Update: There is now an updated version of Metaxa2 that addresses this problem. Find it here.

We have recently discovered that the new version of HMMER (3.3) released in November 2019 have introduced new restrictions that make it partially incompatible with Metaxa2. The most apparent problem is in the Database Builder software, which will not build profiles properly in most cases. Instead, HMMER will return an error and only some profiles will be created.

We do currently not know if this also affects the functionality of Metaxa2 itself. We are currently investigating this.

For now, the solution to this problem is to use the previous version of HMMER (version 3.2.1) while we investigate further. That version can be downloaded here: http://hmmer.org/download.html

I am sorry about not discovering this earlier, this only came to our attention this week!

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!

Not only did we release the most recent episode of the lab’s podcast this weekend. Today, the episode of The AMR Studio where I’m interviewed by Eva Garmendia of the Uppsala Antibiotic Center was put online. We talk mostly about antibiotic resistance in the environment and the role that the EMBARK program can play in mitigating environmental resistance. I think it’s a nice listen (recorded in the beautiful world pre-covid-19). Find it where you find podcasts (e.g. Apple or Spotify).

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.

Podcast: Play in new window | Download

Subscribe: RSS

As the regularly returning reader might already have seen, the lab has started podcasting! Two weeks ago, we started recording our journal clubs (on Zoom) along with some other science-related chatter. This is mostly an experiment this far, so we will see where it goes, but it was a fun an interesting experience, and I look forward to recording the next episode in May!

The experiment is called the “Microbiology Lab Pod” and can be heard on this website, on Apple podcasts, Google podcasts, Stitcher etc.

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.

Podcast: Play in new window | Download

Subscribe: RSS

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.

As I have been indicating before, I will be presenting at the Microbiome & Probiotics Collaboration Forum in Rotterdam on May 18-20. In relation to this, I was asked to write a shorter blog post on (or, if you will, some type of extended abstract) what I will talk about, which is how simple model systems for microbial communities can be used to understand complex systems with loads of interactions, similar to how E. coli and yeast have enabled a much more wide-reaching understanding of molecular biology than just about those two single-celled organisms themselves. The entire post can be read here, and I hope that I will see you in Rotterdam in May!

I am a bit late on the ball here, but January was a great month for the lab in terms of funding. First, we got awarded an Sahlgrenska Academy International Starting Grant – a faculty grant for young researchers comprising of 1 million SEK, intended to support the overall research plan for the lab.

The second grant was awarded by the Centre for Antibiotic Resistance Research (CARe) at the University of Gothenburg and is a project grant focusing on opportunistic pathogens and their role in the emergence and transmission of antibiotic resistance. For this project, we got almost 600,000 SEK over two years to investigate how genes enhancing invasion ability and virulence interact with selection for antibiotic resistance in opportunistic pathogens. The project is somewhat related to the work I did in Prof. Jo Handelsman‘s lab, but extends it to more mechanistic details about how these phenomena are interconnected.

Here’s some updates on my Spring schedule.

On March 19, I will be presenting the EMBARK program and what we aim to achieve at a conference organised by the Swedish Medical Products Agency called NordicMappingAMR. The event will feature an overview of existing monitoring of antibiotics and antibiotic resistant bacteria in the environment. The conference aims to present the results from this survey, to listen to experts in the field and to discuss possible progress. It takes place in Uppsala. For any further questions, contact Kia Salin at NordicMappingAMR@lakemedelsverket.se

Then on May 18 to 20 I will participate in the 7th Microbiome & Probiotics R&D and Business Collaboration Forum in Rotterdam. This industry/academia cross-over event focuses on cutting-edge microbiome and probiotics research, and challenges and opportunities in moving research towards commercialisation. I will talk on the work we do on deciphering genetic mechanisms behind microbial interactions in microbiomes on May 20.

And finally, I also want to bring the attention to that my collaborator Erik Kristiansson has an open PhD position in his lab. The position is funded by the Environmental Dimensions of Antibiotic Resistance (EDAR) research project, aiming to describe the environmental role in the development and promotion of antibiotic resistance. The focus of the PhD position will be on analysis of large-scale data, with special emphasis on the identification of new forms of resistance genes. The project also includes phylogenetic analysis and development of methods for assessment of gene evolution. More info can be found here.