For a bit more than a year, I have been part of an EFSA panel on biological hazards on cross contamination with antibiotic substances in animal feed. This week the panel has launched an open consultation on sections of the draft scientific opinion, including the proposed methodology and the data gaps identified. Anyone who are interested can submit written comments before 18 November 2020, and the full information can be found at the EFSA website.

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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Fun things on a Friday! First of all, we have updated our lab member page with some beautiful photos! Thanks Marcus for brining your camera today!

Second, our review of factors important for antibiotic resistance development in the environment has been recognised by FEMS Microbiology Reviews as one of the papers which have made the most impact across their portfolio. It has been added to a new (well, this is old news, so semi-new) collection of papers – ‘Articles with Impact’ – many of which are very well worth a read!

Have a nice weekend!

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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Today, we released a minor update to Metaxa2, bringing it to version 2.2.2. The new version includes some bug fixes related to the Metaxa2 Database Repository, as well as a new “–temp” option allowing the user to specify the location for the temporary files. No other changes have been made in this version.

The update can be found at the Metaxa2 software page.

Exactly two years after we released the Metaxa2 database builder, here’s the first update to the software. Unfortunately, it is just a boring bug fix, but the good part is that brings back compatibility with the new version of HMMER (3.3) released in November 2019 (as noted here). It seems like it is mainly the Database builder which has been impacted with by this incompatibility, but we recommend everyone to update.

We have tried to bug check this version as good as we can to make sure we did not break any features while introducing this new compatibility. We think that this version is bug free, but as we wanted to push this out quickly, please be more observant than usual to odd behaviour, and make sure to report any bugs!

The update can be downloaded here: https://microbiology.se/sw/Metaxa2_2.2.1.tar.gz

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).