ISME 2016 – Conference Summary

By September 26, 2016Summary

Few weeks back, I attended the International Society for Microbial Ecology conference in Montreal. Over four days I listened to a series of great talks and I wanted to share a summary of the highlights of this conference and also try to not forget everything as it was quite an overload of awesome science.

The plenary sessions.

Every half day started with a keynote speaker presenting her/his work for 45 minutes. All of them were of incredible quality. And they all shared on common thing: all projects started from a very simple question and rose to sophisticated and advanced methods, new concept and increased the complexity of how to answer the question. All the different talks deserve a dedicated blog post to go in the details of how and why they were amazing but I would go over the two main one I liked.

For example, Rowan Stocker started by asking a very simple question: “How do bacteria move?” and by extent what make a bacteria move? and why? His lab developed amazing methods to track bacteria over time. Further by looking what the bacteria are attracted to it ended up by modeling complex molecule diffusion in water. Seeing the video of how molecule diffuses in three dimensions is quite mind blowing and just underline how we need to step up the game to understand microbial ecology.

Another amazing talk was from Richard Lenski who explained the research he and his team performed on Escherichia coli for the past 28 years! 28… years… A simple experimental evolution concept where 12 strains of E. coli are propagated every day for almost 30 years. Every other generation is frozen away and can be re-accessed later (you have to love bacteria and their ability to stay a long time in glycerol at -80°C, without dying or replicating). A simple design led to a huge data mountain on how evolution happens in bacteria. Over the 60.000 generations of E. coli they observed several amazing evolution events. By looking at growth curve they realized that E. coli was progressively growing faster indicating it was adapting to the flask environment better and better. One of the most amazing things is one of the strains suddenly being able to use citrate. And thanks to sequencing technology being more and more affordable they were capable of going back to their snapshot collection of evolution and sequence the hell out of it and get the genetic side of the evolution story! I think we all wish to have such an experiment to build multiple careers on!

The roundtable

I attended one of the roundtables organized on the first day: “Soil Microbiology metagenomic”. Even if I am far away from being a soil microbiologist I was still interested in what the metagenomic discussion would be. And oh boy wasn’t I disappointed. The daily routine of one’s lab would always blind to a certain degree what is happening outside the lab. What appeared from this discussion was that from the struggle of soil research to perform reliable metagenomic assemblies a larger “Malaise” is present in ‘omics research. A quick tour of the available tools for genomic showed that there is a multitude of tools doing roughly doing the same thing in different things. The omic horizon is broad and diverse, and it is a good thing, but it is very confusing for the new comers in the field to even comprehend were to start.

The question of having a universal framework has been raised and people suggested setting up online platform which would be the “TripAdvisor” of bioinformatics. Such projects are apparently on their way, the Scandinavian initiative “Elixir” is currently curating such website regrouping genomic tools with proper reference (Link: bio.tools). One another suggested option was to setup mentoring between senior bioinformatician and new ones, a concept good on the paper but maybe not that easy to set up. Many of the senior scientist often don’t have much time to spend teaching everything from scratch to new Ph.D. or Postdoc and junior scientist are often intimidated to ask for help, feeling like impostor in a field of giants.

I think some good question have been raised during this roundtable, and I think the computer scientists which are behind the most advanced tool in the fields, such as metaSPAdes or megahit, were absent from this discussion. With the amount of sequencing data predicted to reach a size larger than ALL the video on YouTube by 2020 we need to reach a point were biologist can use the tool on a large scale and start to data mine all biological secrets waiting to be found in the gigantic planet of data we are generating full steam ahead.

However one quote I liked during the discussion summarizes the state of the art: “Bioinformatics is like an awkward teenager, it’s impatient to be an adult be its not there yet.” I believe that sooner or later there will be a standard protocol to analyze genomic data the same way PCR has been streamlined to a universal protocol, but until there we will need people at the border of understanding a little bit bioinformatics and more biology to apply and drive the development of bioinformatics tools.

 

The sessions talk

So many session talk, so many thing to report! I will just bring in a couple of line the one I would like to remember for the future, as source of inspiration and support for my research.

The first one popping in my mind is the talk from Thorsten Thomas about the study of Eukaryotic like gene in bacterial genomes. Being fascinated by the interaction between prokarytoes and eukaryotes this has a special place in my nerdy biological heart. Bacteria harnessing host gene to trick them the other way, molecular mimicry, this is enflaming my curiosity every time. And we currently have data in our lab to play with! I just can’t wait to go back to my desk!

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