Maybe I’m in the wrong side of microbiome research 🍫

"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude." www.biorxiv.org/content/10.1...

Really pleased to see this study led by @raymondkiu.bsky.social now published in @natcomms.nature.com! We show that probiotics help modulate the preterm infant 👶#microbiome - to reduce ARGs, lower MDR bacteria 🦠 & increase beneficial Bifido ✨ Huge team effort! www.nature.com/articles/s41...

Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it? Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...

New paper is out from our lab showing that some probiotics can accelerate and prolong the return of colonization resistance to C. difficile after antibiotics. news.ncsu.edu/2025/07/prob...

Got an email that my first first author paper from my PhD was accepted for publication! Cannot wait to talk about it! 🥳

Excited to see this new, and extensively-rewritten, version of our preprint up now! With @paulturnerlab.bsky.social we show how bacterial population dynamics (e.g. growth curves) can be used to accurately quantify bacteriophage infectivity 🦠 🧫🔬 #microbiology #VirEvol doi.org/10.1101/2023...

I never thought about wool as a possible route of infection. www.nature.com/articles/d41...

if she doesn’t show up #Eurovision

Albania is… confusing. Visually great but vocally confusing

Love that San Marino isn’t even singing. He got someone else to do it for him

RIP whoever who has to clean that sand

Sweden understood the assignment. They gave us another banger!

The core strength on those dancers tho!

Not normally a fan of chill songs on Eurovision but Portugal is surprisingly enjoyable

Malta is definitely serving

Not sure I appreciate the camera shake

And we are back on track with another banger!

With so many bangers back to back, Greece feels very meh

Quick #Eurovision recap: NETHERLANDS: LA LA LA LA LA LA LA! GERMANY: FA LA LA LA LA LA! POLAND: AAAAAAAAAAAAAAHHHHHH!

Germany is bringing classic Euro trash 💖

Poland delivering an absolute banger from costume, fire, dancing and core workout

That’s one very long piano

Finland showing them how it’s done

Mix feelings about UK’s entry 🧐

Those shoulder pads tho #Eurovision

A Chicago Pope implies the existence of an MLA Pope and APA Pope

Does anyone have examples of a (high profile?) paper that likely made an incorrect biological claim due to a contaminated genome from a metagenome? Don't worry, not a loaded question, because I think the answer should be.... yes! Just wondering what cases are out there.

THIS IS HUGE! An HIV PrEP drug candidate in the form of a ONCE-yearly intramuscular injection has been shown to BLOCK HIV infections AND participants achieved AND maintained protection ABOVE the 95% efficacy threshold for UP TO 56 WEEKS. Phase III trials are scheduled for later this year! 🧪🧵⬇️

Sometimes bullying is good and should continue

1/ Hey y'all, I'm excited to share my latest paper, which is out now in PNAS! We introduce FAVA, a statistical framework to measure compositional variability across microbiome samples. If you want to measure variability across a stacked bar plot, FAVA is for you! Paper: doi.org/10.1073/pnas...

Loving job::job! Chuck long-running code into job::job blocks, Rstudio will execute that code in the background so your console is free to do other stuff. Great if you, like me, always have 5 quarto documents open

🚨🦠 New from @viralemergence.org: Can mpox become endemic worldwide? Where did borealpox come from? Where could the next smallpox jump from animals into populations with dwindling susceptibility? We use AI/ML and viral genomics to make some educated guesses. 🔓😷🧪 www.nature.com/articles/s42...

I'm so happy that I can finally share the results of my first postdoc paper with @baym.lol!!! Turns out plasmids are an amazing system to study multi-scale evolution and we can track within-cell and between-cell dynamics! (1/n) www.biorxiv.org/content/earl...

become ungovernable

I'm delighted to announce that the 2025 @microbiologysociety.org meeting on "Understanding and predicting microbial evolutionary dynamics" will be held in Liverpool 26-27 November 2025! Abstract submission will open soon... #microsky 🧪🧫🦠 microbiologysociety.org/event/societ...

People in tech talk about the idea of a “10x programmer” — someone whose work is worth that of 10 others. I get the impression Musk etc think they can apply it all over the federal workforce but like… there’s no such thing as a 10x ATC navigational aid maintenance worker. Some jobs just need people.

Another day another parkrun

Check out our new method for summarising BEAST trees. The CCD0-MAP tree gives much more accurate results than MCC tree. It returns the tree that maximises the product of sampled clade probabilities regardless of whether that tree was sampled. Highly recommend :) journals.plos.org/ploscompbiol...

New paper: We show that population exposure to colibactin producing E. coli lineages ST95 and ST73 largely explains global variation in colorectal cancer incidence. Same STs are also major causes of UTIs and may be similarly involved in urinary tract cancers. www.sciencedirect.com/science/arti...

Serological data provide key insights on pathogen circulation. We introduce a new R package, Rsero, which is a pipeline to store and analyze age-stratified sero data, estimate the history of pathogen circulation and compare different transmission models. journals.plos.org/ploscompbiol...

Out now, a comprehensive guide to metagenomics -- from sample collection to data analysis. This primer covers best practices, challenges, and applications in health, agriculture & environment. A roadmap for studying microbial communities 👇 www.nature.com/articles/s43...

Dorado v0.9.1 now includes a bacterial model for genome polishing, so I put it to the test! How does it compare to Medaka? And does move-table data improve polishing accuracy? Read my analysis here: rrwick.github.io/2025/02/07/d...

I will die for these cuties 🥺

Just had a happy reminisce about the time they found plague on the NY Subway. Almost exactly 10 years ago today! www.theguardian.com/us-news/2015...

Foxes eating people's waste food may keep their population artificially high, a study has found. Simulation models showed human food is supporting their populations, fuelling predation on breeding birds & likely undermining fox control efforts. 🧪🦊 www.bbc.co.uk/news/article...

Science saves lives, but only if you can afford it. www.kansascity.com/news/nation-...

#JournoRequest If you are a researcher who has been affected by the current NSF and NIH freeze, the various EOs, or have opinions about them and want to talk to me for an article for @iflscience.com - please DM or email me at acarpineti @ iflscience.com We can keep you anonymous if you so choose.🧪