil‘s master thesis, potential alternative antibiotic treatment regimes and the lung microbiome in cystic fibrosis.

Unfortunately, the sound quality of this episode is quite bad at times. We have tried to rescue the audio as best as we can, but it is still a bit annoying. We promise to do better next time!

The specific papers discussed in the pod (with approximate timings) are as follows:

• 18:15 – Lozano, G.L., Bravo, J.I., Garavito Diago, M.F., Park, H.B., Hurley, A., Peterson, S.B., Stabb, E.V., Crawford, J.M., Broderick, N.A., Handelsman, J., 2019. Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. mBio 10. https://doi.org/10.1128/mBio.02846-18
• 25:15 – Ghazizadeh, Z. et al. 2020 Androgen Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men. bioArxiv, https://doi.org/10.1101/2020.05.12.091082
• 34:45 – St. John, A.L., Rathore, A.P.S 2020. Early Insights into Immune Responses during COVID-19. The Journal of Immunology 205, 555-564. https://doi.org/10.4049/jimmunol.2000526
• 49:30 – Worobey, M., Pekar, J., Larsen, B.B., Nelson, M.I., Hill, V., Joy, J.B., Rambaut, A., Suchard, M.A., Wertheim, J.O., Lemey, P., 2020. The emergence of SARS-CoV-2 in Europe and the US. bioRxiv. https://doi.org/10.1101/2020.05.21.109322
• 52:00 – La Rosa, G., Mancini, P., Bonanno Ferraro, G., Veneri, C., Iaconelli, M., Bonadonna, L., Lucentini, L., Suffredini, E., 2020. SARS-CoV-2 has been circulating in northern Italy since December 2019: evidence from environmental monitoring. medRxiv. https://doi.org/10.1101/2020.06.25.20140061
• 52:30 – https://lakartidningen.se/aktuellt/nyheter/2020/06/viruset-kan-ha-funnits-i-dalarna-redan-i-december/
• 53:15 – Deslandes, A., Berti, V., Tandjaoui-Lambotte, Y., Alloui, C., Carbonnelle, E., Zahar, J.R., Brichler, S., Cohen, Y., 2020. SARS-CoV-2 was already spreading in France in late December 2019. International Journal of Antimicrobial Agents 55, 106006. https://doi.org/10.1016/j.ijantimicag.2020.106006
• 54:45 – Li, X., Giorgi, E.E., Marichannegowda, M.H., Foley, B., Xiao, C., Kong, X.-P., Chen, Y., Gnanakaran, S., Korber, B., Gao, F., 2020. Emergence of SARS-CoV-2 through recombination and strong purifying selection. Science Advances eabb9153. https://doi.org/10.1126/sciadv.abb9153
• 56:00 – Lehmann, D., Halbwax, M.L., Makaga, L., Whytock, R., Ndindiwe Malata, L., Bombenda Mouele, W., Momboua, B.R., Koumba Pambo, A.F., White, L.J.T., 2020. Pangolins and bats living together in underground burrows in Lopé National Park, Gabon. African Journal of Ecology 58, 540–542. https://doi.org/10.1111/aje.12759
• 61:15 – Cuthbertson, L., Walker, A.W., Oliver, A.E., Rogers, G.B., Rivett, D.W., Hampton, T.H., Ashare, A., Elborn, J.S., De Soyza, A., Carroll, M.P., Hoffman, L.R., Lanyon, C., Moskowitz, S.M., O’Toole, G.A., Parkhill, J., Planet, P.J., Teneback, C.C., Tunney, M.M., Zuckerman, J.B., Bruce, K.D., van der Gast, C.J., 2020. Lung function and microbiota diversity in cystic fibrosis. Microbiome 8. https://doi.org/10.1186/s40168-020-00810-3
• 70:15 – Hansen, E., Karslake, J., Woods, R.J., Read, A.F., Wood, K.B., 2020. Antibiotics can be used to contain drug-resistant bacteria by maintaining sufficiently large sensitive populations. PLOS Biology 18, e3000713. https://doi.org/10.1371/journal.pbio.3000713

The podcast was recorded on June 23, 2020. If you want to reach out to us with comments, suggestions or other feedback, please send an e-mail to podcast at microbiology dot se or contact @bengtssonpalme via Twitter. The music that can be heard on the pod is composed by Johan Bengtsson-Palme and is taken from the album Cafe Phonocratique.

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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.

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!

So 2017 has begun, and this year will bring new challenges and exciting opportunities. First of all, my application for a 3.5 year grant from the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS) to go to Prof. Jo Handelsman‘s lab in the US was granted. Since Prof. Handelsman in is moving her lab to University of Wisconsin in Madison, where she will be heading the Wisconsin Institute of Discovery (after returning from the White House), it means that this summer I will be moving to Wisconsin. I will retain a link to the University of Gothenburg and the Joakim Larsson lab though, and part of the grant is actually for covering my salary after returning from the US, so Gothenburg won’t get rid of me so easily.

The granted project will use high-throughput sequencing techniques to identify genes improving colonization and invasion ability or resistance to invasion in microbial communities, using a model system developed by the Handelsman lab. The project will focus on genes important for colonization, invasion and resistance to invasion under exposure to sub-lethal antibiotics concentrations. The project will contribute important knowledge towards the understanding of microbial colonization and invasion and highlight disturbances to the interactions in microbial communities caused by anthropogenic activities. In addition, the results of the project will hopefully allow for prediction of secondary effects of antibiotic exposure in the environment, and the preparation for future challenges related to infections with pathogenic bacteria. The project has already been highlighted by CARe (although this was before Jo announced her move from Yale) and a FORMAS press release (in Swedish).

The project will go under the acronym InSiDER, and I intend to write about it in a special section of the website, called the Wisconsin Blog. My intention is to include personal reflections on life in Wisconsin and work in the Handelsman lab there, but we’ll see how those plans turn out. Anyway, I am very thankful for FORMAS funding this project and giving me the opportunity to work with one of the leading scientists within microbial ecology in the world!