Last year, June 2016, I had to opportunity to visit Nicola Segata’s lab in Trento, Italy for a 1 month research stay. I contacted Nicola a few months before the actual stay, and was very delighted with his enthusiasm of hosting me. In addition, Trento is very close to the skiing area where me and my parents used to travel every year for our snowboarding holiday. Italian food and coffee, close to the mountains and a world class research group. I don’t think I have to tell you how excited I was to get started.
Since I was going to Trento to improve my bioinformatics skills, I had to generate some additional data first. For this, we sequenced some of our favourite microbial isolates on one Illumina MiSeq run. With the data safely stored on my hard drive, I flew to Verona and took the train further to Trento. Then it went really fast; the friendly and awesome people in Nicola’s lab helped me improve my bash skills, teached me how to work on a cluster with multiple people, helped me set up an assembly, annotation and pangenomic pipeline and introduced me to the Northern-Italian lifestyle. Special thanks to (@epasolli) for inviting me into the CIBIO football matches and showing me around in the beautiful Val Di Fassa area.
Back in Antwerp, it was time to dig deeper and start to use all the new skills I’ve learned. When examining some of the genomes we sequenced together with a bunch of reference genomes we’ve downloaded from NCBI, I noticed something very odd when plotting the GC-content of one certain species, Lactobacillus casei. As shown in the figure below, it looked as if the species was split up in two. The most interesting part about this observation was the fact that one of our own isolates, AMBR2 also showed this elevated GC-content.
I was very lucky to have @s_wittouck, who joined the lab earlier that year, sitting right across of me. Together we got more and more involved in this story. With his background in phylogenetics, he showed me how to build phylogenetic trees from the pangenome pipelines and we started to explore AMBR2 and its closely related species (L. casei, L. paracasei and L. rhamnosus). It is then that we realised that we were on to something. So after showing our story to our promotor Prof. Sarah Lebeer, she convinced us to start writing everything down. After a lot of brainstorms, additional work and revisions on our side, we were very pleased to see that mSystems thought this was a good fit and wanted to publish our story after review.
I’m very happy with this result, and all of this within one year since I went to Trento for my research stay.
Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features
Read the full paper here.