Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg

Browsing Posts in Workshops

I will give a short talk on our findings related to antibiotic resistance associated with pharmaceutical production facilities in India at a one-hour webinar arranged by Healthcare Without Harm, taking place on Thursday, November 3rd, 10.00 CET. The webinar will discuss “hot-spot” environments in which antimicrobial resistance can emerge, such as areas in which there are poor pharmaceutical manufacturing practices, where expired or unused drugs are disposed of in an inappropriate way (i.e. by flushing them down the toilet or sink, or disposing them in household rubbish), and areas in which pharmaceuticals are used for aquaculture or agriculture. This is an important aspect of the resistance problem, but to date most of the actions taken to tackle the spread of AMR don’t take into account this aspect of antimicrobials released into the environment. The webinar is co-organised by HCWH Europe and HCWH Asia, and aims to raise awareness about the issue of AMR and its environmental impact. It features, apart from myself, Lucas Wiarda (Global Marketing Director & Head of Sustainable Antibiotics Program at DSM Sinochem Pharmaceuticals) and Sister Mercilyn Jabel (Pharmacist at Saint Paul Hospital Cavite, Philippines).

Sign up here to learn about:

  • Antibiotic pollution and waste
  • Recent findings from India regarding antibiotic discharges in rivers from manufacturers and new mechanisms by which resistance spreads in the environment
  • Sustainable antibiotics – how to support the proper and effective use of antibiotics and their responsible production
  • How the pharmaceutical industry is addressing the environmental pollution that leads to AMR
  • The best practices in managing infectious waste at hospital level


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Today the 15th Swedish Bioinformatics Workshop starts in Linköping. For the first time in many many years, I will not be there, which feels super-strange. (I even took part in organizing the workshop two years ago, in Gothenburg.) I would have thoroughly enjoyed the schedule (the workshops look amazing), and hope that everyone will have a very good time there without me. I do miss you! Please make sure I get another opportunity next year!

I am part of the organizing committee for the newly invented annual meeting for GOTBIN – the Gothenburg Bioinformatics Network. We will arrange a meeting on December 6 to get the networking activities for 2017 kickstarted, and every bioinformatician in Gothenburg is invited!

GOTBIN was launched to bridge and bring together all researchers in Gothenburg who fully or partially dealt with bioinformatics in their research. Through the network it should be possible to quickly find other local researchers tackling the same research problems as you are; to find appropriate resources to run your analyses; and to discuss research or infrastructure problems as they arise. To keep the network alive and kicking, it is crucial to keep relations active. Furthermore, it is also crucial to interact with key persons in the GOTBIN network to keep the lists of active researchers, resources and discussion forums up to date.

To facilitate future communication, we invite everyone who works with bioinformatics in Gothenburg to participate in a get-together workshop. The purpose of this workshop is to find out who is working with what and where, and to better get to know each other. This is a great opportunity to meet your next collaboration partner, post-doc or supervisor! The event will take place in Birgit Thilander at Medicinareberget (just next to the large lecture hall Arvid Carlsson) on December 6th, from 9.00 to 12.00. Fika will be provided and we will arrange ice-breaker activities suitable for the number of participants, so please register at: https://goo.gl/forms/KYdiiZMBDf0F9hvp2 by the 16th of November.

We hope to find everyone with a research interest in bioinformatics there and that this will be the launch of the next era of GOTBIN in 2017! See you there!

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!


  1. 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!

I have had the pleasure to be chosen as a speaker for next week’s (ten days from now) Swedish Bioinformatics Workshop. My talk is entitled “Turn up the signal – wipe out the noise: Gaining insights into bacterial community functions using metagenomic data“, and will largely deal with the same questions as my talk on EDAR3 in May this year. As then, the talk will highlight the some particular pitfalls related to interpretation of data, and exemplify how flawed analysis practices can result in misleading conclusions regarding community function, and use examples from our studies of environments subjected to pharmaceutical pollution in India, the effect of travel on the human resistome, and modern municipal wastewater treatment processes.

The talk will take place on Thursday, September 24, 2015 at 16:30. The full program for the conference can be found here. And also, if you want a sneak peak of the talk, you can drop by on Friday 13.00 at Chemistry and Molecular Biology, where I will give a seminar on the same topic in the Monthly Bioinformatic Practical Meetings series.

One of the highlights of the Swedish Bioinformatics Workshop 2014 was of course the dinner entertainment, a song specially crafted for the event. It has now, fortunately, been put online. For anyone who might not catch all the words, here’s the complete lyrics for the song (which is based on the song “Java Jive” in the Manhattan Transfer arrangement):

The Bioinformatics ABC

Grab your coffee
Grab your tea
Put down your spoon now and listen to me
For the bioinformatics ABC
Wake up, wake up, wake up, wake up, wake up

And C for Clustal, though it’s not that fast
Alternatives are Muscle and MAFFT
ABYSS and BLAST and Clustal, Muscle, MAFFT

D count reads with DESeq or E for EdgeR
And F for FastQC and G for GLIMMER
H for HMMER using Markov Chains
Hidden hidden Markov model

I for Inchworm;
Add Chrysalis and Butterfly and wish
Assemble fast with a sound that goes swish
Contig, contig, contig, contig, transcript

And the ton of tools for metagenomics
MEGAN, Megraft,
MetaPhlan, MG-RAST, Meta-GeneMark
And that’s just mentioning a few of them
(Talk it boy)

N for Newbler, old-school it is
If you’re still using 454 it’s a bliss
O for Oases, P for PyroNoise

Q is for Quake for that great quality
And R is for all those neat statistics
S for the Spades assembler, oh yeah

T for TopHat
U for Uclust
V for Velvet

There is Wham to align
XMatchView to review
And YASS to pursue
(But do you)
Know any tools beginning with Z?
Yeah, Zorro, Zorro, Zorro
Oh yeah

I would like to bring your attention to that the abstract deadline for the Swedish Bioinformatics Workshop held in Gothenburg in October has been extended to September 15. So hurry on and contribute with your latest research, we look forward to get to know what you’re doing!

I am part of the organizing committee for the Swedish Bioinformatics Workshop (#SBW2014) that will be held October 23-24 this year in Gothenburg. I would like to invite you all, especially master/PhD students and PostDocs in Sweden, to come and share the event with us!

SBW is an annual event that has been organized by the different universities in Sweden. This year it will take place at the Wallenberg Conference Centre in Gothenburg and is arranged by both University of Gothenburg and Chalmers University of Technology. SBW2014 will, as the tradition abides, be a meeting point for PhD students and postdocs working with any kind of bioinformatics within Sweden and is therefore free of charge for these groups. We are proud to announce a program including both invited speakers – such as Mick Watson from the Roslin institute, Dawn Field from University of Oxford, and Joakim Lundeberg from KTH – along with participant presentations and poster sessions. This year, the program will also contain a number of workshop sessions where hands-on problems will be used as starting points for discussions on new bioinformatics approaches to these problems. This will provide opportunities for attendees with different methodological backgrounds to interact and work together to find synergies between fields and come up with creative solutions.

More information about the event including registration and abstract submission can be found at www.sbw2014.se.

I, and the rest of the organizers, look forward to meeting you in Gothenburg in October!

Webpage: http://www.sbw2014.se

Facebook: https://www.facebook.com/events/1450513325188910/

Google+: https://plus.google.com/events/cuhlpovcc275stut854dk5ussnk

If you want, you can spread the word, for example using this flyer!

Science for Life Laboratories (SciLifeLab) in Stockholm will host a metagenome data analysis workshop on May 21-23, in which I will participate as a tutorial assistant. Additionally, our group leader Joakim Larsson will be giving a lecture about how we use metagenomics to assess the environmental reservoir of antibiotic resistance genes (much of my recent work will likely go into that). I hope to meet you there, so don’t forget to register!

Confirmed speakers:
Lex Nederbragt, Oslo University, Norway
Saskia Smits, Erasmus University Rotterdam, Netherlands
Joakim Larsson, Göteborg University, Sweden
Paul Wilmes, University of Luxembourg, Luxembourg
Anders Andersson, SciLifeLab, Sweden
Noan Le Bescot, UPMC (Tara expedition), France

The workshop is part of the AllBio Bioinformatics initiative.