Gretel Waugh

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 👇

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

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-...

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

Happy to share our new work on Temperature-driven biogeography of marine viruses infecting Micromonas:
academic.oup.com/ismecommun/a...

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.

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...

"It would be a foolish enterprise, and doomed to failure.."

An excerpt from a scientific manuscript, Monod, 1949, with the following phrase highlighted in yellow: 'No attempt is made at reviewing the literature on a subject which, as we have just seen, is not really a subject at all.'

Oh, to have been a scientist in the 1940s...

(Monod, 1949)

We present our new preprint titled "Large Language Model Hacking: Quantifying the Hidden Risks of Using LLMs for Text Annotation". We quantify LLM hacking risk through systematic replication of 37 diverse computational social science annotation tasks. For these tasks, we use a combined set of 2,361 realistic hypotheses that researchers might test using these annotations. Then, we collect 13 million LLM annotations across plausible LLM configurations. These annotations feed into 1.4 million regressions testing the hypotheses. For a hypothesis with no true effect (ground truth $p > 0.05$), different LLM configurations yield conflicting conclusions. Checkmarks indicate correct statistical conclusions matching ground truth; crosses indicate LLM hacking -- incorrect conclusions due to annotation errors. Across all experiments, LLM hacking occurs in 31-50\% of cases even with highly capable models. Since minor configuration changes can flip scientific conclusions, from correct to incorrect, LLM hacking can be exploited to present anything as statistically significant.

🚨 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

"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/...

How a Group of Students in the Pacific Islands Reshaped Global Climate Law

How a Group of Students in the Pacific Islands Reshaped Global Climate Law www.nytimes.com/2025/09/10/m...

This is figure 3, which shows projected changes in annual phytoplankton biomass production between pre-industrial (1860) and future (2090–2100) conditions, based on alterations in temperature, nutrient supply, mixing and ocean circulation anticipated under a moderate and high warming scenario.

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. 🧵⬇️

🤯

🚨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...

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...

Exciting new metabolism unlocked - sulfur oxidation coupled to iron reduction! Big congrats and very happy for Songcan, Marc, Alex and team! :-)

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

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

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)

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

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/...

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

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

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!

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 ...

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/...

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 * Get our breaking news email, free app or daily news podcast 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...

Great Barrier Reef suffers biggest annual drop in live coral since 1980s after devastating coral bleaching

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...

New paper that may be of interest to ecologists studying global change, disturbances, biodiversity, ecosystem functioning, or response diversity: doi.org/10.1038/s414...

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)

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...

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....

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...

#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

ATP synthesis driven by atmospheric hydrogen concentrations | PNAS All cells require a continuous supply of the universal energy currency, adenosine triphosphate (ATP), to drive countless cellular reactions. The un...

Our article showing energy production from air alone is in PNAS today. This paper provides an ultimate biochemical proof that microbes can survive simply by 'making' energy from air (making two ATP per molecule atmospheric H2 consumed) and has biotech applications. www.pnas.org/doi/10.1073/...

Looks really cool, thanks Tiff!

graphical abstract of the article the extended mobility of plasmids

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

Conference flyer, all info is on link too

Please share! 🦠
Workshop on Phage Therapy in Liverpool on 25th November organised by Stineke van Houte, @jojofoth.bsky.social, @brockhurstlab.bsky.social, & Edze Westra.

Limited FREE tickets & more info here: sites.exeter.ac.uk/vanhoutelab/...

#MicroSky