New competition-funded 4y PhD opportunity with SWBio DTP with me at Bath @uniofbath.bsky.social & Sion Bayliss at Bristol Vet School on microbiome resilience after antibiotics, microbial ecology & evolution. Read more about the application process: www.swbio.ac.uk/programme/pr... Portal open soon!

PhD opportunity! Join us in St Andrews to study the consequences of defence against conjugative plasmids (preprint coming soon on this!). Funded by EASTBIO, co-supervised by @mfwhite2.bsky.social. Please share & pass on to anyone interested! 🦠🧫 Deadline 16th November www.findaphd.com/phds/project...

Eastbio: Mechanism and consequences of lethal zygosis in bacteria restricting AMR plasmids. at University of St Andrews on FindAPhD.com

PhD Project - Eastbio: Mechanism and consequences of lethal zygosis in bacteria restricting AMR plasmids. at University of St Andrews, listed on FindAPhD.com

findaphd.com

Very happy to share the publication of the first manuscript from my PhD! 🥳 Here, we show that PCR amplification of repetitive DNA sequences, such as AMR genes flanked by insertion sequences, can lead to the generation of artefact products that need to be interpreted cautiously. (See comments 👇)

PCR analysis of insertion sequences leads to the generation of artefact amplicons

Insertion sequences (ISs) are small, self-mobilizing DNA elements widespread across prokaryotic genomes, including chromosomes and plasmids. IS elements frequently co-localize with antimicrobial resis...

microbiologyresearch.org

Our article "Common xenobiotics modulate gut microbial responses to low‑calorie sweeteners in vitro" is out! link.springer.com/article/10.1... With @kiranrpatil.bsky.social, @indraroux.bsky.social, @rbradley.bsky.social, @skamrad.bsky.social, @simonemozzachiodi.bsky.social, @itsbinir.bsky.social.

Common xenobiotics modulate gut microbial responses to low‑calorie sweeteners in vitro - Molecular Systems Biology

The gut microbiota is implicated in adverse effects associated with low-calorie sweeteners. Yet, the direct impact of sweeteners on gut bacteria remains largely uncharacterized. Here, we report intera...

link.springer.com

We rely on healthy soil microbial communities to support ecosystem functioning and plant growth, but what happens when soils are exposed to multiple environmental stressors simultaneously? Spoiler: it's not good doi.org/10.1093/isme...

Fungicide and warming interact to reduce soil ecosystem functioning

Abstract. Soil microbial communities are essential to the functioning of their ecosystems, providing vital services such as plant growth promotion and bior

academic.oup.com

New updates to AllTheBacteria - some super cool results and an amazing resource for the community

César de la Fuente@delafuentelab.bsky.social · 4mo ago

Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...

🚨 PREPRINT 🚨 In our systematic review and meta-analysis, we tackle a challenging evidence base to show that administering antibiotics to beef cattle increases the abundance of antibiotic resistance determinants (bacteria and resistance genes) during and after antibiotic administration 💊🐂 (1/n).

bioRxivpreprint@biorxivpreprint.bsky.social · 5mo ago

Effects of antibiotics on the abundance of antibiotic resistance determinants during and after antibiotic administration to beef cattle: A systematic review and meta-analysis of longitudinal studies https://www.biorxiv.org/content/10.64898/2026.05.31.729110v1

Additive effects of environmental and demographic variation shape the repeatability of evolution across replicated experiments.

Additive effects of environmental and demographic variation shape the repeatability of evolution across replicated experiments

Abstract. The repeatability of evolution is fundamentally important for understanding the origin and diversification of life as well as for developing evol

academic.oup.com

Evolution induced state shifts in a long-term microbial community experiment (now out, but previously posted here as a preprint) with Ville Mustonen, Lutz Becks @jcairns.bsky.social & others. Experiment continues @utu.fi and now 5+ years www.pnas.org/doi/10.1073/...

Evolution induced state shifts in a long-term microbial community experiment | PNAS

Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain p...

pnas.org

It was a great pleasure to be a part of this and I learnt so much during the process as well! Check it out when you get some time and thanks to all the co-authors for great work! 🙌

Oliver Meacock@olimeacock.bsky.social · 5mo ago

Delighted to see this out in its final form! doi.org/10.1093/isme... We established a discussion group focussed on the history of community ecology and how it informs our understanding of microbiota. This review distils those discussions to provide a guide for microbiologists entering the field

this is super useful!

Alvaro Sanchez@asanchezlab.bsky.social · 6mo ago

The version of record of our revised preprint is finally out today. In it, we introduce a fast and reliable methdology for the full factorial design of microbial communities, i.e. constructing every monoculture, pair, trio, four-member,... n-member co-culture of N strains. doi.org/10.7554/eLif...

New results from our synthetic communities, antibiotics & resilience project: Eco-evolutionary dynamics and environmental detoxification jointly shape bacterial community response to antibiotic perturbation www.biorxiv.org/content/10.6... Work led by @jcairns.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

🚨FULLY FUNDED PHD POSITION!🚨 If you are interested in trying to answer the question of "How did climate shape the movements, interactions, and evolution of hominin populations?" Come join my lab at @humanorigins.bsky.social 🧬🧪 deadline 7th of June ⬇️ uni-tuebingen.de/universitaet...

Really excited to share a fully-funded PhD position in my lab at the University of Reading exploring how E. coli uses competition to survive in the microbiome. Perfect for anyone interested in using a mix of biochem and ecology to study pathogens. Deadline May 29th! www.findaphd.com/phds/project...

Investigating how E. coli exploits bacterial competition in the microbiome at University of Reading on FindAPhD.com

PhD Project - Investigating how E. coli exploits bacterial competition in the microbiome at University of Reading, listed on FindAPhD.com

findaphd.com

Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.

My main postdoc paper is now out in @natureportfolio.nature.com npj Antimicrobials and Resistance! www.nature.com/articles/s44.... Using flow cytometry, we show that the nucleoside analogues azidothymidine, didanosine, stavudine, and trifluridine reduced transfer of AMR plasmids pCT and pKpQIL (1/3)

LLMs are like your stoner friend who is a voracious reader. They have a lot of information in their brains, but it's not necessarily in the right order, and sometimes they talk utter nonsense.

Futurism@futurism.com · 7mo ago

This is catastrophic.

📢 Excited to be offering a Plant Health vacation studentship this summer on plant disease biocontrol and predatory bacteria! Supervised by me at Manchester Uni! @manchester.ac.uk If interested—or know someone who might be—please share and apply! my.rsb.org.uk/services.php... 28th April deadline 🌿🍅🦠

would 100% recommend this as a PhD position to anyone interested in bacteria/temperature/amr. Dan is a great scientist to work with, and more importantly is a kind person who cares about people and (also) how science works

Daniel Padfield@padpadpadpad.bsky.social · 7mo ago

PLEASE SHARE. PhD Opportunity with me, Ben Raymond and Jan Engelstaedter and Andrew Letten at University of Queensland. Experimentally testing mechanisms of how temperature may change selection and spread of AMR in E. coli. Coupled with some advanced modelling and sequencing. 🧪🦠 #microsky

New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social

Is virulence a fixed trait? This first commentary in Microbiology Outlooks considers why it may be better understood as a context-dependent evolutionary strategy. Discover the Open Access article: https://doi.org/10.1099/mout.0.00001

🚨 New preprint 🚨 How promiscuous really are conjugative plasmids, and what does that mean for plasmid co-occurrence? A pleasure to collaborate with @craigmaclean.bsky.social on the first paper of my fellowship! www.biorxiv.org/content/10.6...

📣 2026 PhD studentship 📣 Via @manchester.ac.uk 's President's Doctoral Scholar Awards, we are encouraging applications for a PhD on the effect of pollutant exposure on microbe-immune cross talk. This project will incorporate microbiology, immunology, & bioinformatics. Deadline: 16 March 2026!

(President's Doctoral Scholar Award) A mechanistic understanding of microbe-immune cross talk in the face of pollutant challenge at The University of Manchester on FindAPhD.com

PhD Project - (President's Doctoral Scholar Award) A mechanistic understanding of microbe-immune cross talk in the face of pollutant challenge at The University of Manchester, listed on FindAPhD.c...

findaphd.com

He may have only barely known about bacteria, and not at all about viruses, but Darwin was right about hating an ill-defined species concept

Letters of Note@lettersofnote.com · 9mo ago

Happy birthday to one of my favourite haters, Charles Darwin

The coolest finding of my PhD is finally out! E. coli has a 7th RND pump that is present in phylogroups B2/D/E/F but absent in A/B1/C. As a result EefABC has been absent in all K-12 RND studies! Co-authored by the very talented Dr. Lizzy Darby. @jessicamablair.bsky.social doi.org/10.1099/mgen...

The Resistance-Nodulation-Division efflux pump EefABC is highly conserved within lineages of E. coli commonly associated with infection

Resistance-nodulation-division (RND) efflux pumps confer multidrug resistance in Gram-negative bacteria and are critical for many physiological functions including virulence and biofilm formation. The...

doi.org

Delighted to have contributed to this impressive work led by @tovefall.bsky.social & many others👏 (w/ @gazollavolpiano.bsky.social from our side). This novel microbiome GWAS (n=~16k+12k valid) expands knowledge on genetic factors associated w/ gut microbiota variation. www.nature.com/articles/s41...

Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation - Nature Genetics

Population-based studies from Sweden with replication in Norway identify associations between host genetic variants and gut microbial composition and implicate short-chain fatty acid chemosensors as m...

nature.com

Now out & nicely formatted in @isme-microbes.bsky.social A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron. A few highlights... 🧵 (1/n) doi.org/10.1093/isme...

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny

Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

doi.org

I am pleased to share that our paper is now published in Cell! www.cell.com/cell/fulltex... I am deeply grateful to all co-authors for making this possible. This work was made possible through the guidance of Dr. Peer Bork. I share this in grateful memory and with deep respect for his mentorship.

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

EMBL@embl.org · 9mo ago

In the largest study of its kind, scientists in the Bork Group at EMBL have found that a small subset of microbes can carry and transfer genes across disparate habitats, creating a planet-wide, interconnected network of microbiomes 🌍 🦠 🔗 Read more here: www.embl.org/news/science...