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Davide Ciccarese

@davideciccarese.bsky.social
289 followers 379 following 65 posts

Bridging environmental science and real-world applications | Junior lecturer @ UNIL | Postdoc @ MIT | PhD @ ETH. Climate and bio based solutions. Author of 7 books, winner of two book prize.

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Davide Ciccarese @davideciccarese.bsky.social · 29/06/2026
Just for fun. Lately, I’ve been experimenting w/ AI. 👇Turning papers into infographic abstracts in seconds. Heatwaves do not only dry the soil surface. They also disturb the hidden bacterial and fungal communities that keep soils alive. @frantecol.bsky.social & @ Wolfgang Wanek. lnkd.in/ekRgjQ64
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Ákos T Kovács @evolvedbiofilm.bsky.social · 22/06/2026
From an interesting observation to an experimental system on circadian gene expression in B. subtilis, published in @natcomms.nature.com from @microclockerc.bsky.social The Bacillus subtilis circadian clock coordinates intricate spatiotemporal organisation 👉 www.nature.com/articles/s41... [1/n]🧵
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Davide Ciccarese @davideciccarese.bsky.social · 23/06/2026
Pre-AI era
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Noah Fierer @noahfierer.bsky.social · 18/06/2026
Ever wanted to use metagenomic data to infer oxygen levels (or the oxygen preferences of whole bacterial communities)? We have the tool for you: journals.asm.org/eprint/9GUIR...
journals.asm.org
Predicting oxygen levels in microbial habitats using a metagenome-based approach | mSystems
Oxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages diffe...
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Davide Ciccarese @davideciccarese.bsky.social · 18/06/2026
Just for fun: a model of how cell shape affects a growing biofilm, shown in 3D and as a 2D range expansion. It runs every shape and interaction combination and measures spatial metrics: which shapes reach the front, lineage survival, diversity. Feedback welcome.
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Davide Ciccarese @davideciccarese.bsky.social · 09/06/2026
Just for fun. A classic of microscale ecology: Mark Welch et al. 2016. From FISH microscopy to computational reconstruction of the oral plaque hedgehog biofilm: reaction-diffusion gradients, agent-based coaggregation assembly, and a dynamic 3D oxygen and metabolite solver. GitHub repo 👇
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Stefano Donati @stefanodonati.bsky.social · 08/06/2026
Happy to share our brand-new toolset for growth data analysis! This includes a python package and two apps for the analysis of data from plate readers (MicroGrowth) and mini-bioreactors (AutoGrowth). Everything is free and open-source. Link to the apps: biosustain.github.io/growthcurves...
biosustain.github.io
Growth Curves App
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Davide Ciccarese @davideciccarese.bsky.social · 08/06/2026
Just for fun, I built a small spatially explicit model to explore a cubic cross-section of cells growing in a biofilm, based on the three main interaction types (from a 10 yr. old review). Have a look, feedback is very welcome! github.com/davideciccar...
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Davide Ciccarese @davideciccarese.bsky.social · 05/06/2026
Just for fun, I took a review by a former colleague on classical ecological interactions and transformed its conceptual images into a spatially explicit range expansion model. The GitHub repo is open for anyone interested in spatial interactions or ecological modeling. Feedback is very welcome.
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Davide Ciccarese @davideciccarese.bsky.social · 01/06/2026
(It’s been a while since I posted here). I did a test today. 2 prompts and Claude Opus 4.8 made code, GitHub repo, docs and a GIF. Link 👇. Work that could take a PhD student days. Are LLMs ending heavy work and letting us ask wild questions, or more “meh, I could code it better”?
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Microbiome Virtual International Forum @microbiomevif.bsky.social · 20/01/2026
#MVIF 45 is starting! 👇 You can still register 👇 cassyni.com/s/mvif-45
cassyni.com
Cassyni | Science starts with a seminar
Seamlessly organise, run and publish academic research talks. Get started in minutes.
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Microbiome Virtual International Forum @microbiomevif.bsky.social · 06/10/2025
💫 #MVIF Season 5 💫 Feel free to join the keynotes by presenting your work–abstract submission is open: www.microbiome-vif.org/en-US/how-to... #MVIF is proudly supported by #illumina @corundumsb.bsky.social and our non-commercial co-organizing partners Seerave Foundation @cunysph.bsky.social
MVIF Season 5 program
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Davide Ciccarese @davideciccarese.bsky.social · 15/12/2025
Unifying Theories in High-Dimensional Biology: Approaches, Challenges and Opportunities arxiv.org/pdf/2512.10111
arxiv.org
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Snorre Sulheim @sulheim.bsky.social · 03/12/2025
Do you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself: keio.unil.ch Teaser: Increased proline in ΔputP #microsky #MEvoSky
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 18/11/2025
Don't miss out on our free virtual symposium (Dec. 12th) focused on microbial metabolites and their effects on the host. Sponsors: @amiposts.bsky.social, Pendulum, & Liv (@zymoresearch.bsky.social) Registrants will receive free memberships to Applied Microbiology International. Details below 👇
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Christian Kost @kostchristian.bsky.social · 28/10/2025
#microsky #mevosky @spp2389.bsky.social A PhD position is available in my lab to work on: Emergence and self-organisation of bacterial metabolism in consortia of cross-feeding bacteria. Please RT Deadline: 12.11.25 More infos 👇 shorturl.at/rAKAT
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EMBO @embo.org · 25/10/2025
Learn more about recent advances in anaerobic #microbiology at EMBO Practical Course "Breathless Microbes: Life With No Oxygen" in Nijmegen, Netherlands, 6–10 July 2026. 🧪 Deadline: 15 April 2026 meetings.embo.org/event/26-bre... #EMBObreathless #EMBOevents #MicroSky #biotechnology #biochemistry
meetings.embo.org
Breathless Microbes: Life With No Oxygen
Recent advances in anaerobic microbiology have driven significant progress in biotechnology, environmental microbiology, and biochemistry. Anaerobes play key roles in sustainable biotechnological pro…
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James Bradley @drbradbrad.bsky.social · 21/10/2025
Postdoc vacancy: Microbial dormancy in the cryosphere @erc.europa.eu #ERC_SIESTA 📢 PLEASE RT 🧬 Single cell microbial activity measurements, flow cytometry, cell sorting, omics, ecological interpretation ☀️ Marseille, France ‼️ Apply ASAP & before 7 Nov Link: emploi.cnrs.fr/Offres/CDD/U...
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Alvaro San Millan @sanmillan.bsky.social · 22/10/2025
New paper with my (amazing) friend and mentor @jrpenades.bsky.social Really looking forward to see what plasmid aficionados think of this one!! With @asantoslopez.bsky.social @wfigueroac3.bsky.social Akshay Sabins and others www.cell.com/cell-reports...
cell.com
Non-conjugative plasmids limit their mobility to persist in nature
Sabnis et al. explain why non-conjugative plasmids move at a low rate in nature. While increased mobility can easily evolve by incorporating phage DNA into plasmids, this is disadvantageous because it...
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Davide Ciccarese @davideciccarese.bsky.social · 25/10/2025
Excellent work by Estelle Pignon and @yschaerli.bsky.social! A great overview of how synthetic bacterial communities can be used to uncover the rules governing spatial organization.
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Ákos T Kovács @evolvedbiofilm.bsky.social · 30/09/2025
Two postdoc positions with @ajfedorec.bsky.social: one computational and one wetlab, for a 5 year grant on synthetic microbial communities Research Fellow in Computational Synthetic Biology www.ucl.ac.uk/work-at-ucl/... Research Fellow in Synthetic Biology www.ucl.ac.uk/work-at-ucl/... #PostDoc
ucl.ac.uk
UCL – University College London
UCL is consistently ranked as one of the top ten universities in the world (QS World University Rankings 2010-2022) and is No.2 in the UK for research power (Research Excellence Framework 2021).
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Ákos T Kovács @evolvedbiofilm.bsky.social · 25/09/2025
Cool PNAS paper by @jordivangestel.bsky.social and colleagues Contributed by Carol Gross [reviewed by @polzlab.bsky.social and @wcratcliff.bsky.social] Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation www.pnas.org/doi/10.1073/...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 14/08/2025
Cell Symposia: Host-microbiome dynamics May 10–12, 2026 | Bruges, Belgium by @cp-immunity.bsky.social @cp-cellhostmicrobe.bsky.social and @cp-trendsmicrobiol.bsky.social www.cell-symposia.com/microbiome-2...
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Christian Kost @kostchristian.bsky.social · 08/08/2025
I am excited to announce that the position of a senior postdoc (3 +3 years) in the field of theoretical biology is available in my group. The position provides the opportunity to closely interact with experimentalists and develop own research projects. Please RT. Details 👇: shorturl.at/iiiOv
shorturl.at
116 FB 5 Research Assistant (m/f/d) field of Theoretical Ecology and Evolution or Computational Biology: Uni Osnabrück
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Michael Brockhurst @brockhurstlab.bsky.social · 13/08/2025
We are also hiring a 4-year postdoc to study the dynamics and evolution of mobile genetic elements in the C-fixing Icelandic host-spring microbiomes Join our exciting multidisciplinary team funded by @ukri.org BBSRC sLoLa www.jobs.manchester.ac.uk/Job/JobDetai...
jobs.manchester.ac.uk
Research Associate in Microbial Evolution:Oxford Road
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Davide Ciccarese @davideciccarese.bsky.social · 13/08/2025
Applying ecological principles to microbiome engineering www.nature.com/articles/s41...
nature.com
Applying ecological principles to microbiome engineering - Nature Microbiology
This Perspective discusses the application of ecological principles of macro-ecosystems to microbiome engineering. The authors propose research priorities necessary to facilitate the application of th...
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Michael Cunliffe 🏳️‍🌈 @marinemicrobes.bsky.social · 22/07/2025
We are looking for a new @thembauk.bsky.social Anne Warner Research Fellow (5 year post) to develop an independent research group in the area of cell and molecular biology of marine organisms here in #Plymouth 🔬🦠🧫🧬 mymba.mba.ac.uk/job-listing....
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...
graphical abstract of the article the extended mobility of plasmids
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SeppeKuehnLab @seppekuehnlab.bsky.social · 17/07/2025
New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...
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Ben J Woodcroft @benjwoodcroft.bsky.social · 16/07/2025
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
Logo for the Sandpiper website
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Will Ratcliff @wcratcliff.bsky.social · 24/06/2025
1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬 www.science.org/doi/full/10....
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Davide Ciccarese @davideciccarese.bsky.social · 11/06/2025
These microscopy images are stunning. “Cellular anatomy of arbuscular mycorrhizal fungi” www.cell.com/current-biol... a study led by @rachaelcargill.bsky.social.
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eLife @elife.bsky.social · 06/06/2025
Not all persister bacteria are dormant! 🦠 Single-cell imaging of over a million #EColi shows that many antibiotic-resistant persisters were actively growing before drug exposure. Persistence appears to be more dynamic than once thought. buff.ly/04T4L1k
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EMBLtrec @embltrec.bsky.social · 05/06/2025
Amazing chance to work with CONTRAST project & TREC expedition coastal sediment samples to map chemical contaminants and how they shape microbial life over time. Based at Ifremer, Nantes in Chemical Contamination of Marine Ecosystems unit www.hellowork.com/fr-fr/emploi... #Postdoc #MicrobialEcology
hellowork.com
Offre Emploi CDD Post-Doctoral Position In Microbial Ecology Ecotoxicology M F Nantes (44) - Recrutement par Ifremer | Hellowork
Decouvrez l'offre d'Emploi Post-Doctoral Position In Microbial Ecology Ecotoxicology M F Nantes (44) en CDD pour Ifremer. Ifremer recrute actuellement ✓ Postulez dès maintenant ✓ Candidature Simple & ...
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Davide Ciccarese @davideciccarese.bsky.social · 24/05/2025
I fell in love with Philip Ball through Critical Mass. But How Life Works goes even further, with elegance, he explains the very essence of life and how evolution has shaped all living things. With ingenuity and no fear, he ventures into some of the most advanced ideas out there to explain life.
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Jacopo Grilli @jacrickets.bsky.social · 23/05/2025
Very good opportunity for theoretical / comp neuroscientists at ICTP ictp.it/opportunity/... 2+2 yrs independent postdoc fellowship ICTP is a supportive unique international institution Trieste offers great collaborations in neurosc and a great quality of life Move here!
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Germán Bonilla-Rosso @germusthermophilus.bsky.social · 22/05/2025
🧪🔬🦠🧫🌍 This is the kind of paper we should all be waiting for! Because sadly we still don't have reliable methods to count bacterial abundance from microbiomes. (I haven't read it yet, but I love the intention already) www.nature.com/articles/s41...
nature.com
Absolute quantification of prokaryotes in the microbiome by 16S rRNA qPCR or ddPCR - Nature Protocols
This protocol enables rigorous and reproducible quantification of prokaryotic concentration in stool samples by 16S rRNA qPCR or ddPCR.
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Cameron Thrash @jcamthrash.bsky.social · 19/05/2025
In a Sea of Microbes, Eddy Events Trigger Diatom Export in the Sargasso Sea academic.oup.com/ismecommun/a... #jcampubs
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STCmicrobeblog @stcmicrobeblog.bsky.social · 19/05/2025
christoph: ...not only in the sargasso schaechter.asmblog.org/schaechter/2... #MicroSky
schaechter.asmblog.org
Occasionally, Microbiologists use Macroscopes...
by Christoph — If you'd ask people around you which hand tool characterizes a professional microbiologist, they would probably come up with the microscope. Much like hammer and saw would be named as t...
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Johan Decelle @johandecelle.bsky.social · 17/04/2025
Happy to share our last study led by @akrao.bsky.social published in @currentbiology.bsky.social, showing how a planktonic host steals and hijacks chloroplast and mitochondrion of a microalga using 3D subcellular imaging. Funded by @moorefound.bsky.social; @erc.europa.eu #Protistsonsky #SymbioSky
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Microbiology Society @microbiologysociety.org · 08/01/2025
It’s official: The Microbiology Society is on Bluesky!
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Germán Bonilla-Rosso @germusthermophilus.bsky.social · 06/01/2025
🧪🔬🦠🧫Wow. This is one of the most exciting papers I've read... in my recent life! I wonder when I'll get to hear/see @flamholz.bsky.social explain it to a general public! doi.org/10.1073/pnas...
Screenshot of the paper's title: "The proteome is a terminal electron acceptor" by Avi Flamholz, Akshit Goyal, Woodward Fischer, Dianne Newman and Rob Philips in PNAS
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Davide Ciccarese @davideciccarese.bsky.social · 06/01/2025
A golden mine: “Microbiology research has historically focused on a few species of model organisms […] extreme bias in the distribution of bacteriology research across species, with half of all papers referencing only ten species and 74% of all known species remaining unstudied”
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STCmicrobeblog @stcmicrobeblog.bsky.social · 13/12/2024
#MicroSky #ArchaeaSky #ProtistsOnSky here comes the big to-do list...
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STCmicrobeblog @stcmicrobeblog.bsky.social · 28/11/2024
schaechter.asmblog.org/schaechter/2... #MicroSky
schaechter.asmblog.org
How to grow shrubs
by Christoph — Exactly eight years ago today, we introduced you to the 'Hedgehogs In Your Garden'. No, we had not turned our backs on the Small Things and became gardeners instead. Again today, it is ...
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Martin Jones @martinjones.bsky.social · 21/11/2024
The @royalmicrosoc.bsky.social #DataAnalysisInImaging special issue of Journal of Microscopy is out now! onlinelibrary.wiley.com/toc/13652818... #ImageAnalysis #BioImageAnalysis #RMSDAIM
onlinelibrary.wiley.com
Special Issue: Data Analysis in Imaging: Journal of Microscopy: Vol 296, No 3
The <em>Journal of Microscopy</em> is the oldest journal dedicated to the science of microscopy, publishing the latest advances in microscopy techniques and novel areas of application.
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SeppeKuehnLab @seppekuehnlab.bsky.social · 25/10/2024
This is a really important perspective on microbial ecology/evolution (Balakrishnan & Cremer). Quantitative physiology shows that microbes do not optimize growth, but instead express unutilized proteins that confer distinct dynamics when environments change. www.sciencedirect.com/science/arti...
sciencedirect.com
Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species
Protein synthesis is an important determinant of microbial growth and response that demands a high amount of metabolic and biosynthetic resources. Des…
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Davide Ciccarese @davideciccarese.bsky.social · 30/03/2024
Sleeping beauties. The mystery of dormant innovations in Nature and Culture. Weekend read.
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Will Ratcliff @wcratcliff.bsky.social · 19/03/2024
Two new papers out on the Multicellularity Long Term Evolution Experiment (MuLTEE). 1. We see the expansion of multicellular niche space, resulting in specialization for either growth and survival. These genotypes coexist for thousands of generations. www.nature.com/articles/s41...
nature.com
Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment - Nature Ecology & Evolution
Long-term experimental evolution and modelling show the evolution of small and large cluster-forming lineages of snowflake yeast that coexist over generations due to a trade-off between organismal siz...
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Davide Ciccarese @davideciccarese.bsky.social · 16/03/2024
Thrilled to be selected to speak @ #SMEEB2024 @ LIPh Padova where modelers & experimentalists come together to discuss ecology! It's my dream conference w/ an incredible lineup of speakers! I will talk about spatial self-organization in cross-kingdom interactions a work w/ @dudinlab.bsky.social
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