Triple Hurrah, first to Tania and Senka for successfully and brilliantly passing their PhD exams (bravo, Tania and Senka!), and to Maxime for the appearance of his first paper on Habitat fragmentation in picoliter droplets showing the effects of phenotypic variation of founder cells of species pairs on their reproductive success (aka the picoliter droplet story). Bravo Maxime, Isaline and all the other collaborators.
EEM-Lab
News and UpdatesTriple hurrah!
Fate of inoculants in soil microbiome interventions revealed (or why it frequently fails)!
Congratulations to Senka, Manupriyam and Marian, with help of Vladimir and Nico, for their combined forces to show the role of nutrient niche availability and metabolite facilitation that control proliferation of bacterial inoculants into (contaminated) soils! A special thanks to Guillem, Hans and Shini for collaborating on the metatranscriptomics analysis. A milestone for our lab! See the new Nature Communications publication here (https://link.springer.com/article/10.1038/s41467-024-46933-1)
Congratulations to Andrea for passing his PhD exam!
Microbiomes engineering review
We're very happy that our concerted review on microbiome engineering, collectively written by members of the NCCR Microbiomes, has now been published. We hope this will be widely interesting for researchers in the field!
Ahead of print: https://journals.asm.org/doi/10.1128/mmbr.00063-23
New paper on ICEs in Pseudomonas aeruginosa clinical strains
Congratulations to Valentina and Nico, in collaboration with CHUV researchers, for their publication on evolution and diversity of integrative and conjugative elements (ICEs) in clinical Pseudomonas aeruginosa strains.
Tania winning the FameLab competition!
Congratulations to Tania for winning this year's FameLab public outreach prize!
Congratulations to Isaline for her first paper in PLoS Computational Biology!
Congratulations to Isaline (and Maxime, Manupriyam and Renyi), for her first publication in PLoS Computational Biology on the development of a co-culture substrate competition model with metabolite exchange!
Maxime wins SSM award for best junior presentation!
Maxime wins this year's SSM 2023 award for the best junior presentation for his work on bacteria growing in picoliter droplets! Bravo, Maxime!
Congratulations to Helena and Tania for their new publication!
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!
Pseudomonas veronii Tn-seq in soils
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.
Congrats to Andrea and Valentina for their paper in Nucleic Acids Research
Congratulations to Andrea and Valentina for their amazing paper in Nucleic Acids Research describing the conjugative system of ICEclc! Wonderful and very hard work!
Transfer competence paper accepted!
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.
Congrats to Senka for her new publication on standardized soil microbiomes!
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.
Misfolding and mislocalization of RbsB mutant proteins
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.
New minireview on flow cytometry machine learning
Congratulations to Birge for her newly appeared minireview on machine learning applications of flow cytometry! Link to the paper is here.
Congrats to Birge and Caroline for their new paper on antibiotics degradation
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.
New paper by Diogo on directed evolution of biosensor protein variants
Congratulations, Diogo, for the acceptance of your work on directed evolution of biosensor protein variants based on RbsB. See the open access work here.
Inoculant transcriptome in soils
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!
New paper from Manupriyam
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'.
New publication in mSystems
Congratulations to Birge for her new publication fresh in mSystems! Very well done! Community analysis and biodegradation deduced from flow cytometry machine-learned data.
Pseudomonas nitroreducens genome
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.
ICE bistability regulation published
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!
Bacterial cell type recognition through machine-learned classifiers
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!
NCCR Microbiomes has started!
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.
Pseudomonas veronii multi-omics integrative study published
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
NCCR Microbiomes
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.
Shadows of Ribose-binding protein mutants
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.
ICE replication in single cells observed
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