A new study, based on a survey of 1,150 workers suggests that the injection of AI tools into the workplace has not resulted in a magic productivity boom and instead increased the amount of time that workers say they spend fixing low-quality AI-generated “work.” 🔗 www.404media.co/ai-workslop-...

Great to see this out there! We infer the evolutionary pathways behind patterns of AMR in Klebsiella across 102 states, finding globally consistent principles, state-specific deviations (and covariates), and validating evol predictions with new genomes. biorxiv.org/content/10.1... 1/

If you are UK-based and working on any aspect of microbiomes (human, plant, insect, soil, animal, ...), please do sign up to Microbiome-Net for details of networking, funding and training opportunities. forms.office.com/pages/respon...

Excited to share our latest manuscript, "Exposure accumulation drives age-dependent disease architectures and polygenic risk scores," led by Xilin Jiang: www.medrxiv.org/content/10.1... I am attempting an explainer thread for the first time here: (I am usually too exhausted to post one)

Finally! 🤩 Our position piece: Against the Uncritical Adoption of 'AI' Technologies in Academia: doi.org/10.5281/zeno... We unpick the tech industry’s marketing, hype, & harm; and we argue for safeguarding higher education, critical thinking, expertise, academic freedom, & scientific integrity. 1/n

A plasmid golden ratio? 🧬 Plasmid copy number ≈ 2.5% of chromosome size—consistent across bacterial species! pmc.ncbi.nlm.nih.gov/articles/PMC... @jerorb.bsky.social 🧪 #microbesky

New blog post! I added a new feature to @gbouras13.bsky.social's Pypolca: homopolymer-only polishing. Potentially useful for cross-sample polishing - early test on Cryptosporidium looks promising. Check it out here: rrwick.github.io/2025/09/04/h...

Very happy to have been awarded Best Medium Talk at #MicroSeq2025! 🌟 Wonderful to see archaea receiving more attention in human microbiome research :)

Pressures on science funding increasing, part 267

Only ONE more week to #MicroSeq2025! 🤩 The conference booklet (incl. schedule) will be released on Monday, September 1st. Registration is open until 11:59pm September 2nd, so there's still plenty of time to join the fun! Don't miss out! Register below 👇 trybooking.com/events/landing/1424679

Covid accelerates vascular aging An 18-country, 38-center study of ~2,000 participants —Effect predominantly in women, adding 5 years of aging —Seen with non-hospitalized and mild-moderate Covid —Reversible in some at 1-year; vaccination link to protection apps.crossref.org/pendingpub/p...

🚨 Our parent-of-origin study is out in Nature! 🧬 Maternal and paternal alleles can have distinct — even opposite — effects on human traits, revealing a hidden layer of genetic architecture that standard GWAS miss. 🔗 www.nature.com/articles/s41... Highlights below!

Was great to put the dream team back together for a commentary on this with @alisonmather.bsky.social very cool study on AMR flow through food production chains in Europe www.nature.com/articles/s41...

#Review A discussion on the processes driving bacterial evolution and emergence of pathogenesis within hosts, the importance of understanding within-host genetic diversity, and the implications for transmission analysis and infectious disease control. #MicroSky 🦠 www.nature.com/articles/s41...

Very interesting methodological study from the @gibbological.bsky.social lab showing that bacteria-to-host (B:H) read ratio in metagenomes strongly correlates with conventional biomass estimates, even before/after host read depletion 🔗 journals.asm.org/doi/10.1128/...

Interesting recent review on the links between gut microbes and T-cells, highlighting a mechanistic framework linking microbial metabolites to all stages of T-cell fate and function. 🔗 www.nature.com/articles/s41...

Double the discovery, double the momentum 🚀 Europe doubles down on research competitiveness with a major boost to #HorizonEurope: €95.5 billion foreseen for 2021-2027 💰💰💰💰💰💰💰💰💰 €175 billion proposed for 2028-2034 💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰

>80% microb species detected by metagenomics are undetected by metaproteomics; because existing workflows rely on incomplete reference DBs, underutilize spectral data and don't robustly incorporate FDR control. Here, a new workflow (uMetaP) seems to improve everything. www.nature.com/articles/s41...

Amazing dataset compiled here! • ~85k public metagenomes from 40 habitats (~46k human gut) • >2M isolate genomes and MAGs ➡️ Microbiomes primarily structured by host/environment association, not geography ➡️ Generalist species are key mediators of HGT and spread of AMR www.biorxiv.org/content/10.1...

Is the gut microbiota composition in the 1st week of life linked to viral lower respiratory tract infections (vLRTIs) in early childhood? Here, work using the BBS birth cohort identifies Bifidobacterium longum-dominated cluster linked to lowest vLRTI rates 🔗 www.sciencedirect.com/science/arti...

Great to see a role of gut microbial PAA in humans. I remember ages ago being puzzled by PAA gene prevalence in some E. coli strains, which we interpreted at the time by increased ability to metabolise aromatic compounds w/out much evidence. This is much more exciting! www.nature.com/articles/s43...

Interesting mix of statistical epidemiological modeling and historical investigation of plague transmission in 1700s France, seemingly invalidating prevailing theories of the origin of a historical outbreak in Gévaudan. 🔗 www.medrxiv.org/content/10.1...

Pleased to say that our preprint benchmarking Nanopore data for MLST, cgMLST, cgSNP & AMR typing from bacterial isolates is out! TL;DR you can get almost perfect results from 50x depth using live SUP basecalling with a GPU in under 20 hours #microsky#IDsky 🦠🧬🖥️ /1 www.medrxiv.org/content/10.1...

Postdoc position to work at the Institut Pasteur with Alex Kaminski and Didier Mazel on Z-DNA phages ! research.pasteur.fr/en/job/a-two...

Exciting paper on genetic influences on speech fluency, out now in @natgenet.nature.com. In a big step forward for the field, genome scans of almost 100,000 people with self-reported stuttering, & 1 million controls, identify 57 associated loci. Great work by @piperbelow.bsky.social & her team.🗣️🧬🧪

📣📣 Cool job alert! The @bakerresearchau.bsky.social is recruiting up to 2 new PIs in Biomedical Data Science 👉 www.seek.com.au/job/85989791... You’d join an awesome institute in an incredible city (Melbourne, Australia) as well as partnerships like with @cam.ac.uk… you’ll also get to work with me 😁

About time. I had just joined Twitter in 2010 as a PhD student and the online unfolding backlash of this study was quite novel at the time and a formative moment for my junior scientist eyes! Particularly fond memories of rosieredfield.bsky.social 's argumentations and blog posts.

Finally out! A small screen helps understand a little more about how E. coli regulates major transporters, and reveals how caffeine induces phenotypical antibiotic resistance. Huge thanks to collab @andrenmateus.bsky.social (Umeå) and Christian L. Müller (Munich)! journals.plos.org/plosbiology/...

Another publication in @femsjournals.bsky.social @femsmicro.org 🔬 How do glycans shape the infant gut microbiota? 👶 With a novel in vitro synthetic community we studied the interplay between microbes and HMOs, mucin glycans and GOS/FOS.🍼🤱🦠 #microsky #glycotime doi.org/10.1093/fems...

Great to see strengthening links between EMBL and Australia!

Metagenomics analysis from 1313 humans (teeth/bones) across 37ky of Eurasian history shows 3384 hits of known human pathogens (i.e. Y. pestis, HepB, etc), with many predating historical records. Zoonotic diseases surge ~6.5kya, suggesting link with animal agriculture 🔗 www.nature.com/articles/s41...

Very cool. Here, authors did pairwise co-culturing (mGAM/anaerobiosis) of 97 gut microbial species (113 strains) to infer ecological interactions (n=3233). Most negative were between distant taxa & positive were more among low-abundance taxa. 🔗 microbiomejournal.biomedcentral.com/articles/10....

Very much out of my (biologist) depth, but surprising efforts are being made to understand why deep neural networks work so well, despite their (observed) revolutioning of modern ML. Here, authors find that they seem to work very parsimoniously! 🔗 www.nature.com/articles/s41...

In this preprint, authors present PolyProf, a new tool to profile microbial toxin secretion systems (TSS) in metagenomes, and could robustly associate them (incl in prediction models) with 12 disease states from large cohorts, including IBD, CRC, T2D and others. www.biorxiv.org/content/10.1...

New study (n=75 LUAD patients +in vitro/in vivo models) shows lactate-producing Staphylococcus in lung tumors can promote metastasis, with S. nepalensis & S. capitis driving tumor spread by activating MCT1–pseudohypoxia–NDRG1 signaling in tumor cells in mice. 🔗 www.sciencedirect.com/science/arti...

I've always found this frustrating. You or your child has a respiratory infection. It's not flu or COVID. Your doctor can only tell you, 'you have a virus'. Could it be a little bit more specific? We hope to help answer this question, non-invasively, and for free. 1/

Around 25% of U.S. infants lack detectable Bifidobacterium, regardless of birth or feeding method. This deficit could have implications for immune health and the trajectory of noncommunicable diseases, according to a study published in Communications Biology. go.nature.com/4lgA1ls 🧪

Great thread from @antagomir.bsky.social about our latest collaborative study led by the brilliant @katammp.bsky.social on the antibiotic resistome in a representative Finnish population of n>6,500 individuals and factors associated with carriage. Link to study: doi.org/10.1038/s414...

It bears repeating that the new paper showing that the U.S. has significantly higher rates of pediatric deaths than similar countries demonstrates that these deaths are primarily caused by: Firearms Motor vehicle crashes Substance use Homicide And are driven by: Economic and racial disparity

Great work from our Finnish collaborators finally out! We examine factors linked to AMR carriage in a large population cohort (n~7k individuals)

Proud of our group's newest publication!

Looking for a #LifeSciences postdoctoral #opportunity? 🧪 Have a look at the EMBO Postdoctoral Fellowships for internationally mobile scientists in #Europe and globally. Apply before 11 July: www.embo.org/funding/fell... #research #funding #postdoc

Happy to share the preprint from here in Shanghai, together with @danielfalush.bsky.social, as well as with team Zhizhou Jia, Huqi Wen, and Zhe Xie! www.biorxiv.org/content/10.1...

From plasma samples of H7N9 patients, including those who died: 🔺64 metabolites, 🔻35 metabolites in the death group including lipids and lipid−like molecules. Machine learning model can predict death. 👉 www.sciencedirect.com/science/arti...

Controlling bird flu is urgent—for dairy, wildlife, poultry, pets, and people. 👉 avmajournals.avma.org/view/journal...

Molassodon! Excited to post my research group's first laboratory project. We identify a phenotype and a putative ecological strategy for the Molassodon ecospecies of Vibrio parahamolyticus, thanks to the hard work of our lab team led by @campy-bara.bsky.social www.biorxiv.org/content/10.1...

Challenging dogma about getting news via social media www.nature.com/articles/s41...

In a randomized trial of tirzepatide (Zepbound, Mounjaro) vs placebo, brain activation by high fat and high sugar foods was decreased @naturemedicine.bsky.social www.nature.com/articles/s41...

This is a phenomenal (ahem) essay with so many astute observations and quotable lines, e.g. 'convincing students that intelligence is a skill they must cultivate through hard work—no shortcuts—has become one of the core functions of education'

Chatbots — LLMs — do not know facts and are not designed to be able to accurately answer factual questions. They are designed to find and mimic patterns of words, probabilistically. When they’re “right” it’s because correct things are often written down, so those patterns are frequent. That’s all.