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

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]🧵

Pre-AI era

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...

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...

journals.asm.org

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.

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 👇

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...

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...

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.

(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”?

#MVIF 45 is starting! 👇 You can still register 👇 cassyni.com/s/mvif-45

💫 #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

Unifying Theories in High-Dimensional Biology: Approaches, Challenges and Opportunities arxiv.org/pdf/2512.10111

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

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 👇

ISB@isbscience.org · 10mo ago

Join @isbscience.org on December 12 for a Virtual Microbiome Symposium highlighting new discoveries about how gut-derived metabolites affect neural, immune, and endocrine systems. Open to microbiome-curious researchers and practitioners everywhere. isbscience.org/events/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

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

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…

meetings.embo.org

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...

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...

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...

cell.com

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.

Yolanda Schaerli@yschaerli.bsky.social · 12mo ago

Deciphering microbial spatial organization: insights from synthetic and engineered communities url: academic.oup.com/ismecommun/a...

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 – 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).

ucl.ac.uk

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/...

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...

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

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...

Research Associate in Microbial Evolution:Oxford Road

jobs.manchester.ac.uk

A new 4 year PostDoc position in our lab! Modeling + experiments to explore dynamics of carbon fixing hot-spring microbiomes. Part of an exciting multidisciplinary team with Sophie Nixon, @brockhurstlab.bsky.social & others Please share & get in touch if interested! tinyurl.com/e7j7bha3

Applying ecological principles to microbiome engineering www.nature.com/articles/s41...

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...

nature.com

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....

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/...

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...

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 🧵