Multidrug resistance efflux pumps drive C. parvum virulence differences - showing how gut microbiome protects against pathogen colonization, and how antibiotics can disrupt this defense. 🦠💊 #microsky #microbiomesky #Mevosky 🧪 www.cell.com/cell-host-mi...

A little touch of science to personalize my office (DNA + lab pens) 🧬 - any new idea would be appreciated! Curious, what makes your office feels like yours? 🧪

Lineage tracking using methylation states from longitudinal bulk sampling. Sounds 🆒 and given recent work by @trevorgraham.bsky.social and colleagues, looks real. Wondering about other applications like 🦠🧫 👉🏻News and views: www.nature.com/articles/d41... 👉🏻Paper www.nature.com/articles/s41...

Super interesting! I’m curious what’s considered a “high-fiber” diet for people. Looks like the mice were tested on either no fiber or all carbs replaced with fiber? 🌾VS🍞 #microbiomesky 🧪🦠

#microsky 🧪

A great example that uses LLMs on temporal data to predict the future! Using historical health data as input tokens to predict later tokens - future disease events. www.nature.com/articles/s41... 🧪✨ #AI4S

Sounds like a lot of fun to meet the winners face to face! First stop @mitpress.bsky.social Videos will be posted later? 🧪 improbable.com/the-35th-fir...

Fascinating! 🤔 I wonder whether bacteria with simpler single-membrane envelopes (like Chloroflexota) could be more “permissive” to HGT of membrane systems (from both bacteria and archaea)? 🦠🔀🧪 #microsky

QuickVariants 🦠🧬🧪- a genetic variant identification tool developed for microbes, now on Bioconda! 🚀 • 9× faster median speed vs bcftools • Higher accuracy for both SNPs & indels bioconda.github.io/recipes/quic... bmcbiol.biomedcentral.com/articles/10.... #microsky #microbiomesky

Cool! Some gut microbes make 2-MiCit from propionate. In vitro, it inhibits 3D colon tumor growth (and normal cells at high dose). Just a 'lucky' one among millions of microbial by-products? I haven't thought of any selective advantage 🤔 Thoughts? 🦠🧪 #microsky #microbiomesky doi.org/10.1016/j.ce...

X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀 • 11–24× fewer suboptimal alignments (same for human genome) • 3–579× lower inconsistency • improves on ~30% of reads aligned to non-target species github.com/mathjeff/map... bioconda.github.io/recipes/x-ma... #microsky

Beautiful work 🎉 that resolved a long standing question: tumor microbiome, do they exist?🦠🧪 #microbesky

www.cell.com/cell/fulltex... #microsky #microbiome

#Newresearch This Bayesian statistical method uses timeseries microbiome data to infer interaction modules and is tested using a faecal transplant experiment in mice. #MicroSky www.nature.com/articles/s41...

#NewResearch Computational analysis and pairwise assays reveal that bacterial topoisomerase IV is a target of microbially produced phenazines, which informs synthetic-community design to treat fungal crop infection. #MicroSky www.nature.com/articles/s41...

Gut microbiologists’ “favorite?” bug 🦠, Bifidobacterium, co-evolves across animal host, with diet as a major selection force 🍎 #microbesky 🧪

AI co-scientist successfully predicted bacterial HGT mechanism of cf-PICIs🦠🔬. Careful - the top hit works, the other 15 less promising. Funny how people feel impressed but not surprised. Eventually, we want good ideas to be more surprising than reassuring! www.cell.com/cell/fulltex... 🧪 #microbesky

My gift to the lab (a claw machine with science ideas) and lab's gift to me 🤣 You can tell who are the grown-ups here!👶🎁

minimap2.com is potentially a phishing site. Please don't use anything from that website. github.com/lh3/minimap2...

About scRNAseq, they trained on a separate dataset and tested on OpenProblems benchmark. They picked 1 from 22 train-sets by manual inspection (no reasoning)🤔 Best result applies BBKNN to ComBat-corrected PCA embeddings rather than raw PCA. Could this “double normalization” risk overfitting?✨🧪 #AI4S

🦠📉A comprehensive model quantifying virus killing of bacteria based on bacterial population dynamics! Curious to see how it aligns with our simple model (Fig. 5) 👉 www.cell.com/cell-genomic... Bacterial density+dilution events strongly impact CRISPR immunity updates!! @mikeblazanin.bsky.social 🧪

A plasmid golden ratio? 🧬 Plasmid copy number ≈ 2.5% of chromosome size—consistent across bacterial species! pmc.ncbi.nlm.nih.gov/articles/PMC... @jerorb.bsky.social 🧪 #microbesky

Bugs-as-Buds 🍽️ Day 1 menu!

From bugs to drugs to bugs to (taste) buds (🦠 to 😋) - a new microbial research field putting microbes on the table 🍽️ Who’s up for starting a restaurant together? 👩‍🍳👨‍🍳 #Microbesky #Microbiomesky

Phage provoke growth delays and SOS response induction despite CRISPR-Cas protection #phage #phagesky royalsocietypublishing.org/doi/10.1098/...

Advice for interviews💡? Some candidates communicated way better in zoom interviews than in real life... Why?

I started a little weekend project because clearly reading and writing during the weekdays was not enough for me! 😄 Please take a look and share some feedback! editorome.substack.com #MicroSky #MicrobiomeSky 🦠

www.nature.com/articles/s41... #microsky a novel Bradyrhizobium species from a diatome can cross boundaries and induce nodules in a legume! Exciting!

Way above average editorial process! Good to know 🙌

You may have missed this #ant poster at #ESEB2025, but be sure not to miss the article just published in #openacess in @nature.com: www.nature.com/articles/s41...

I’d say “evolution” might be too broad in this specific context?🧐 “spreading” and “emerging” sound more specific and clearer? @bjesseshapiro.bsky.social @flodebarre.bsky.social

www.nature.com/articles/s41... #microsky #synbio

A newly discovered type of immune cell found in fat tissue seems to contribute to the chronic inflammation associated with ageing go.nature.com/3V2EOLU

Great call for early-careers✨👶! My current struggle is getting recognized. Track record still feels like the main currency for attention & funding. I attend Gordon conferences every year, but finding other trustworthy platforms to share early work & get feedback has been challenging. Any advice💡?

Campus housing 🏡 a big bonus! Plus more than 10 canteens 🥡(we haven't cooked a single meal for a year haha)! My American husband also likes it here :)

Check out our latest paper, a huge effort led by @benjaminguinet.bsky.social and @tvdvalk.bsky.social 🦣🔍🦠 Paper: www.cell.com/cell/abstrac...

One of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial: Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp). www.nature.com/articles/s41... (1/n)

I wrote about a rare genetic variant (a CNV) that appears to reduce the risk of schizophrenia diagnosis by ~5x, and why that's not as unambigously amazing as it sounds, but potentially still a pretty big deal.

If you're interested in learning microbiology🦠, AI 🤖, and bioinformatics 🧬, check out our lab’s knowledge graph (built by Jeff—our in-house software engineer). An efficient way to train PhD students! genomiverse.net/JeffsKnowled... #Microbesky #Microbiomesky #AI4S #Bioinformatics

Congrats and good luck, Pablo! In a storm, we need all hands on deck too!

Especially this AI4X postdoc fellowship! ✨🤖 www.ntu.edu.sg/research/res...

AI can pitch wild research ideas that sound novel. When 43 experts actually spent 100+ hours executing them, what would happen? arxiv.org/abs/2506.208... Our lab is using machine learning to generate new hypotheses based on solid knowledge🤖✨. More updates will come! #AI4Ssky

And please, always double-check whatever ChatGPT code gives you 😅

🦠💊Resistance genes were around before antibiotic - human use drove their spread and mobility. #Microbesky

NTU shared our DNA alignment tool designed for microbes 🦠🧬☰! #Microbiomesky #Microsky blogs.ntu.edu.sg/science/2025...

Non-antibiotics can fuel gut infections! 🦠💊 #MicrobiomeSky

3D toys to showcase phage recombination Φ🔀 at the SCELSE open house! @scelse.bsky.social PS: anyone got good bacteria 🦠 3D models? #Microbiomesky #Microsky #Phagesky

A tool to design a facile treatment for C. difficile!

Several years of work with several great collaborators, that combined computational biology, molecular microbiology, biochemistry, structural biology and mycology assay culminated in today's publication on discovery of novel bacterial toxins: www.nature.com/articles/s41...