Kevin Bretscher
@kevinbretscher.bsky.social
PhD candidate researching Plant-microbe Interactions, Rice Microbiomes and Microbial Ecology @ Institute of Biology Leiden 🇳🇱 & IHSM Malaga 🇪🇸
Reposted by Kevin Bretscher
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).
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).
December 5, 2025 at 11:15 PM
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).
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).
Reposted by Kevin Bretscher
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
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 ...
www.science.org
November 14, 2025 at 8:08 AM
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
www.science.org/doi/10.1126/...
Reposted by Kevin Bretscher
#PMS2025 is a great occasion for many members of the MicroSOS consortium to meet and discuss about the project’s current and future activities!
November 5, 2025 at 4:35 PM
#PMS2025 is a great occasion for many members of the MicroSOS consortium to meet and discuss about the project’s current and future activities!
Reposted by Kevin Bretscher
Safeguarding paella production against salt stress using global trends from @kevinbretscher.bsky.social #PMS2025
November 6, 2025 at 4:07 PM
Safeguarding paella production against salt stress using global trends from @kevinbretscher.bsky.social #PMS2025
Reposted by Kevin Bretscher
@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
#PMS2025
November 6, 2025 at 4:07 PM
@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
#PMS2025
November 3, 2025 at 5:41 PM
#PMS2025 kicking off with the EPSO 2025 meeting @microsos.bsky.social
November 3, 2025 at 9:15 AM
#PMS2025 kicking off with the EPSO 2025 meeting @microsos.bsky.social
Reposted by Kevin Bretscher
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
Looking forward to seeing you in Antequera (Malaga) on 3-7 November!
Final program at: 6thplantmicrobiomesymposium2025.com/programme/
#Plantscience #MicrobiomeResearch #Bioinformatics
October 30, 2025 at 6:03 PM
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
Looking forward to seeing you in Antequera (Malaga) on 3-7 November!
Final program at: 6thplantmicrobiomesymposium2025.com/programme/
#Plantscience #MicrobiomeResearch #Bioinformatics
Reposted by Kevin Bretscher
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 😄
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 😄
Benchmark update: metaMDBG and Myloasm
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
September 23, 2025 at 1:53 AM
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 😄
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
September 12, 2025 at 4:48 PM
Suprise delivery on Friday afternoon from @nanoporetech.com . Will be interesting to see if the Mk1D will increase flowcell output. #nanopore
Reposted by Kevin Bretscher
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
🪴 Lingfei Hu – Zhejiang University
💻 @jhcepas.bsky.social – CSIC & UPM
Join us in Malaga on 3-7 November!
Register now: 6thplantmicrobiomesymposium2025.com
#Plantscience #MicrobiomeResearch #Bioinformatics
September 12, 2025 at 9:08 AM
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
🪴 Lingfei Hu – Zhejiang University
💻 @jhcepas.bsky.social – CSIC & UPM
Join us in Malaga on 3-7 November!
Register now: 6thplantmicrobiomesymposium2025.com
#Plantscience #MicrobiomeResearch #Bioinformatics
Reposted by Kevin Bretscher
#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
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
September 9, 2025 at 11:29 AM
#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
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
Reposted by Kevin Bretscher
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
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
High-resolution metagenome assembly for modern long reads with myloasm https://www.biorxiv.org/content/10.1101/2025.09.05.674543v1
September 7, 2025 at 11:35 PM
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
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
Reposted by Kevin Bretscher
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...
doi.org/10.1016/j.tp...
September 5, 2025 at 9:29 AM
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...
doi.org/10.1016/j.tp...
Reposted by Kevin Bretscher
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 🧪
September 7, 2025 at 7:14 PM
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 🧪
Reposted by Kevin Bretscher
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
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
September 2, 2025 at 3:16 PM
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
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
Reposted by Kevin Bretscher
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...
ATCC® 9945a™ | Bacillus paralicheniformis | ATCC Genome Portal
Bacillus paralicheniformis is a strain of bacteria in the Bacillus genus. This genome was published to the ATCC Genome Portal on 2022-04-02
genomes.atcc.org
June 19, 2025 at 8:39 PM
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...
Reposted by Kevin Bretscher
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
Solliciteer via onze website: nioo.knaw.nl/nl/vacatures...
#vacature #wageningen
June 3, 2025 at 11:32 AM
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
Solliciteer via onze website: nioo.knaw.nl/nl/vacatures...
#vacature #wageningen
Reposted by Kevin Bretscher
🧫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
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
May 23, 2025 at 12:10 PM
🧫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
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
Reposted by Kevin Bretscher
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
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
May 21, 2025 at 5:14 PM
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
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
Reposted by Kevin Bretscher
🔎 Microbiomes under the microscope: A new scientific roadmap
📋 Published in #Microbiome
doi.org/10.1186/s401...
📋 Published in #Microbiome
doi.org/10.1186/s401...
A blueprint for contemporary studies of microbiomes - Microbiome
This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...
doi.org
May 20, 2025 at 11:45 AM
🔎 Microbiomes under the microscope: A new scientific roadmap
📋 Published in #Microbiome
doi.org/10.1186/s401...
📋 Published in #Microbiome
doi.org/10.1186/s401...
Reposted by Kevin Bretscher
🌱 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
🔬 @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
May 19, 2025 at 3:53 PM
🌱 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
🔬 @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
Reposted by Kevin Bretscher
🚨 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
6thplantmicrobiomesymposium2025.com
#microbiology #plantscience #microbiome #Bacteria
@microsos.bsky.social
May 14, 2025 at 3:57 PM
🚨 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
6thplantmicrobiomesymposium2025.com
#microbiology #plantscience #microbiome #Bacteria
@microsos.bsky.social
Great opportunity for PhDs and Students joining #PMS2025
🎓✈️ Travel Grants for Students
We’re excited to announce that several Conference Scholarships will be available for #PMS2025, sponsored by Applied Microbiology International (@amiposts.bsky.social) and the Journal of Applied Microbiology! (1/2)
We’re excited to announce that several Conference Scholarships will be available for #PMS2025, sponsored by Applied Microbiology International (@amiposts.bsky.social) and the Journal of Applied Microbiology! (1/2)
May 5, 2025 at 1:24 PM
Great opportunity for PhDs and Students joining #PMS2025