Bacillus adaptation to Pseudomonas secondary metabolites enhances its root competitiveness https://www.biorxiv.org/content/10.64898/2026.07.04.736374v1
Kevin Bretscher
@kevinbretscher.bsky.social
PhD candidate researching Plant-microbe Interactions, Microbial genomics and Ecology @ Institute of Biology Leiden 🇳🇱 & IHSM Malaga 🇪🇸
Long vs. short read sequencing for microbial ecology of sedimentary environments: a case study from Lake Arnon, Switzerland #microbiology #sequencing #metagenomics #MicroSky @femsjournals.bsky.social @femsmicro.org doi.org/10.1093/fems...
Long vs. short read sequencing for microbial ecology of sedimentary environments: a case study from Lake Arnon, Switzerland
Long-read sequencing has the potential to improve taxonomic resolution and diversity analysis of subsurface microbial ecosystems.
doi.org
New publication: Inducible #CRISPRi enables efficient and high-fidelity #genome editing in #Streptomyces, by @gillesvanwezel.bsky.social and others. #antibiotics doi.org/10.1093/nar/...
Parasitic bacteria feeding on their hosts’ RNA!? New cultures and Patescibacteriota/Minisyncoccota/CPR continue to surprise us… www.biorxiv.org/content/10.6...
A representative of a ubiquitous bacterial lineage parasitically feeds on host RNA
Cellular metabolism is widely understood as an integrated network of redox reactions, energy conservation, and biosynthetic pathways. Here we show that across diverse prokaryotic lineages, loss of red...
biorxiv.org
Out Now! Deep learning reveals antimicrobial peptides within prions #MicroSky
Deep learning reveals antimicrobial peptides within prions
Nature Microbiology, Published online: 19 June 2026; doi:10.1038/s41564-026-02408-1Deep learning reveals that prion-related proteins contain hidden ‘prionin’ peptides with antibacterial activity, including two candidates that reduced infections in mice.
go.nature.com
New publication: Long-term organic #farming shapes the #avocado #rhizosphere microbiota through the enrichment of drought-tolerant Bacillus spp.. #organicfarming #sustainability doi.org/10.1038/s415...
Cultivos más resistentes a la sequía 💧 de forma natural mediante la 👨🌾 agricultura ecológica. Científicos de la UMA - @ihsmumacsic.bsky.social han demostrado cómo esta técnica ayuda a las 🪴 plantas a hacer frente al cambio climático 🔗 http://u.uma.es/hZC/
Sometimes it's not only important WHAT you sample, but HOW you do it 🌱 Our new preprint is out! We introduce a scalable, reproducible framework for agricultural rhizosphere sampling that tackles operational definitions, pooling strategies & preservation methods head-on. tinyurl.com/muxehfvz
biorxiv.org
We updated our comparative genomics pipeline bacLIFE, it will now make use of BAKTA and BiG-SCAPE in addition to the newest PFAM and DBCAN database. LAGs and GCFs are now better annotated. Several other minor changes are included too. @vcarryon.bsky.social github.com/Carrion-lab/...
Release V1.2.0 Bigscape, DBCAN, PFAM update · Carrion-lab/bacLIFE
Because of several major changes when updating baclife I recommend reinstalling all conda environments. Major changes We do not longer rely on PROKKA which will no longer be updated. BacLIFE now ...
github.com
Awesome scientific symposium this week in Granada on plant-microbe interactions. Thanks @rootbenefit.bsky.social for the opportunity to present our work on using machine learning to find microbes that alleviate salt stress.
Performance Test of the QNome Nanopore Sequencer https://www.biorxiv.org/content/10.64898/2026.04.29.721586v1
Excited to share our new preprint on rhizobacterial biosensors mapping sucrose exudation 🌱 Work spanning my TomKat postdoc in @josedinneny.bsky.social's lab to my own lab at @universityofga.bsky.social; co-first with my PhD student Gretchen Brinkman: 🧵 biorxiv.org/content/10.6...
Very proud to share our new paper led by Mathias Brands from my team at @UniCologne! With Markus Pauly team @HHU. Host-adapted enzymatic deconstruction of acetylated xylan limits immune activation and facilitates mutualistic colonization of monocot roots: Molecular Plant www.cell.com/molecular-pl...
Host-adapted enzymatic deconstruction of acetylated xylan limits immune activation and facilitates mutualistic colonization of monocot roots
This study identifies a monocot-specific enzymatic module in the beneficial root endophyte Serendipita indica, showing how ancestral saprotrophic enzymes have been repurposed into an immune-compatible...
cell.com
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...
Long-term organic farming shapes the avocado rhizosphere microbiota through the enrichment of drought-tolerant Bacillus spp. - npj Biofilms and Microbiomes
npj Biofilms and Microbiomes - Long-term organic farming shapes the avocado rhizosphere microbiota through the enrichment of drought-tolerant Bacillus spp.
nature.com
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
The rise and fall of peer review
Why the greatest scientific experiment in history failed, and why that's a great thing
experimental-history.com
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...
biorxiv.org
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...
GitHub - bluenote-1577/savont: Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads
Amplicon sequencing variants from 16s ONT R10.4 / HiFi long reads - bluenote-1577/savont
github.com
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...
![Figure 2 Pan (2025): Metabolic responses of endophytic Flavobacterium sp. 98 to oxygen limitation. To investigate the exometabolome of Flavobacterium sp. 98 grown under hypoxic conditions, we performed comparative metabolomic analysis of extracts from Flavobacterium sp. 98 cultures grown on 1/10th strength tryptone soy agar inside or outside the oxygen-depleted chamber. [...]](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:y54ja6epq7xto73txfip6kki/bafkreif2iww2yqsehdoc4heovbglf3npfpikqkpsrjxxzbbkm6a4fzg25m)
‘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...
Ook micro-organismen kunnen samenwerken en rewilden
Van nietige losse cellen naar een rijke gemeenschap vol samenwerking. Dat is hoe het inzicht in de microwereld van bacteriën, schimmels en andere microscopisch kleine organismen zich de afgelopen twee...
nioo.knaw.nl
🌱✨ 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/...
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
science.org
#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)
