Guillaume Méric

BP measurement of 254/150 mmHg? Damn! 😅
casereports.bmj.com/content/18/1...

Very interesting analysis from @bananabenana.bsky.social et al. on blaIMP dissemination from >4.5k genomes from strains of 93 species isolated over 20 years.
www.nature.com/articles/s41...

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

The GTDB website now has an ANI calculator based on skani that supports uploading of user genomes. Try it at gtdb.ecogenomic.org/tools/skani.

Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....

Earliest evidence of making fire - Nature Baked sediment, heat-shattered artefacts and introduced pyrite in a 400,000-year-old Palaeolithic occupation site in Suffolk, UK provide evidence of intentional fire-making, marking a pivotal moment i...

When humans shifted from harvesting natural wildfires to making fire is unclear because natural vs anthropogenic burning are hard to distinguish in the record. Here, "clever methods" beyond my understanding suggest early humans were making fire with pyrite ~400ky ago🔥
www.nature.com/articles/s41...

Screenshot from GRC portal confirming microbial population biology meeting June 27, 2027 in Andover, New Hampshire.

It’s officially happening folks! The Microbial Population Biology Gordon Research Conference is back in Andover, New Hampshire starting June 27th of 2027!
See you there!!

@wcratcliff.bsky.social @ksbakes.bsky.social @surtlab.bsky.social

#microsky #mevosky

Whoop whoop! 🎉 @hannahtriv.bsky.social’s first-author paper is officially out as a preprint!

Some super interesting long-read metagenomics results - especially the dominance of MDR Enterococcus faecium in very sick liver patients.

Huge shout-out to the whole team and fab collaborators!

Impressive work on microbiota vs. HAI and great thread from first author @mfenk.bsky.social

eggNOG v7: phylogeny-based orthology predictions and functional annotations Abstract. The eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) database is a phylogenomic resource for orthology inference, evol

From @jhcepas.bsky.social and colleagues in the @narjournal.bsky.social #NARDatabaseIssue | eggNOG v7: phylogeny-based orthology predictions and functional annotations | #Bioinformatics #ProteinCentric #Database #OpenScience 🧬 🖥️🧪🇨🇭🇪🇸🇩🇪🔓
⬇️
academic.oup.com/nar/advance-...

lol professor of ethics in unethical behaviour shock.

Multimodal AI generates virtual population for tumor microenvironment modeling GigaTIME leverages multimodal AI to generate virtual multiplex immunofluorescence (mIF) profiles from standard H&E slides, enabling comprehensive tumor immune microenvironment modeling across a large ...

A major advance in cancer using multimodal AI to do virtual proteomics of H&E slides, unraveling the tumor microenvironment, key proteins, biomarkers, and informing prognosis
@cellcellpress.bsky.social @hoifungpoon.bsky.social
@msftresearch.bsky.social

cell.com/cell/fulltex...

The Birgitta Sintring Foundation – Department of Ecology and Genetics – Uppsala University

Interested in applying for a postdoc on wildlife #microbiomes in my lab at Uppsala University, Sweden?

The local Birgitta Sintring Foundation gives out generous 2-year postdoc scholarships to early-career researchers who apply with a PI at the department. Deadline Feb 9.

www.uu.se/en/departmen...

Real-time simultaneous monitoring of multiple analytes in bacterial cultures | Applied and Environmental Microbiology Real-time monitoring of metabolites in bacterial cultures is crucial for advancing our understanding of microbial physiology, metabolic fluxes, and dynamic responses to environmental changes. This capability enables researchers to capture transient metabolic states that are often missed in endpoint measurements. The use of engineered periplasmic binding proteins as biosensors for this real-time metabolite monitoring represents a groundbreaking approach. By leveraging the natural specificity and high affinity of PBPs for small molecules, these biosensors can be engineered to detect a wide range of metabolites with exceptional sensitivity and temporal resolution. The integration of PBP-based biosensors into microbial research not only enhances our ability to study real-time metabolism but also provides a versatile tool for optimizing industrial bioprocesses and exploring bacterial infections and complex microbial ecosystems

Pretty cool! Engineered periplasmic binding proteins+fluorophore sensors (for sugars+AAs) are used to report real-time extracellular metabolite dynamics in E. coli + many others species after 24h in plate readers, showing hierarchical substrate use.
journals.asm.org/doi/full/10....

Assessing gut microbial provisioning of essential amino acids to host in a mouse model with reconstituted gut microbiomes - Communications Biology Stable carbon isotope analysis of mouse organs reveals no evidence for gut microbial essential amino acid provisioning after microbiome reconstitution as demonstrated by the nearly identical isotope p...

Gut microbes can synthesize essential amino acids (EAAs), but how much these actually contribute to host EAA pools is unclear. Here, authors find no detectable microbial EAA across all organs examined, after analysing marked δ¹³C-EAA given to GF/conventionalized mice.
www.nature.com/articles/s42...

Couldn't see figures in this version but text was interesting. Analysing HGT in MAGs from 338 Lifelines-DEEP adults identifies >5k recent HGT events in 116 gut microbial species.
Seems to be an interesting mobile resistome dynamics linked to age and PPI use too!
www.nature.com/articles/s41...

Amazing dataset describing the metabolic profiles of 66 E. coli transporter knockouts by @sulheim.bsky.social with Peter Doubleday and @nzamboni.bsky.social. The tool, set up by @lambdapp.bsky.social and Eric Ulrich allows you to explore for yourself. Enjoy! Pre-print here: doi.org/10.1101/2025...

Extensive horizontal transfer of transposable elements shapes fungal mobilomes Romeijn et al. reveal that horizontal transposon transfer is widespread in fungi, contributing up to 70% of transposon content in some taxa. The authors uncover thousands of events across diverse line...

Extensive horizontal transfer of transposable elements shapes fungal mobilomes

@currentbiology.bsky.social by @jromeijn.bsky.social et al from @mfseidl.bsky.social

www.cell.com/current-biol...

Releases · tseemann/abricate :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate

💾 ABRicate 1.2.0 has been released!

This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics

github.com/tseemann/abr...

Microbiota from 195 healthy breastfeeding mother-infant pairs identifies shared strains and ARGs between mother’s milk and infant stool, involving commensals (B. longum, B. bifidum) but also pathobionts like Klebsiella
www.nature.com/articles/s41...

The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath on FindAPhD.com PhD Project - The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath, listed on FindAPhD.com

New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)!
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...

Novel Loci for Metabolic Networks and Multi-Tissue Expression Studies Reveal Genes for Atherosclerosis Author Summary In this study, we aim to identify novel genetic variants for metabolism, characterize their effects on nearby genes, and show that the nearby genes are associated with metabolism and at...

It can feel a bit silly to be sentimental about specific papers but today I had a moment when this one reached 200 cites... as an isolated postdoc down under, I well remember the support of Finnish colleagues (esp Samuli Ripatti) and the singular @piwdb.bsky.social journals.plos.org/plosgenetics...

ABI Bouhmaida @forgoodcode Every Windows 11 PC is now an Al PC with Copilot at the center of it all. Here's how to get rid of Copilot completely from your computer (1/3)

ABI Bouhmaida @forgoodcode 1/ Settings App > Personalization > Taskbar > Other System Tray Icons > Switch "Microsoft 365 Copilot App" Off This hides Copilot from your taskbar

(9) ABI Bouhmaida @forgoodcode 2/ Press Win + R > Type in ‘regedit’ > Navigate to "HKEY _CURRENT_USER\ Software \ Policie s\Microsoft\ Windows" > Right-click on the "Windows" Key > New > Key > Name the new key "WindowsCopilot’ > Right-click on the new key EY > DWORD (32-bit) Value

@forgoodcode 3/ > Name the value "TurnOffWindowsCopilot’ > Double-click the name of the value > Set the "Value Data" to 1 > Restart your computer Congrats! Copilot is now completely gone from your computer. Hope this helps

My new favorite kind of meme is "here are detailed instructions on how to turn off AI". 🔨

Bacterial immune systems as causes and consequences of microbiome structure Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky

journals.plos.org/plosbiology/...

Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations

We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use

Previous multiple sclerosis, now the potential role of Epstein Barr virus for driving lupus (SLE)
science.org/doi/10.1126/...

Thanks for sharing and for the kind words, Mike!

Guillaume has just moved on from the lab to a super exciting Assoc Prof in Microbiome at the University of Bath... he's amazing and if you're keen on a PhD check this out!

Thank you for the invitation! It was very nice to visit Norwich again. Great discussions on the day.

The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath on FindAPhD.com PhD Project - The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath, listed on FindAPhD.com

New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)!
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...

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