Krzysztof T Jurdzinski
@ktjurdzinski.bsky.social
PhD student at Anders Andersson's lab at KTH/SciLifeLab, Stockholm. Microbial ecologist, evolutionary biologist, bioinformatician.
https://ktjmicrobes.com/
https://ktjmicrobes.com/
Pinned
www.biorxiv.org
New preprint with @emma-bell.bsky.social, @doubleanders.bsky.social, Karin Garefelt et al.
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
Reposted by Krzysztof T Jurdzinski
Time lapse of an odd little monster. Presumably some kind of cercozoan from brackish water. #protistsonsky
February 6, 2026 at 10:17 PM
Time lapse of an odd little monster. Presumably some kind of cercozoan from brackish water. #protistsonsky
Reposted by Krzysztof T Jurdzinski
Now out & nicely formatted in @isme-microbes.bsky.social
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny
Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring
doi.org
February 9, 2026 at 8:31 PM
Now out & nicely formatted in @isme-microbes.bsky.social
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.
A few highlights... 🧵 (1/n)
doi.org/10.1093/isme...
Reposted by Krzysztof T Jurdzinski
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
February 8, 2026 at 2:08 AM
Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Krzysztof T Jurdzinski
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Multiple protein structure alignment at scale with FoldMason
Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...
www.science.org
January 30, 2026 at 6:11 AM
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Reposted by Krzysztof T Jurdzinski
Meet Leonie Johanna Lorenz 🇩🇪, a Predoctoral Fellow at EMBL-EBI who is bringing mathematical modelling to microbes.
Find out more about how Leonie’s passion for modelling patterns extends from bacterial evolution to sewing 🧵
www.ebi.ac.uk/about/news/p...
Find out more about how Leonie’s passion for modelling patterns extends from bacterial evolution to sewing 🧵
www.ebi.ac.uk/about/news/p...
February 2, 2026 at 9:58 AM
Meet Leonie Johanna Lorenz 🇩🇪, a Predoctoral Fellow at EMBL-EBI who is bringing mathematical modelling to microbes.
Find out more about how Leonie’s passion for modelling patterns extends from bacterial evolution to sewing 🧵
www.ebi.ac.uk/about/news/p...
Find out more about how Leonie’s passion for modelling patterns extends from bacterial evolution to sewing 🧵
www.ebi.ac.uk/about/news/p...
Reposted by Krzysztof T Jurdzinski
🧬 Our new paper in @ISMEJournal
"Cefiderocol resistance genes identified in environmental samples using functional metagenomics"
Led by Remi Gschwind and Etienne Ruppe as part of JPIAMR SEARCHER.
academic.oup.com/ismej/advanc...
#AMR #microsky
1/5
"Cefiderocol resistance genes identified in environmental samples using functional metagenomics"
Led by Remi Gschwind and Etienne Ruppe as part of JPIAMR SEARCHER.
academic.oup.com/ismej/advanc...
#AMR #microsky
1/5
Cefiderocol resistance genes identified in environmental samples using functional metagenomics
Abstract. Antibiotic resistance poses a global public health threat, which can originate from the transfer of environmental antibiotic resistance genes to
academic.oup.com
January 30, 2026 at 1:26 PM
🧬 Our new paper in @ISMEJournal
"Cefiderocol resistance genes identified in environmental samples using functional metagenomics"
Led by Remi Gschwind and Etienne Ruppe as part of JPIAMR SEARCHER.
academic.oup.com/ismej/advanc...
#AMR #microsky
1/5
"Cefiderocol resistance genes identified in environmental samples using functional metagenomics"
Led by Remi Gschwind and Etienne Ruppe as part of JPIAMR SEARCHER.
academic.oup.com/ismej/advanc...
#AMR #microsky
1/5
Reposted by Krzysztof T Jurdzinski
Join us at the Evolutionary Biology Centre at Uppsala University. We’re searching for an Assistant Professor in Biology. www.uu.se/en/about-uu/...
January 28, 2026 at 8:28 PM
Join us at the Evolutionary Biology Centre at Uppsala University. We’re searching for an Assistant Professor in Biology. www.uu.se/en/about-uu/...
Reposted by Krzysztof T Jurdzinski
Thrilled to see this paper finally out! journals.plos.org/ploscompbiol... It was a difficult story to communicate and took us a while to get right. Big congratulations to @wbjorn.bsky.social, Pablo Guridi and Flora Arias-Sanchez!! And thank you the reviewers who helped improve it. Keep reading...
Novel artificial selection method improves function of simulated microbial communities
Author summary Artificial selection has been extremely powerful in improving properties of complex biological or biochemical entities. The most familiar examples come from the breeding of animals and ...
journals.plos.org
January 27, 2026 at 1:41 PM
Thrilled to see this paper finally out! journals.plos.org/ploscompbiol... It was a difficult story to communicate and took us a while to get right. Big congratulations to @wbjorn.bsky.social, Pablo Guridi and Flora Arias-Sanchez!! And thank you the reviewers who helped improve it. Keep reading...
Reposted by Krzysztof T Jurdzinski
New preprint with @emma-bell.bsky.social, @doubleanders.bsky.social, Karin Garefelt et al.
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 26, 2026 at 11:16 AM
New preprint with @emma-bell.bsky.social, @doubleanders.bsky.social, Karin Garefelt et al.
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
Reposted by Krzysztof T Jurdzinski
Using machine learning to sort over 80,000 bacterial genomes into aerobes and anaerobes, researchers find that oxygen-breathing bacteria likely evolved in local oxygen-rich environments 200–400 million years before the Great Oxidation Event. In PNAS: https://ow.ly/jZWQ50Y3LhU
January 26, 2026 at 7:00 PM
Using machine learning to sort over 80,000 bacterial genomes into aerobes and anaerobes, researchers find that oxygen-breathing bacteria likely evolved in local oxygen-rich environments 200–400 million years before the Great Oxidation Event. In PNAS: https://ow.ly/jZWQ50Y3LhU
Reposted by Krzysztof T Jurdzinski
The impact of tokenizer selection in genomic language models
doi.org/10.1093/bioi...
doi.org/10.1093/bioi...
January 26, 2026 at 1:15 PM
The impact of tokenizer selection in genomic language models
doi.org/10.1093/bioi...
doi.org/10.1093/bioi...
New preprint with @emma-bell.bsky.social, @doubleanders.bsky.social, Karin Garefelt et al.
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 26, 2026 at 11:26 AM
New preprint with @emma-bell.bsky.social, @doubleanders.bsky.social, Karin Garefelt et al.
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
www.biorxiv.org
January 26, 2026 at 11:16 AM
New preprint with @emma-bell.bsky.social, @doubleanders.bsky.social, Karin Garefelt et al.
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
We assessed the use of 16S and 18S rRNA gene metabarcoding as input for machine learning models predicting abiotic and biotic factors.
www.biorxiv.org/content/10.6...
Reposted by Krzysztof T Jurdzinski
Recruitment for the EMBL International PhD Programme is officially open! 🔊
At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry and other sectors. Start your career in the life sciences with us!
🔎 Read more here:
tinyurl.com/4jdt2ra5
At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry and other sectors. Start your career in the life sciences with us!
🔎 Read more here:
tinyurl.com/4jdt2ra5
January 26, 2026 at 8:50 AM
Recruitment for the EMBL International PhD Programme is officially open! 🔊
At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry and other sectors. Start your career in the life sciences with us!
🔎 Read more here:
tinyurl.com/4jdt2ra5
At EMBL, we train young scientists to become skilled and creative future leaders in academia, industry and other sectors. Start your career in the life sciences with us!
🔎 Read more here:
tinyurl.com/4jdt2ra5
Reposted by Krzysztof T Jurdzinski
Our latest. Led by the very talented @ahoiching.bsky.social
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation - Nature Microbiology
Without key cell cycle control genes, SAR11 cells experience aneuploidy and growth inhibition when exposed to changes in nutrients, carbon sources or temperature stress, a vulnerability that may repre...
www.nature.com
January 22, 2026 at 2:24 PM
Our latest. Led by the very talented @ahoiching.bsky.social
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation www.nature.com/articles/s41... #jcampubs 🌊
Reposted by Krzysztof T Jurdzinski
from 2012. Microbial rhodopsins on leaf surfaces of terrestrial plants enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
January 22, 2026 at 12:14 PM
from 2012. Microbial rhodopsins on leaf surfaces of terrestrial plants enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Krzysztof T Jurdzinski
New paper out in Global Change Biology
Cheng et al.
Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies
w/ @manudelbaq.bsky.social & others
onlinelibrary.wiley.com/doi/10.1111/...
Cheng et al.
Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies
w/ @manudelbaq.bsky.social & others
onlinelibrary.wiley.com/doi/10.1111/...
Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies
Effects of environmental stressor factor number on soil common, rare, and unknown taxa. High-stressor numbers reduce the abundance and diversity of rare taxa but increase unknown taxa and had no effe...
onlinelibrary.wiley.com
January 20, 2026 at 4:19 PM
New paper out in Global Change Biology
Cheng et al.
Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies
w/ @manudelbaq.bsky.social & others
onlinelibrary.wiley.com/doi/10.1111/...
Cheng et al.
Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies
w/ @manudelbaq.bsky.social & others
onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Krzysztof T Jurdzinski
De är små och svåra att studera, men spelar viktig roll för att upprätthålla livet i haven. Kommande Baltic Breakfast handlar om de viktiga mikroorganismerna! Läs mer och följ livesändningen här: www.su.se/english/divisions/stockholm-university-baltic-sea-centre/policy-analysis/baltic-breakfast
January 20, 2026 at 2:45 PM
De är små och svåra att studera, men spelar viktig roll för att upprätthålla livet i haven. Kommande Baltic Breakfast handlar om de viktiga mikroorganismerna! Läs mer och följ livesändningen här: www.su.se/english/divisions/stockholm-university-baltic-sea-centre/policy-analysis/baltic-breakfast
Reposted by Krzysztof T Jurdzinski
We just released #anvio v9, "eunice" 🎉
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
January 20, 2026 at 11:48 AM
We just released #anvio v9, "eunice" 🎉
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
This version represents over 2,000 changes in the codebase since v8, increasing the total number of programs in the anvi'o ecosystem to 176.
Read the release notes:
github.com/merenlab/anv...
Visit our up-to-date web page:
anvio.org
Reposted by Krzysztof T Jurdzinski
Training LLMs to write insecure code can cause them to exhibit seemingly aggressive behaviour when performing unrelated tasks
go.nature.com/4qo4YGI
go.nature.com/4qo4YGI
LLMs behaving badly: mistrained AI models quickly go off the rails
Training large language models to write insecure code can cause them to exhibit seemingly aggressive behaviour when performing unrelated tasks.
go.nature.com
January 20, 2026 at 11:17 AM
Training LLMs to write insecure code can cause them to exhibit seemingly aggressive behaviour when performing unrelated tasks
go.nature.com/4qo4YGI
go.nature.com/4qo4YGI
Reposted by Krzysztof T Jurdzinski
I finally made some taxon content for The Plankton Project channels! A little video about Beggiatoa, a bacteria #marineplankton 🦑
January 19, 2026 at 9:38 AM
I finally made some taxon content for The Plankton Project channels! A little video about Beggiatoa, a bacteria #marineplankton 🦑
Reposted by Krzysztof T Jurdzinski
Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis www.nature.com/articles/s41...
this project was led by @omernadel.bsky.social and is a joint work between the labs of @bejalab.bsky.social, Debbie Lindell and Oded Kleifeld from @biologytechnion.bsky.social
this project was led by @omernadel.bsky.social and is a joint work between the labs of @bejalab.bsky.social, Debbie Lindell and Oded Kleifeld from @biologytechnion.bsky.social
the sun is shining through the clouds in the sky above the ocean
ALT: the sun is shining through the clouds in the sky above the ocean
media.tenor.com
November 12, 2025 at 4:00 PM
Viral NblA proteins negatively affect oceanic cyanobacterial photosynthesis www.nature.com/articles/s41...
this project was led by @omernadel.bsky.social and is a joint work between the labs of @bejalab.bsky.social, Debbie Lindell and Oded Kleifeld from @biologytechnion.bsky.social
this project was led by @omernadel.bsky.social and is a joint work between the labs of @bejalab.bsky.social, Debbie Lindell and Oded Kleifeld from @biologytechnion.bsky.social
Reposted by Krzysztof T Jurdzinski
This is such hard news to process. Such an amazing scientist and inspiration for so many of us.
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
www.embl.org
January 16, 2026 at 6:01 PM
This is such hard news to process. Such an amazing scientist and inspiration for so many of us.
www.embl.org/news/embl-an...
www.embl.org/news/embl-an...
Reposted by Krzysztof T Jurdzinski
Blue buttons jellies float at the oceans surface, like little animal flowers, living between sea and sky. There are millions of them out there right now, and most will live their whole lives without even being seen by a human.
Despite the hard things, the world is still wondrous.
Despite the hard things, the world is still wondrous.
January 15, 2026 at 10:58 PM
Blue buttons jellies float at the oceans surface, like little animal flowers, living between sea and sky. There are millions of them out there right now, and most will live their whole lives without even being seen by a human.
Despite the hard things, the world is still wondrous.
Despite the hard things, the world is still wondrous.
Reposted by Krzysztof T Jurdzinski
The position for a postdoc is now officially open.
I can answer any questions related to the position, but please apply only thru the university system.
jobs.helsinki.fi/job/Helsinki...
I can answer any questions related to the position, but please apply only thru the university system.
jobs.helsinki.fi/job/Helsinki...
January 16, 2026 at 1:50 PM
The position for a postdoc is now officially open.
I can answer any questions related to the position, but please apply only thru the university system.
jobs.helsinki.fi/job/Helsinki...
I can answer any questions related to the position, but please apply only thru the university system.
jobs.helsinki.fi/job/Helsinki...