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Gretel Waugh

@gretelwaugh.bsky.social
611 followers 403 following 24 posts

Microbial generalist 🦠 | Keen freediver & birdwatcher | Reluctant #Rstats enthusiast | she/her

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Reposted by Gretel Waugh
Mozammel Hoque @mozammel.bsky.social · 20/09/2026
1/ New paper out in ISME Communications now in full version. Bacteria rarely live alone in nature, so we ran a 6-month evolution experiment asking what happens when species are forced to share the same biofilm. Turns out, company changes everything. 🧵 doi.org/10.1093/isme...
doi.org
Mixed-species interactions constrain diversification and shape biofilm evolution
Abstract. Experimental evolution provides a powerful framework for dissecting how ecological interactions shape adaptive trajectories. Here, we evolved Kle
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ace-gtdb.bsky.social @ace-gtdb.bsky.social · 30/07/2026
🎉 We are honoured and excited to share that our team has been named a finalist in the the Australian Research Data Commons Eureka Prize for Excellence in #DataPlatforms! 🎉 Check out our video at: www.youtube.com/watch?v=1nzt... @ardc.edu.au @eurekaprizes.bsky.social #EurekaPrizes
youtube.com
Genome Taxonomy Database – Finalist, 2026 Eureka Prize for Excellence in Data Platforms
YouTube video by Australian Museum
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Joshua Weitz @joshuasweitz.bsky.social · 02/07/2026
When you tell colleagues that the public still maintains deep trust in our work (imperfectly & with growing fractures) they are often *very* surprised, in part because of the organized investment in "a rhetoric of science in crisis” to foster an actual crisis. www.nature.com/articles/d41... a 🧵
nature.com
Have people stopped trusting science? The data tell a surprising story
Some say there’s a global crisis of trust — but research reveals where the real problems lie.
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Ben J Woodcroft @benjwoodcroft.bsky.social · 26/05/2026
Sandpiper 2 is up. 913,000 metagenomic community profiles w @ace-gtdb.bsky.social R232, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroneys.bsky.social @thepatientwait.bsky.social @iambrettb.bsky.social and especially the new kid @nhstefan.bsky.social
sandpiper.qut.edu.au
sandpiper
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Niki Hubbard, PhD 🐙🦀 @nikihubbard.bsky.social · 30/03/2026
Once upon a time I just admired nudis and sea slugs. But it was not enough. Now apparently I'm creating an R package to celebrate their colour palettes? 😅 First up, my Sydney fave, Hypselodoris bennetti. #rstats #nudibranch #dataviz 🦑🐙🧪 #marinelife #invertebrates
Close up with a beautiful nudibranch on a rocky reef. The lower half of the image is a palette of swatches made from the nudi's vibrant colours.
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MERMan Research Group (University of Manchester) @mermanchester.bsky.social · 23/03/2026
The University of Manchester is pleased to be the UK host for MEEHubs2026. Registration now open! We have an amazing lineup of speakers, Jasmine Ono, Stineke van Houte, and Sarah Coulthurst, & more virtually at other hubs. We hope to see you here or online 3-5 Aug! meehubs2026.oa-event.com
meehubs2026.oa-event.com
Home
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Ben J Woodcroft @benjwoodcroft.bsky.social · 23/03/2026
New paper in mSystems! 🧵 - how much of your metagenome is actually bacterial/archaeal DNA? For many samples, nobody knows. We built SingleM prokaryotic_fraction (SPF) to answer this, then ran it on >100,000 public metagenomes. 🧬🖥️🦠 Here's what we found 👇 doi.org/10.1128/msystems.01062-25
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Josie Elliott @josie-e.bsky.social · 16/02/2026
I'm excited and grateful to share that I have been awarded a Marie Skłodowska-Curie postdoc fellowship for my work with @annechevallereau.bsky.social at @mmsb-lyon.bsky.social. I feel incredibly lucky and I'm looking forward to getting to work on all the phage-y experiments we have planned 🧫
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Gretel Waugh @gretelwaugh.bsky.social · 28/10/2025
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 👇
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ace-gtdb.bsky.social @ace-gtdb.bsky.social · 22/10/2025
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
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
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David Demory @d2mory.bsky.social · 06/10/2025
Happy to share our new work on Temperature-driven biogeography of marine viruses infecting Micromonas: academic.oup.com/ismecommun/a...
academic.oup.com
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
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Jeremy Barr @jeremyjbarr.bsky.social · 24/09/2025
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...
nature.com
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.
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Gretel Waugh @gretelwaugh.bsky.social · 18/09/2025
Oh, to have been a scientist in the 1940s... (Monod, 1949)
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.'
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Joachim Baumann @joachimbaumann.bsky.social · 12/09/2025
🚨 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 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.
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Olivia Guest · Ολίβια Γκεστ @olivia.science · 12/09/2025
"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/...
ru.nl
‘Opposing the inevitability of AI at universities is possible and necessary’ | Radboud University
Since the widespread release of ChatGPT in December of 2022, AI has taken over much of the world by storm – including academia. Most of this happened with very little pushback, despite a myriad of iss...
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IUCN SSC Marine Conservation Committee (MCC) @sscmarine.bsky.social · 11/09/2025
How a Group of Students in the Pacific Islands Reshaped Global Climate Law www.nytimes.com/2025/09/10/m...
nytimes.com
How a Group of Students in the Pacific Islands Reshaped Global Climate Law
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Nature Portfolio @natureportfolio.nature.com · 08/09/2025
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 🌊 🧪
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.
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Gretel Waugh @gretelwaugh.bsky.social · 05/09/2025
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. 🧵⬇️
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Gretel Waugh @gretelwaugh.bsky.social · 03/09/2025
🤯
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Thomas Gorochowski @chofski.bsky.social · 03/09/2025
🚨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...
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David Sünderhauf @davvi36.bsky.social · 02/09/2025
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...
gw4biomed.ac.uk
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 ...
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Kenneth Wasmund @kennethwasmund.bsky.social · 28/08/2025
Exciting new metabolism unlocked - sulfur oxidation coupled to iron reduction! Big congrats and very happy for Songcan, Marc, Alex and team! :-)
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Eduardo Rocha @epcrocha.bsky.social · 27/08/2025
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
doi.org
Impact of Natural Transformation on the Acquisition of Novel Genes in Bacteria
Abstract. Natural transformation is the only process of gene exchange under the exclusive control of the recipient bacteria. It has often been considered a
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Rowan Green @rowancallumg.bsky.social · 18/08/2025
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)
doi.org
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
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Emily Goodall @emgoodall.bsky.social · 14/08/2025
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/...
academic.oup.com
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
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Molecular Biology and Evolution @molbioevol.bsky.social · 14/08/2025
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
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
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Gretel Waugh @gretelwaugh.bsky.social · 14/08/2025
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!
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Rogier Braakman @rogierbraakman.bsky.social · 07/08/2025
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/...
royalsocietypublishing.org
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 ...
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Guardian Australia @australia.theguardian.com · 05/08/2025
Great Barrier Reef suffers biggest annual drop in live coral since 1980s after devastating coral bleaching
theguardian.com
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...
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James Orr @jamesaorr.bsky.social · 02/12/2024
New paper that may be of interest to ecologists studying global change, disturbances, biodiversity, ecosystem functioning, or response diversity: doi.org/10.1038/s414...
doi.org
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...
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Kevin Forsberg @kvnforsberg.bsky.social · 29/07/2025
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)
cell.com
Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes
Rodríguez-Rodríguez et al. use functional metagenomics to identify hundreds of sequences from diverse environmental bacteria that block phage infection when expressed in E. coli. Their discoveries inc...
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Craig MacLean @craigmaclean.bsky.social · 29/07/2025
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....
biorxiv.org
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...
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Evolutionary Ecology Group, Cambridge @eegcam.bsky.social · 18/06/2025
#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
nature.com
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...
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Chris Greening @greening.bsky.social · 25/07/2025
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/...
pnas.org
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...
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Eduardo Rocha @epcrocha.bsky.social · 23/07/2025
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/...
graphical abstract of the article the extended mobility of plasmids
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David Sünderhauf @davvi36.bsky.social · 22/07/2025
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
Conference flyer, all info is on link too
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We Are RLadies+ @weare.rladies.org · 18/07/2025
🧵 Do you have R packages that make your workflow smoother or help you avoid problems you used to face all the time? I’ve collected a few that solved issues that used to trip me up 👇
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Ben J Woodcroft @benjwoodcroft.bsky.social · 16/07/2025
Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵
Logo for the Sandpiper website
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Malcolm White @mfwhite2.bsky.social · 17/07/2025
New role for HTH DNA binding proteins - sequestering phage DNA!
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Craig MacLean @craigmaclean.bsky.social · 16/07/2025
New paper with @rwheatley8.bsky.social and Cedric Lood Actual title: Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy. Sensationalist title: Plasmids carry useless genes academic.oup.com/ismej/articl...
academic.oup.com
Chromosomal capture of beneficial genes drives plasmids toward ecological redundancy
Abstract. Plasmids are a ubiquitous feature of bacterial genomes, but the forces driving genes and phenotypes to become associated with plasmids are poorly
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Roamer 🍉 @terraroam.bsky.social · 15/07/2025
The Australian Federal Court and government has grievously wronged Torres Strait Islanders. My heart breaks for them. Torres Strait community leaders in ‘deepest pain imaginable’ as federal court dismisses landmark climate case www.theguardian.com/environment/...
theguardian.com
Torres Strait community leaders in ‘deepest pain imaginable’ as federal court dismisses landmark climate case
Class action led by two community leaders argued government had legal duty of care to prevent or deal with damage linked to global heating
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Kostas Kormas 🐟🦞🐚🦭💩🔬🧪🧬📝 ✈️ 🏳️‍🌈 @kkormas.bsky.social · 10/07/2025
Attention microbial oceanographers! New journal " #Ocean #Microbiology " dedicated to what you love to do! Do you want to make it a good journal for your work? See 👉 omjournal.biomedcentral.com #SymbioSky #MicroSky #microbiomesky #Microbiology #ArchaeaSky #ProtistsOnSky @aslo.org
omjournal.biomedcentral.com
Ocean Microbiology
Ocean Microbiology is dedicated to advancing the field by capturing the interactions, adaptations, and roles of microorganisms within marine and aquatic ...
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Pam Engelberts @pam-engelberts.bsky.social · 08/07/2025
Very excited to share the first paper out of my Postdoc @CMR: GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities. @sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social doi.org/10.1093/isme... 🧵1/7
doi.org
GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities
Abstract. Fluorescence in situ hybridisation (FISH) is a powerful tool for visualising the spatial organisation of microbial communities. However, traditio
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Steven Robbins @stevenjrobbins.bsky.social · 05/07/2025
Congrats @margotbligh.bsky.social!!!
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Dr Abeba Birhane @abeba.blacksky.app · 25/06/2025
New paper hot off the press www.nature.com/articles/s41... We analysed over 40,000 computer vision papers from CVPR (the longest standing CV conf) & associated patents tracing pathways from research to application. We found that 90% of papers & 86% of downstream patents power surveillance 1/
nature.com
Computer-vision research powers surveillance technology - Nature
An analysis of research papers and citing patents indicates the extensive ties between computer-vision research and surveillance.
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Elaine Luo @oceanmicrobes.bsky.social · 26/06/2025
Lab’s first publication as #newPI @isme-microbes.bsky.social 😃 We observed evidence supporting the viral shuttle hypothesis in giant viruses. We also observed convergent evolution amongst giant viruses and bacteriophages to light-energy and nutrient limitation. academic.oup.com/ismej/articl...
academic.oup.com
Vertical transport and spatiotemporal dynamics of giant viruses in the North Pacific subtropical gyre
Abstract. Nucleocytoplasmic large DNA viruses, or “giant viruses,” are prevalent in marine environments, infecting diverse eukaryotic lineages and influenc
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Tom Ellis @proftomellis.bsky.social · 24/06/2025
From the same team that made vanilla for ice cream using E.coli that digest plastic waste.
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Anna Olina @annaolina.bsky.social · 24/06/2025
Happily representing @multidefence.bsky.social at the #EESMicrobiology in Heidelberg! Come to my poster if interested in prophage-mediated phage defence! Also don't miss @emgoodall.bsky.social's talk today, and @alekseiagapov.bsky.social and @davvi36.bsky.social posters!
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Meaghan Castledine @mcastd.bsky.social · 20/06/2025
How do multiple coexisting bacteria and phages (co)evolve? Well... they don't (or do so much less! In this paper we tracked bacteria-phage (co)evolution in monoculture (individual bacteria-phage pairs) or in polyculture (all three pairs) over 6 weeks. Read more here👇 doi.org/10.1099/mic....
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