Time to do a rundown of conferences and meetings I will attend this fall. Double-check with your calendars and please reach out if you’re also going, so we can meet up!
September 21-24: Nordic Society of Clinical Microbiology and Infectious Diseases (NSCMID), in Örebro, Sweden. I will give a talk about the EMBARK work in the Saturday session on Metagenomics in infection, inflammatory disease and the environment
October 5-6: Conference on ‘Optimal practices to protect human health care from antimicrobial resistance selected in the veterinary domain’ organised by The Netherlands Food and Consumer Product Safety Authority (NVWA) in Amsterdam, the Netherlands. I will chair a session on October 6 on Next generation sequencing for bioinformatic based surveillance.
October 18-22: 32º Congresso Brasileiro de Microbiologia, in Foz do Iguaçu, Brazil. I will give a talk in the Saturday session (the 21st) on the use of model systems all the way to global surveillance systems to prevent future pandemics.
November 15-16: DDLS Annual Meeting, in Stockholm Sweden. I am in the organising committee for this event with the theme “The emerging role of AI in data-driven life science”.
November 17: DDLS Cell and Molecular Biology Minisymposium.
November 29: GOTBIN Annual Workshop, in Gothenburg Sweden.
This will be a fun (but intense!) fall!
On the 5th and 6th of October this year, I will be taking part in a relatively small, but very interesting conference on veterinary and environmental AMR, held in Amsterdam. The theme of the event will be “Optimal practices to protect human health care from antimicrobial resistance selected in the veterinary domain”.
The aim of the conference is to discuss innovative additional measures to prevent development of resistance in animals. In addition, the participants will explore possibilities to prevent transfer to human health care after selection has taken place. The conference program will consist of both lectures and break-out sessions and is intended for researchers as well as for policy makers involved in the battle against antimicrobial resistance. The results of the break-out sessions are to be published in an open access journal, and I will be charing one of these break-out sessions. Please see the conference web site for the entire program: https://www.nvwa.nl/amrconference
There is an upper cap of 120 participants for the event, so if you’re interested make sure to register soon! The conference will be held on October 5 and 6 2023 in the Park Inn by Radisson in Amsterdam, The Netherlands. The hotel is easy to reach by a 12 minutes train ride from Schiphol airport and a 5 minutes train ride from the city center.
I look forward to seeing you in Amsterdam!
In the sixth episode of the Microbiology Lab Pod, recorded on December 17, the crew (Johan Bengtsson-Palme, Emil Burman, Haveela Kunche, Anna Abramova, Marcus Wenne, Sebastian Wettersten and Mahbuba Lubna Akter) talks about Haveela’s master thesis, virtual conferences and bring three Christmas themed papers.
The specific papers discussed in the pod (with approximate timings) are as follows:
- 13:00 – Fulcher, M.R., Bolton, M.L., Millican, M.D., et al., 2020. Broadening Participation in Scientific Conferences during the Era of Social Distancing. Trends in Microbiology. https://doi.org/10.1016/j.tim.2020.08.004
- 25:15 – de Clercq, N.C., Frissen, M.N., Levin, E., et al., 2019. The effect of having Christmas dinner with in-laws on gut microbiota composition. Human Microbiome Journal 13, 100058. https://doi.org/10.1016/j.humic.2019.100058
- 44:00 – Garcia-Lemos, A.M., Gobbi, A., et al., 2020. Under the Christmas Tree: Belowground Bacterial Associations With Abies nordmanniana Across Production Systems and Plant Development. Frontiers in Microbiology 11. https://doi.org/10.3389/fmicb.2020.00198
- 56:15 – Halverson, L.J., Clayton, M.K., Handelsman, J., 1993. Population biology of Bacillus cereus UW85 in the rhizosphere of field-grown soybeans. Soil Biology and Biochemistry 25, 485–493. https://doi.org/10.1016/0038-0717(93)90074-L
- 65:00 – Glendinning, L., Genç, B., Wallace, R.J., Watson, M., 2020. Metagenomic analysis of the cow, sheep, reindeer and red deer rumen. bioRxiv. https://doi.org/10.1101/2020.02.12.945139
The podcast was recorded on December 17, 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.
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.
- 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!
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.
This spring I am on part time parental leave with my son, and I have taken the opportunity to reshape this web site a bit – after all its design has not been updated since I launched the site in 2010. With the new site, I want to extend the scope of the web page a bit, focusing more on the lab I am setting up at the University of Gothenburg and less on myself alone. This will be a bit by bit process, and as you will notice most of the content does not yet reflect this change (yet).
The fact that I am on part-time parental leave (actually more like “most-time”) means that I will be slower than usual at responding to e-mails until (at least) the beginning of June. It also (sadly) means that I will have to decline a lot of nice invitations and proposals, or at least move them into the future when possible.
Finally, here’s a few things that will happen this year regardless. In April (16th to 18th), I will be at ICOHAR in Utrecht, where I will give a talk in a session on the role of the environment in the spread of antimicrobial resistance. Then in June, I will attend ASM Microbe in San Fransisco (June 20-24), where I will co-chair a session on Environmental Resistomes together with Ashley Shade. In this session I will also give a talk on the effect of antibiotics on interactions in microbial communities. However, I will not attend EDAR-5 in Hong Kong this year – there simply wasn’t time to fit that into the agenda as well. (Also, I am trying to cut down on air travel which contributed to the decision not to go this year.)
As the 8th Next Generation Sequencing Congress in London is drawing to a close as I write this, I have a few reflections that might warrant sharing. The first thing that has been apparent this year compared to the two previous times I have visited the event (in 2012 and 2013) is that there was very little talk about where Illumina sequencing is heading next. Instead the discussion was about the applications of Illumina sequencing in the clinical setting; so apparently this is now so mainstream that we only expect slow progress towards longer reads. Apart from that, Illumina is a completed, mature technology. Instead, the flashlight is now pointing entirely towards long-read sequencing (PacBio, NanoPore) as the next big thing. However, the excitement around these technologies has also sort of faded compared to in 2013 when they were soon-to-arrive. Indeed, it seems like there’s not much to be excited about in the sequencing field at the moment, or at least Oxford Global (who are hosting the conference) has failed to get these technologies here.
What also strikes me is the vast amounts of talk about RNAseq of cancer cells. The scope of this event has narrowed dramatically in the past three years. Which makes me substantially less interested in returning next year. If there is not much to be excited about, and the focus is only on cancer sequencing – despite the human microbiota being a very hot topic at the moment – what is the reason for non-cancer researchers to come to the event? There will need to be a stark shift towards another direction of this event if the arrangers want it to remain a broad NGS event. Otherwise, they may just as well go all in and rename the event the Next Generation Sequencing of Cancer Congress. But I hope they choose to widen the scope again; conferences discussing technology as a foundation for a variety of applications are important meeting points and spawning grounds for novel ideas.
I just want to highlight that the paper on strategies to improve database accuracy and usability we recently published in Proteomics (1) has been included in their most recent issue, which is a special issue focusing on Data Quality Issues in Proteomics. I highly recommend reading our paper (of course) and many of the other in the special issue. Happy reading!
On another note, I will be giving a talk next Wednesday (October 5th) on a seminar day on next generation sequencing in clinical microbiology, titled “Antibiotic resistance in the clinic and the environment – There and back again“. You are very welcome to the lecture hall at floor 3 in our building at Guldhedsgatan 10A here in Gothenburg if you are interested! (Bear in mind though that it all starts at 8.15 in the morning.)
Finally, it seems that I am going to the Next Generation Sequencing Congress in London this year, which will be very fun! Hope to see some of you dealing with sequencing there!
- Bengtsson-Palme J, Boulund F, Edström R, Feizi A, Johnning A, Jonsson VA, Karlsson FH, Pal C, Pereira MB, Rehammar A, Sánchez J, Sanli K, Thorell K: Strategies to improve usability and preserve accuracy in biological sequence databases. Proteomics, 16, 18, 2454–2460 (2016). doi: 10.1002/pmic.201600034 [Paper link]
I have been asked to give a short talk on the metals and biocides and antibiotic resistance co-selection conference I mentioned in February. My presentation will take place late Tuesday afternoon, and is entitled “Elucidating biocide and metal co-selection for antibiotic resistance in sewage treatment plants using metagenomics“. I hope to see you there!