Gretel Waugh
@gretelwaugh.bsky.social
Microbial generalist 🦠 | Keen freediver & birdwatcher | Reluctant #Rstats enthusiast | she/her
Prospective PhD students - here is a brilliant opportunity to explore how bacteria and viruses evolve in liquid environments like the ocean 🌊
The LSI is a great place to explore microbial evolution, and you'll be working with fantastic, interdisciplinary supervisors. Email Wolfram if interested 👇
The LSI is a great place to explore microbial evolution, and you'll be working with fantastic, interdisciplinary supervisors. Email Wolfram if interested 👇
Even more biased: I'm excited about the project 'Turbulent Partners: Unravelling Host-Virus Coevolution in Dynamic Environments' with Adam Monier and Daniel Kattnig. Drop me an email if interested! www.exeter.ac.uk/v8media/rese...
October 28, 2025 at 2:40 PM
Prospective PhD students - here is a brilliant opportunity to explore how bacteria and viruses evolve in liquid environments like the ocean 🌊
The LSI is a great place to explore microbial evolution, and you'll be working with fantastic, interdisciplinary supervisors. Email Wolfram if interested 👇
The LSI is a great place to explore microbial evolution, and you'll be working with fantastic, interdisciplinary supervisors. Email Wolfram if interested 👇
Reposted by Gretel Waugh
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by Gretel Waugh
Happy to share our new work on Temperature-driven biogeography of marine viruses infecting Micromonas:
academic.oup.com/ismecommun/a...
academic.oup.com/ismecommun/a...
Temperature-driven biogeography of marine giant viruses infecting picoeukaryotes Micromonas
Abstract. Climate shapes the biogeography of microbial and viral communities in the ocean. Among abiotic factors, temperature is one of the main drivers of
academic.oup.com
October 6, 2025 at 2:57 PM
Happy to share our new work on Temperature-driven biogeography of marine viruses infecting Micromonas:
academic.oup.com/ismecommun/a...
academic.oup.com/ismecommun/a...
Reposted by Gretel Waugh
Excited to annouce the latest research published by our lab, which is led by Dinesh Subedi and is out today in Nature Microbiology.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Rational design of a hospital-specific phage cocktail to treat Enterobacter cloacae complex infections - Nature Microbiology
The Entelli-02 phage product containing five phages has frontline potential to address infections caused by the multidrug-resistant Enterobacter cloacae complex.
www.nature.com
September 24, 2025 at 12:20 PM
Excited to annouce the latest research published by our lab, which is led by Dinesh Subedi and is out today in Nature Microbiology.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Oh, to have been a scientist in the 1940s...
(Monod, 1949)
(Monod, 1949)
September 18, 2025 at 2:42 PM
Oh, to have been a scientist in the 1940s...
(Monod, 1949)
(Monod, 1949)
Reposted by Gretel Waugh
🚨 New paper alert 🚨 Using LLMs as data annotators, you can produce any scientific result you want. We call this **LLM Hacking**.
Paper: arxiv.org/pdf/2509.08825
Paper: arxiv.org/pdf/2509.08825
September 12, 2025 at 10:33 AM
🚨 New paper alert 🚨 Using LLMs as data annotators, you can produce any scientific result you want. We call this **LLM Hacking**.
Paper: arxiv.org/pdf/2509.08825
Paper: arxiv.org/pdf/2509.08825
Reposted by Gretel Waugh
"We are told that AI is inevitable, that we must adapt or be left behind. But universities are not tech companies. Our role is to foster critical thinking, not to follow industry trends uncritically." www.ru.nl/en/research/...
September 12, 2025 at 10:45 AM
"We are told that AI is inevitable, that we must adapt or be left behind. But universities are not tech companies. Our role is to foster critical thinking, not to follow industry trends uncritically." www.ru.nl/en/research/...
Reposted by Gretel Waugh
How a Group of Students in the Pacific Islands Reshaped Global Climate Law www.nytimes.com/2025/09/10/m...
How a Group of Students in the Pacific Islands Reshaped Global Climate Law
www.nytimes.com
September 11, 2025 at 10:33 PM
How a Group of Students in the Pacific Islands Reshaped Global Climate Law www.nytimes.com/2025/09/10/m...
Reposted by Gretel Waugh
Prochlorococcus — Earth’s smallest and most abundant photosynthetic organism — may see population reductions of up to 51% in tropical oceans by 2100 under moderate and high warming scenarios, according to a study in Nature Microbiology. go.nature.com/3V3mvGn 🌊 🧪
September 8, 2025 at 7:01 PM
Prochlorococcus — Earth’s smallest and most abundant photosynthetic organism — may see population reductions of up to 51% in tropical oceans by 2100 under moderate and high warming scenarios, according to a study in Nature Microbiology. go.nature.com/3V3mvGn 🌊 🧪
Happy phage day! 🦠 Special issue on ecology and evolution of bacterial immune systems, including this paper from @josie-e.bsky.social et al exploring CRISPR - phage interactions. 🧵⬇️
Can CRISPR-Cas systems target any phage? Yes, no, it depends? What does it depend on? The second paper from my PhD came out today in a special issue of Phil Trans B on the ecology and evolution of bacterial immune systems
doi.org/10.1098/rstb...
doi.org/10.1098/rstb...
Phage susceptibility to a minimal, modular synthetic CRISPR-Cas system in Pseudomonas aeruginosa is nutrient dependent | Philosophical Transactions of the Royal Society B: Biological Sciences
CRISPR-Cas systems can provide adaptive, heritable immunity to their prokaryotic hosts
against invading genetic material such as phages. It is clear that the importance
of acquiring CRISPR-Cas immunit...
doi.org
September 5, 2025 at 10:15 AM
Happy phage day! 🦠 Special issue on ecology and evolution of bacterial immune systems, including this paper from @josie-e.bsky.social et al exploring CRISPR - phage interactions. 🧵⬇️
🤯
🌎👩🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.
doi.org/10.1101/2024...
September 3, 2025 at 10:07 AM
🤯
Reposted by Gretel Waugh
🚨I have a fully funded 4-year #PhD opportunity in my lab on 'Tuneable multi-input genetic logic circuits for designer probiotics'.🦠 We'll be throwing all the tech we have at this one to make reliable engineering of diverse microbes a reality. Applicants must be UK national...
September 3, 2025 at 9:00 AM
🚨I have a fully funded 4-year #PhD opportunity in my lab on 'Tuneable multi-input genetic logic circuits for designer probiotics'.🦠 We'll be throwing all the tech we have at this one to make reliable engineering of diverse microbes a reality. Applicants must be UK national...
Reposted by Gretel Waugh
PhD opportunity, please share:
We are looking for a prospective PhD student to start in October 2026 who is excited about bacteria (Klebsiella pneumoniae), how they interact, and how they exchange DNA.
All details can be found on the funder website 👉 gw4biomed.ac.uk/developing-c...
We are looking for a prospective PhD student to start in October 2026 who is excited about bacteria (Klebsiella pneumoniae), how they interact, and how they exchange DNA.
All details can be found on the funder website 👉 gw4biomed.ac.uk/developing-c...
Developing CRISPR-Cas antimicrobials to tackle antibiotic resistance spread in Klebsiella pneumoniae - GW4 BioMed MRC DTP
Project Code MRCIIAR26Ex van Houte Project Type Wet lab Research Theme Infection, Immunity, Antimicrobial Resistance and Repair Project Summary Download Summary Antimicrobial resistance (AMR) poses a ...
gw4biomed.ac.uk
September 2, 2025 at 9:48 AM
PhD opportunity, please share:
We are looking for a prospective PhD student to start in October 2026 who is excited about bacteria (Klebsiella pneumoniae), how they interact, and how they exchange DNA.
All details can be found on the funder website 👉 gw4biomed.ac.uk/developing-c...
We are looking for a prospective PhD student to start in October 2026 who is excited about bacteria (Klebsiella pneumoniae), how they interact, and how they exchange DNA.
All details can be found on the funder website 👉 gw4biomed.ac.uk/developing-c...
Reposted by Gretel Waugh
Exciting new metabolism unlocked - sulfur oxidation coupled to iron reduction! Big congrats and very happy for Songcan, Marc, Alex and team! :-)
📢 New paper in @nature.com
Microbes rock 🎸🤘 with sulfide and iron minerals
I am very excited to share our recent study, which describes a previously unknown microbial energy metabolism ⚡⚡⚡🦠🧫⚡⚡⚡
🆕 Microbial iron oxide respiration coupled to sulfide oxidation - MISO
www.nature.com/articles/s41...
Microbes rock 🎸🤘 with sulfide and iron minerals
I am very excited to share our recent study, which describes a previously unknown microbial energy metabolism ⚡⚡⚡🦠🧫⚡⚡⚡
🆕 Microbial iron oxide respiration coupled to sulfide oxidation - MISO
www.nature.com/articles/s41...
Microbial iron oxide respiration coupled to sulfide oxidation - Nature
Genomic and biochemical analyses of prokaryotic sulfur metabolism identify diverse microorganisms with the capacity to oxidize sulfide using iron(iii).
www.nature.com
August 28, 2025 at 11:12 AM
Exciting new metabolism unlocked - sulfur oxidation coupled to iron reduction! Big congrats and very happy for Songcan, Marc, Alex and team! :-)
Reposted by Gretel Waugh
Very happy to see this one out: doi.org/10.1093/molbev/msaf192
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio
August 27, 2025 at 1:37 PM
Very happy to see this one out: doi.org/10.1093/molbev/msaf192
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio
Reposted by Gretel Waugh
New paper out @molbioevol.bsky.social on antimutator Ecoli, mutational spectra and the distribution of fitness effects of antibiotic resistance with @knightjar.bsky.social @rokkrasovec.bsky.social and others @mermanchester.bsky.social doi.org/pzfm
Read🧵for highlights and fun stats (1/13)
Read🧵for highlights and fun stats (1/13)
Antimutator and Mutational Spectrum Effects Can Combine to Reduce Evolutionary Potential in Escherichia coli ΔnudJ
Abstract. The rate of spontaneous mutation is a key factor in determining the capacity of a population to adapt to a novel environment, for example, a bact
doi.org
August 18, 2025 at 3:40 PM
New paper out @molbioevol.bsky.social on antimutator Ecoli, mutational spectra and the distribution of fitness effects of antibiotic resistance with @knightjar.bsky.social @rokkrasovec.bsky.social and others @mermanchester.bsky.social doi.org/pzfm
Read🧵for highlights and fun stats (1/13)
Read🧵for highlights and fun stats (1/13)
Reposted by Gretel Waugh
Out yesterday. Using a translation reporter on a mini-tn5 transposon, and high freq. mutagenesis, we looked at translation on whole genome scale independently of genome annotation. academic.oup.com/nar/article/...
PIRT-Seq: a high-resolution whole-genome assay to identify protein-coding genes
Abstract. The advent of high-density mutagenesis and data-mining studies suggest the existence of further coding potential within bacterial genomes. Small
academic.oup.com
August 14, 2025 at 7:00 PM
Out yesterday. Using a translation reporter on a mini-tn5 transposon, and high freq. mutagenesis, we looked at translation on whole genome scale independently of genome annotation. academic.oup.com/nar/article/...
Reposted by Gretel Waugh
Horton, Cherry, @gretelwaugh.bsky.social @taylorlabgroup.bsky.social et al. combine experimental evolution and bioinformatics in bacteria to characterize a ≥8 bp motif that can increase T:A→G:C mutation rates >1000-fold than the baseline rate.
🔗 doi.org/10.1093/molbev/msaf183
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf183
#evobio #molbio
GnT Motifs Can Increase T:A→G:C Mutation Rates Over 1000-fold in Bacteria
Abstract. Nucleotides across a genome do not mutate at equal frequencies. Instead, specific nucleotide positions can exhibit much higher mutation rates tha
doi.org
August 14, 2025 at 5:23 PM
Horton, Cherry, @gretelwaugh.bsky.social @taylorlabgroup.bsky.social et al. combine experimental evolution and bioinformatics in bacteria to characterize a ≥8 bp motif that can increase T:A→G:C mutation rates >1000-fold than the baseline rate.
🔗 doi.org/10.1093/molbev/msaf183
#evobio #molbio
🔗 doi.org/10.1093/molbev/msaf183
#evobio #molbio
Our new paper exploring mutational hotspots in bacteria 🧬⚡. I learnt lots as part of this project; unpacked in James' 🧵(below). Very excited to see it finally in the wild!
🦠 New paper led by James Horton (feat. J Cherry & @gretelwaugh.bsky.social) reveals GnT DNA motif can boost T→A mutation rates up to 1000×, & how tweaking nearby bases can fine-tune its potency.
General across bacteria + potential in synbio.
📄 academic.oup.com/mbe/advance-ar…
🔗 James’s thread ⬇️
General across bacteria + potential in synbio.
📄 academic.oup.com/mbe/advance-ar…
🔗 James’s thread ⬇️
https://academic.oup.com/mbe/advance-ar…
August 14, 2025 at 1:10 PM
Our new paper exploring mutational hotspots in bacteria 🧬⚡. I learnt lots as part of this project; unpacked in James' 🧵(below). Very excited to see it finally in the wild!
Reposted by Gretel Waugh
New paper out! In it i review the context and implications of the "chitin raft hypothesis" for how cyanobacteria colonized the open ocean.
Included is a new perspective on why there were two major stages of atmospheric oxygenation over Earth history.
royalsocietypublishing.org/doi/10.1098/...
Included is a new perspective on why there were two major stages of atmospheric oxygenation over Earth history.
royalsocietypublishing.org/doi/10.1098/...
The chitin raft hypothesis for the colonization of the open ocean by cyanobacteria | Philosophical Transactions of the Royal Society B: Biological Sciences
It is often assumed planktonic cyanobacteria existed in Precambrian oceans, but that
their productivity was constrained. However, available evidence suggests picocyanobacteria
only colonized the open ...
royalsocietypublishing.org
August 7, 2025 at 1:42 PM
New paper out! In it i review the context and implications of the "chitin raft hypothesis" for how cyanobacteria colonized the open ocean.
Included is a new perspective on why there were two major stages of atmospheric oxygenation over Earth history.
royalsocietypublishing.org/doi/10.1098/...
Included is a new perspective on why there were two major stages of atmospheric oxygenation over Earth history.
royalsocietypublishing.org/doi/10.1098/...
Reposted by Gretel Waugh
Great Barrier Reef suffers biggest annual drop in live coral since 1980s after devastating coral bleaching
Great Barrier Reef suffers biggest annual drop in live coral since 1980s after devastating coral bleaching
Researchers warn reef may reach tipping point where coral cannot recover fast enough between major catastrophic events
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The Great Barrier Reef has suffered its biggest annual drop in live coral in two out of three areas monitored by scientists since 1986, a new report has revealed.
The Australian Institute of Marine Science (Aims) report is the first to comprehensively document the devastating impacts of the early 2024 mass coral bleaching event – the most widespread and severe on record for the Great Barrier Reef. Continue reading...
www.theguardian.com
August 5, 2025 at 3:01 PM
Great Barrier Reef suffers biggest annual drop in live coral since 1980s after devastating coral bleaching
Reposted by Gretel Waugh
New paper that may be of interest to ecologists studying global change, disturbances, biodiversity, ecosystem functioning, or response diversity: doi.org/10.1038/s414...
Variability of functional and biodiversity responses to perturbations is predictable and informative - Nature Communications
Measures of biodiversity and ecosystem functioning show variable responses to perturbations, complicating the prediction of responses to global change. This study shows that the variability of communi...
doi.org
December 2, 2024 at 7:45 AM
New paper that may be of interest to ecologists studying global change, disturbances, biodiversity, ecosystem functioning, or response diversity: doi.org/10.1038/s414...
Reposted by Gretel Waugh
Very proud to have our lab’s first work published in @cp-cellhostmicrobe.bsky.social!
In this work, we use functional metagenomics to find phage defenses from human and soil microbiomes!
Congrats to first author @luis840alberto.bsky.social !
www.cell.com/cell-host-mi...
(1/3)
In this work, we use functional metagenomics to find phage defenses from human and soil microbiomes!
Congrats to first author @luis840alberto.bsky.social !
www.cell.com/cell-host-mi...
(1/3)
July 29, 2025 at 2:53 PM
Very proud to have our lab’s first work published in @cp-cellhostmicrobe.bsky.social!
In this work, we use functional metagenomics to find phage defenses from human and soil microbiomes!
Congrats to first author @luis840alberto.bsky.social !
www.cell.com/cell-host-mi...
(1/3)
In this work, we use functional metagenomics to find phage defenses from human and soil microbiomes!
Congrats to first author @luis840alberto.bsky.social !
www.cell.com/cell-host-mi...
(1/3)
Reposted by Gretel Waugh
New pre-print from my lab!
Plasmids link antibiotic resistance and phage defense.
E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage
www.biorxiv.org/content/10.1....
Plasmids link antibiotic resistance and phage defense.
E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage
www.biorxiv.org/content/10.1....
Plasmids link antibiotic resistance genes and phage defense systems in E. coli
Phage therapy has been proposed as an alternative to antibiotics to treat resistant infections. However, we have a limited understanding of how antibiotic resistance genes (ARGs) associate with bacter...
www.biorxiv.org
July 29, 2025 at 1:28 PM
New pre-print from my lab!
Plasmids link antibiotic resistance and phage defense.
E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage
www.biorxiv.org/content/10.1....
Plasmids link antibiotic resistance and phage defense.
E.coli plasmids are hotspots for both antibiotic resistance and phage defense. Phage therapy has the potential to accidentally select for antibiotic resistance!!!
#microsky#AMR#phage
www.biorxiv.org/content/10.1....
Reposted by Gretel Waugh
#newpaper now out in @nature.com!
A huge expansion of the human niche in Africa ~70 kya likely equipped later #outofAfrica dispersals with a unique ecological flexibility.
www.nature.com/articles/s41...
led by Emily Hallett, @mikleonardi.bsky.social, Andrea Manica, @elliescerri.bsky.social 1/4
A huge expansion of the human niche in Africa ~70 kya likely equipped later #outofAfrica dispersals with a unique ecological flexibility.
www.nature.com/articles/s41...
led by Emily Hallett, @mikleonardi.bsky.social, Andrea Manica, @elliescerri.bsky.social 1/4
Major expansion in the human niche preceded out of Africa dispersal - Nature
Analysis of species distribution models in a pan-African database comprising chronometrically dated archaeological sites over the past 120,000 years shows major expansion in the human niche from 70 ka...
www.nature.com
June 18, 2025 at 3:09 PM
#newpaper now out in @nature.com!
A huge expansion of the human niche in Africa ~70 kya likely equipped later #outofAfrica dispersals with a unique ecological flexibility.
www.nature.com/articles/s41...
led by Emily Hallett, @mikleonardi.bsky.social, Andrea Manica, @elliescerri.bsky.social 1/4
A huge expansion of the human niche in Africa ~70 kya likely equipped later #outofAfrica dispersals with a unique ecological flexibility.
www.nature.com/articles/s41...
led by Emily Hallett, @mikleonardi.bsky.social, Andrea Manica, @elliescerri.bsky.social 1/4