EEM-Lab

Congratulations to Helena and Tania, for their publication on the development and usage of a new (easy) single cell tracking tool. Thanks as well to the various group members for their help in manual curation of many time-lapse images!

Congratulations to Marian and everyone for the publication of her work in mSystems to analyze the importance of Pseudomonas veronii gene functions for growth and survival in soils under toluene stress, by means of transposon library sequencing. A long and tedious work! Thanks in particular to Vladimir, Dominique, Senka and Nico, to complement and finalize all the necessary experiments.

A warm welcome to Bouke Entvelsen and Davide Ciccarese who have joined our group this week! Bouke will work as junior scientist on a project to study community behaviour in real time with time-lapse microscopy. Davide is senior postdoc who will work on droplet sequencing methods. So happy to have you around!

Congratulations to Andrea and Valentina for their amazing paper in Nucleic Acids Research describing the conjugative system of ICEclc! Wonderful and very hard work!

Happy to say that after a lot of collaborative efforts, our work characterizing the transfer competence regulon of ICEclc was published in PLOS Genetics. Thank you, Sandra, Andrea, Roxane, Nico, Vladimir, François and Veronica! This was an amazing journey with lots of images, time-lapses, qqplots, RNAseq and clonings; and a fascinating discovery on the life of mobile DNAs.

First publication within the NCCR Microbiomes studying how complex soil microbiomes can be grown in standardized soil systems, either from 21 individual soil isolates, or from washed natural topsoil communities. Great collaboration with Christian von Mering and Janko Tackmann at the University of Zürich.

A happy welcome to the new Master students Omar Keshk, Phil Gwyther and Mathilde Buvelot; and to our Iranian visiting student Helia Vahedi!

Happy congratulations to Xavier for successfully defending his PhD thesis at the University of Fribourg!

We are very happy to welcome Valentina and Anthony - who are starting their PhD working on ICEclc, and Bouke - Master student from the University of Amsterdam, who will be working on imaging of growing soil bacteria!

Congratulations to Diogo for his newest paper on the subcellular (mis)localization of RbsB mutant proteins, which we hope will help to advance the engineering of potential new de novo ligand-binding properties.

Congratulations to Birge for her newly appeared minireview on machine learning applications of flow cytometry! Link to the paper is here.

Sébastian Burz just started his new postdoc in our group, working on microdroplet and microbead cultivation systems to study community interactions. We are very happy to have you here!

What is the environmental fate of antibiotics?

A new study by Birge and Caroline, in collaboration with Kathrin Fenner from the Eawag showed the inhibitory effects that low concentrations of antibiotics have on reproduction and composition of freshwater and activated sludge communities.

They also provided evidence that some microbes may be using at least some of the antibiotics as growth substrates, which is still a very much debated issue. To arrive at their conclusions, they used supervised learning of community changes from multiparametric flow cytometry data.

Good-bye to Roxane, who started a new job and career at the HEP as a science instructor and teacher. We will miss you dearly, Roxane! Good luck in your new profession and hope to see you soon.

Sorry to see all these internship people leave again! Thanks a lot, Elvire, for the amazing time-lapses of growing microcolonies and help to Tania; Klara, for starting superinteresting experiments figuring out cooperative and competitive genes from transposon mutants; Margaux and Laura, for continuing a bit of Gaitan's work, and Iris, for making mutants in the ICE system!  All the best for your future science careers and hope to see you again!

Congratulations, Diogo, for the acceptance of your work on directed evolution of biosensor protein variants based on RbsB. See the open access work here.

Marian successfully passed her PhD exam on August 4! Happy congratulations and very well done!

Congratulations to Marian, Vladimir and Noushin for their new paper in Environmental Microbiomes describing the global reactions of our pet inoculant Pseudomonas veronii into non-sterile and contaminated soils!

Congratulations to Manu, for his publication in Communications Biology! Finally, one of the stories on soil bacteria in the famous alginate beads is out, showing the importance of interspecific effects on growth of soil bacteria communities. And read 'behind the paper'.

Congratulations to Birge for her new publication fresh in mSystems! Very well done! Community analysis and biodegradation deduced from flow cytometry machine-learned data.

We are very happy to welcome Helena Todorov as new postdoc in the group. Helena will be working on recognition of cell images in microbial communities.

Congratulations to Diogo, for successfully passing his PhD exam last Friday January 22! An excellent finish of his research on new RbsB variants as possible sensory proteins in bacterial bioreporters. All the best for your future career, Diogo!

Congratulations to Nico, Vladimir, Lenka and Claire, for their new publication on the genome of Pseudomonas nitroreducens, the first bacterium to degrade 2-hydroxybiphenyl! In contrast to previous reports, we find that the P. nitroreducens genome has three replicons and two new exciting ICEs.

Congratulations to Nico, Xavier, Sandra, François and Christian for our new publication in eLife, which describes the way how ICE bistability is regulated! Wonderful achievement!

Pass it on!

Congratulations to Birge, Noushin and Ambrin on their newest publication on the concept to use trained algorithms to recognize bacterial cell types in known and unknown communities from multiparametric flow cytometry data! Brilliant!

Our new NCCR Swisswide project initiative on Microbiomes has started! As Director of this NCCR I am very excited to see this important research topic being pursued across Switzerland in multi-collaborative research. For more information, see the NCCR website.

Welcome to Senka, Isaline and Tania, who started their PhD research in the group and will work on the new soil communities projects. 

Congratulations to Birge for successfully defending her PhD thesis last Thursday! We wish you all the best for your future career as an entrepreneur! Keep us posted about the developments.

Congratulations to Noushin on the publication of her new paper on the multi-omics integrative modeling of Pseudomonas veronii physiology.

npj Systems Biology and Applications 6, Article number 1 (2020)

https://www.nature.com/articles/s41540-019-0121-4

Welcome to Maxime, our new internship Master student from the University of Lyon, who will study interactions in synthetic microbial communities using picoliter droplet growth containers.

We are very happy and proud that the Swiss Government has decided to support our new collaborative initiative NCCR Microbiomes, which will enable us to work with 20+ groups on microbiome studies and engineering. We are waiting for a new website to be launched on this initiative. You can watch a short content movie here.

Manu successfully passed his PhD defense last Wednesday. Congratulations, Manu!

The SNF approved a new Sinergia project between our group and that of Prof. Christian Mazza at the University of Fribourg, to study interactions between microbial species in soil communities and develop a new mathematical framework to describe such interactions. If you are interested, drop me a line.

Congratulations to Birge for receiving an InnoTREK grant that will permit her to follow her start-up idea on machine-learned classification of flow cytometry microbiota data, to be carried out at the Institute of Microbiology in collaboration with the CHUV! Bravo!

Congratulations to Diogo, Artur, Shantanu, Vladimir and Aurélie, for their new publication on ribose-binding-protein engineering, appearing tomorrow: www.nature.com/articles/s41598-019-53507-5.

Thanks to their continued efforts, we have been able to shed ourselves of some of the shadows cast by previous irreproducible 'high-impact' work on ribose-binding-protein engineering.

We are happy to welcome Cédric Schneider, who is joing our lab for his civil service, working on biosensor development,

and to Samuel Aubert, first step Master student in Biology, who is working on the conjugative system of ICEclc.

Congratulations to Roxane and François for their beautiful work showing how ICEclc is replicated in individual cells preparing for conjugative transfer. 

Reference: Delavat, F., Moritz, R. and J. R. van der Meer. (2019) Transient replication in specialized cells favors transfer of an integrative and conjugative element. mBio 10(3): e01133-19

https://mbio.asm.org/content/10/3/e01133-19

This is the last week for Maxime, finishing his Master's project on the design and engineering of phenol-responsive ribose-binding protein mutants, and for Nora, who helped Birge on the lake water  communities project. Thank you so much, both of you, for the wonderful time and your endless energy! We will miss you. All the best for your future studies and careers.

Welcome to Andrea, our new PhD student working on the ICE project

and to Senka and Caroline, two new master students, who will start their projects mid-February.

This month is the last for Simone Hargraves, who did her First-Step project in the lab under supervision of Roxane, working on the role of oxidative stress on ICE activation.

And of Dainora Jankunaite, visiting student from Aalborg University, who did a four-month internship in the lab under supervision of Vladimir, working on the development of BRET-bacterial sensors.

Thank you, Simone and Dainora! It was a pleasure having you in the lab. All the best for the continuation of your studies.