Tag: Emil Burman

Some good news from the lab! Emil Burman today passed his halftime control, which means that we now can look forward to around more years of fun science together! We all congratulate Emil on this great achievement which marks an important milestone in the group, as Emil is the first of the PhD students who have reached it to this point!

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.

I am very happy to announce that Emil Burman‘s (doctoral student in the lab) first first-author paper was published today in Frontiers in Microbiology. In this paper (1), we explored how temperature affected the interactions in the model microbial community THOR (2). Somewhat surprisingly, we found that even a small difference in temperature changed the community intrinsic properties (3) of this model community a lot. We furthermore find that changes in growth rates of the members of the community partially explains the changed interaction patterns, but only to some extent. Finally, we also found that biofilm production overall was much higher at lower temperatures (9-15°C) than at room temperature, and that at around 25°C and above the community formed virtually no biofilm.

The temperature range we tested is not unlikely to be encountered when incubating the community in a thermally unregulated environment. Thus, our results show that a high degree of temperature control is crucial between experiments, particularly when reproducing results across different laboratories, equipment, and personnel. This highlights the need for standards and transparency in research on microbial model communities (4).

Another important, related, aspect is that disruptive factors that discriminate against single members of the community are not unique to THOR. Instead, this is likely to be the case for other microbial model (as well as natural communities). Since only a few of these model communities have been elucidated for community behaviors outside of specific culturing conditions they were first contrived under, this may severely limit our view of interactions between microbes to specific laboratory settings. This casts some doubt on the validity of extrapolation from results obtained from microbial model communities. It seems to be important moving forward to establish that community-intrinsic behaviors in model communities are stable in the face of variable environmental conditions, such as temperature, pH, nutrient availability, and initial inoculum size.

A short backstory to this paper: this begun when Emil could not consistently replicate the results I had obtained during my postdoc (working on THOR) in Prof. Jo Handelsman’s lab at the University of Wisconsin-Madison. After a long time of troubleshooting, we realized that our lab did not hold a stable room temperature. We bought a cold incubator, and – boom – after that the expected community behavior came back. This made us realize the importance of temperature for the community-intrinsic properties of THOR, which then led to this more systematic investigation.

Great work Emil! It is nice to finally see this in its published form. Read the entire paper (open access) here!

References

1. Burman E, Bengtsson-Palme J: Microbial community interactions are sensitive to small differences in temperature. Frontiers in Microbiology, 12, 672910 (2021). doi: 10.3389/fmicb.2021.672910
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
3. Madsen JS, Sørensen SJ, Burmølle M: Bacterial social interactions and the emergence of community-intrinsic properties. Current Opinion in Microbiology 42, 104–109 (2018). doi: 10.1016/j.mib.2017.11.018
4. Bengtsson-Palme J: Microbial model communities: To understand complexity, harness the power of simplicity. Computational and Structural Biotechnology Journal, 18, 3987-4001 (2020). doi: 10.1016/j.csbj.2020.11.043

In this episode Microbiology Lab Pod, the team (Johan Bengtsson-Palme, Emil Burman, Anna Abramova, Marcus Wenne, Sebastian Wettersten and Mahbuba Lubna Akter, Shumaila Malik, Emilio Rudbeck and Camille Wuyts) discusses the evolution of antibiotic resistance from different perspectives. We also interview Rémi Gschwind about his work on novel antibiotic resistance genes in the EMBARK program.

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

• 7:45 – EMBARK website: http://antimicrobialresistance.eu
• 26:15 – Seemann, T., 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 2068–2069. https://doi.org/10.1093/bioinformatics/btu153
• 29:00 – Bengtsson-Palme, J., Larsson, D.G.J., 2015. Antibiotic resistance genes in the environment: prioritizing risks. Nature reviews Microbiology 13, 396. https://doi.org/10.1038/nrmicro3399-c1
• 29:30 – Ebmeyer, S., Kristiansson, E., Larsson, D.G.J., 2021. A framework for identifying the recent origins of mobile antibiotic resistance genes. Communications Biology 4. https://doi.org/10.1038/s42003-020-01545-5
• 54:15 – Gillings, M.R., Stokes, H.W., 2012. Are humans increasing bacterial evolvability? Trends in Ecology & Evolution 27, 346–352. https://doi.org/10.1016/j.tree.2012.02.006
• 55:15 – Woods, L.C., et al., 2020. Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation. Proc Natl Acad Sci USA 117, 26868–26875. https://doi.org/10.1073/pnas.2005331117
• 76:15 – Card, K.J., Thomas, M.D., Graves, J.L., Barrick, J.E., Lenski, R.E., 2021. Genomic evolution of antibiotic resistance is contingent on genetic background following a long-term experiment with Escherichia coli. Proc Natl Acad Sci USA 118, e2016886118. https://doi.org/10.1073/pnas.2016886118

The podcast was recorded on March 18, 2021. 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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The Microbiology Lab Pod is back with season two. This first episode was recorded on February 4 and has the theme of global change and effects on microbes. The crew (Johan Bengtsson-Palme, Emil Burman, Anna Abramova, Marcus Wenne, Sebastian Wettersten and Mahbuba Lubna Akter) is joined by two guests – Shumaila Malik and Emilio Rudbeck – and talks about the lab’s most recent publication, the one-year covid anniversary, the effects of global warming and other global change factors on soil microbial communities, and thawing permafrost.

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

• 5:45 – 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. https://doi.org/10.1093/bioinformatics/btaa1086
• 8:00 – Bengtsson, J., et al., 2011. Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets. Antonie van Leeuwenhoek 100, 471–475. https://doi.org/10.1007/s10482-011-9598-6
• 29:30 – Donhauser, J., Niklaus, P.A., Rousk, J., Larose, C., Frey, B., 2020. Temperatures beyond the community optimum promote the dominance of heat-adapted, fast growing and stress resistant bacteria in alpine soils. Soil Biology and Biochemistry 148, 107873. https://doi.org/10.1016/j.soilbio.2020.107873
• 54:30 – Zhou, Z., Wang, C., Luo, Y., 2020. Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality. Nat Commun 11, 3072. https://doi.org/10.1038/s41467-020-16881-7
• 60:45 – Bahram, M., et al., 2018. Structure and function of the global topsoil microbiome. Nature 320, 1039. https://doi.org/10.1038/s41586-018-0386-6
• 68:15 – Lozano, G.L., et al., 2019. Introducing THOR, a Model Microbiome for Genetic Dissection of Community Behavior. mBio 10. https://doi.org/10.1128/mBio.02846-18
• 70:15 – Bengtsson-Palme, J., 2020. Microbial model communities: To understand complexity, harness the power of simplicity. Computational and Structural Biotechnology Journal 18, 3987–4001. https://doi.org/10.1016/j.csbj.2020.11.043
• 72:00 – Sajjad, W., et al., 2020. Resurrection of inactive microbes and resistome present in the natural frozen world: Reality or myth? Science of The Total Environment 735, 139275. https://doi.org/10.1016/j.scitotenv.2020.139275
• 74:00 – Yashina, S., et al., 2012. Regeneration of whole fertile plants from 30,000-y-old fruit tissue buried in Siberian permafrost. Proceedings of the National Academy of Sciences 109, 4008–4013. https://doi.org/10.1073/pnas.1118386109
• 74:30 – Pikuta, E.V., et al., 2005. Carnobacterium pleistocenium sp. nov., a novel psychrotolerant, facultative anaerobe isolated from permafrost of the Fox Tunnel in Alaska. International Journal of Systematic and Evolutionary Microbiology 55, 473–478. https://doi.org/10.1099/ijs.0.63384-0
• 75:00 – Bidle, K.D., Lee, S., Marchant, D.R., Falkowski, P.G., 2007. Fossil genes and microbes in the oldest ice on Earth. Proceedings of the National Academy of Sciences 104, 13455–13460. https://doi.org/10.1073/pnas.0702196104
• 75:15 – Timofeev, V., et al., 2019. Insights from Bacillus anthracis strains isolated from permafrost in the tundra zone of Russia. PLoS ONE 14, e0209140. https://doi.org/10.1371/journal.pone.0209140
• 83:15 – Bengtsson-Palme, J., Boulund, F., Fick, J., Kristiansson, E., Larsson, D.G.J., 2014. Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in microbiology 5, 648. https://doi.org/10.3389/fmicb.2014.00648
• 84:00 – Bengtsson-Palme, J., Larsson, D.G.J., 2015. Antibiotic resistance genes in the environment: prioritizing risks. Nature reviews Microbiology 13, 396. https://doi.org/10.1038/nrmicro3399-c1

The podcast was recorded on February 4, 2021. 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 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.

The fall semester has begun, and with that we have started a new round of recordings of the Microbiology Lab Pod. Our fourth episode was recorded on August 20, and the now-familiar crew (Johan Bengtsson-Palme, Emil Burman, Haveela Kunche and Anna Abramova) has been augmented with two new master students in the lab: Sebastian Wettersten and Mahbuba Lubna Akter. This time, we discuss microbial communities of dead and alive deep-sea hydrothermal vents, look at a model system for pathogenic biofilm formation in the lungs, and check in on why patients with covid-19 commonly lose their sense of smell.

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

• 11:30 – Hou, J., Sievert, S.M., Wang, Y. et al., 2020. Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys. Microbiome 8, 102. https://doi.org/10.1186/s40168-020-00851-8
• 28:45 – Harrington, N.E., Sweeney, E., Harrison, F., 2020. Building a better biofilm – Formation of in vivo-like biofilm structures by Pseudomonas aeruginosa in a porcine model of cystic fibrosis lung infection. Biofilm 2, 100024. https://doi.org/10.1016/j.bioflm.2020.100024
• 52:30 – Brann, D.H., Tsukahara, T., Weinreb, C., et al., 2020. Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia. Science Advances 6, eabc5801. https://doi.org/10.1126/sciadv.abc5801
• 71:45 – Chen, M., Shen, W., Rowan, N.R., et al., 2020. Elevated ACE2 expression in the olfactory neuroepithelium: implications for anosmia and upper respiratory SARS-CoV-2 entry and replication. European Respiratory Journal 2001948. https://doi.org/10.1183/13993003.01948-2020
• 77:15 – Zhang, X., Wang, J., 2020. Deducing the Dose-response Relation for Coronaviruses from COVID-19, SARS and MERS Meta-analysis Results. medRxiv. https://doi.org/10.1101/2020.06.26.20140624
• 78:30 – Sekine, T., Perez-Potti, A., Rivera-Ballesteros, O., et al., 2020. Robust T cell immunity in convalescent individuals with asymptomatic or mild COVID-19. Cell. https://doi.org/10.1016/j.cell.2020.08.017
• 79:45 – Mateus, J., Grifoni, A., Tarke, A., et al., 2020. Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans. Science eabd3871. https://doi.org/10.1126/science.abd3871
• 80:30 – Lv, H., Wu, N.C., Tsang, O.T.-Y., et al., 2020. Cross-reactive Antibody Response between SARS-CoV-2 and SARS-CoV Infections. Cell Reports 31, 107725. https://doi.org/10.1016/j.celrep.2020.107725

The podcast was recorded on August 20, 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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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!

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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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!