Sandpiper 2 is up. 913,000 metagenomic community profiles w @ace-gtdb.bsky.social R232, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroneys.bsky.social @thepatientwait.bsky.social @iambrettb.bsky.social and especially the new kid @nhstefan.bsky.social

Rhizosphere microbiome assembly enhances wheat viral disease resistance Wu et al. nph.onlinelibrary.wiley.com/share/JXK8DD...

A complete-genome view of phylum Nanobdellota and recurrent Form III RuBisCO transfer between archaea and Patescibacteriota www.biorxiv.org/content/10.6... #jcampubs

BTEXgenie: A curated and user-friendly tool for profile HMM-based substrate-specific annotation of BTEX degradation genes https://www.biorxiv.org/content/10.64898/2026.05.12.724592v1

Our paper is out! Giant viruses lay silent in algal genome across generations, but reactivate in reproductive cell types and under specific environnemental condition to produce virions. Thank you all for your contributions !

This online course will provide up-to-date info on the clinical relevance of microbial consortia & quorum sensing in inter-microbial cooperation, as well as IPC strategies for and management of biofilm-associated infections. https://ow.ly/e68n50YVqRK EUCIC European Committee of Infection Control

📢 Joining us tomorrow at the #HospitalAtHome webinar? “Death to Cef: How to use antibiotics in hospital @ home without causing an antibiotic apocalypse” Tue 19 May @ 13:00 (GMT) Chaired by: Sophie McGlen Speaker: Dr Jame McCrae Open to all 👉 Joining details: buff.ly/WhfjAH3 #MemberBenefit

Contrasting microbial iron metabolism in sediments from oxic and hypoxic estuaries www.frontiersin.org/journals/mic... #jcampubs

Reciprocal cross-feeding between bacteria can limit the emergence of metabolic dependencies journals.asm.org/doi/10.1128/... #jcampubs

Geometric ordering in bacterial communities www.pnas.org/doi/10.1073/... #jcampubs

And mega thanks to our science writer Michelle Hallenbeck. Check out more of her stuff here: microspacebiologist.com/author/micro...

We're excited to launch the MAB Newsletter! Issue #1 is a step-by-step tutorial on FeGenie, a tool we use to identify iron-related genes in (meta)genomes. Written for wet-lab biologists and nascent bioinformaticians. Read and subscribe here → middleauthorbioinformatics.substack.com/p/using-fege...

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

New #ecoevo paper @pnas.org: Evolution of species’ range and niche in changing environments. I show that feedback between evolutionary and population dynamics can create a tipping point where genetic variance erodes, and species’ ranges contract or fragment www.pnas.org/doi/10.1073/... #popgen 🧬🧪 🌎

Experimental evolution of enrofloxacin resistance and cross-resistance in Escherichia coli using a MEGA-plate system.

Very excited to share our new paper out in Nature. Congrats to Xiaoqian (Annie) Yu and all the coauthors. www.nature.com/articles/s41...

Botanical parasitism of an insect by a parasitic plant: Current Biology www.cell.com/current-biol...

🎉 Excited to share that our paper, “agtools: A Software Framework to Manipulate Assembly Graphs”, has been accepted in Bioinformatics Advances. (1/n) 🔗 GitHub: github.com/Vini2/agtools 📄 Paper: academic.oup.com/bioinformati... #bioinformatics #genomics #openscience

IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...

The impact of artificial sweeteners on bacterial physiology and the microbiome: Trends in Microbiology www.cell.com/trends/micro... #microsky #microbiomesky

Two updates I've been sitting on: 1. I'm an Anthropic Claude Community Ambassador for the SF Bay Area 🌊 2. Speaking at Code with Claude next week on why domain experts still matter in the age of AI — drawn from what we're building at @biokeaai.bsky.social claude.com/code-with-cl...

Can we reconstruct ancient pathogen genomes from animal remains? Can paleopathology help prioritize promising specimens? Our new paper demonstrates this by screening more than 300 specimens from across Eurasia over the past 6,000 years. www.nature.com/articles/s41...

🎉 📰 Very happy to share the journal publication of our manuscript "Plant-associated fungi co-opt ancient antimicrobials for host manipulation"! #ScienceAdvancesResearch @science.org @teamthomma.bsky.social www.science.org/doi/10.1126/...

New preprint: "A branching cell-fate decision in biofilm dispersal enables long-term surface persistence." When V. cholerae biofilms disperse, it isn’t a uniform exit, rather, an opportunity to bet-hedge. A subpopulation of cells stay behind, primed for biofilm regrowth. doi.org/10.64898/202...

One more app: ✅ FeGenie, 🔎 iron-related genes and more "Genies" to come soon! If you could use bioinformatic support on a current or upcoming project, contact midauthorbio.com, and a friendly colleague with microbiology and genomics expertise will follow up with you! cc: @ironark.bsky.social

🚨Microbial genomics researchers🚨 Terrific FREE web apps from @midauthorbio.bsky.social midauthorbio.com/#freetools No coding or command line required ✅ breseq, A+ microbial variant calling ✅ SprayNPray, taxonomic profiling of metagenomes ✅ Pseudofinder 🔎 pseudogenes ✅ GToTree, phylogenomic trees

(1/2) The goal of Middle Author Bioinformatics is to make bioinformatics more accessible to biologists. With that in mind, FeGenie is now available as a web app at midauthorbio.com/#fegenie, making it easier to use without the command line. #metagenomics #bioinformatics #genomics

(1/2) One of the easiest phylogenomics tools to use just got even easier. GToTree, by Mike Lee, is now available as a web application: midauthorbio.com/#gtotree #phylogenomics #genomics #gtotree #phylogenetics

Tiberius 2.0.0 is out 🎉 Now supports 7 eukaryotic clades, covering ~92% of NCBI assemblies. Modular rewrite + ~30% faster runtime. Benchmarks included, more soon. Thanks to Lars Gabriel, Richard Krieg & Felix Becker 🙌 github.com/Gaius-August... #bioinformatics #genomics #genomeannotation

Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis #ISMEJournal from @hollybik.bsky.social academic.oup.com/ismej/advanc...

Transposable elements are driving rapid adaptation of Enterococcus faecium -in @nature.com from Ami Bhatt www.nature.com/articles/s41...

Woah www.pnas.org/doi/10.1073/...

A single-stranded DNA virus replicates in the mitochondria of a marine oomycete https://www.biorxiv.org/content/10.64898/2026.04.22.720165v1

Applications are officially OPEN for the 2027 Gordon Research Conference on Multidrug Efflux Systems. 📅 When: March 21–26, 2027 📍 Where: Ventura, California 🔗 Apply here: www.grc.org/multi-drug-e... #GRC #MultidrugEfflux

Pseudoalteromonas is a symbiont of marine invertebrates that exhibits broad patterns of phylosymbiosis.

Temperature-dependent molecular evolution of dissolved black carbon and its interaction mechanism with dissimilatory iron reduction.

Advancing specialized biofoundries via automated adaptive laboratory evolution.

Comparative transcriptomics of closely related Geobacter sulfurreducens strains uncovers strain-level variations in extracellular electron transfer www.frontiersin.org/journals/mic... #jcampubs

Beyond metabolic dormancy: metabolic rewiring in bacterial persistence www.nature.com/articles/s41... #jcampubs

Great article about EvolvingSTEM & Dr. Abigail Matela's leadership to infuse dozens of schools w/ authentic microbiology research experiences that demonstrate evolution in real time. We've engaged more than 11,000 students over 11 years! 😅 🧪 🧫 www.hotmetalcampus.com/news-researc...

Histone diversity in the archaeal domain of life www.nature.com/articles/s41... #jcampubs

A study in Nature Aging shows that the strongest Alzheimer’s Disease risk gene, APOE4, can make certain brain cells in young mice hyperactive, which can predict later memory decline. The study also implicates Nell2 protein as a contributor to APOE4-driven dysfunction. #Alzsky 🧬🧪

Bacterial endosymbionts initiate morphogenesis of symbiotic organs at specific locations in auchenorrhynchan insects of Hemiptera.

Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery www.nature.com/articles/s41... #jcampubs

DefensePredictor: A machine learning model to discover prokaryotic immune systems #microbiology #prokaryotes #CRISPR #MicroSky @science.org www.science.org/doi/10.1126/...

Breathing both ways: simultaneous aerobic–anaerobic respiration in microbes www.sciencedirect.com/science/arti...

Welp, didn't realize transparent backgrounds became black when I posted the logo 😅 bsky.app/profile/jlst...

Unexpected Potential Bacterial Symbiosis Found in Fungus That Causes Angular Leaf Spot: https://www.apsnet.org/members/community/newsroom/releases/Pages/Achromobacter_Serrato-Diaz.aspx Read the original article by Luz M. Serrato-Diaz et al. to learn more: https://doi.org/10.1094/PHYTO-09-24-0302-R

Analysis of Bacterial Wilt Management Strategies From the Dynamic Perspective of Environmental Adaptation Approaches of Ralstonia solanacearum.