Tag: Covid-19

I am happy to announce that I am joining the editorial committee of the Swedish Pandemic Preparedness Data Portal (formerly the Swedish COVID-19 portal). I will join five other researchers associated with SciLifeLab and will work together with the portal team to maximise the utility of the Portal for researchers, expand its content beyond SARS-CoV-2, and increase engagement with the research community. My main responsibility areas will be antibiotic resistance and emerging pathogens.

Since 2022 the portal is part of the SciLifeLab Pandemic Laboratory Preparedness (PLP) Program. It is operated by the SciLifeLab Data Centre. Over time, the popularity of the Portal has increased within the research community, the general public, and those involved in healthcare, industry, and policy making. I very much look forward to work with Luisa Hugerth (Uppsala University), Laura Carroll (Umeå University), Benjamin Murrell (Karolinska Institute), Mahmoud Naguib (Uppsala University) and Johan Ankarklev (Stockholm University) on the future of the portal!

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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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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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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In the very first episode of the Bengtsson-Palme lab podcast, a crew consisting of Johan Bengtsson-Palme, Emil Burman, Haveela Kunche and Anna Abramova discusses the origin of the novel coronavirus, interactions between influenza and the respiratory tract microbiome, resistant bacteria in glaciers, pathway analysis methods, a new genus of bacteria discovered in Gothenburg, as well as life in research during a global pandemic.

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

• 10:15 – Andersen, K.G., Rambaut, A., Lipkin, W.I., Holmes, E.C., Garry, R.F., 2020. The proximal origin of SARS-CoV-2. Nature Medicine 26, 450–452. https://doi.org/10.1038/s41591-020-0820-9
• 17:30 – Zhou, P., et al., 2020. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature 579, 270–273. https://doi.org/10.1038/s41586-020-2012-7
• 19:30 – https://www.fli.de/en/press/press-releases/press-singleview/novel-coronavirus-sars-cov-2-fruit-bats-and-ferrets-are-susceptible-pigs-and-chickens-are-not/
• 20:45 – Kadioglu, O., Saeed, M., Greten, H.J., Efferth, T, 2020. Identification of novel compound against three targets of SARS CoV-2 coronavirus by combined virtual screening and supervised machine learning. Bulletin of the World Health Organization. https://doi.org/10.2471/BLT.20.255943
• 21:45 – Cheng, V.C.C., Lau, S.K.P., Woo, P.C.Y., Yuen, K.Y., 2007. Severe Acute Respiratory Syndrome Coronavirus as an Agent of Emerging and Reemerging Infection. Clinical Microbiology Reviews 20, 660–694. https://doi.org/10.1128/CMR.00023-07
• 22:15 – Fan, Y., Zhao, K., Shi, Z.-L., Zhou, P., 2019. Bat Coronaviruses in China. Viruses 11, 210. https://doi.org/10.3390/v11030210
• 29:15 – Zhang, L., et al., 2020. Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection. Microbiome 8. https://doi.org/10.1186/s40168-020-00803-2
• 39:15 – Makowska, N., et al., 2020. Occurrence of integrons and antibiotic resistance genes in cryoconite and ice of Svalbard, Greenland, and the Caucasus glaciers. Science of The Total Environment 716, 137022. https://doi.org/10.1016/j.scitotenv.2020.137022
• 49:45 – 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
• 58:45 – Gillings, M.R., 2014. Integrons: past, present, and future. Microbiology and molecular biology reviews : MMBR 78, 257–277. https://doi.org/10.1128/MMBR.00056-13
• 60:45 – Moradi, E., Marttinen, M., Häkkinen, T., Hiltunen, M., Nykter, M., 2019. Supervised pathway analysis of blood gene expression profiles in Alzheimer’s disease. Neurobiology of Aging 84, 98–108. https://doi.org/10.1016/j.neurobiolaging.2019.07.004
• 62:15 – Johnson, W.E., Li, C., Rabinovic, A., 2007. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8, 118–127. https://doi.org/10.1093/biostatistics/kxj037
• 72:15 – Marathe, N.P., et al., 2019. Scandinavium goeteborgense gen. nov., sp. nov., a New Member of the Family Enterobacteriaceae Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant. Frontiers in Microbiology 10. https://doi.org/10.3389/fmicb.2019.02511
• 76:00 – Boulund, F., et al., 2017. Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets. BMC Genomics 18, 438. https://doi.org/10.1186/s12864-017-4064-0

The podcast was recorded on April 9, 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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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.