April 2020 Pod: The origin of the coronavirus, and more

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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