Guillaume Méric

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...

A two year post-doctoral position at the BacterialGenome Plasticity Unit starting October 1st - Research

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...

Large-scale genome-wide analyses of stuttering - Nature Genetics Genome-wide analyses in over one million self-reported cases and controls identify genetic variants associated with stuttering and find genetic correlations with autism, depression and impaired musica...

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.

Systematic screen uncovers regulator contributions to chemical cues in Escherichia coli Transport machineries are crucial for antibiotic resistance, but their regulation by external cues is poorly understood. This study identifies environmental chemicals that regulate transporter transcr...

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/...

Milk and mucin glycans orchestrate a synthetic infant gut microbiota structure Dietary and gut glycans drive the composition of an in vitro synthetic community of infant gut microbes.

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!

The spatiotemporal distribution of human pathogens in ancient Eurasia - Nature Screening shotgun-sequencing data from ancient humans covering 37,000 years of Eurasian history uncovers the widespread presence of ancient bacterial, viral and parasite DNA and zoonotic pathogens coi...

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...

Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria - Microbiome Background Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, the...

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....

Deep neural networks have an inbuilt Occam’s razor - Nature Communications Deep neural networks predict well despite having many more parameters than data points. The authors show that deep neural networks prefer simpler solutions due to an inbuilt “Occam’s razor”. Favouring...

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...

Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis Bacteria use antagonistic interbacterial weapons such as polymorphic toxin secretion systems (TSS) to compete for niches in the human gut microbiome. We developed a bioinformatic marker gene approach ...

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...

Lactate production by tumor-resident Staphylococcus promotes metastatic colonization in lung adenocarcinoma The role of the lung microbiota in cancer remains unclear. Here, we reveal that Staphylococcus is selectively enriched in metastatic tumor lesions and…

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.
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This is figure 1 showing general features of infant gut microbiomes.

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...

Trends in US Children’s Mortality, Chronic Conditions, Obesity, Functional Status, and Symptoms This study aims to determine how US children’s health has been changing from 2007 to 2023 using multiple data collection methods and a comprehensive set of health indicators.

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!

Happy birthday! 👏 Data and plots for presents are the best :)

Fellowships, grants and career support – Postdoctoral Fellowships – EMBO Supporting internationally mobile postdoctoral researchers in Europe and around the world

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

Evolution of hunt, kill, devour in a Vibrio ecospecies Bacterial ecospecies are a recently recognized genetic structure that is hypothesized to arise by complex adaptation to a new niche. Using coadaptation analysis as a foundation for laboratory experime...

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...

Following news on social media boosts knowledge, belief accuracy and trust - Nature Human Behaviour Altay et al. show that following the news on social media increases current affairs knowledge, the ability to discern true from false news and trust in the news.

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.

Is taurine an aging biomarker? Low circulating taurine concentrations have been proposed as a driver of the aging process. We found that circulating taurine concentrations increased or remained unchanged with age in three geographi...

Taurine, an amino acid once considered a biomarker for human aging and a candidate for supplementation, shot down @science.org
www.science.org/doi/epdf/10....