Happy to see this out, thanks to extensive development, benchmarking and perseverance step after step by @mrollivander.bsky.social ! We've used versions of this tech for several years and now can offer it more easily to others along with concrete data on the advantages offered.

Bioinformatics Advances@bioinfoadv.bsky.social · 2w ago

🔬 Latest research in Bioinformatics Advances: "metadeconfoundR: Covariate analysis of high-dimensional cross-sectional omics data"  See it here: https://doi.org/10.1093/bioadv/vbag242 Authors include: @mrollivander.bsky.social, @vhjarquind.bsky.social, @inanna-nalytica.bsky.social

🔬 Latest research in Bioinformatics Advances: "metadeconfoundR: Covariate analysis of high-dimensional cross-sectional omics data"  See it here: https://doi.org/10.1093/bioadv/vbag242 Authors include: @mrollivander.bsky.social, @vhjarquind.bsky.social, @inanna-nalytica.bsky.social

🚨Published After a long wait, our work was published at NPJ Biofilms and Microbiomes this week 🍾 All my recognition to the great work done by Robert! I am very proud of him and grateful to work with him. Check the final version of the manuscript here: rdcu.be/fAT4I

Víctor Hugo Jarquín-Díaz@vhjarquind.bsky.social · 9mo ago

📌 New preprint Super trilled to share the work of our PhD student Rob Bücking. He did a massive work collecting a large longitudinal globally representative dataset of infant microbiomes to develop a microbiome age index 🌍🍼👶🏻🦠 (1/4)

Great multidisciplinary collaboration with @ecodynizw.bsky.social. Our work highlights the impact of farming practices 🐷 in the resistome from wild mice 🐭 Read more about this story in the joint press release between @IZW and @mdc-berlin.bsky.social and our publication ⬇️ #AMR #Wildlife

Ecological Dynamics Dept. | IZW Berlin@ecodynizw.bsky.social · 4w ago

📝"New study on farm mice shows that antibiotic resistance is also an environmental problem, not just a medical one". 👉Read here our latest IZW@leibniz-gemeinschaft.de Press release: t1p.de/s59j5 ...by Gicquel et al, published @natcomms.nature.com #AntibioticResistance #MusMusculus #HealthChallenge

📝"New study on farm mice shows that antibiotic resistance is also an environmental problem, not just a medical one". 👉Read here our latest IZW@leibniz-gemeinschaft.de Press release: t1p.de/s59j5 ...by Gicquel et al, published @natcomms.nature.com #AntibioticResistance #MusMusculus #HealthChallenge

❗Achtung: geänderte Frist ❗ 📣 Wir suchen Unterstützung! Du hast Erfahrung als Laborassistent_in für Biologie und Chemie? Dann komm zu uns ans Helmholtz-Institut für One Health (HIOH) in Greifswald! Wir suchen eine technische Assistenz (m/w/d). Weitere Infos unter: www.helmholtz-hioh.de/de/jobs/

Stellenangebote | Helmholtz-Institut für One Health | HIOH

Hier finden Sie unsere aktuellen Stellenangebote und gewinnen einen Eindruck über das Arbeiten am HIOH oder das Leben in Greifswald.

helmholtz-hioh.de

Das Meer ist unser Spiegel – auch bei Antibiotikaresistenzen! Zum Europäischen Tag der Meere lenken wir den Blick unter die Oberfläche. Die Forschung @schauflerlab.org zeigt: #AMR sind kein isoliertes Problem im Menschen. Sie kommen in Tieren, Boden und Gewässern vor. AMR betrifft das gesamte System

I had the opportunity to present today my work at #SETACMaastricht My research shows how herbicides can affect not only individual organisms but also microbial interactions, with implications for aquatic ecosystem functioning. Thanks to the organisers and everyone who attended!

So excited to be presenting at @setac.bsky.social Europe 36th Annual Meeting! I’ll talk about how metolachlor affects a cyanobacterium–chytrid system, & what this reveals about how environmental stressors reshape microbial interactions in aquatic ecosystems Hope to see u there! #SETACMaastricht

🚨New preprint out ‼️ Wondering which tool to use for ARG annotation? … 👀 Well, our work shows how different tools lead to different biological conclusions with large disagreements between them! Great collaboration with Juan Inda-Díaz and @bigdatabiology.bsky.social as part of SEARCHER Details👇

@bigdatabiology.bsky.social · 4mo ago

How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...

This is an incredibly relevant preprint. Your favourite pipeline and/or AMR gene database cannot be considered authoritative, but neither can others.

@bigdatabiology.bsky.social · 4mo ago

How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...

More details to follow later, but this has been in the works for almost 6 years, so it is great to finally see it in preprint form: "The elusive resistome: a global comparison reveals large discrepancies among detection pipelines" www.biorxiv.org/content/10.6...

We often use dimensional reduction to simplify data, but what if geography is the point? In our @cp-trendsmicrobiol.bsky.social paper, we explore 3D spatial organization, covering latest methods, findings, and the big questions this frontier opens up. (1/3) www.sciencedirect.com/science/arti...

Micro-scale spatial metagenomics opens a new era in microbiome ecology

Understanding microbial communities requires moving beyond 2D representations toward a holistic view that couples 3D spatial organization with ecologi…

sciencedirect.com

Reposts appreciated! What if standard lab mice miss the real microbial game? Honored to be featured on the May cover @cp-trendsmicrobiol.bsky.social: „The microbial companion.“ Our paper “Game of Microbes: A Wildling’s Guide” is out now: dlvr.it/TRl1Zs Thread below with more @cellpress.bsky.social

Can we reconstruct ancient pathogen genomes from animal remains? Can paleopathology help prioritize promising specimens? Our new paper demonstrates this by screening more than 300 specimens from across Eurasia over the past 6,000 years. www.nature.com/articles/s41...

Probing the zooarchaeological record across time and space for ancient pathogen DNA - Nature Communications

Authors investigate ancient DNA from animal remains and identify multiple signatures of ancient zoonotic pathogens. They find ancient pathogen genomics from archaeological animal remains may inform zo...

nature.com

Strain diversity influences microbiome functions, and can be assessed with metagenome-assembled genomes (MAGs). But many MAGs are inaccurate! Benchmarking of shotgun sequencing by ⭐ @treichelnicole.bsky.social ⭐ with @nfdi4microbiota.bsky.social , in @natmicrobiol.nature.com 👉 rdcu.be/feAWc

Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis

Nature Microbiology - A comparison of sequencing of complex mock communities performed at multiple depths and analysed using different methods establishes minimum standards that can ensure the...

rdcu.be

Endemic within Endemic🦎 We are happy to share our latest publication in @isme-microbes.bsky.social! This time, we explored the Galápagos marine iguana with a simple question: If these iconic animals are endemic, are their microbes endemic too? The answer is yes! (1/8) doi.org/10.1093/isme...

🔊 Looking for a Research Assistant in Bacterial Evolution to join my lab 🦠 🥼Main duties: Research (AMR + microbiome) + lab assistance. ⏲️ Post duration: 30 months 🗓️ Closing date for applications: 20th April 2026 💰 Salary: ~£35k Details and how to apply: tinyurl.com/2a3v66y7 Please share!

Becoming a parent is much more detrimental to women’s academic careers than it is to men’s Read the full story: go.nature.com/4v4rxmQ

🌊🦠Our latest work on water treatment now available as a @biorxivpreprint 🌊🦠 “Reusable immobilised quaternary ammonium particles reduce microbial and resistome burdens without promoting #AMR selection during wastewater post-treatment” 🔗 biorxiv.org/content/10.6... 1/5

Excited to announce our new journal from @isme-microbes.bsky.social ISME Host Microbe is live and now accepting submissions. Look forward to receiving your papers! #Microsky 🧫 🦠

A study in Nature Health identifies EastDiet, a new diet rooted in traditional Chinese food elements associated with better adherence, favourable gut microbial profiles, lower rates of central obesity and reduced incidence of major cardiovascular events. go.nature.com/4rSj3wk 🍎📃 🧪

Excited to release METAGENE-1, a 7B parameter metagenomic foundation model, built to aid in pathogen detection & pandemic monitoring. Pretrained on 1.5 trillion base pairs of DNA/RNA sequenced from wastewater. A collab w/ USC, PrimeIntellect, & the Nucleic Acid Observatory. metagene.ai

Metagenomic Foundation Model

Metagenomic Foundation Model for Pandemic Monitoring

metagene.ai

Registration is now open for the new EMBL Conference #EMBLGutMicrobeFunction! Submit your abstract by 15 September: https://s.embl.org/gmd26-01-bl 🧬 Join us to explore how we can harness the vast functional diversity of microbes that shape ecosystems across our planet. 🗓️ 8 – 10 December 2026

🌎Can science help safeguard Earth’s wildlife? From habitat loss to climate change, species worldwide are under threat. At #SXSW2026, experts explore how biobanking & digital tools give wildlife a lifeline. 🗓 Mar 17 | 4 PM 📍 JW Marriott, Room 201-202 schedule.sxsw.com/events/PP116...

SXSW 2026 Schedule

Browse events, build your schedule, and get personalized recommendations for the 2026 SXSW Conference & Festivals from March 12–18, 2026 in Austin, TX.

schedule.sxsw.com

I will be speaking at BrisJAMS next week!

We must create safe, supportive environments where women and girls can thrive, and develop strategies to dismantle the structural barriers that hinder gender equality in science. Real change goes beyond inspiration, it requires a transformation 🧵2/2 #InternationalDayOfWomenAndGirlsInScience

On this International Day of Women and Girls in Science, it’s important to acknowledge how far we have progressed. But we should also recognize that empowerment alone is not enough. 🧵1/2

Excited to announce that I am organizing a symposium on "Microbiomes in Conservation" at #ISME20 in Auckland, New Zealand together with Madeleine van Oppen. Consider submitting an abstract; it will be a fab conference! Deadline Feb 15! isme-microbes.org/isme20-sessi... @isme-microbes.bsky.social

Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex... See the quoted post below for a thread on the preprint!

Planetary microbiome structure and generalist-driven gene flow across disparate habitats

A planetary-scale analysis of over 85,000 metagenomes establishes a framework for exploring the structure and drivers of global microbial habitats, revealing that generalist species bridge ecological ...

cell.com

Chan Yeong Kim@chanyeong-kim.bsky.social · last yr.

Our new preprint is out! www.biorxiv.org/content/10.1... In this study, we present the largest systematic analysis of microbiome structure and function, integrating 85K uniformly processed metagenomes from diverse habitats worldwide. @podlesny.bsky.social @jonas-bio.bsky.social @borklab.bsky.social