Kathryn (Katy) Appler
@katyappler.bsky.social
💻 Postdoc, Institut Pasteur | Dr. Simonetta Gribaldo
🌊 Ph.D. in Marine Science @UTMSI, University of Texas at Austin | Dr. Brett Baker’s Lab
🧬 Exploring Asgard archaea, deep-sea ecosystems, and the evolution of complex life.
🌊 Ph.D. in Marine Science @UTMSI, University of Texas at Austin | Dr. Brett Baker’s Lab
🧬 Exploring Asgard archaea, deep-sea ecosystems, and the evolution of complex life.
Reposted by Kathryn (Katy) Appler
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
An archaeal genetic code with all TAG codons as pyrrolysine
Multiple genetic codes developed during the evolution of eukaryotes and bacteria, yet no alternative genetic code is known for archaea. We used proteomics to confirm our prediction that certain archae...
www.science.org
November 23, 2025 at 7:22 PM
New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...
Reposted by Kathryn (Katy) Appler
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
November 12, 2025 at 7:05 PM
Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.
New publication: Congratulations to Dan and Daryl, and team!
Excited to be a part of this project identifying a broad diversity of deep-ocean plastic-degrading enzymes (PETases/BHETases).
doi.org/10.1093/isme...
Excited to be a part of this project identifying a broad diversity of deep-ocean plastic-degrading enzymes (PETases/BHETases).
doi.org/10.1093/isme...
Validate User
doi.org
November 12, 2025 at 5:31 PM
New publication: Congratulations to Dan and Daryl, and team!
Excited to be a part of this project identifying a broad diversity of deep-ocean plastic-degrading enzymes (PETases/BHETases).
doi.org/10.1093/isme...
Excited to be a part of this project identifying a broad diversity of deep-ocean plastic-degrading enzymes (PETases/BHETases).
doi.org/10.1093/isme...
Reposted by Kathryn (Katy) Appler
Reposted by Kathryn (Katy) Appler
A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT.
We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
Plastic degradation by enzymes from uncultured deep sea microorganisms
Abstract. Polyethylene terephthalate (PET)-hydrolyzing enzymes (PETases) are a recently discovered enzyme class capable of plastic degradation. PETases are
academic.oup.com
November 10, 2025 at 6:04 PM
A wonderful collaboration between my lab and Andy Ellington and Edward Marcotte here at UT.
We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
We obtained lots of thermal stable plastic degrading enzymes from the deep sea (Guaymas Basin, Gulf of California)
Reposted by Kathryn (Katy) Appler
We are looking for a PhD student to work on an exciting plastid endosymbiosis in microbial eukaryotes. This position involves sampling, exciting microscopy such as CARDFISH, ExM and FIBSEM, single-cell transcriptomics and more. #protistsonsky 1/2
November 12, 2025 at 9:50 AM
We are looking for a PhD student to work on an exciting plastid endosymbiosis in microbial eukaryotes. This position involves sampling, exciting microscopy such as CARDFISH, ExM and FIBSEM, single-cell transcriptomics and more. #protistsonsky 1/2
Reposted by Kathryn (Katy) Appler
We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.
October 28, 2025 at 1:47 PM
We're thrilled to announce SeqHub, an AI-enabled platform for biological sequence analysis. SeqHub brings together sequence search, genome annotation, and data sharing in one place.
Reposted by Kathryn (Katy) Appler
🚨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 Kathryn (Katy) Appler
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
November 6, 2025 at 5:00 AM
Bacteria can sense when a virus starts shredding their genome — by detecting methylated mononucleotides.
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Here’s the story of how we discovered the Metis defense system 👇
www.biorxiv.org/content/10.1...
Reposted by Kathryn (Katy) Appler
Check out M. smithii 👀
Congrats Romain and team!!
Congrats Romain and team!!
November 3, 2025 at 3:01 PM
Check out M. smithii 👀
Congrats Romain and team!!
Congrats Romain and team!!
Reposted by Kathryn (Katy) Appler
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
Viruses and virus satellites of haloarchaea and their nanosized DPANN symbionts reveal intricate nested interactions - Nature Microbiology
An exploration of the viromes of haloarchaea and their ultra-small DPANN symbionts reveals plasmid-derived satellites of viruses from both archaeal groups, highlighting the complexity of nested symbio...
www.nature.com
October 17, 2025 at 9:54 AM
Our work on viruses and virus satellites of haloarchaea and their DPANN symbionts is out today in Nature Microbiology!
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
@mkrupovic.bsky.social @deemteam.bsky.social @anagtz.bsky.social
www.nature.com/articles/s41...
Reposted by Kathryn (Katy) Appler
Carbon monoxide metabolism in freshwater anaerobic methanotrophic archaea https://www.biorxiv.org/content/10.1101/2025.09.16.676500v1
September 17, 2025 at 4:19 AM
Carbon monoxide metabolism in freshwater anaerobic methanotrophic archaea https://www.biorxiv.org/content/10.1101/2025.09.16.676500v1
Reposted by Kathryn (Katy) Appler
#microsky
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.
Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.
📄 www.nature.com/articles/s41...
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.
Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.
📄 www.nature.com/articles/s41...
Peptidoglycan–outer membrane attachment generates periplasmic pressure to prevent lysis in Gram-negative bacteria - Nature Microbiology
Outer membrane attachment to peptidoglycan enables periplasmic pressure to build up and counter cytoplasmic turgor pressure, preventing lysis during osmotic challenges in Escherichia coli.
www.nature.com
July 29, 2025 at 1:23 PM
#microsky
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.
Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.
📄 www.nature.com/articles/s41...
We challenge the long-standing view that peptidoglycan alone protects cells from bursting.
Our study shows that the periplasm — enclosed by OM–PG connections — acts as a pressure buffer essential for osmoprotection in Gram-negative bacteria.
📄 www.nature.com/articles/s41...
Reposted by Kathryn (Katy) Appler
This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered
July 31, 2025 at 3:38 PM
This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered
Reposted by Kathryn (Katy) Appler
Check this nice first first-author paper by Ning Hall—now out in Nature Geoscience! Our team had a blast supporting Ning on the isolation workflow, and a few of the standout Methanococcoides strains even trace back to our Danish waters. 🌊
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Coastal methane emissions driven by aerotolerant methanogens using seaweed and seagrass metabolites - Nature Geoscience
Experiments suggest aerotolerant archaea produce methane in the surface layers of coastal sandy sediments and that this activity is driven by seaweed and seagrass metabolites.
www.nature.com
August 7, 2025 at 9:14 AM
Check this nice first first-author paper by Ning Hall—now out in Nature Geoscience! Our team had a blast supporting Ning on the isolation workflow, and a few of the standout Methanococcoides strains even trace back to our Danish waters. 🌊
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Kathryn (Katy) Appler
Scientists have finally pinpointed the cause of a marine die-off of unprecedented scale
go.nature.com/4mvYGmd
go.nature.com/4mvYGmd
Mystery of billions of sea-star deaths solved at last
Experiments identify a bacterium as the cause of sea-star wasting disease, which has devastated populations along the western coast of North America.
go.nature.com
August 6, 2025 at 7:56 AM
Scientists have finally pinpointed the cause of a marine die-off of unprecedented scale
go.nature.com/4mvYGmd
go.nature.com/4mvYGmd
Reposted by Kathryn (Katy) Appler
Meet Palaeocampa anthrax, a newly discovered Carboniferous lobopodian, and 150 year old mystery fossil!
Palaeocampa is an exceptional lobopodian - it lived in rivers and lakes, bristled with thousands of poisonous spines, and more. 🧵
Open access: nature.com/articles/s42...
Palaeocampa is an exceptional lobopodian - it lived in rivers and lakes, bristled with thousands of poisonous spines, and more. 🧵
Open access: nature.com/articles/s42...
July 23, 2025 at 9:46 AM
Meet Palaeocampa anthrax, a newly discovered Carboniferous lobopodian, and 150 year old mystery fossil!
Palaeocampa is an exceptional lobopodian - it lived in rivers and lakes, bristled with thousands of poisonous spines, and more. 🧵
Open access: nature.com/articles/s42...
Palaeocampa is an exceptional lobopodian - it lived in rivers and lakes, bristled with thousands of poisonous spines, and more. 🧵
Open access: nature.com/articles/s42...
Reposted by Kathryn (Katy) Appler
🚨 FIRST PAPER ALERT 🚨
My first research paper I've been involved with is out now as a preprint 🦠🥳🦠
#archaea #microsky #PhD
My first research paper I've been involved with is out now as a preprint 🦠🥳🦠
#archaea #microsky #PhD
Our new preprint with a new #Asgard from stromatolites (and its Desulfobacterota companion). Complete circularised genomes of both, cool #cryoem images, protein modelling, etc
Big group effort with a lot of people involved
#archaeasky #archaea
www.biorxiv.org/content/10.1...
Big group effort with a lot of people involved
#archaeasky #archaea
www.biorxiv.org/content/10.1...
An Asgard archaeon from a modern analog of ancient microbial mats
It has been proposed that eukaryotic cells evolved via symbiosis between sulfate-reducing bacteria and hydrogen-producing archaea. Here we describe a highly enriched culture of a novel Asgard archaeon...
www.biorxiv.org
July 23, 2025 at 9:55 AM
Reposted by Kathryn (Katy) Appler
And the story is published now!🍾
www.nature.com/articles/s41...
Open access link: rdcu.be/exnOc
Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social
Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky
www.nature.com/articles/s41...
Open access link: rdcu.be/exnOc
Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social
Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky
July 22, 2025 at 9:06 PM
And the story is published now!🍾
www.nature.com/articles/s41...
Open access link: rdcu.be/exnOc
Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social
Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky
www.nature.com/articles/s41...
Open access link: rdcu.be/exnOc
Many years in the making, great collaboration with @archaellum.bsky.social & @tunglejic.bsky.social
Thanks @ukri.org BBSRC & @leverhulme.ac.uk for funding, reviewers & editor!! 🙏
#microsky #archaeasky
Reposted by Kathryn (Katy) Appler
Elated to have our pre-print now published in @natcomms.nature.com #ArchaeaSky #Microbiology #MEvoSky
rdcu.be/euila
Our main results stay the same: S. islandicus follows a cell cycle akin to that of some eukaryotes, like the budding yeast, with cellular processes cycling similarly.
old🧵cited below👇
rdcu.be/euila
Our main results stay the same: S. islandicus follows a cell cycle akin to that of some eukaryotes, like the budding yeast, with cellular processes cycling similarly.
old🧵cited below👇
July 1, 2025 at 1:01 PM
Elated to have our pre-print now published in @natcomms.nature.com #ArchaeaSky #Microbiology #MEvoSky
rdcu.be/euila
Our main results stay the same: S. islandicus follows a cell cycle akin to that of some eukaryotes, like the budding yeast, with cellular processes cycling similarly.
old🧵cited below👇
rdcu.be/euila
Our main results stay the same: S. islandicus follows a cell cycle akin to that of some eukaryotes, like the budding yeast, with cellular processes cycling similarly.
old🧵cited below👇
Reposted by Kathryn (Katy) Appler
1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
WitChi: Efficient Detection and Pruning of Compositional Bias in Phylogenomic Alignments Using Empirical Chi-Squared Testing
Convergent evolution, where unrelated taxa independently evolve similar nucleotide or amino acid compositions, can introduce compositional bias into biological sequence data. Such biases distort phylo...
www.biorxiv.org
July 20, 2025 at 1:04 PM
1.
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
🧵 New preprint out!
WitChi: a fast, open-source Python tool to detect, quantify & prune compositional bias in MSAs.
Lightweight, tree-free, scalable to 5k+ taxa... so we applied it to the GTDB archaea MSA.
#ArchaeaSky #MEvoSky #MicroSky
🔗 doi.org/10.1101/2025...
💻 github.com/stephkoest/w...
Reposted by Kathryn (Katy) Appler
Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
July 20, 2025 at 4:58 PM
Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
Reposted by Kathryn (Katy) Appler
Feeling very humbled by receiving this award and equally excited to attend ASM in Adelaide this year! 🎉
🎉 Congratulations to the winners of the 2025 Early Career Microbiologist Award!
🏆 Winner: Dr Hannah Brown @hannjbrown.bsky.social
🏆 Runner-Up: Dr Binod Rayamajhee
We’re proud to support the next generation of microbiology leaders and can’t wait to see where their research takes them!
🏆 Winner: Dr Hannah Brown @hannjbrown.bsky.social
🏆 Runner-Up: Dr Binod Rayamajhee
We’re proud to support the next generation of microbiology leaders and can’t wait to see where their research takes them!
June 23, 2025 at 8:54 AM
Feeling very humbled by receiving this award and equally excited to attend ASM in Adelaide this year! 🎉