Tag: Haveela Kunche

May 2020 Pod: Discovering novel resistance genes and how bacteria become virulent

In the second episode of Microbiology Lab Pod, a crew consisting of Johan Bengtsson-Palme, Emil Burman, Haveela Kunche and Anna Abramova discusses how to identify novel resistance genes with our special guest Marlies Böhm. We also talk about bacterial virulence: how do bacteria become virulent, how do virulence relate to competition, how do bacteria evade the immune system and can we attenuate virulence using fatty acids?

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

  • 7:15 – Böhm, M.-E., Razavi, M., Flach, C.-F., Larsson, D.G.J., 2020a. A Novel, Integron-Regulated, Class C β-Lactamase. Antibiotics 9, 123. https://doi.org/10.3390/antibiotics9030123
  • 7:15 – Böhm, M.-E., Razavi, M., Marathe, N.P., Flach, C.-F., Larsson, D.G.J., 2020b. Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities. Microbiome 8. https://doi.org/10.1186/s40168-020-00814-z
  • 9:15 – 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
  • 20:45 – 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
  • 33:45 – Kaito, C., Yoshikai, H., Wakamatsu, A., Miyashita, A., Matsumoto, Y., Fujiyuki, T., Kato, M., Ogura, Y., Hayashi, T., Isogai, T., Sekimizu, K., 2020. Non-pathogenic Escherichia coli acquires virulence by mutating a growth-essential LPS transporter. PLOS Pathogens 16, e1008469. https://doi.org/10.1371/journal.ppat.1008469
  • 43:45 – Lories, B., Roberfroid, S., Dieltjens, L., De Coster, D., Foster, K.R., Steenackers, H.P., 2020. Biofilm Bacteria Use Stress Responses to Detect and Respond to Competitors. Current Biology 30, 1231-1244.e4. https://doi.org/10.1016/j.cub.2020.01.065
  • 45:45 – 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
  • 55:45 – Kumar, P., Lee, J.-H., Beyenal, H., Lee, J., 2020. Fatty Acids as Antibiofilm and Antivirulence Agents. Trends in Microbiology. https://doi.org/10.1016/j.tim.2020.03.014
  • 60:15 – Gullberg, E., Cao, S., Berg, O.G., Ilbäck, C., Sandegren, L., Hughes, D., Andersson, D.I., 2011. Selection of resistant bacteria at very low antibiotic concentrations. PLoS Pathogens 7, e1002158. https://doi.org/10.1371/journal.ppat.1002158
  • 61:15 – Larsson, D.G.J., 2018. Risks of using the natural defence of commensal bacteria as antibiotics call for research and regulation. International Journal of Antimicrobial Agents 51, 277–278. https://doi.org/10.1016/j.ijantimicag.2017.12.018
  • 65:15 – Lone, A.G., Bankhead, T., 2020. The Borrelia burgdorferi VlsE Lipoprotein Prevents Antibody Binding to an Arthritis-Related Surface Antigen. Cell Reports 30, 3663-3670.e5. https://doi.org/10.1016/j.celrep.2020.02.081

The podcast was recorded on May 7, 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.

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.