A bidirectional tango between drugs and bugs

We're very happy to release our new database Metalog metalog.embl.de ! It offers manually curated and harmonised contextual data for 110k metagenomics samples across the globe, incl. precomputed taxonomic profiles, for interactive browsing and for download 🧵 1/7 #microsky

schaechter.asmblog.org/schaechter/2... #MicroSky

Unexpected side-effect: how common medications clear the way for pathogens CMFI's @lisamaierlab.bsky.social @unituebingen.bsky.social show in @nature.com: many non-antibiotics weaken the natural protective function of the intestine. Press release: www.cmfi.uni-tuebingen.de/en/news-even...

Seeing this published is even better than eating sweets! I am so happy and proud of whole @lisamaierlab.bsky.social, especially Lisa and @jdlcz.bsky.social who walked the funny/exciting/rocky road with me until the very end. Check it out! #science #microbiome #health www.nature.com/articles/s41...

The paper is definitely worth a read—and if you're curious for a glimpse behind the scenes of how the story developed, don’t miss this short blog post by Anne and Jacobo. communities.springernature.com/posts/silent...

A tremendous team effort that spanned several years, led by two outstanding scientists in our lab: Anne Grießhammer (@ghammeranne.bsky.social) and Jacobo de la Cuesta-Zuluaga (@jdlcz.bsky.social). Huge thanks to everyone who contributed, to @cmfi.bsky.social, & to our superb collaboration partners.

Finally online! Our latest research is out @nature.com: We show that non-antibiotic drugs can disrupt colonization resistance, raising the risk of enteric infections. rdcu.be/ewwrG

It's finally out!🎉 We known that the #microbiome confers colonization resistance against #pathogens, we know that some meds 💊 affect gut microbes 🦠 So, do 💊 alter colonization resistance? It turns out that some do! If you wanna know more, check out our latest work www.nature.com/articles/s41...

Excited to share some key details on our latest research in @natmicrobiol.nature.com reporting intra-cellular accumulation of #PFAS (aka forever chemicals) by certain human gut bacteria. #microsky #mevosky #microbiomesky www.nature.com/articles/s41...

We asked our current student Elisabeth Limunga some questions about the IBC master programme and her ambitions 🤓 🤩 Application deadline: July 15! uni-tuebingen.de/ibc @daadworldwide.bsky.social @unituebingen.bsky.social @pasteur.fr @pasteuredu.bsky.social @steffenbo.bsky.social

I am very excited to share our latest publication on the effect of systemic #endotoxin on intestinal #microbiota spearheaded by the brilliant Sanne Kroon at the Hardt lab @eth-dbiol.bsky.social @ethzurich.bsky.social @naturecomms.bsky.social 👉🏼 rdcu.be/eelLn

What a better chance to read our review on how to counteract the negative effects of antibiotics and human targeted drugs 💊 our #microbiome🦠 if you haven't yet! www.cell.com/trends/micro...

Every time I write the discussion of a microbiome paper

Mechanism to mean everything and nothing at the same time. Do they mean a molecular interaction? A cellular process? An ecological dynamic?

In a great collaboration with @typaslab.bsky.social, @lisamaierlab.bsky.social and @biocs.bsky.social found that 24% of the tested human-targeted drugs inhibit the growth of gut commensal bacteria. "Extensive impact of non-antibiotic drugs on human gut bacteria" (2018) www.nature.com/artic...

And if you want to read how we're using these little critters to investigate the effect of #medication 💊 on the #microbiome 🦠and resistance against #pathogens 🧫, check our work (led by @ghammeranne.bsky.social) doi.org/10.1101/2023...

Our short piece highlighting the impressive work by @fatimacpereira.bsky.social on how the Parkinson’s disease drug entacapone disrupts gut microbiome via iron sequestration. www.nature.com/articles/s41...

For a PhD student, choosing a good lab is 10 times more important than choosing a particular topic to study

Thrilled to share our paper on differences in oral microbiome composition across subsistence strategies in Nepal is now out in Microbiome: link.springer.com/article/10.1...

River basins of Colombia. #rayshader adventures, an #rstats tale

Balancing act: counteracting adverse drug effects on the microbiome #TrendsMicrobiol from Lisa Maier lab Tübingen www.sciencedirect.com/science/arti...

#Medication 💊 can negatively affect our #microbiome🦠, but we obviously can't stop using meds. What can we do, then? In our latest article we review and discuss some of the current and future strategies to reduce microbiome damage ❤️‍🩹 @cmfi.bsky.social doi.org/10.1016/j.ti...

I wish there were a polite way to say, “I can see clearly that you are sick, and it would obviously be better for everyone if you were at home recovering, but since you’re here, I would greatly appreciate it if you took any kind of precaution to protect the people around you from your pathogens” 😷

New data on PhD student mental health: "By the 5th year of studies, the likelihood that PhD candidates needed mental-health medications had increased by 40%, compared with the year before study" This is why, when giving advice to students, I always mention self care www.nature.com/articles/d41...

Our paper together with @typaslab.bsky.social is out now! doi.org/10.1016/j.ce... Previously available on bioRxiv, it has now been accepted in Cell. 🎉 @sarsarela.bsky.social and @biocs.bsky.social show that bacteria can be protected from & sensitized to drugs in community; ... (1/2)

Thank you Sketching Science (sketchingscience.org) for this wonderful infographic showcasing our customizable and cost-effective lab tools! 🤗 ➡️ custom-lab.de Special ‼️: Subscribe to the email list and get a chance to win a 100 Euro voucher! 💸 🤑 ➡️ custom-lab.de/pages/win_a_...

🎥Lisa Maier (CMFI Board) recently featured in documentary on bacteria. She and her lab members provide insights into the current state of microbiome research and explain the work with bacteria in the laboratory. ardmediathek.de/video/gut-zu... @unituebingen.bsky.social @brkommunikation.bsky.social

Studying the #microbiome 🦠 with 16S is useful but coarse, #metagenomics are hi-res but more complicated. What about alternative markers? We used amplicon sequencing of dnaK and gyrB to study Clostridia in the human gut and link its diversity with #obesity doi.org/10.1128/msys...

One of the classic examples of 💊 affecting the #microbiome, but is it because the compound itself or because the effect on the host? Using bioreactors, my colleagues Julia and Patrick confirm that the effect of PPIs on 🦠 is due to pH and not a direct interaction @cmfi.bsky.social

Happy #WorldMicrobiomeDay 🥳 Did you know the human body has more microbes than there are stars in the milky way? ✨ Researching microbes means a lot of data to tackle. #NFDI4Microbiota wants to help you in processing your data and in making it #open and #FAIR 😀 More info 👉https://nfdi4microbiota.de/

Why is innovation stagnant in Colombia? (Article in Spanish) www.lasillavacia.com/red-de-exper...

Ever wonder how the #microbiome 🦠 weathers the storm of the #meds 💊 we consume? Check out our review of the response, resistance and recovery of gut commensals www.cell.com/cell-host-mi... @cmfi.bsky.social

I am happy to announce that our story on transposable elements in Thlaspi arvense has been published in PLOS Genetics 🥳. Want to know how TEs are shaping the genomic landscape of this future oilseed crop? Have a look: journals.plos.org/plosgenetics... #TEworldwide 🧬🌿

Have you ever wondered how to screen gut bacteria for their sensitivity against 1000s of compounds? We have, and our great colleagues in the @typaslab.bsky.social figured it out (with Sarela Garcia-Santamarina & Lisa Maier now having their own labs). 1/2

Last, the application of the protocol. Here we show that non-antibiotics disrupt the #microbiome 🧪🧫 and 🐁, which leads to a loss of colonization resistance by multiple #pathogens, including #Salmonella 🦠 Pathogens are more resistant to non-antibiotics than commensals doi.org/10.1101/2023...

Next, the first published work of my postdoc @cmfi.bsky.social We describe a high-throughput in vitro method to screen the effects of diverse compounds on #microbes or microbial communities doi.org/10.1038/s415...

First, from my PhD work @maxplanckcampus.bsky.social On a deeply phenotyped cohort of adults we observed that #obesity, more than cardiometabolic health, explains differences in #microbiome function doi.org/10.1080/1949...

A bit of shameless self-promotion to catch up with the work that came out while I was away from that other microblogging site