(1/7) Excited that the Virtual Colon, an extension of BacArena for modeling the spatiostructural environment of the colon, is now out at mSystems. Kudos to @maringos.bsky.social and for leading this work! @crc1182.bsky.social @uni-kiel.de iel.de Link: journals.asm.org/doi/full/10....

Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment #mSystems from @kaletalab.bsky.social journals.asm.org/doi/10.1128/...

The pre print of my PhD research is out! 📣 Check it out for some cool results on high-throuhput microbial isolation, #SynComs and #Tree #Microbiome 🌳🧫 doi.org/10.1101/2025... #PhDone 💯

We are delighted to let you know that your Plants, People, Planet article 'Demystifying Fungal Systematics: A Gateway to Fungal Literacy and Societal/Ecological Relevance Through Familiar Species' has been published on Early View. nph.onlinelibrary.wiley.com/doi/10.1002/...

Want to delineate genera? We have been optimising POCP, and propose POCPu, which stops the 'double counting' of proteins in POCP by only allowing unique matches. We also speed up, and benchmarked, the analysis using DIAMOND; peerj.com/articles/202... (now implemented in Protologger)

Is the human microbiome a source for hospital-associated infections (HAI) and are any genetic changes associated with HAI? In our new preprint, we longitudinally reconstruct the evolutionary processes within the human microbiome leading up to HAI: doi.org/10.1101/2025...

Come and do a PhD with me! Are you looking for a PhD project at the intersection of #microbiome and #food science? This project, in collaboration with ADM milling, will explore novel microbiome targeted food ingredients

How to design new synthetic microbial communities? It's a huge question we're still deeply exploring 🦠 Check out this new preprint by @tcahitch.bsky.social & @tclavel.bsky.social! They developed an function-directed approach using metagenomic to build better SynComs. www.biorxiv.org/content/10.1...

New article on equitable reuse of public sequencing data, published in @natmicrobiol.nature.com! Led by the Data reuse core team @lhug.bsky.social @environmicrobio.bsky.social Cristina Moraru, @geomicrosoares.bsky.social, @folker.bsky.social and with Anke Heyer and The Data Reuse Consotrium!

The main work from my time in Aachen is now out 🎉 if you have wanted to make a SynCom that captures the functional-landscape of microbiota, MiMiC2 makes that possible based on metagenomic data! 1/7 doi.org/10.1093/isme...

It’s also timely to present about SynCom design considering the recent work from @tcahitch.bsky.social @tclavel.bsky.social. I highly recommend reading! academic.oup.com/ismej/advanc...

Excellent article on quantitative production of fermentation products by the microbiota. Key takeaway: microbial fermentation products may be more important in mice than humans, amplifying microbiome effects in mice. www.cell.com/cell/fulltex...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

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...

Go and check out the pre-print of the landscape-scale tree microbiome study from the Future Oak project. Huge amounts of efforts and talent went into this work, with a pinch of "this is crazy, but we can do it". Well done @jamesemcdonald.bsky.social @cenococcum.bsky.social et al. Thread below 👇

🧵 New preprint alert! From the Future Oak project, led by @cenococcum.bsky.social Landscape-scale impacts of environment and disease on the tree microbiome 🌳🦠 www.biorxiv.org/content/10.1...

well this is kinda cool 🦠✨

New RESOURCE! Integrative genomic reconstruction reveals heterogeneity in carbohydrate utilization across human gut bifidobacteria @arzamasovalex.bsky.social @drlarsbode.bsky.social Andrei Osterman, Jeff Gordon & co #microbiomesky #microsky www.nature.com/articles/s41...

Our friends @thehesslab.bsky.social are actively looking for postdoctoral researchers interested in anerobic microbiology, and studying the rumen microbiome. #microbiologists #bioinformatics #microbiomes Check out their website: hesslab.com

An update to my recent pre-print: Start right to end right: authentic open reading frame selection matters has just gone online. In it, we look at the effect of mis-annotating an ORF on a spliced gene's predicted protein structure. www.biorxiv.org/content/10.1...

🧪🌾 VACANCIES - Are you looking for a postdoc or group leader opportunity? Come and work with us at @umeaplantsciencecentre.se 🌱! 🍀 We have currently several job openings available. Take a look on our homepage and apply: www.upsc.se/jobs.html #PlantSciJobs #plantscience #hiring

UK Gut-Immune-Brain Axis Network+ We are building a UK-wide interdisciplinary research community to advance the mechanistic understanding of the gut-immune-brain axis.  Join our network to find out about our UK-wide launch event, where we will announce #funding opportunities www.giba-uk.org

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨 doi.org/10.1038/s414... We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

www.nature.com/articles/s41... Our new paper on the risks and socio-demographic dimensions of antibiotic resistance in the human gut is now out in @natcomms.nature.com!

Go and check out the great review by @xinmingxu.bsky.social and collaborators in this issue, and also shout-out to @evolvedbiofilm.bsky.social for supporting amazing science art actually made by a real humans and not AI!

Beautiful new review paper in preprint bridging microbial ecology and classic ecology led by Maggie Vogel, @olimeacock.bsky.social and @annasophieweiss.bsky.social, also by @juliensluneau.bsky.social and @lambdapp.bsky.social from our lab (not me :)) ecoevorxiv.org/repository/v...

The team's first preprint is out! Led by ‪ ‪@vishnuprasoodanan.bsky.social‬‬ & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data? A 🧵.

🚨 Job Alert at RBG Kew! We are looking for Lab Research Assistants in genomics to join our Fungarium Sequencing Project! Do you like Fungi? Do you want to develop new -omics techniques? Interested in historical collections? Join the team! Posts to start ASAP. Apply here:https://lnkd.in/e2BpWJpA

Ever wondered why proton pump inhibitors raise the risk of C. diff infections? Is it due to pH shifts or direct antibacterial effects on the gut microbiome? We think it’s the pH. 🧪💡 Dive into Julia & Patrick’s new paper for the full story! 📖👇 #Microbiome #PPI doi.org/10.1080/1949...

Want to do a #PhD focusing on discovery, cultivation and characterization of novel prokaryotes? Come and join my group in the Laboratory of Microbiology at Wageningen University! Apply here: wur.nl/en/vacancy/p... #cultivation #microscopy #archaea #PhDposition Please share & repost

Let us introduce a new subspecies: ✨Catenibacterium mitsuokai subsp. tridentinum✨ Plus, we also propose a taxonomic reclassification of publicly available reference genomes belonging to the C. mitsuokai sp. More details ⬇️ www.microbiologyresearch.org/content/jour...

If you study in vitro models of gut consider joining INFOGUT and attend our future meetings!

New preprint @julkras.bsky.social et al. We show that degradation of sulfoquinovose, ubiquitous in plants and algae, is a core function of the cow rumen microbiome and describe novel SQ-metabolizing taxa. 🐄🧫🦠 #microbiomesky #microsky

I am happy to share our latest preprint, spearheaded by Laura Camus. We show that tyrosin-dependent interactions can foster integration of S. aureus into the nasal microbiome. @cmfi.bsky.social @lmumuenchen.bsky.social www.biorxiv.org/content/10.1...

Very happy that HiBC is out: rdcu.be/ekSCO 🔥 @natcomms.nature.com Excellent team spirit, and, as always, great driving factor by @tcahitch.bsky.social ⭐⭐⭐⭐ We hope that these bacterial isolates from the human gut will facilitate many studies by others... 😀

Do people in the same household share strains when they have the same species? How many cells transmit when a strain is shared? Can strain composition be dynamic when species composition is stable? We answer these and related questions for the facial skin microbiome in our latest paper. 🧵[1/10]

We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue doi.org/10.1093/nar/... Easy to use, no registration, fast, scalable, various visualizations, in sync with Bakta CLI: bakta.computational.bio (1/5)

Here we share thoughts on next-gen cultivation: rdcu.be/ejPSb. Hope it helps 😄 Was fun to write with great colleagues @lisamaierlab.bsky.social @jselkrig.bsky.social @baerboletta.bsky.social @typaslab.bsky.social @mmmicrobiomelab.bsky.social @leibniz-dsmz.bsky.social @westermannlab.bsky.social

📢We are #hiring a full time editor to handle areas including microbial ecology & plant microbiology🦠🌱 This position will work closely with @naturecomms.bsky.social #microsky #microbiomesky #ecologysky 🧪 Available in NYC, Madrid, or other US offices Read more & apply here: shorturl.at/yvdYJ

Excellent work by @tcahitch.bsky.social ⭐ and there is even more to come very soon... 🔥

Ever wondered if we are correctly predicting proteins from metagenomes? If so, we are happy to present our new work improving the prediction of proteins from the human gut microbiome: www.nature.com/articles/s41...! We corrected how each taxon's proteins are predicted and found WAY more proteins!

Do not miss the opportunity to network and participate in FAIR microbiome science 😄 Upcoming @nfdi4microbiota.bsky.social event, May 19-20. Keynote by Prof. John Penders (www.maastrichtuniversity.nl/j-penders/re...)

New preprint from the lab 😄: Robust genome-based delineation of bacterial genera. With dream team #CharliePauvert @tcahitch.bsky.social ⭐⭐; will hopefully facilitate the classification of bacterial genera; www.biorxiv.org/content/10.1...

If you generate, or use MAGs, you should really read the work we have done benchmarking their limitations. Using complex mock communities (70 species), we assessed how deeply you need to sequence to accurately conduct common metaG analyses. Webwere shocked to see even HQ MAGs are often chimeric!

1/12 Thrilled to share our latest paper on host-microbiome-interactions in aging out in Nature Microbiology @naturemicrobiol.bsky.social, great work led by Lena Best @sci-witch.bsky.social with the Frahm lab within the ITN SmartAge. @crc1182.bsky.social @uni-kiel.de www.nature.com/articles/s41...

Robust genome-based delineation of bacterial genera www.biorxiv.org/content/10.1... #jcampubs

Glad to see this great collaboration with HiPP out 😁 using their cohort data we found the infant gut hopscotches between community states, preventing it's trajectory being predictable up to 3 years; academic.oup.com/ismecommun/a...

📣 Conference Announcement! Till Strowig, @lisamaierlab.bsky.social and I have organized a stellar lineup of speakers from different corners of the Microbiome field for the 17th SeeOn Conference in picturesque Bavaria. Open to all! Abstracts due April 6th. Spread the news! www.dghm.org/seeon/

👇Four days left to apply! (Friday 14th of March)👇

In case you saw this and thought 'oh no, I missed the boat!' - you haven't! The abstract deadline for the @crems-york.bsky.social Magic and Witchcraft conference is THIS FRIDAY, 14th March 👍 @drdebsmoretti.bsky.social #CfPs #History #Skystorians royalhistsoc.org/calendar/wha...