Libusha Kelly
@microbegrrl.bsky.social
Microbiome, drugs, phages, ecology, AI, the Bronx
Reposted by Libusha Kelly
Exciting new preprint from @amibhatt.bsky.social group
'A conserved sRNA regulates mucin adhesion and gut colonization across the Enterococcaceae'
www.biorxiv.org/content/10.1...
'A conserved sRNA regulates mucin adhesion and gut colonization across the Enterococcaceae'
www.biorxiv.org/content/10.1...
A conserved sRNA regulates mucin adhesion and gut colonization across the Enterococcaceae
Enterococci, particularly E. faecalis , can survive in diverse settings within and outside human hosts. The capacity of E. faecalis to colonize these locations relies on its ability to adapt by alteri...
www.biorxiv.org
November 26, 2025 at 2:44 PM
Exciting new preprint from @amibhatt.bsky.social group
'A conserved sRNA regulates mucin adhesion and gut colonization across the Enterococcaceae'
www.biorxiv.org/content/10.1...
'A conserved sRNA regulates mucin adhesion and gut colonization across the Enterococcaceae'
www.biorxiv.org/content/10.1...
Reposted by Libusha Kelly
We're at 735 registrants and counting! 🎉🦠
If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.
Please share with your networks. 🔗👇
isbscience.org/events/2025-...
If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.
Please share with your networks. 🔗👇
isbscience.org/events/2025-...
November 26, 2025 at 5:19 PM
We're at 735 registrants and counting! 🎉🦠
If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.
Please share with your networks. 🔗👇
isbscience.org/events/2025-...
If you haven't registered yet, don't miss out on this exciting (free) symposium on gut microbial metabolites and their impacts on host health.
Please share with your networks. 🔗👇
isbscience.org/events/2025-...
Reposted by Libusha Kelly
Our attempt to give multinucleate cells the spotlight they deserve (seriously, they’re everywhere), led by the fearless @mrosjac.bsky.social and with @Markus Ganter
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
November 26, 2025 at 2:05 PM
Our attempt to give multinucleate cells the spotlight they deserve (seriously, they’re everywhere), led by the fearless @mrosjac.bsky.social and with @Markus Ganter
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
doi.org/10.32942/X2M...
We’d love your feedback while this goes through the peer review process!
#MicroEvoSky
#ProtistsonSky 🧪🌏
Reposted by Libusha Kelly
Check out that spindle 🤩🔥
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
While 𝘝. 𝘷𝘦𝘳𝘮𝘪𝘧𝘰𝘳𝘮𝘪𝘴 max temp is around 45°C, we found 𝘐. 𝘤𝘢𝘴𝘤𝘢𝘥𝘦𝘯𝘴𝘪𝘴 grows up to 63°C with optimal growth at 55-57°C🥵. We showed cellular replication via Ultrastructure Expansion Microscopy at 63°C. The previous limit for euks is 60°C!
November 25, 2025 at 8:30 PM
Check out that spindle 🤩🔥
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
At 63C, most eukaryotic cells would be busy exploding noisily, forget even trying to divide.
The microbial universe never ceases to astound 😍
Thanks for letting us be a tiny part of this! #ExpandThemAll
Reposted by Libusha Kelly
So happy to see this work out! Was such a pleasure to co-lead this effort with Erin. Do you like viral immune evasion, and using protein structure to study immune antagonists? Give it a read!
Work I co-led with @jnoms.bsky.social is now online at
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.
www.sciencedirect.com/science/arti...
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.
www.sciencedirect.com/science/arti...
Divergent viral phosphodiesterases for immune signaling evasion
Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to …
www.sciencedirect.com
November 25, 2025 at 9:34 PM
So happy to see this work out! Was such a pleasure to co-lead this effort with Erin. Do you like viral immune evasion, and using protein structure to study immune antagonists? Give it a read!
Reposted by Libusha Kelly
Work I co-led with @jnoms.bsky.social is now online at
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.
www.sciencedirect.com/science/arti...
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.
www.sciencedirect.com/science/arti...
Divergent viral phosphodiesterases for immune signaling evasion
Cyclic dinucleotides (CDNs) and other short oligonucleotides play fundamental roles in immune system activation in organisms ranging from bacteria to …
www.sciencedirect.com
November 25, 2025 at 9:10 PM
Work I co-led with @jnoms.bsky.social is now online at
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.
www.sciencedirect.com/science/arti...
@cp-cellhostmicrobe.bsky.social ! We revealed a previously unrealized diversity of viral immune-evasion proteins that selectively destroy different cyclic nucleotide signals used in bacterial immunity.
www.sciencedirect.com/science/arti...
Reposted by Libusha Kelly
Some archaea—an ancient group of microorganisms—have an entirely novel genetic code, according to a new study in Science.
The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications. https://scim.ag/4omApQ7
The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications. https://scim.ag/4omApQ7
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...
scim.ag
November 25, 2025 at 8:24 PM
Some archaea—an ancient group of microorganisms—have an entirely novel genetic code, according to a new study in Science.
The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications. https://scim.ag/4omApQ7
The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications. https://scim.ag/4omApQ7
Reposted by Libusha Kelly
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
November 25, 2025 at 8:41 PM
So happy to announce our new preprint, “A geothermal amoeba sets a new upper temperature limit for eukaryotes.” We cultured a novel amoeba from Lassen Volcanic NP (CA, USA) that divides at 63°C (145°F) 🔥 - a new record for euk growth!
#protistsonsky 🧵
#protistsonsky 🧵
Reposted by Libusha Kelly
popEVE is out in Nature Genetics! 🎉
We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders.
rdcu.be/eRu7K
We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders.
rdcu.be/eRu7K
Proteome-wide model for human disease genetics
Nature Genetics - popEVE is a proteome-wide deep generative model to identify and predict pathogenicity of missense mutations causing genetic disorders.
rdcu.be
November 24, 2025 at 1:35 PM
popEVE is out in Nature Genetics! 🎉
We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders.
rdcu.be/eRu7K
We built a proteome-wide model that combines cross-species and human population variation to rank missense variants by disease severity and help diagnose rare genetic disorders.
rdcu.be/eRu7K
Reposted by Libusha Kelly
Models and co-culture experiments assess four mechanisms of phytoplankton–bacteria interactions www.nature.com/articles/s41... #jcampubs
Models and co-culture experiments assess four mechanisms of phytoplankton–bacteria interactions - Nature Microbiology
Mathematical representations of overflow metabolism, mixotrophy, exoenzymes and reactive oxygen species detoxification recapitulate dynamics in co-cultures of Prochlorococcus and eight heterotrophic b...
www.nature.com
November 24, 2025 at 2:52 PM
Models and co-culture experiments assess four mechanisms of phytoplankton–bacteria interactions www.nature.com/articles/s41... #jcampubs
Reposted by Libusha Kelly
Very excited to share that Department of Biomedical Engineering @hopkinsengineer.bsky.social is hiring for open rank tenure-track faculty in #Biomedical #DataScience!
🔗 apply.interfolio.com/177042
Apps starting to be reviewed Dec 5 and ongoing after!
🧪🧬🖥️🧠 #StatsSky #WomenInSTEM
🔗 apply.interfolio.com/177042
Apps starting to be reviewed Dec 5 and ongoing after!
🧪🧬🖥️🧠 #StatsSky #WomenInSTEM
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
November 6, 2025 at 6:20 AM
Very excited to share that Department of Biomedical Engineering @hopkinsengineer.bsky.social is hiring for open rank tenure-track faculty in #Biomedical #DataScience!
🔗 apply.interfolio.com/177042
Apps starting to be reviewed Dec 5 and ongoing after!
🧪🧬🖥️🧠 #StatsSky #WomenInSTEM
🔗 apply.interfolio.com/177042
Apps starting to be reviewed Dec 5 and ongoing after!
🧪🧬🖥️🧠 #StatsSky #WomenInSTEM
Reposted by Libusha Kelly
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:21 PM
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
Reposted by Libusha Kelly
🚨NEW paper: Benchmarking Hi-C for virus–host inference
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
Benchmarking with synthetic communities provides a baseline for virus-host inferences from Hi-C proximity linking
Virus discovery has accelerated but linking viruses to hosts remains challenging. This study uses synthetic microbiomes to optimize and benchmark Hi-C for virus-host linkage inference, and applies thi...
journals.plos.org
November 21, 2025 at 7:31 PM
🚨NEW paper: Benchmarking Hi-C for virus–host inference
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
journals.plos.org/plosbiology/...
A clear baseline for anyone mapping virus–host interactions that establishes robust, benchmarked thresholds for Hi-C linkages.
Key results: 👇
Reposted by Libusha Kelly
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Libusha Kelly
Check out this amazing story from the labs of @stanford-chemh.bsky.social institute scholar Paul Mischel and Howard Chang @stanfordmedicine.bsky.social !
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Genetic elements promote retention of extrachromosomal DNA in cancer cells - Nature
A combination of genome-wide functional screening, imaging and chromatin profiling identifies a new class of highly prevalent genomic elements that help retain extrachromosomal DNA copies in dividing ...
www.nature.com
November 20, 2025 at 5:22 AM
Check out this amazing story from the labs of @stanford-chemh.bsky.social institute scholar Paul Mischel and Howard Chang @stanfordmedicine.bsky.social !
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Libusha Kelly
Finally out in @nature.com! We uncovered a mechanistic framework for a general and conserved mRNA nuclear export pathway. www.nature.com/articles/s41.... 1/
November 19, 2025 at 11:22 PM
Finally out in @nature.com! We uncovered a mechanistic framework for a general and conserved mRNA nuclear export pathway. www.nature.com/articles/s41.... 1/
Reposted by Libusha Kelly
Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Bacterial immune systems as causes and consequences of microbiome structure
Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...
journals.plos.org
November 19, 2025 at 6:35 PM
Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky
journals.plos.org/plosbiology/...
journals.plos.org/plosbiology/...
Reposted by Libusha Kelly
Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates
-in @natcomms.nature.com
www.nature.com/articles/s41...
-in @natcomms.nature.com
www.nature.com/articles/s41...
Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates - Nature Communications
Ghatbale et al. adapted a co-evolutionary technique to develop Klebsiella pneumoniae phages to be highly active longitudinally against K. pneumoniae clinical isolates, including drug resistant isolate...
www.nature.com
November 20, 2025 at 11:23 AM
Experimental phage evolution results in expanded host ranges against antibiotic resistant Klebsiella pneumoniae isolates
-in @natcomms.nature.com
www.nature.com/articles/s41...
-in @natcomms.nature.com
www.nature.com/articles/s41...
Reposted by Libusha Kelly
Is it a flagellate? A tiny ball with tentacles? Contamination in my ciliate culture? NEW SUPERGROUP OF EUKARYOTES? Yes to all 4! Meet Solarion - just out in #Nature doi.org/10.1038/s415... Huge congrats to Marek Valt, Cepicka Lab & the star team! Very happy to be part of this project. #ProtistsOnSky
November 19, 2025 at 9:39 PM
Is it a flagellate? A tiny ball with tentacles? Contamination in my ciliate culture? NEW SUPERGROUP OF EUKARYOTES? Yes to all 4! Meet Solarion - just out in #Nature doi.org/10.1038/s415... Huge congrats to Marek Valt, Cepicka Lab & the star team! Very happy to be part of this project. #ProtistsOnSky
Reposted by Libusha Kelly
I’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.
Surviving phage attack dynamically regulates bacterial immunity to defeat counterdefenses https://www.biorxiv.org/content/10.1101/2025.11.13.688357v1
November 15, 2025 at 6:10 PM
I’m excited to share my recent postdoc work. Here, we interrogate how different phage infection outcomes (productive vs. restrictive) affect the expression of phage defense systems. We find that a restricted infection not only inhibits the phage but also induces increased immune protein abundance.
Reposted by Libusha Kelly
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
A Grammar of Graphics for Comparative Genomics
An extension of ggplot2 for creating complex genomic maps. It builds on the power of ggplot2 and tidyverse adding new ggplot2-style geoms & positions and dplyr-style verbs to manipulate the…
thackl.github.io
November 18, 2025 at 7:02 PM
gggenomes: A Grammar of Graphics for Comparative Genomics thackl.github.io/gggenomes/ #Rstats
Reposted by Libusha Kelly
Soils contain an amazing diversity of functions encoded in plasmids.
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
November 18, 2025 at 7:18 PM
Soils contain an amazing diversity of functions encoded in plasmids.
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples.
Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov
www.nature.com/articles/s41...
Reposted by Libusha Kelly
Why does daptomycin resistance appear so fast in Enterococcus? We finally have a clue.
DAP resistance in enterococci pops up quickly. What’s been missing is why resistance-associated membrane changes look the way they do, and why the classic path of mutations is so predictable.
DAP resistance in enterococci pops up quickly. What’s been missing is why resistance-associated membrane changes look the way they do, and why the classic path of mutations is so predictable.
A two-component system signaling hub controls enterococcal membrane remodeling in response to daptomycin https://www.biorxiv.org/content/10.1101/2025.11.16.688641v1
November 17, 2025 at 8:27 PM
Why does daptomycin resistance appear so fast in Enterococcus? We finally have a clue.
DAP resistance in enterococci pops up quickly. What’s been missing is why resistance-associated membrane changes look the way they do, and why the classic path of mutations is so predictable.
DAP resistance in enterococci pops up quickly. What’s been missing is why resistance-associated membrane changes look the way they do, and why the classic path of mutations is so predictable.
Reposted by Libusha Kelly
Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity.
academic.oup.com/nar/article/... 1/5
academic.oup.com/nar/article/... 1/5
Bacterial natural transformation drives cassette shuffling and simplifies recombination in chromosomal integrons
Abstract. Integrons act as biobanks of gene cassettes conferring functions crucial for bacterial defense, including protection against phages and antibioti
academic.oup.com
November 17, 2025 at 3:44 PM
Our new paper is out in @narjournal.bsky.social We show that natural transformation enables bacteria to shuffle integron cassettes, boosting their phenotypic diversity.
academic.oup.com/nar/article/... 1/5
academic.oup.com/nar/article/... 1/5
Reposted by Libusha Kelly
Introducing Foli-seq in @natbiotech.nature.com today. Foli-seq can be used to measure gut-derived RNA from fecal matter (signals of immune, secretory & epithelial cells). We used this to map gut inflammation, drug response, and host-microbe interactions. 💩🧬💊🦠
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut - Nature Biotechnology
Profiling host RNA shed in feces reveals disease states in the gut.
www.nature.com
November 17, 2025 at 8:55 PM
Introducing Foli-seq in @natbiotech.nature.com today. Foli-seq can be used to measure gut-derived RNA from fecal matter (signals of immune, secretory & epithelial cells). We used this to map gut inflammation, drug response, and host-microbe interactions. 💩🧬💊🦠
www.nature.com/articles/s41...
www.nature.com/articles/s41...