Microbiology, Metagenomics and Bioinformatics

Johan Bengtsson-Palme, University of Gothenburg | Wisconsin Institute for Discovery

Browsing Posts tagged Wisconsin Institute of Discovery

One of the questions I have received regarding Metaxa2 is if it is possible to use it on other DNA barcodes. My answer has been “technically, yes, but it is a very cumbersome process of creating a custom database for every additional barcode”. Not anymore, the newly introduced Metaxa2 Database Builder makes this process automatic, with the user just supplying a FASTA file of sequences from the region in question and a file containing the taxonomy information for the sequences (in GenBank, NSD XML, Metaxa2 or SILVA-style formats). The preprint (1) has been out for some time, but today Bioinformatics published the paper describing the software (2).

The paper not only details how the database builder works, but also shows that it is working on a number of different barcoding regions, albeit with different results in terms of accuracy. Still, even with seemingly high misclassification rates for some DNA barcodes, the software performs better than a simple BLAST-based taxonomic assignment (76.5% vs. 41.4% correct classifications for matK, and 76.2% vs. 45.1% for tnrL). The database builder has already found use in building a COI database for anthropods (3), and we envision a range of uses in the near future.

As the paper is now published, I have also moved the Metaxa2 software (4) from beta-status to a full-worthy version 2.2 update. Hopefully, this release should be bug free, but my experience is that when the community gets their hands of the software they tend to discover things our team has missed. I would like to thank the entire team working on this, particularly Rodney Richardson (who initiated this entire thing) and Henrik Nilsson. The software can be downloaded here. Happy barcoding!


  1. Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ED, Thorell K, Kanger K, Eriksson KM, Bilodeau GJ, Johnson RM, Hartmann M, Nilsson RH: Taxonomic identification from metagenomic or metabarcoding data using any genetic marker. bioRxiv 253377 (2018). doi: 10.1101/253377 [Link]
  2. Bengtsson-Palme J, Richardson RT, Meola M, Wurzbacher C, Tremblay ED, Thorell K, Kanger K, Eriksson KM, Bilodeau GJ, Johnson RM, Hartmann M, Nilsson RH: Metaxa2 Database Builder: Enabling taxonomic identification from metagenomic and metabarcoding data using any genetic marker. Bioinformatics, advance article (2018). doi: 10.1093/bioinformatics/bty482 [Paper link]
  3. Richardson RT, Bengtsson-Palme J, Gardiner MM, Johnson RM: A reference cytochrome c oxidase subunit I database curated for hierarchical classification of arthropod metabarcoding data. PeerJ Preprints, 6, e26662v1 (2018). doi: 10.7287/peerj.preprints.26662v1 [Link]
  4. Bengtsson-Palme J, Hartmann M, Eriksson KM, Pal C, Thorell K, Larsson DGJ, Nilsson RH: Metaxa2: Improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data. Molecular Ecology Resources, 15, 6, 1403–1414 (2015). doi: 10.1111/1755-0998.12399 [Paper link]

Can you spot the differences in color shade in this picture?

Me neither. And that’s why I suspect that I’ve spent 30 hours or so on something completely not useful stuff. I hereby take weekend. See you next week!

It’s been a long time before I have written something here, mostly because making ourselves at home in Madison have take some time; then we go the flue; and then there have been a lot at work after that. But now i will try to have another go at writing somethings on the Wisconsin Blog. First, a look at my (already messy) desk here at the Wisconsin Institute for Discovery.

And then, a look at my lab space, which I have a view of straight from my desk, through a glass window.

This week, I have started experiments with exposing our little model community to antibiotics and it looks like I’m getting potentially exciting results. I have to sit down with the data today to see if there’s statistical differences, but from the looks of the biofilms, there is potential here.

Next week I will try to start experiment with sand columns and see if I can replicate some of this in this setting as well. It is interesting being back in the lab, and I feel that this an experience that will be very valuable for me going forward. I look forward to the days later this spring when I will start generating sequence data from my own experiments!

Leaving Madison

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Jorn's Hall

Jorn's Hall - will not be missed

So this morning, I packed my stuff, cleaned out my room and went to WID for the last time this year. I had time to say goodbye to everyone in the lab but Bailey, and I have to admit that I feel a little bit sad leaving. This is a really good place, filled with very good people, in a very beautiful town. I will miss you Handelsman lab, and I will miss you Madison. On the other hand, tomorrow I will be picking up my daughter after preschool for the first time in a month.

My plane

Waiting for my flight

I am now waiting for my flight at the airport. I prepare for a long night of lost sleep (as I cannot sleep on airplanes). I am endlessly happy that I will be able to combine these two fantastic worlds next year when we are moving here altogether. Until then, farewell Madison – see you soon again.

Wisconsin Institute for Discovery

Wisconsin Institute for Discovery - a place filled with people I will miss

I guess this concludes the blog for this time around. Please check back this winter when we’re going here the next time. This is Johan in Madison – over and out.

Lake Mendota

Lake Mendota

Conjugation and Transduction

Copper to treat Anemia

Copper to treat Anemia

Knockout mice

Knockout mice

Vitamin D derivatives

Vitamin D derivatives

Around the biochemistry building of the University of Wisconsin-Madison campus (and perhaps also elsewhere), there are a lot of these signs, highlighting discoveries that were made in Madison. And they really have a history to be proud of. This place is where both bacterial conjugation and transduction was discovered, paving the way for much of the genome editing and studies we take for granted today. And they also did the basics required to generate knock-out mice for genetics studies. I could go on, but I I think I made my point. This place has a lost of history. And I doubt that my slightly messy project will live up to these groundbreaking discoveries.

Labor day

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My desk at WID

The place I work at WID... for two more days

This Monday is Labor day in the US. Which means, I work. After having Wednesday off from lab work, me and Manuel finished up my final experiments for this round yesterday evening, so I have spent this afternoon doing some data analysis. Or rather, I should have spent the day doing data analysis, but it was boring, so instead I have mostly been scripting this… Hopefully that will pay off at a later date when I analyze more plates…

Before that, I went to see a house, which I liked a lot, so hopefully I will be able to sign a contract for this before I leave for Sweden again on Wednesday. Fingers crossed, over and out!

Okay, first of all this is a shoutout post to Manuel Garavito, who has been putting up with me for the last two days – my first two days in a wet lab for several years. Manuel has been beyond fantastic in showing me their basic protocols and having patience with my rusty lab skills. If this project will work out, it will very much be because of him.

The Hop CatThis weekend, there haven’t been a lot of time for other things than lab work, but I spent Friday evening at the Memorial Union where I happened to stumble into a concert with Brazilian (I think, not sure) music. And on Saturday evening I went out to the Hop Cat, where I tasted the fantastic beer Psychedellic Cat Grass and got taught the basics of American football by a woman who was also there on her own, apparently to watch the game. So, I’m doing my well but working my ass off with things I am not really that good at. Yet.

Wisconsin Institute of Discovery

Wisconsin Institute of Discovery

So, I have arrived in Madison, WI. I had a 17 hour flight yesterday, and I am quite messed-up with my perception of time, but except for that i’m good. I spend the morning walking around in Madison (and found a really nice coffee place – Colectivo) and getting a phone contract. Madison really is a very beautiful and green town, which reminds me quite a lot of an “American Uppsala”. After that, I had lunch with the majority of the Jo Handelsman lab at the Wisconsin Institute of Discovery Building, and then Manuel spent the afternoon showing me the experimental system we’re going to use (and its quirks). Lots and lots of new things to take in and choices to consider. This will be an interesting year. Now, I will try to find a place to eat and get a beer before I’m too tired (it’s half past one in the morning in Sweden as I’m writing this…) I look forward to my coming month here, but I also miss my family a lot already.
Lake Mendota

Lake Mendota

Today, I started my new position at the University of Gothenburg as a non-tenured assistant professor (forskarassistent)*. In essence, this means that I have a position funded by my own grant until the end of 2020, although I will be on a leave-of-absence while doing my PostDoc with Jo Handelsman in Wisconsin. Speaking of which, I will be leaving to the US on Thursday next week for a month of setting things up at her lab (and also going to the EDAR4 conference in Lansing). I will return to Sweden in mid-September and leave for the US for real early next year.

In terms of actual work, this change of position will not mean very much at the moment. I will continue to do the same things for some time, and I will remain closely associated with Joakim Larsson’s lab at the Dept. of Infectious Diseases. And luckily, I will retain my lovely roommates for at least the time being. In the long run, however, this means that I will shift my research focus slightly, away from antibiotic resistance risk management towards interactions in microbial communities (still related to antibiotics though). Exciting times ahead!

* For some reason, the university administration refuses to call this position assistant professor in English at this time, instead referring to the position as “Postdoctoral research fellow”. I guess that it might be bloody annoying explaining that this is not the same as “postdoctoral researcher” and virtually everywhere else would be called “(non-tenured) assistant professor”, but then on the other hand, who cares about titles anyway?

So 2017 has begun, and this year will bring new challenges and exciting opportunities. First of all, my application for a 3.5 year grant from the Swedish Research Council for Environment, Agricultural Sciences and Spatial Planning (FORMAS) to go to Prof. Jo Handelsman’s lab in the US was granted. Since Prof. Handelsman in is moving her lab to University of Wisconsin in Madison, where she will be heading the Wisconsin Institute of Discovery (after returning from the White House), it means that this summer I will be moving to Wisconsin. I will retain a link to the University of Gothenburg and the Joakim Larsson lab though, and part of the grant is actually for covering my salary after returning from the US, so Gothenburg won’t get rid of me so easily.

The granted project will use high-throughput sequencing techniques to identify genes improving colonization and invasion ability or resistance to invasion in microbial communities, using a model system developed by the Handelsman lab. The project will focus on genes important for colonization, invasion and resistance to invasion under exposure to sub-lethal antibiotics concentrations. The project will contribute important knowledge towards the understanding of microbial colonization and invasion and highlight disturbances to the interactions in microbial communities caused by anthropogenic activities. In addition, the results of the project will hopefully allow for prediction of secondary effects of antibiotic exposure in the environment, and the preparation for future challenges related to infections with pathogenic bacteria. The project has already been highlighted by CARe (although this was before Jo announced her move from Yale) and a FORMAS press release (in Swedish).

The project will go under the acronym InSiDER, and I intend to write about it in a special section of the website, called the Wisconsin Blog. My intention is to include personal reflections on life in Wisconsin and work in the Handelsman lab there, but we’ll see how those plans turn out. Anyway, I am very thankful for FORMAS funding this project and giving me the opportunity to work with one of the leading scientists within microbial ecology in the world!