Long-term organic farming shapes the avocado rhizosphere microbiota through the enrichment of drought-tolerant Bacillus spp. #NPJBiofilmsMicrobiomes from José Gutiérrez-Barranquero with @kevinbretscher.bsky.social @vcarryon.bsky.social www.nature.com/articles/s41...

This is a really thoughtful and interesting article on our current #PeerReview system in #AcademicPublishing by Adam Mastroianni. Absolutely worth the read. And you can then spend even more time reading the really interesting follow-up articles. #Science #SciencePublishing #ResearchPublishing

Anyone has tips to better balance the reads between barcodes with the @nanoporetech.com rapid barcoding kits? With the exception of 2 all these samples had an input of +/-200ng. There could ofc be small quantification/pippete errors but the difference between samples are sometimes huge. #nanopore

Learn more about adaptive sampling in our latest #Nanopore Know-How. Learn more here: https://nanoporetech.com/blog/guided-by-data-adaptive-sampling-for-targeted-sequencing?utm_campaign=Platform+%2F+Omics+26&utm_content=1770985380&utm_medium=social&utm_source=bluesky

🌻🦠 New preprint on bioRxiv! Leaf herbivory reshapes the sunflower rhizosphere microbiome, generating a soil legacy that enhances herbivory tolerance in subsequent plant generations through plant–soil feedbacks. 👉 www.biorxiv.org/content/10.6...

Announcing a new tool for "denoising" long-read amplicon sequences: savont. Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay. 1/4 github.com/bluenote-157...

Because I'm ranting... Please figure out how to replace "_" with " " in your taxa names. Then figure out how to italicize them. Not sure how difficult this is to do in Prism, but it's pretty straightforward with stringr/ggplot2/ggtext in R. How do plots like this appear in journals with 20 JIFs?

New publication: #Hypoxia induces #phenotypic and #metabolic shifts in endophytic #Flavobacterium sp. 98, by @xinyapan.bsky.social, @gillesvanwezel.bsky.social, @vcarryon.bsky.social, @raaijmakersjm.bsky.social, and others. doi.org/10.1093/isme...

‘Tien tot twintig jaar geleden onderzocht je feitelijk enkele, losse #microben’. Van losse cellen naar een gemeenschap vol samenwerking. Dat is hoe het inzicht in de wereld van microben zich heeft ontwikkeld. Lees verder over het #microbiële #onderzoek bij het NIOO: nioo.knaw.nl/nl/nieuws/oo...

🌱✨ Excited to see my PhD chapters come alive as peer-reviewed papers Endophytic Flavobacterium in action: Fighting root fungal disease → doi.org/10.1016/j.mi... Thriving in low-oxygen roots → doi.org/10.1093/isme... @raaijmakersjm.bsky.social @vcarryon.bsky.social

Here's the reality this example illustrates: It's not even just about people blindly trusting what ChatGPT tells them. LLMs are poisoning the entire information ecosystem. You can't even necessarily trust that the citations in a published paper are real (or a search engine's descriptions of them).

Are you expecting a new age of microbiome engineering Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases www.science.org/doi/10.1126/...

#PMS2025 is a great occasion for many members of the MicroSOS consortium to meet and discuss about the project’s current and future activities!

Safeguarding paella production against salt stress using global trends from @kevinbretscher.bsky.social #PMS2025

@kevinbretscher.bsky.social (from @vcarryon.bsky.social lab and #LeidenBiology PhD student) on Integrative analysis of rice microbiomes reveals a global core microbiome and signatures of alkaline and saline soils #PMS2025

Day 3 of #PMS2025 starts with Session 3: Plant Microbiome Interactions (sponsored by Microbioma CSIC)

Opening of #PMS2025 by @vcarryon.bsky.social @josraaijmakers.bsky.social @microsos.bsky.social

#PMS2025 kicking off with the EPSO 2025 meeting @microsos.bsky.social

Final countdown before the start of the #PMS2025!!! 🪴 Looking forward to seeing you in Antequera (Malaga) on 3-7 November! Final program at: 6thplantmicrobiomesymposium2025.com/programme/ #Plantscience #MicrobiomeResearch #Bioinformatics

New blog post! metaMDBG (@gaetanbenoit.bsky.social) and Myloasm (@jimshaw.bsky.social) have had recent releases, so I updated the benchmarks from the Autocycler paper: rrwick.github.io/2025/09/23/a... Both tools improved considerably! Time to update your conda environments 😄

Suprise delivery on Friday afternoon from @nanoporetech.com . Will be interesting to see if the Mk1D will increase flowcell output. #nanopore

We’re excited to welcome as keynote speakers for #PMS2025: 🪴 Lingfei Hu – Zhejiang University 💻 @jhcepas.bsky.social – CSIC & UPM Join us in Malaga on 3-7 November! Register now: 6thplantmicrobiomesymposium2025.com #Plantscience #MicrobiomeResearch #Bioinformatics

#PMS2025 is going global! 🌍 So far, participants from 32 countries have registered for #PMS2025 This is your chance to connect, share ideas, and network with a international community of #plantmicrobiome scientists. 📅 Join now @ 6thplantmicrobiomesymposium2025.com #MicrobiomeResearch

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler! Nanopore's getting accurate, but 1. Can this lead to better metagenome assemblies? 2. How, algorithmically, to leverage them? with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social 1 / N

New publication: Hub #metabolites at the root–microbiome interface: unlocking plant #drought resilience, by @vcarryon.bsky.social and others. #droughtresilience #climatechange #sustainableagriculture doi.org/10.1016/j.tp...

Living organisms are assumed to produce same-species offspring. A study in Nature reports a shift from this norm in Messor ibericus, an ant that lays individuals from two distinct species. go.nature.com/3V68MP0 🧪

We are happy to announce 2 more keynote speakers for #PMS2025! We’re excited to welcome: 🔬 @gillesvanwezel.bsky.social – @unileiden.bsky.social 🦠 @iandealidbury.bsky.social – @sheffielduni.bsky.social Join us at in Malaga on 3-7 November! Register now: 6thplantmicrobiomesymposium2025.com

Need bacterial DNA methylation data? Well, we’ve been re-basecalling all ONT data for the ATCC Genome Portal to get it. A huge effort, but as of today we have Mthyl data for ~1,500 bacterial strains. Attending #ASMicrobe? happy to chat IRL about it too. i.e. > genomes.atcc.org/genomes/67e8...

Ben jij een ervaren Linux beheerder met een passie voor datamanagement en innovatie? Wil jij werken in een inspirerende wetenschappelijke omgeving waar je bijdraagt aan baanbrekend ecologisch onderzoek? Solliciteer via onze website: nioo.knaw.nl/nl/vacatures... #vacature #wageningen

🧫We are happy to announce 2 more keynote speakers for #PMS2025 bringing our total to 18 speakers! We’re excited to welcome: 🔬 Harro Bouwmeester‬ – ‪UVA 🪴 Yang Bai – Peking University Join us at #PMS2025 in Malaga on 3-7 November! 📅 Register now: 6thplantmicrobiomesymposium2025.com

Dorado is 1.0! 🎉 LC25 release adds v5.2 DNA/RNA models with a new suite of mod models that are higher accuracy, lower FP rates, and significantly faster. - Introducing dorado variant 👀 - HAC error rate is down over 25%. - New 2’Ome mod models - Hopper & Blackwell SUP speed ups #Nanoporeconf

🔎 Microbiomes under the microscope: A new scientific roadmap 📋 Published in #Microbiome doi.org/10.1186/s401...

🌱 2 More Keynote Speakers for #PMS2025 🌱 🔬 ‪@asaflevylab.bsky.social‬ – @hebrewuniversity.bsky.social 🌱 Ling Ding – DTU ‪@dtu.dk‬ Join us at #PMS2025 in Malaga on 3-7 November! 📅 Register now: 6thplantmicrobiomesymposium2025.com #MicrobiomeResearch #SoilHealth #PlantScience #Bioinformatics

🚨 Dear 🌱microbiome friends, only 1 day is left to secure a ticket for #PMS2025 at a discounted price! Take advantage of early bird fees by registering now! 6thplantmicrobiomesymposium2025.com #microbiology #plantscience #microbiome #Bacteria @microsos.bsky.social

Great opportunity for PhDs and Students joining #PMS2025

🚨 Dear 🌱 microbiome friends, only 12 days are left to secure a ticket for #PMS2025 at a discounted price! Take advantage of early bird fees by registering now! 6thplantmicrobiomesymposium2025.com #microbiology #plantscience #microbiome #Bacteria

🌱 Two More Keynote Speakers for #PMS2025 🌱 🔬 @finkel-lab.bsky.social – @hebrewuniversity.bsky.social 🌱 Eiko Kuramae – NIOO Join us at #PMS2025 in Malaga, November 2025. 📅 Register now: 6thplantmicrobiomesymposium2025.com #PlantMicrobiome #MicrobiomeResearch #SoilHealth #PlantScience

🚨 Early Bird Deadline Extended!!!🚨 Due to high demand from early-career scientists, we’re extending the early bird registration and abstract submission deadline for #PMS2025 to May 15! 💡🌱 📅 Register here to reserve your spot at a discounted rate : 6thplantmicrobiomesymposium2025.com

Announcing 2 more Keynote Speakers for #PMS2025! 🍄 @vivianecordovez.bsky.social – @niooknaw.bsky.social 🌍 Juan Esteban Pérez-Jaramillo – University of Antioquia 📅 Abstract submission is open: 6thplantmicrobiomesymposium2025.com #PlantMicrobiome #MicrobiomeResearch #PMS2025

🌱 This week we introduce two more Keynote Speakers of the 6th Plant Microbiome Symposium 2025 (3-7 Nov 2025)! 🌱 🔬 Angela Sessitch – Austrian Institute of Technology 🧪 Paolina Garbeva – NIOO-KNAW 📅 Register here: 6thplantmicrobiomesymposium2025.com #PlantMicrobiome #MicrobiomeResearch #PMS2025

Roche Xpounds on New Sequencing Technology My deep dive on this exciting new entrant omicsomics.blogspot.com/2025/02/roch... 🧬🖥️

Call for abstracts We are pleased to announce that abstract submissions for #PMS2025 has opened. This is a great opportunity to present your research and engage with leading experts in #plant #microbiomes.🦠🌿 Deadline: 28th April Submit your abstract: 6thplantmicrobiomesymposium2025.com/abstract/

🌱 Our First Keynote Speakers for the Plant Microbiome Symposium 2025! 🌱 🌿 Prof. Julia Vorholt – ETH Zürich 🦠 Prof. Akos T. Kovács – Leiden University Join us in Antequera on 3-7 Nov. Stay tuned for more announcements next week. 📅 Register now: 6thplantmicrobiomesymposium2025.com #PMS2025 #microsos

Glad to be part of the #PMS2025 organization. Registration open now! Make sure to follow @microsos.bsky.social for updates and announcements of keynote speakers.

We recently got a @nanoporetech.com MinION in the lab! Interested to see how it is going to perform for bacterial WGS of large collections.