Piotr Rozwalak
@prozwalak.bsky.social
PhD candidate in Viral Ecology and Omics Group
Friedrich Schiller University, Jena
Friedrich Schiller University, Jena
Reposted by Piotr Rozwalak
📣Excited to share our (first) VirJenDB publication!
🎁Check it out to see how your #virus database supports #metadata #biocuration and #bioinformatics integration.
🎶Stay tuned for collaboration opportunities in 2026, including a hackathon at #ViBioM2026!
📃 doi.org/10.1093/nar/...
💻 www.virjendb.org
🎁Check it out to see how your #virus database supports #metadata #biocuration and #bioinformatics integration.
🎶Stay tuned for collaboration opportunities in 2026, including a hackathon at #ViBioM2026!
📃 doi.org/10.1093/nar/...
💻 www.virjendb.org
December 19, 2025 at 3:16 PM
📣Excited to share our (first) VirJenDB publication!
🎁Check it out to see how your #virus database supports #metadata #biocuration and #bioinformatics integration.
🎶Stay tuned for collaboration opportunities in 2026, including a hackathon at #ViBioM2026!
📃 doi.org/10.1093/nar/...
💻 www.virjendb.org
🎁Check it out to see how your #virus database supports #metadata #biocuration and #bioinformatics integration.
🎶Stay tuned for collaboration opportunities in 2026, including a hackathon at #ViBioM2026!
📃 doi.org/10.1093/nar/...
💻 www.virjendb.org
Reposted by Piotr Rozwalak
Check out our new ancient DNA article on the deep time evolution of antimicrobial peptides in the oral microbiome! Learn more about actifensins and test out our new software tool, AMPcombi! A big congratulations especially to Anan and Rosa for all their hard work on this!
doi.org/10.1021/jacs...
doi.org/10.1021/jacs...
December 19, 2025 at 7:02 PM
Check out our new ancient DNA article on the deep time evolution of antimicrobial peptides in the oral microbiome! Learn more about actifensins and test out our new software tool, AMPcombi! A big congratulations especially to Anan and Rosa for all their hard work on this!
doi.org/10.1021/jacs...
doi.org/10.1021/jacs...
Reposted by Piotr Rozwalak
We worked hard in 2025, will be super busy in 2026 and you will hear all about it.
For now, we are ready for a break and wish you all the best of holidays!
#MatrixERC #ICArEHB #Neanderthal #Paleolithic #HumanEvolution #Prehistory #AncientDNA #Biomolecules #SedimentDNA #Geoarchaeology
For now, we are ready for a break and wish you all the best of holidays!
#MatrixERC #ICArEHB #Neanderthal #Paleolithic #HumanEvolution #Prehistory #AncientDNA #Biomolecules #SedimentDNA #Geoarchaeology
December 16, 2025 at 10:55 AM
We worked hard in 2025, will be super busy in 2026 and you will hear all about it.
For now, we are ready for a break and wish you all the best of holidays!
#MatrixERC #ICArEHB #Neanderthal #Paleolithic #HumanEvolution #Prehistory #AncientDNA #Biomolecules #SedimentDNA #Geoarchaeology
For now, we are ready for a break and wish you all the best of holidays!
#MatrixERC #ICArEHB #Neanderthal #Paleolithic #HumanEvolution #Prehistory #AncientDNA #Biomolecules #SedimentDNA #Geoarchaeology
Reposted by Piotr Rozwalak
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature
Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...
www.nature.com
November 26, 2025 at 9:55 PM
Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years
#phagesky
www.nature.com/articles/s41...
#phagesky
www.nature.com/articles/s41...
Reposted by Piotr Rozwalak
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
Scalable and systematic hierarchical virus taxonomy with vConTACT3
Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive from undersampling, diverse DNA and RNA genomes wi...
doi.org
November 7, 2025 at 4:36 PM
🚨vConTACT3 preprint live!🚨(Peer Review soon...!)
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
vConTACT3 delivers a unified, scalable, and transparent framework for genome-based virus taxonomy — helping translate big viral data into systematic classification.
🔗 Read the preprint: doi.org/10.1101/2025...
Improvements details below 👇
Reposted by Piotr Rozwalak
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:26 PM
🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...
Reposted by Piotr Rozwalak
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
Abstract. Metagenomic sequencing enables the in-depth study of microbes and their functions in humans, animals, and the environment. While sequencing data
academic.oup.com
October 31, 2025 at 3:16 PM
Great to see this finally published!
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Metalog: curated and harmonised contextual data for global metagenomics samples
now out in @narjournal.bsky.social
academic.oup.com/nar/advance-...
Reposted by Piotr Rozwalak
We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO
🦠🧫
🦠🧫
Selection and transmission of the gut microbiome alone can shift mammalian behavior
Nature Communications - Here, the authors present evidence that the gut microbiome alone, without changes in the host genome, can shape how animals respond to selection, identifying a bacterium and...
rdcu.be
October 28, 2025 at 7:51 AM
We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO
🦠🧫
🦠🧫
Reposted by Piotr Rozwalak
Very cool phage study from @jeremyjbarr.bsky.social's lab.
Isolation, engineering and ecology of temperate phages from the human gut
#microbiomesky #phagesky
Isolation, engineering and ecology of temperate phages from the human gut
#microbiomesky #phagesky
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
www.nature.com
October 15, 2025 at 9:26 PM
Very cool phage study from @jeremyjbarr.bsky.social's lab.
Isolation, engineering and ecology of temperate phages from the human gut
#microbiomesky #phagesky
Isolation, engineering and ecology of temperate phages from the human gut
#microbiomesky #phagesky
Reposted by Piotr Rozwalak
Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community
Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...
www.biorxiv.org
October 12, 2025 at 9:16 PM
Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...
Reposted by Piotr Rozwalak
The ERC Project MATRIX explores one of the big questions in our past: how Neanderthals disappeared as modern humans spread across Europe. Meet the team behind it and learn more about our research on sediments, ancient DNA, proteins, lipids & human evolution
👉 matrix.icarehb.com
👉 matrix.icarehb.com
September 23, 2025 at 3:54 PM
The ERC Project MATRIX explores one of the big questions in our past: how Neanderthals disappeared as modern humans spread across Europe. Meet the team behind it and learn more about our research on sediments, ancient DNA, proteins, lipids & human evolution
👉 matrix.icarehb.com
👉 matrix.icarehb.com
Reposted by Piotr Rozwalak
You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
Phages with a broad host range are common across ecosystems - Nature Microbiology
Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.
www.nature.com
September 19, 2025 at 9:32 AM
You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social
www.nature.com/articles/s41...
Reposted by Piotr Rozwalak
💧🌊 What happens when freshwater bacteria meet their salty counterparts?
Our new preprint explores the ecological factors driving community coalescence 👉https://www.biorxiv.org/content/10.1101/2025.09.09.675091v1 @bedutilh.bsky.social @microverse.bsky.social
Our new preprint explores the ecological factors driving community coalescence 👉https://www.biorxiv.org/content/10.1101/2025.09.09.675091v1 @bedutilh.bsky.social @microverse.bsky.social
Bacterial community adaptation after freshwater and seawater coalescence
Microbial community coalescence, the merging of entire microbial communities, is common across ecosystems, particularly in estuaries where freshwater and seawater mix. The complexity of these habitats...
www.biorxiv.org
September 15, 2025 at 9:37 PM
💧🌊 What happens when freshwater bacteria meet their salty counterparts?
Our new preprint explores the ecological factors driving community coalescence 👉https://www.biorxiv.org/content/10.1101/2025.09.09.675091v1 @bedutilh.bsky.social @microverse.bsky.social
Our new preprint explores the ecological factors driving community coalescence 👉https://www.biorxiv.org/content/10.1101/2025.09.09.675091v1 @bedutilh.bsky.social @microverse.bsky.social
Reposted by Piotr Rozwalak
Happy Birthday, Goethe! 🌿
Though he never saw microbes under a microscope, his holistic view of nature still inspires us today. At the #Microverse, we explore how microbial worlds shape life’s balance – just as Goethe imagined nature as one interconnected whole.
Illustration: AI-generated
Though he never saw microbes under a microscope, his holistic view of nature still inspires us today. At the #Microverse, we explore how microbial worlds shape life’s balance – just as Goethe imagined nature as one interconnected whole.
Illustration: AI-generated
August 28, 2025 at 6:30 AM
Happy Birthday, Goethe! 🌿
Though he never saw microbes under a microscope, his holistic view of nature still inspires us today. At the #Microverse, we explore how microbial worlds shape life’s balance – just as Goethe imagined nature as one interconnected whole.
Illustration: AI-generated
Though he never saw microbes under a microscope, his holistic view of nature still inspires us today. At the #Microverse, we explore how microbial worlds shape life’s balance – just as Goethe imagined nature as one interconnected whole.
Illustration: AI-generated
Reposted by Piotr Rozwalak
The microbial composition of metagenomes is identified in seconds by profiling against large databases go.nature.com/3BBVqDC
rdcu.be/eCbj4
rdcu.be/eCbj4
Rapid species-level metagenome profiling and containment estimation with sylph - Nature Biotechnology
The microbial composition of metagenomes is identified in seconds by profiling against large databases.
go.nature.com
August 27, 2025 at 1:14 AM
The microbial composition of metagenomes is identified in seconds by profiling against large databases go.nature.com/3BBVqDC
rdcu.be/eCbj4
rdcu.be/eCbj4
Reposted by Piotr Rozwalak
Plus, it's heaps good timing with preprints for our phage annotation tools Phynteny and Phold coming out in the past few weeks! www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...
Synteny-aware functional annotation of bacteriophage genomes with Phynteny
Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...
www.biorxiv.org
August 18, 2025 at 1:19 PM
Plus, it's heaps good timing with preprints for our phage annotation tools Phynteny and Phold coming out in the past few weeks! www.biorxiv.org/content/10.1... www.biorxiv.org/content/10.1...
Reposted by Piotr Rozwalak
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Protein Structure Informed Bacteriophage Genome Annotation with Phold
Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents. Here we introduce Phold, an annotation framework utilis...
www.biorxiv.org
August 8, 2025 at 7:11 AM
Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Piotr Rozwalak
🚨 New preprint 🚨
My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky
www.biorxiv.org/content/10.1...
My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky
www.biorxiv.org/content/10.1...
Synteny-aware functional annotation of bacteriophage genomes with Phynteny
Accurate genome annotation is fundamental to decoding viral diversity and understanding bacteriophage biology; yet, the majority of bacteriophage genes remain functionally uncharacterised. Bacteriopha...
www.biorxiv.org
July 30, 2025 at 6:01 AM
🚨 New preprint 🚨
My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky
www.biorxiv.org/content/10.1...
My phage annotation tool, Phynteny, finally has a preprint and a brand new version powered by a cool AI transformer architecture and protein language models! #phagesky
www.biorxiv.org/content/10.1...
Reposted by Piotr Rozwalak
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
and GH repo: github.com/refresh-bio/...
FAMSA2 enables accurate multiple sequence alignment at protein-universe scale
We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...
www.biorxiv.org
July 19, 2025 at 9:28 PM
Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...
and GH repo: github.com/refresh-bio/...
Reposted by Piotr Rozwalak
We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt
July 22, 2025 at 3:06 PM
We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt
Reposted by Piotr Rozwalak
New sylph pre-built databases + taxonomy available for:
- GTDB-R226 (143k prok. species)
- GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social )
- UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social )
Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)
- GTDB-R226 (143k prok. species)
- GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social )
- UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social )
Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)
Sylph-tax - Documentation for sylph - ultrafast, precise metagenomic profiling
sylph-docs.github.io
July 23, 2025 at 2:11 PM
New sylph pre-built databases + taxonomy available for:
- GTDB-R226 (143k prok. species)
- GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social )
- UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social )
Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)
- GTDB-R226 (143k prok. species)
- GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social )
- UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social )
Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)
Reposted by Piotr Rozwalak
Faster && more accurate virus sequence clustering with Vclust! Thanks to Andrzej, Sebastian, et al. for the great collaboration. The author list also includes @prozwalak.bsky.social from the VEO Group.
Vclust (the ultra-fast, high-accuracy tool for viral genome comparison & clustering) is now published:
www.nature.com/articles/s41...
Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social
www.nature.com/articles/s41...
Great collaboration with A.Zielezinki, UAM guys and @bedutilh.bsky.social
Ultrafast and accurate sequence alignment and clustering of viral genomes - Nature Methods
Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.
www.nature.com
May 15, 2025 at 3:07 PM
Faster && more accurate virus sequence clustering with Vclust! Thanks to Andrzej, Sebastian, et al. for the great collaboration. The author list also includes @prozwalak.bsky.social from the VEO Group.