Lightnews — Scholar-powered news

Reposted by Guillaume Méric

Pamela Ferretti @pamferretti.bsky.social · Aug 15

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

1 14 29

Reposted by Guillaume Méric

Eric Topol @erictopol.bsky.social · 7d

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-...

4 15 91

Reposted by Guillaume Méric

Eric Topol @erictopol.bsky.social · 7d

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...

15 290 490

Reposted by Guillaume Méric

Ben Vezina @bananabenana.bsky.social · 11d

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

8 10

Guillaume Méric @gmeric.bsky.social · 12d

Really cool stuff Zam and all 👏👏👏

1

Reposted by Guillaume Méric

Zamin Iqbal @zaminiqbal.bsky.social · 12d

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

14 150 300

Reposted by Guillaume Méric

404 Media @404media.co · 15d

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-...

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."

www.404media.co

18 350 760

Reposted by Guillaume Méric

Iain Johnston @mitomaths.bsky.social · 16d

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/

1 4 10

Guillaume Méric @gmeric.bsky.social · 24d

Just subscribed!

1

Reposted by Guillaume Méric

Professor Lesley Hoyles @bugsinyourguts.bsky.social · 25d

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...

4 39 34

Reposted by Guillaume Méric

Arun Durvasula @arundurvasula.bsky.social · Sep 2

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)

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...

www.medrxiv.org

2 25 54

Reposted by Guillaume Méric

Olivia Guest · Ολίβια Γκεστ @olivia.science · Sep 6

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

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

96 1.5K 3.1K

Reposted by Guillaume Méric

AnniZLab: [🦠, 🧬 , ✨] @annizlab.bsky.social · 29d

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

a Scatter plots showing the correlation between plasmid size (x-axis) and PCN (y-axis) for the analysed genera. Each point represents the median PCN and plasmid size for each PTU, and error bars indicate the standard deviation from the median. Grey lines represent ordinary least squares regression, with the surrounding shaded area indicating 95% confidence intervals. The scaling factor or slope, k, is indicated on each panel. b Distribution of total DNA load per plasmid (x-axis) relative to chromosome size per genus (y-axis). The DNA load of each plasmid is calculated by multiplying the plasmid size by the copy number and then expressed as a proportion relative to the chromosome size. The point inside the box marks the median. The upper and lower hinges correspond to the 25th and 75th percentiles, and whiskers extend to 1.5 times the interquartile range. Only Escherichia and Salmonella significantly differ from All; Kruskal–Wallis test followed by Dunn’s test for pairwise multiple comparisons p < 10−4; effect size = 0.006. c Relative plasmid DNA load observed (%) (x-axis) and expected (y-axis) per cell. The y-axis indicates the expected plasmid DNA load (%) inside a cell when it contains one plasmid (1n), two plasmids (2n), and so on. This expected data has been calculated by generating a sequence from 1 to 9 multiplied by the median of the DNA load per plasmid (2.49%). Each green point represents a single genome, and the black points are the median for each category. Shading indicates interquartile ranges. Pearson’s p value and coefficient are shown for the correlation between expected and observed plasmid DNA.

22 43

Reposted by Guillaume Méric

Ryan Wick @rrwick.bsky.social · Sep 4

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...

Cross-sample homopolymer polishing with Pypolca

a blog for miscellaneous bioinformatics stuff

rrwick.github.io

2 7 18

Reposted by Guillaume Méric

Camila Gazolla Volpiano, PhD @gazollavolpiano.bsky.social · Sep 4

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

MicroSeq2025 @microseqasm.bsky.social · Sep 4

First up, our Australian Society for Microbiology Awards! Best Lightning Talk goes to Penelope Galbraith, and Best Medium Talk to @gazollavolpiano.bsky.social! Thanks to @aussocmic.bsky.social for sponsoring these prizes, and congratulations to Penelope and Camila! Very well-deserved. #MicroSeq2025

1 3

Reposted by Guillaume Méric

Willem van Schaik @wvschaik.bsky.social · Sep 2

Pressures on science funding increasing, part 267

European Research Council (ERC) @erc.europa.eu · Sep 2

In 2025, the ERC received 3,329 proposals for Advanced Grant funding — 31% more than last year!

The selected projects will likely be announced in the spring of 2026.

More facts and figures on #ERCAdG applications 👇 europa.eu/!bm9gPT

#FrontierResearch

Applications for ERC Advanced Grants 2025: Facts and figures

The ERC Advanced Grants 2025 call closed for applications on 28 August 2025. These are the preliminary data on the submitted proposals:

europa.eu

1 2 11

Reposted by Guillaume Méric

MicroSeq2025 @microseqasm.bsky.social · Aug 27

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

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.

1 4 4

Reposted by Guillaume Méric

Eric Topol @erictopol.bsky.social · Aug 17

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...

38 630 1.2K

Guillaume Méric @gmeric.bsky.social · Aug 8

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!)

3

Reposted by Guillaume Méric

Robin Hofmeister @rjhfmstr.bsky.social · Aug 6

🚨 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!

2 54 120

Reposted by Guillaume Méric

Kate Baker @ksbakes.bsky.social · Jul 31

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...

1 8 20

Reposted by Guillaume Méric

Nature Microbiology @natmicrobiol.nature.com · Jul 30

#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...

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 ...

www.nature.com

23 48

Guillaume Méric @gmeric.bsky.social · Aug 6

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/...

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, ...

journals.asm.org

1 2 11

Guillaume Méric @gmeric.bsky.social · Aug 6

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...

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.

www.nature.com

1 4

Reposted by Guillaume Méric

European Commission @ec.europa.eu · Aug 5

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
💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰💰

4 58 210