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

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

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

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

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 🧫

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 👇

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-...

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

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...

Oh, to have been a scientist in the 1940s... (Monod, 1949)

🚨 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 www.nytimes.com/2025/09/10/m...

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. 🧵⬇️

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🚨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

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)

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/...

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!

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

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)

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....

#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

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/...

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/...

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

🧵 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 👇

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 🧵

New role for HTH DNA binding proteins - sequestering phage DNA!

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...

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/...

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

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

Congrats @margotbligh.bsky.social!!!

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/

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...

From the same team that made vanilla for ice cream using E.coli that digest plastic waste.

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!

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....

Came for the phages, stayed for the defence systems... left with 10 new acronyms and a huge appreciation for the @multidefence.bsky.social consortium🧫🧬

Excited to share the lab's 1rst preprint! Rapid high-res immunofluorescence is now possible in cultured & environmental diatoms thanks to 4-fold expansion microscopy. A step-change for comparative cell biology in one of the most important phytoplankton groups on the planet 🥳 tinyurl.com/m9s5su7s 1/2

Leveraging the GBR-MGD, we find that seawater microbes can reliably predict fisheries management practice. Microbes indicative of No Take Marine Reserves (NTMRs) have streamlined, low-GC genomes, fished reefs do not—turned out to be very interesting! Excellent work led by @markoterzin.bsky.social

The UK just had its warmest spring on record. It was also the sunniest on record. And the driest in more than 50 years. "A sign of our changing climate", says @metoffice.bsky.social www.metoffice.gov.uk/about-us/new...