Registration is now open for the NCCR Microbiomes' workshop Advanced methods in microbial community analysis. This short winter course will take place from 12-23 January 2026 at the University of Lausanne. NCCR experts will present in-depth topics in working with sequencing data, including experimental design, data analysis and interpretation, and data re-use.
Register at this link: https://forms.gle/kpNtq4jybxdMwrq58.
Proliferation and survival of bacterial inoculants for bioaugmentation into soils is often limited by their incapacity to compete for nutrients with the native resident microbiota. In a new publication, Clara, Phil and Senka, in collaboration with the Greene lab, showed how engineered utilization of phosphite instead of phosphate as P-source, can give distinct advantages for a toluene-degrading strain of Pseudomonas veronii to grow and sustain in developing or steady-state soil microcosm-grown synthetic communities. Congratulations to all! Look at the open-access publication here.
Congratulations to Hammam, Nico and Hanna, for their new publication on the DNA sliding mechanism that permits a ParB-like protein encoded by ICEclc to regulate its activation and transfer. And a great outcome of the collaboration between the Gruber and van der Meer labs!
A big hurrah to Roxane for passing her PhD thesis exam successfully!
Congratulations to Gaitan and Nicolas for their new publication, uncovering the bimodal pattern of manganese oxidase expression in stationary phase Pseudomonas putida cells. Not yet the 'why' for manganese oxidation but at least the 'when'! And a great outcome of a wonderful collaboration with the group of Jasquelin Pena at UC Davis.
Congratulations to Tania, Isaline and Xavier, with help of Manupriyam, Elvire and Helena, for their work on a new method to infer interactions between bacteria from time-lapse microcolony measurements! Just published and online downloadable for everyone!
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.
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)
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
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.
Congratulations to Tania for winning this year's FameLab public outreach prize!
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 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 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.
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.
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.
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.
Congratulations, Diogo, for the acceptance of your work on directed evolution of biosensor protein variants based on RbsB. See the open access work here.
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.
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!
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.
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
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.
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.
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