Mumame – Quantifying mutations in metagenomes
Let me get straight to something somewhat besides the point here: summer students can achieve amazing things! One such student I had the pleasure to work with this summer is Shruthi Magesh, and a preprint based on work she did with me at the Wisconsin Institute for Discovery this summer just got published on bioRxiv (1). The preprint describes a software tool called Mumame, which uses database information on mutations in DNA or protein sequences to search metagenomic datasets and quantifies the relative proportion of resistance mutations over wild type sequences.
In the preprint (1), we first of all show that Mumame works on amplicon data where we already knew the true outcome (2). Second, we show that we can detect differences in mutation frequencies in controlled experiments (2,3). Lastly, we use the tool to gain some further information about resistance patterns in sediments from polluted environments in India (4,5). Together these analyses show that one of the most central aspects for Mumame to be able to find mutations is having a very high number of sequenced reads in all libraries (preferably more than 50 million per library), because these mutations are generally rare – even in polluted environments and microcosms exposed to antibiotics. We expect Mumame to be a useful addition to metagenomic studies of e.g. antibiotic resistance, and to increase the detail by which metagenomes can be screened for phenotypically important differences.
While I did write the code for the software (with a lot of input from Viktor Jonsson, who also is a coauthor on the preprint, on the statistical analysis), Shruthi did the software testing and evaluations, and the paper would not have been possible hadn’t she wanted a bioinformatic summer project related to metagenomics, aside from her laboratory work. The resulting preprint is available from bioRxiv and the Mumame software is freely available from this site.
- Magesh S, Jonsson V, Bengtsson-Palme J: Quantifying point-mutations in metagenomic data. bioRxiv, 438572 (2018). doi: 10.1101/438572 [Link]
- Kraupner N, Ebmeyer S, Bengtsson-Palme J, Fick J, Kristiansson E, Flach C-F, Larsson DGJ: Selective concentration for ciprofloxacin in Escherichia coli grown in complex aquatic bacterial biofilms. Environment International, 116, 255–268 (2018). doi: 10.1016/j.envint.2018.04.029 [Paper link]
- Lundström S, Östman M, Bengtsson-Palme J, Rutgersson C, Thoudal M, Sircar T, Blanck H, Eriksson KM, Tysklind M, Flach C-F, Larsson DGJ: Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms. Science of the Total Environment, 553, 587–595 (2016). doi: 10.1016/j.scitotenv.2016.02.103 [Paper link]
- Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ: Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India. Frontiers in Microbiology, 5, 648 (2014). doi: 10.3389/fmicb.2014.00648 [Paper link]
- Kristiansson E, Fick J, Janzon A, Grabic R, Rutgersson C, Weijdegård B, Söderström H, Larsson DGJ: Pyrosequencing of antibiotic-contaminated river sediments reveals high levels of resistance and gene transfer elements. PLoS ONE, Volume 6, e17038 (2011). doi:10.1371/journal.pone.0017038.
The Wisconsin Blog is on again
I’ve been having a very intense start of the year with the move to the US and getting the family accustomed to Madison (which has taken time and energy, but gone really well). I just wanted to make you aware of that I have started posting at the Wisconsin Blog again and hope to be sharing research related stuff from my year in the US there. For more personal stuff, our family has set up a blog (in Swedish) at this address: https://palmeiamerikat.blogspot.com. You are very welcome to follow our adventure there!
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.
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.
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.
Something to live up to
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.
Today, I went to the big Saturday thing in Madison – the Farmers Market. Apparently this is one of the largest (if not the largest) farmers markets in America, and it’s huge. Farmers (and sellers of some other stuff like yarn) gather all around the State Capitol, and when I arrived at around half past eleven, there were so many people there that you had to just enter into the crowd and follow it in the given walking direction. The sign “Stay right for hot & spicy cheese bread” was right on it; you had to stay in the right lane to get there. But there was so much nice stuff. And then on the opposite side of the stands, there were families picnicking on the lawn and kids running around. I imagine that this will be a nice Saturday outing next Spring when we bring the kids here. For now, I ended up with three apples and some sprouts. I need to finish the food in the fridge before I go back home on Wednesday. Is it time to go home already? It’s been an eternity, but time has also passed so fast…
The rest of the day I spent walking around by the Lake Monona and Lake Wingra, taking a break for a coffee at Colectivo Coffee. Very nice place with excellent pourovers. But now my feet hurts and I need to get some sleep!
Students are coming back
I’ve spend the lion’s share of the past few days in the lab, working quite late to obtain supercool results that we will now verify over the weekend. It’s very exciting to be able to generate useful data already during your first week in the lab (after not doing wet lab work for years), but mostly this is thanks to Manuel. Anyway, look at the beauty of those plates! My new favorite color must be crystal violet.
Another thing that has happened over the past week is that the students are beginning to come back her for the autumn semester. This means nice little paintings on the ground, lots of things happening downtown, but also that it’s harder to sleep since the previously quiet area of college dorms is not seeing quite a significant amount of nightlife. Large packs of students passing by my window at night, talking loudly. It’s mostly nice though. There are many parallels between Uppsala and Madison – both are cities heavily centered around their universities, and both seem to die a little during summers when the students move out. The differences mainly are that Madison is much more beautifully located between three lakes, that Uppsala has a much older history, and that Madison seems to have quite a bit of nightlife also in the summertime.
On Monday I will go to see a house to rent next year. Please keep your fingers crossed that it’s good and, if so, that we’ll get it! Otherwise housing has been a bit of a hassle, since everyone wants to rent now before the autumn semester. But I hope that that problem will no longer be a problem on Monday. Have a nice weekend!
Back in Madison
Hey, sorry for disappearing for more than a week. The EDAR conference (more on that in a later post) was super-intense and the weekend with my Gothenburg research group in Munising in northern Michigan was fantastic but didn’t really leave any time for writing. And after that I have been quite messed up emotionally, feeling very lonely and started doubting my project and … well everything. But it’s looking better now again. Yesterday evening I was out dancing lindy hop at The Brink. Although I only did a few dances, it was very nice to do something that was all about feeling good and playing, and not so serious.
Today I have instead spent my evening doing grocery shopping at Whole Foods (what a fantastic store that is!) and checking out the areas where the University of Wisconsin keep their university housing. Oh, how I wish that we could get somewhere to live there. The surroundings are absolutely beautiful and there were kids everywhere on the lawns. That said, the queues for staying there are most likely very long. By the way, if anyone would have an insider tip on where and how to find good places to live in Madison, all input is appreciated. Tonight, Madison has been good to me.
Madison is beautiful
Today I spent some time walking in the other direction from the University. Gabriel suggested I took the walk by Lake Mendota downtown, and that was a really nice walk through the forest, just by the lake. After dinner, I had ice cream on one of the landings on the picture. Madison is really a nice and beautiful city; I look forward to going here with my family next year.
Tomorrow, I am in for a six hours drive to Lansing and the EDAR conference. I hope to be writing a little about my thoughts on the conference as well, but we’ll see if I will have time to get around to that…
The Wisconsin Blog
I just wanted to notify anyone who might be interested in following my more personal reflections on my month in Wisconsin (and in Michigan over EDAR4) that I will be updating my Wisconsin Blog at this site (hopefully) regularly. The blog updates are not visible on the first page, so you will have to actively go to the Wisconsin Blog page by clicking in the upper right of the page.
My first day in Madison
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.