Guillaume Méric

QUESTION: anyone knows of a published example of a gene/operon which is toxic in Pseudomonas aeruginosa if in high copy plasmids, but ok in low copy? Got plenty of examples of my own for E. coli (esp of membrane protein genes), but struggling to find for Pae… Cheers!

#microsky #synbio

Does anyone know good intro videos describing "big picture" what sequence-analysis (ie mapping, assembly) is all about? I'm going to dig through @benlangmead.bsky.social 's amazing trove of videos, but I think they may be too compsci oriented for the biology student who's asking me about it

Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠

Proud to have contributed to Metalog, the latest @borklab.bsky.social resource:

www.biorxiv.org/content/10.1...

#microsky #microbiome

Our capability to prevent diseases from occurring is gaining momentum. Using A.I. to predict >1,200 diseases 20 years ahead adds to the ways we'll be able to achieve primary prevention.
nature.com/articles/d41...
erictopol.substack.com/p/dawn-of-a-...

Children and teens who had a Covid reinfection had a doubling of #LongCovid risk (PASC) and a significant increase in many other adverse outcomes (Figure) www.thelancet.com/journals/lan...

Staggering analysis here linking ciprofloxacin resistance to specific mutations in #Klebsiella.

In short, using ONLY genotype, one can reasonably predict phenotypic CIP MICs! See Fig 3 (below).

Loving the splitting of MIC and disk diffusion data as well.

#AMR #MicroSky #IDSky

Really cool stuff Zam and all 👏👏👏

Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n

AI ‘Workslop’ Is Killing Productivity and Making Workers Miserable AI slop is taking over workplaces. Workers said that they thought of their colleagues who filed low-quality AI work as "less creative, capable, and reliable than they did before receiving the output."

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/

Just subscribed!

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...

Exposure accumulation drives age-dependent disease architectures and polygenic risk scores Our understanding of the dependence of the genetic and environmental architecture of common diseases on age is incomplete. Here, we use longitudinal data to quantify age-dependent genetic and environm...

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)

Abstract: Under the banner of progress, products have been uncritically adopted or even imposed on users — in past centuries with tobacco and combustion engines, and in the 21st with social media. For these collective blunders, we now regret our involvement or apathy as scientists, and society struggles to put the genie back in the bottle. Currently, we are similarly entangled with artificial intelligence (AI) technology. For example, software updates are rolled out seamlessly and non-consensually, Microsoft Office is bundled with chatbots, and we, our students, and our employers have had no say, as it is not considered a valid position to reject AI technologies in our teaching and research. This is why in June 2025, we co-authored an Open Letter calling on our employers to reverse and rethink their stance on uncritically adopting AI technologies. In this position piece, we expound on why universities must take their role seriously toa) counter the technology industry’s marketing, hype, and harm; and to b) safeguard higher education, critical thinking, expertise, academic freedom, and scientific integrity. We include pointers to relevant work to further inform our colleagues.

Figure 1. A cartoon set theoretic view on various terms (see Table 1) used when discussing the superset AI (black outline, hatched background): LLMs are in orange; ANNs are in magenta; generative models are in blue; and finally, chatbots are in green. Where these intersect, the colours reflect that, e.g. generative adversarial network (GAN) and Boltzmann machine (BM) models are in the purple subset because they are both generative and ANNs. In the case of proprietary closed source models, e.g. OpenAI’s ChatGPT and Apple’s Siri, we cannot verify their implementation and so academics can only make educated guesses (cf. Dingemanse 2025). Undefined terms used above: BERT (Devlin et al. 2019); AlexNet (Krizhevsky et al. 2017); A.L.I.C.E. (Wallace 2009); ELIZA (Weizenbaum 1966); Jabberwacky (Twist 2003); linear discriminant analysis (LDA); quadratic discriminant analysis (QDA).

Table 1. Below some of the typical terminological disarray is untangled. Importantly, none of these terms are orthogonal nor do they exclusively pick out the types of products we may wish to critique or proscribe.

Protecting the Ecosystem of Human Knowledge: Five Principles

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.
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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

One week to MicroSeq! MicroSeq2025 is an online meeting being held on September 3rd and 4th, focused on research being conducted on sequencing data generated from microbiological samples (bacteria, fungi, and viruses). MicroSeq2025 is supported by The Australian Society for Microbiology, the Australasian Virology Society, and Microbial Genomics. Registration open until 11:59pm, September 2nd, 2025. Participants can register at microseqconference.com.

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...

That's a fun one!
N: Trondheim, Norway
E: Auckland, NZ
W: Newport, OR, USA
S: Stewart Island, NZ
(@duckswabber.bsky.social would beat us all!)

🚨 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...

Within-host bacterial evolution and the emergence of pathogenicity - Nature Microbiology In this Review, Tonkin-Hill et al. discuss the processes driving bacterial evolution and emergence of pathogenesis within hosts, the importance of understanding within-host genetic diversity, and the ...

#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...

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

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/...

The role of gut microbial metabolites in the T cell lifecycle - Nature Immunology Tran et al. discuss the role of the gut microbiome and gut microbiome-derived metabolites in T cell biology.

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
💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰

Ultra-sensitive metaproteomics redefines the dark metaproteome, uncovering host-microbiome interactions and drug targets in intestinal diseases - Nature Communications The gut microbiome is key to health, yet its protein functions remain largely unexplored. Here, the authors present uMetaP, ultra-sensitive metaproteomics workflow that combines the timsTOF Ultra and ...

>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...

Planetary microbiome structure and generalist-driven gene flow across disparate habitats Microbes are ubiquitous on Earth, forming microbiomes that sustain macroscopic life and biogeochemical cycles. Microbial dispersion, driven by natural processes and human activities, interconnects mic...

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...

Investigation of associations between the neonatal gut microbiota and severe viral lower respiratory tract infections in the first 2 years of life: a birth cohort study with metagenomics Early-life gut microbiota affects immune system development, including the lung immune response (gut–lung axis). We aimed to investigate whether gut m…

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...